From 2f619e5647509d200879529c66c3f75f09f0ca0d Mon Sep 17 00:00:00 2001 From: rodche Date: Fri, 21 Oct 2022 00:32:44 -0400 Subject: [PATCH 01/20] Paxtools-6: refactoring - - now java compatibility level 11 (was 8); - use Collections interface where possible; - add BiopaxSafeCollection (will try to replace Set in biopax object props); - upgraded biopax-search (full-text) module to use Lucene 7.5; - remove deprecated code, debug comments, etc. polish. - fixed some minor bugs (e.g. in TR), removed useless code/comments, etc. --- gsea-converter/pom.xml | 2 +- .../biopax/paxtools/io/gsea/GMTConverter.java | 37 +- .../paxtools/io/gsea/GSEAConverter.java | 66 +- json-converter/pom.xml | 2 +- normalizer/pom.xml | 2 +- .../paxtools/normalizer/MiriamLink.java | 16 +- .../paxtools/normalizer/Normalizer.java | 15 +- pattern/pom.xml | 4 +- .../org/biopax/paxtools/pattern/Match.java | 2 +- .../org/biopax/paxtools/pattern/Pattern.java | 12 +- .../biopax/paxtools/pattern/PatternBox.java | 2 +- .../org/biopax/paxtools/pattern/Searcher.java | 73 +- .../paxtools/pattern/constraint/AND.java | 2 +- .../ActivityModificationChangeConstraint.java | 2 +- .../paxtools/pattern/constraint/ConBox.java | 2 +- .../pattern/constraint/ConstraintAdapter.java | 10 +- .../pattern/constraint/ConstraintChain.java | 6 +- .../constraint/ControlToControllerER.java | 6 +- .../pattern/constraint/ConversionSide.java | 4 +- .../pattern/constraint/InterToPartER.java | 10 +- .../paxtools/pattern/constraint/LinkedPE.java | 2 +- .../ModificationChangeConstraint.java | 2 +- .../paxtools/pattern/constraint/OR.java | 2 +- .../pattern/constraint/Participant.java | 4 +- .../constraint/ParticipatesInConv.java | 2 +- .../pattern/constraint/PathConstraint.java | 2 +- .../pattern/constraint/RelatedControl.java | 2 +- .../paxtools/pattern/constraint/XOR.java | 4 +- .../example/DeltaFeatureExtractor.java | 8 +- .../pattern/miner/BlacklistGenerator.java | 14 +- .../pattern/miner/BlacklistGenerator2.java | 109 ++- .../pattern/miner/CommonIDFetcher.java | 2 +- .../pattern/miner/ConfigurableIDFetcher.java | 6 +- .../biopax/paxtools/pattern/miner/Dialog.java | 2 +- .../pattern/miner/ExtendedSIFWriter.java | 16 +- .../paxtools/pattern/miner/MinerAdapter.java | 28 +- .../paxtools/pattern/miner/OutputColumn.java | 4 +- .../RelatedGenesOfInteractionsMiner.java | 2 +- .../pattern/miner/SIFInteraction.java | 32 +- .../paxtools/pattern/miner/SIFSearcher.java | 8 +- .../paxtools/pattern/util/Blacklist.java | 6 +- .../pattern/util/ChemicalNameNormalizer.java | 151 +---- .../util/DifferentialModificationUtil.java | 10 +- .../pattern/util/PhysicalEntityChain.java | 4 +- .../paxtools/pattern/PCSiteSIFTest.java | 12 +- .../biopax/paxtools/pattern/TempTests.java | 32 +- .../paxtools/pattern/UbiqueStatHelper.java | 16 +- .../biopax/paxtools/pattern/DBParsers.java | 64 +- .../biopax/paxtools/pattern/SPIKEParser.java | 8 +- .../pattern/constraint/TestParent.java | 2 +- .../pattern/miner/SIFSearcherTest.java | 10 +- paxtools-archetype/README.md | 2 +- paxtools-archetype/pom.xml | 2 +- .../resources/archetype-resources/pom.xml | 4 +- paxtools-console/pom.xml | 2 +- .../org/biopax/paxtools/PaxtoolsMain.java | 70 +- ...cationXREFtoRelationshipXREFConverter.java | 125 ++-- .../examples/PathwayGenesExtractor.java | 10 +- .../paxtools/examples/ProteinNameLister.java | 7 +- .../ReactomeEntitySetUnificationXrefFix.java | 4 +- .../biopax/paxtools/examples/Tutorial.java | 25 +- .../examples/UnificationIDtoRDFIDLister.java | 5 +- .../paxtools/examples/UseOfReflection.java | 2 +- .../examples/tutorial-pom-examples.xml | 2 +- paxtools-core/pom.xml | 3 +- .../controller/AbstractPropertyEditor.java | 25 +- .../controller/AbstractTraverser.java | 2 +- .../biopax/paxtools/controller/Cloner.java | 23 +- .../biopax/paxtools/controller/Completer.java | 13 +- .../paxtools/controller/EditorMapImpl.java | 4 +- .../biopax/paxtools/controller/Fetcher.java | 305 ++++----- .../biopax/paxtools/controller/IdFetcher.java | 6 +- .../paxtools/controller/Integrator.java | 30 +- .../biopax/paxtools/controller/Merger.java | 46 +- .../paxtools/controller/ModelUtils.java | 223 +++--- .../paxtools/controller/PathAccessor.java | 11 +- .../controller/PropertyAccessorAdapter.java | 2 +- .../paxtools/controller/SimpleMerger.java | 8 +- .../TransitivePropertyAccessor.java | 2 +- .../biopax/paxtools/controller/Traverser.java | 2 +- .../controller/TraverserBilinked.java | 17 +- .../controller/UnionPropertyAccessor.java | 2 +- .../paxtools/converter/LevelUpgrader.java | 4 +- .../paxtools/impl/BioPAXElementImpl.java | 131 ++-- .../org/biopax/paxtools/impl/MockFactory.java | 4 +- .../org/biopax/paxtools/impl/ModelImpl.java | 232 +++---- .../impl/level2/BioPAXLevel2ElementImpl.java | 2 +- .../paxtools/impl/level2/ReferenceHelper.java | 4 +- .../impl/level2/biochemicalReactionImpl.java | 12 +- .../paxtools/impl/level2/catalysisImpl.java | 4 +- .../paxtools/impl/level2/complexImpl.java | 2 +- .../paxtools/impl/level2/controlImpl.java | 8 +- .../paxtools/impl/level2/conversionImpl.java | 8 +- .../paxtools/impl/level2/dataSourceImpl.java | 2 +- .../paxtools/impl/level2/entityImpl.java | 8 +- .../paxtools/impl/level2/evidenceImpl.java | 6 +- .../impl/level2/experimentalFormImpl.java | 2 +- .../impl/level2/interactionAdapter.java | 17 +- .../paxtools/impl/level2/interactionImpl.java | 4 +- .../level2/openControlledVocabularyImpl.java | 2 +- .../paxtools/impl/level2/pathwayImpl.java | 4 +- .../paxtools/impl/level2/pathwayStepImpl.java | 8 +- .../impl/level2/physicalEntityImpl.java | 4 +- .../level2/physicalEntityParticipantImpl.java | 2 +- .../level2/physicalInteractionAdapter.java | 2 +- .../impl/level2/physicalInteractionImpl.java | 4 +- .../paxtools/impl/level2/processImpl.java | 8 +- .../impl/level2/publicationXrefImpl.java | 6 +- .../impl/level2/sequenceFeatureImpl.java | 4 +- .../impl/level2/sequenceParticipantImpl.java | 2 +- .../impl/level2/smallMoleculeImpl.java | 2 +- .../biopax/paxtools/impl/level2/xrefImpl.java | 2 +- .../impl/level3/BiochemicalReactionImpl.java | 2 +- .../paxtools/impl/level3/ControlImpl.java | 17 +- .../paxtools/impl/level3/ConversionImpl.java | 22 +- .../paxtools/impl/level3/InteractionImpl.java | 34 +- .../impl/level3/MolecularInteractionImpl.java | 24 +- .../impl/level3/TemplateReactionImpl.java | 110 +-- .../biopax/paxtools/io/SimpleIOHandler.java | 5 +- .../biopax/paxtools/model/BioPAXElement.java | 17 +- .../java/org/biopax/paxtools/model/Model.java | 38 +- .../model/level2/InteractionHelper.java | 4 +- .../model/level3/TemplateReaction.java | 15 +- .../paxtools/util/AbstractFilterSet.java | 8 +- .../biopax/paxtools/util/BPCollections.java | 87 ++- .../paxtools/util/BiopaxSafeCollection.java | 74 ++ .../biopax/paxtools/util/BiopaxSafeSet.java | 52 +- .../biopax/paxtools/util/ClassFilterSet.java | 5 +- .../paxtools/util/EquivalenceGrouper.java | 15 +- .../paxtools/util/SetEquivalenceChecker.java | 2 +- .../controller/CommandManagerTest.java | 2 +- .../controller/CompleterClonerTest.java | 9 +- .../paxtools/controller/PathAccessorTest.java | 2 +- .../paxtools/impl/level3/EqualsEtcTest.java | 108 ++- paxtools-query/pom.xml | 4 +- .../biopax/paxtools/query/QueryExecuter.java | 158 ++--- .../biopax/paxtools/query/algorithm/BFS.java | 26 +- .../query/algorithm/CommonStreamQuery.java | 18 +- .../query/algorithm/CycleBreaker.java | 9 +- .../query/algorithm/NeighborhoodQuery.java | 9 +- .../query/algorithm/PathsBetweenQuery.java | 16 +- .../query/algorithm/PathsFromToQuery.java | 22 +- .../paxtools/query/algorithm/Prune.java | 12 +- .../paxtools/query/model/AbstractGraph.java | 2 +- .../paxtools/query/model/AbstractNode.java | 6 +- .../biopax/paxtools/query/model/Graph.java | 7 +- .../paxtools/query/wrapperL3/GraphL3.java | 10 +- .../wrapperL3/PhysicalEntityWrapper.java | 10 +- .../query/wrapperL3/StringFieldFilter.java | 2 +- .../GraphL3Undirected.java | 10 +- .../PhysicalEntityWrapper.java | 4 +- .../org/biopax/paxtools/query/QueryTest.java | 39 +- paxtools-search/pom.xml | 4 +- .../biopax/paxtools/search/SearchEngine.java | 633 +++++++++--------- .../paxtools/search/SearchEngineTest.java | 28 +- pom.xml | 7 +- psimi-converter/pom.xml | 2 +- .../paxtools/converter/psi/EntryMapper.java | 48 +- .../paxtools/converter/psi/TestMapping.java | 2 +- sbgn-converter/pom.xml | 2 +- .../paxtools/io/sbgn/L3ToSBGNPDConverter.java | 75 +-- .../paxtools/io/sbgn/SBGNLayoutManager.java | 6 +- .../org/biopax/paxtools/io/sbgn/VNode.java | 2 +- .../paxtools/io/sbgn/SBGNConverterTest.java | 32 +- 164 files changed, 2002 insertions(+), 2180 deletions(-) create mode 100644 paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java diff --git a/gsea-converter/pom.xml b/gsea-converter/pom.xml index 368351d2c..096e63d04 100644 --- a/gsea-converter/pom.xml +++ b/gsea-converter/pom.xml @@ -2,7 +2,7 @@ org.biopax.paxtools paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT 4.0.0 diff --git a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java index fba256248..da5baa1f5 100644 --- a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java +++ b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java @@ -112,7 +112,7 @@ public void writeToGSEA(final Model model, OutputStream out) throws IOException if ((minNumIdsPerEntry <= 1 && !entry.identifiers().isEmpty()) || entry.identifiers().size() >= minNumIdsPerEntry) { - writer.write(entry.toString() + "\n"); + writer.write(entry + "\n"); } } writer.flush(); @@ -126,12 +126,9 @@ public void writeToGSEA(final Model model, OutputStream out) throws IOException */ public Collection convert(final Model model) { - final Collection toReturn = new TreeSet(new Comparator() { - @Override - public int compare(GMTEntry o1, GMTEntry o2) { - return o1.toString().compareTo(o2.toString()); - } - }); + final Collection toReturn = new TreeSet<>( + Comparator.comparing(GMTEntry::toString) + ); Model l3Model; // convert to level 3 in necessary @@ -143,9 +140,9 @@ public int compare(GMTEntry o1, GMTEntry o2) { //a modifiable copy of the set of all PRs in the model - //after all, it has all the ERs that do not belong to any pathway final Set entityReferences = - new HashSet(l3Model.getObjects(EntityReference.class)); + new HashSet<>(l3Model.getObjects(EntityReference.class)); - final Set pathways = l3Model.getObjects(Pathway.class); + final Collection pathways = l3Model.getObjects(Pathway.class); for (Pathway pathway : pathways) { String name = (pathway.getDisplayName() == null) ? pathway.getStandardName() : pathway.getDisplayName(); @@ -156,7 +153,7 @@ public int compare(GMTEntry o1, GMTEntry o2) { final String currentPathwayName = name; LOG.debug("Begin converting " + currentPathwayName + " pathway, uri=" + currentPathway.getUri()); - final Set ers = new HashSet(); + final Set ers = new HashSet<>(); final Traverser traverser = new AbstractTraverser(SimpleEditorMap.L3, Fetcher.nextStepFilter, Fetcher.objectPropertiesOnlyFilter) { @Override @@ -198,19 +195,23 @@ protected void visit(Object range, BioPAXElement domain, Model model, PropertyEd //organize PRs by species (GSEA s/w can handle only same species identifiers in a data row) if(!entityReferences.isEmpty() && !skipOutsidePathways) { LOG.info("Creating entries for the rest of PRs (outside any pathway)..."); - toReturn.addAll(createGseaEntries("other","other", getDataSource(l3Model.getObjects(Provenance.class)),entityReferences)); + toReturn.addAll(createGseaEntries("other","other", + getDataSource(l3Model.getObjects(Provenance.class)), entityReferences)); } return toReturn; } - private Collection createGseaEntries(String uri, final String name, final String dataSource, - final Set ers) + private Collection createGseaEntries(String uri, String name, + String dataSource, + Collection ers) { - final Collection toReturn = new ArrayList(); - GMTEntry entry = new GMTEntry(uri, "", "", String.format("name: %s; datasource: %s",name, dataSource)); - for (EntityReference er : ers) + Collection toReturn = new ArrayList<>(); + GMTEntry entry = new GMTEntry(uri, "", "", + String.format("name: %s; datasource: %s", name, dataSource)); + for (EntityReference er : ers) { entry.identifiers().addAll(idFetcher.fetchID(er)); + } toReturn.add(entry); return toReturn; } @@ -218,11 +219,11 @@ private Collection createGseaEntries(String uri, final String name, fi /* * Gets datasource names, if any, in a consistent way/order, excl. duplicates */ - private String getDataSource(Set provenances) + private String getDataSource(Collection provenances) { if(provenances.isEmpty()) return "N/A"; - Set dsNames = new TreeSet(); + Set dsNames = new TreeSet<>(); for (Provenance provenance : provenances) { String name = provenance.getDisplayName(); diff --git a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java index 7a5ad6095..6423d0b99 100644 --- a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java +++ b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java @@ -48,9 +48,9 @@ public class GSEAConverter private final String idType; private final boolean crossSpeciesCheckEnabled; - private Set allowedOrganisms; + private Collection allowedOrganisms; private final boolean skipSubPathways; - private final Set skipSubPathwaysOf; + private final Collection skipSubPathwaysOf; private boolean skipOutsidePathways = false; private int minNumOfGenesPerEntry = 1; @@ -115,13 +115,11 @@ public GSEAConverter(String idType, boolean crossSpeciesCheckEnabled, boolean sk * @param skipSubPathwaysOf - do not look inside sub-pathways of pathways of given data sources to collect entity references * (useful when a model, such as converted to BioPAX KEGG data, has lots of sub-pathways, loops.) */ - public GSEAConverter(String idType, boolean crossSpeciesCheckEnabled, Set skipSubPathwaysOf) + public GSEAConverter(String idType, boolean crossSpeciesCheckEnabled, Collection skipSubPathwaysOf) { this.idType = idType; this.crossSpeciesCheckEnabled = crossSpeciesCheckEnabled; - if(skipSubPathwaysOf == null) - skipSubPathwaysOf = Collections.emptySet(); - this.skipSubPathwaysOf = skipSubPathwaysOf; + this.skipSubPathwaysOf = (skipSubPathwaysOf == null) ? Collections.emptySet() : skipSubPathwaysOf; this.skipSubPathways = false; } @@ -138,7 +136,7 @@ public void setSkipOutsidePathways(boolean skipOutsidePathways) { this.skipOutsidePathways = skipOutsidePathways; } - public Set getAllowedOrganisms() { + public Collection getAllowedOrganisms() { return allowedOrganisms; } @@ -178,7 +176,7 @@ public void writeToGSEA(final Model model, OutputStream out) throws IOException if ((minNumOfGenesPerEntry <= 1 && !entry.identifiers().isEmpty()) || entry.identifiers().size() >= minNumOfGenesPerEntry) { - writer.write(entry.toString() + "\n"); + writer.write(entry + "\n"); } } writer.flush(); @@ -192,12 +190,7 @@ public void writeToGSEA(final Model model, OutputStream out) throws IOException */ public Collection convert(final Model model) { - final Collection toReturn = new TreeSet(new Comparator() { - @Override - public int compare(GMTEntry o1, GMTEntry o2) { - return o1.toString().compareTo(o2.toString()); - } - }); + final Collection toReturn = new TreeSet<>(Comparator.comparing(GMTEntry::toString)); Model l3Model; // convert to level 3 in necessary @@ -208,10 +201,10 @@ public int compare(GMTEntry o1, GMTEntry o2) { //a modifiable copy of the set of all PRs in the model - //after all, it has all the PRs that do not belong to any pathway - final Set sequenceEntityReferences = - new HashSet(l3Model.getObjects(SequenceEntityReference.class)); + final Collection sequenceEntityReferences = + new ArrayList<>(l3Model.getObjects(SequenceEntityReference.class)); - final Set pathways = l3Model.getObjects(Pathway.class); + final Collection pathways = l3Model.getObjects(Pathway.class); for (Pathway pathway : pathways) { String name = (pathway.getDisplayName() == null) ? pathway.getStandardName() : pathway.getDisplayName(); @@ -236,14 +229,14 @@ public int compare(GMTEntry o1, GMTEntry o2) { if(!pathwaySers.isEmpty()) { LOG.debug("For pathway: " + currentPathwayName + " (" + currentPathway.getUri() + "), got " + pathwaySers.size() + " sERs; now - grouping by organism..."); - Map> orgToPrsMap = organismToProteinRefsMap(pathwaySers); + Map> orgToPrsMap = organismToProteinRefsMap(pathwaySers); // create GSEA/GMT entries - one entry per organism (null organism also makes one) String dataSource = getDataSource(currentPathway.getDataSource()); Collection entries = createGseaEntries(currentPathway.getUri(), currentPathwayName, dataSource, orgToPrsMap); if(!entries.isEmpty()) toReturn.addAll(entries); - sequenceEntityReferences.removeAll(pathwaySers);//keep not processed PRs (a PR can be processed multiple times) + sequenceEntityReferences.removeAll(pathwaySers);//keep not processed PRs (can be processed multiple times) LOG.debug("- collected " + entries.size() + "entries."); } } @@ -252,7 +245,8 @@ public int compare(GMTEntry o1, GMTEntry o2) { //organize PRs by species (GSEA s/w can handle only same species identifiers in a data row) if(!sequenceEntityReferences.isEmpty() && !skipOutsidePathways) { LOG.info("Creating entries for the rest of PRs (outside any pathway)..."); - Map> orgToPrsMap = organismToProteinRefsMap(sequenceEntityReferences); + Map> orgToPrsMap = + organismToProteinRefsMap(sequenceEntityReferences); if(!orgToPrsMap.isEmpty()) { // create GSEA/GMT entries - one entry per organism (null organism also makes one) if(model.getUri()==null) { @@ -268,11 +262,12 @@ public int compare(GMTEntry o1, GMTEntry o2) { return toReturn; } - private Collection createGseaEntries(String uri, final String name, final String dataSource, - final Map> orgToPrsMap) + private Collection createGseaEntries( + String uri, String name, String dataSource, + Map> orgToPrsMap) { // generate GSEA entries for each species - final Collection toReturn = new ArrayList(); + final Collection toReturn = new ArrayList<>(); for (final String org : orgToPrsMap.keySet()) { if(orgToPrsMap.get(org).size() > 0) { GMTEntry GMTEntry = new GMTEntry(uri, org, idType, @@ -286,9 +281,10 @@ private Collection createGseaEntries(String uri, final String name, fi //warn: there can be many equivalent BioSource objects (same taxonomy id, different URIs) - private Map> organismToProteinRefsMap(Set seqErs) + private Map> organismToProteinRefsMap( + Collection seqErs) { - Map> map = new HashMap>(); + Map> map = new HashMap<>(); if(seqErs.isEmpty()) throw new IllegalArgumentException("Empty set"); @@ -297,21 +293,23 @@ private Map> organismToProteinRefsMap(Set sers = map.get(key); + if(allowedOrganisms==null || allowedOrganisms.isEmpty() || allowedOrganisms.contains(key)) + { + Collection sers = map.get(key); if (sers == null) { - sers = new HashSet(); + sers = new HashSet<>(); map.put(key, sers); } sers.add(r); } } } else { - final Set sers = new HashSet(); + final Set sers = new HashSet<>(); for (SequenceEntityReference r : seqErs) { String key = getOrganismKey(r.getOrganism()); //collect PRs only from allowed organisms - if(allowedOrganisms==null || allowedOrganisms.isEmpty() || allowedOrganisms.contains(key)) { + if(allowedOrganisms==null || allowedOrganisms.isEmpty() || allowedOrganisms.contains(key)) + { sers.add(r); } } @@ -322,7 +320,7 @@ private Map> organismToProteinRefsMap(Set sers, GMTEntry targetEntry) + void processEntityReferences(Collection sers, GMTEntry targetEntry) { prs_loop: for (SequenceEntityReference ser : sers) { @@ -379,11 +377,11 @@ void processEntityReferences(Set sers, GMTEntry targetE /* * Gets datasource names, if any, in a consistent way/order, excl. duplicates */ - private String getDataSource(Set provenances) + private String getDataSource(Collection provenances) { if(provenances.isEmpty()) return "N/A"; - Set dsNames = new TreeSet(); + Set dsNames = new TreeSet<>(); for (Provenance provenance : provenances) { String name = provenance.getDisplayName(); @@ -433,7 +431,7 @@ private String getOrganismKey(BioSource org) { return key; } - private boolean shareSomeObjects(Set setA, Set setB) { + private boolean shareSomeObjects(Collection setA, Collection setB) { return (!setA.isEmpty() && !setB.isEmpty()) ? !CollectionUtils.intersection(setA, setB).isEmpty() : false; } } diff --git a/json-converter/pom.xml b/json-converter/pom.xml index caeaaceb2..e329100ef 100644 --- a/json-converter/pom.xml +++ b/json-converter/pom.xml @@ -3,7 +3,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT json-converter BioPAX to/from JSON Converter diff --git a/normalizer/pom.xml b/normalizer/pom.xml index 6f5065a76..523e85b7f 100644 --- a/normalizer/pom.xml +++ b/normalizer/pom.xml @@ -9,7 +9,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT https://biopax.github.io/Paxtools diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java index b9c252897..536041934 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java @@ -143,7 +143,7 @@ public static String getDataTypeURI(String datatypeKey) */ public static String[] getDataTypeURIs(String datatypeKey) { - Set alluris = new HashSet(); + Set alluris = new HashSet<>(); Datatype datatype = getDatatype(datatypeKey); for(Uris uris : datatype.getUris()) { for(Uri uri : uris.getUri()) { @@ -232,7 +232,7 @@ public static String getDataTypeDef(String datatypeKey) */ public static String[] getLocations(String datatypeKey, String entityId) { - Set locations = new HashSet(); + Set locations = new HashSet<>(); Datatype datatype = getDatatype(datatypeKey); for (Resource resource : getResources(datatype)) { String link = resource.getDataEntry(); @@ -257,7 +257,7 @@ public static String[] getLocations(String datatypeKey, String entityId) */ public static String[] getDataResources(String datatypeKey) { - Set locations = new HashSet(); + Set locations = new HashSet<>(); Datatype datatype = getDatatype(datatypeKey); for (Resource resource : getResources(datatype)) { String link = resource.getDataResource(); @@ -319,7 +319,7 @@ public static String getName(String datatypeKey) */ public static String[] getNames(String datatypeKey) { - Set names = new HashSet(); + Set names = new HashSet<>(); Datatype datatype = getDatatype(datatypeKey); names.add(datatype.getName()); Synonyms synonyms = datatype.getSynonyms(); @@ -338,7 +338,7 @@ public static String[] getNames(String datatypeKey) */ public static String[] getDataTypesName() { - Set dataTypeNames = new HashSet(); + Set dataTypeNames = new HashSet<>(); for(Datatype datatype : miriam.getDatatype()) { dataTypeNames.add(datatype.getName()); } @@ -354,7 +354,7 @@ public static String[] getDataTypesName() */ public static String[] getDataTypesId() { - Set dataTypeIds = new HashSet(); + Set dataTypeIds = new HashSet<>(); for(Datatype datatype : miriam.getDatatype()) { dataTypeIds.add(datatype.getId()); } @@ -460,7 +460,7 @@ else if(containsUri(datatypeKey)) */ public static String[] getResourcesId() { - Set ids = new HashSet(); + Set ids = new HashSet<>(); for(Datatype datatype : miriam.getDatatype()) { for (Resource resource : getResources(datatype)) { ids.add(resource.getId()); @@ -522,7 +522,7 @@ public static boolean containsUri(String searchUri) { * @return the list of MIRIAM Resources in that datatype */ private static List getResources(Datatype datatype) { - List toReturn = new ArrayList(); + List toReturn = new ArrayList<>(); Resources resources = datatype.getResources(); if (resources != null) { diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index 4bfd84e5e..cfdf937a4 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -111,7 +111,7 @@ private void normalizeXrefs(Model model) { final String xmlBase = getXmlBase(model); //current base, the default or model's one, if set. // use a copy of the xrefs set (to avoid concurrent modif. exception) - Set xrefs = new HashSet(model.getObjects(Xref.class)); + Set xrefs = new HashSet<>(model.getObjects(Xref.class)); for(Xref ref : xrefs) { //skip not well-defined ones (incl. PublicationXrefs w/o db/id - won't normalize) @@ -334,7 +334,7 @@ private String convertToOWL(Model model) { private Collection getUnificationXrefsSorted(XReferrable r) { - List urefs = new ArrayList(); + List urefs = new ArrayList<>(); for(UnificationXref ux : new ClassFilterSet(r.getXref(), UnificationXref.class)) { if(ux.getDb() != null && ux.getId() != null) { @@ -460,7 +460,7 @@ public void normalize(Model model) { normalizeBioSources(model); // auto-generate missing entity references: - for(SimplePhysicalEntity spe : new HashSet(model.getObjects(SimplePhysicalEntity.class))) { + for(SimplePhysicalEntity spe : new HashSet<>(model.getObjects(SimplePhysicalEntity.class))) { //it skips if spe has entityReference or memberPE already ModelUtils.addMissingEntityReference(model, spe); } @@ -733,8 +733,8 @@ private static class NormalizerMap { final ShallowCopy copier; NormalizerMap(Model model) { - subs = BPCollections.I.createMap(); - uriToSub = BPCollections.I.createMap(); + subs = BPCollections.I.createMap(100); + uriToSub = BPCollections.I.createMap(100); this.model = model; copier = new ShallowCopy(); } @@ -774,13 +774,14 @@ void doSubs() { try { ModelUtils.replace(model, subs); } catch (Exception e) { - log.error("Failed to replace BioPAX elements.", e); + log.error("Failed to replace BioPAX elements", e); return; } for(BioPAXElement e : subs.values()) { - if(!model.contains(e)) + if(!model.containsID(e.getUri())) { model.add(e); + } } for(BioPAXElement e : model.getObjects()) { diff --git a/pattern/pom.xml b/pattern/pom.xml index 8998aa0d8..cbcb73c2b 100644 --- a/pattern/pom.xml +++ b/pattern/pom.xml @@ -5,7 +5,7 @@ org.biopax.paxtools paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT pattern @@ -26,6 +26,6 @@ paxtools-core ${project.version} - + diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/Match.java b/pattern/src/main/java/org/biopax/paxtools/pattern/Match.java index 3e77b6cb9..b4f20befd 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/Match.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/Match.java @@ -71,7 +71,7 @@ public List get(String[] label, Pattern p) { if (label == null) return Collections.emptyList(); - List list = new ArrayList(label.length); + List list = new ArrayList<>(label.length); for (String lab : label) { list.add(variables[p.indexOf(lab)]); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java b/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java index 96547969a..f49781f57 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java @@ -39,7 +39,7 @@ private Pattern(Class startingClass) { this.startingClass = startingClass; this.labelMap = new HashMap(); - this.constraints = new ArrayList(); + this.constraints = new ArrayList<>(); this.lastIndex = 0; } @@ -134,7 +134,7 @@ public void optimizeConstraintOrder() for (MappedConst con1 : constraints) { - preMap.put(con1, new HashSet()); + preMap.put(con1, new HashSet<>()); int m1 = con1.getMaxInd(); for (MappedConst con2 : constraints) @@ -152,11 +152,11 @@ public void optimizeConstraintOrder() // determine ordered levels - List> levels = new ArrayList>(); + List> levels = new ArrayList<>(); do { - Set level = new HashSet(); + Set level = new HashSet<>(); for (MappedConst con : preMap.keySet()) { @@ -179,11 +179,11 @@ public void optimizeConstraintOrder() // build new constraints list - List newList = new ArrayList(constraints.size()); + List newList = new ArrayList<>(constraints.size()); for (Set level : levels) { - List temp = new ArrayList(constraints); + List temp = new ArrayList<>(constraints); temp.retainAll(level); newList.addAll(temp); } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/PatternBox.java b/pattern/src/main/java/org/biopax/paxtools/pattern/PatternBox.java index ba2c9dc8e..7323ff796 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/PatternBox.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/PatternBox.java @@ -385,7 +385,7 @@ public boolean satisfies(Match match, int... ind) if (blacklist != null) { - Set set = new HashSet(input1); + Set set = new HashSet<>(input1); set = blacklist.getNonUbiques(set, RelType.INPUT); set.removeAll(output2); if (set.isEmpty()) diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java index ead13b3b2..764679032 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java @@ -66,7 +66,7 @@ public static List search(BioPAXElement ele, Pattern pattern) */ public static List searchRecursive(Match match, List mc, int index) { - List result = new ArrayList(); + List result = new ArrayList<>(); Constraint con = mc.get(index).getConstr(); int[] ind = mc.get(index).getInds(); @@ -118,7 +118,7 @@ public static List searchRecursive(Match match, List mc, int */ public static List searchPlain(Model model, Pattern pattern) { - List list = new LinkedList(); + List list = new LinkedList<>(); Map> map = search(model, pattern); for (List matches : map.values()) @@ -137,7 +137,7 @@ public static List searchPlain(Model model, Pattern pattern) */ public static List searchPlain(Collection eles, Pattern pattern) { - List list = new LinkedList(); + List list = new LinkedList<>(); Map> map = search(eles, pattern); for (List matches : map.values()) @@ -151,7 +151,7 @@ public static List searchPlain(Collection eles, * Searches the given pattern in the given model. * @param model model to search in * @param pattern pattern to search for - * @return map from starting elements to the list matching results + * @return map from starting elements to the list of results */ public static Map> search(Model model, Pattern pattern) { @@ -163,33 +163,31 @@ public static Map> search(Model model, Pattern patter * @param model model to search in * @param pattern pattern to search for * @param prg progress watcher to keep track of the progress - * @return map from starting elements to the list matching results + * @return map from starting elements to the ordered list of results */ public static Map> search(final Model model, final Pattern pattern, final ProgressWatcher prg) { - final Map> map = new ConcurrentHashMap>(); + final Map> map = new ConcurrentHashMap<>(); final ExecutorService exec = Executors.newFixedThreadPool(20); - Set eles = model.getObjects(pattern.getStartingClass()); + Collection eles = model.getObjects(pattern.getStartingClass()); if (prg != null) prg.setTotalTicks(eles.size()); for (final BioPAXElement ele : eles) { - exec.execute(new Runnable() { - @Override - public void run() { - List matches = search(ele, pattern); - if (!matches.isEmpty()) - { - map.put(ele, matches); - } - if (prg != null) prg.tick(1); + exec.execute(() -> { + List matches = search(ele, pattern); + if (!matches.isEmpty()) + { + map.put(ele, matches); } + if (prg != null) prg.tick(1); }); } exec.shutdown(); + try { exec.awaitTermination(10, TimeUnit.MINUTES); } catch (InterruptedException e) { @@ -205,35 +203,33 @@ public void run() { * @param pattern pattern to search for * @return map from starting element to the matching results */ - public static Map> search(final Collection eles, - final Pattern pattern) + public static Map> search( + Collection eles, Pattern pattern) { - final Map> map = new ConcurrentHashMap>(); + final Map> map = new ConcurrentHashMap<>(); final ExecutorService exec = Executors.newFixedThreadPool(10); for (final BioPAXElement ele : eles) { if (!pattern.getStartingClass().isAssignableFrom(ele.getModelInterface())) continue; - exec.execute(new Runnable() { - @Override - public void run() { - List matches = search(ele, pattern); - if (!matches.isEmpty()) { - map.put(ele, matches); - } + exec.execute(() -> { + List matches = search(ele, pattern); + if (!matches.isEmpty()) { + map.put(ele, matches); } }); } exec.shutdown(); + try { exec.awaitTermination(10, TimeUnit.MINUTES); } catch (InterruptedException e) { throw new RuntimeException("search, failed due to exec timed out.", e); } - return Collections.unmodifiableMap(new HashMap>(map)); + return Collections.unmodifiableMap(new HashMap<>(map)); } /** @@ -247,7 +243,7 @@ public void run() { * @param c type of the element to collect * @return set of the elements at the specified index of the matching results */ - public static Set searchAndCollect( + public static Collection searchAndCollect( Model model, Pattern pattern, int index, Class c) { return searchAndCollect(model.getObjects(pattern.getStartingClass()), pattern, index, c); @@ -264,10 +260,10 @@ public static Set searchAndCollect( * @param c type of the element to collect * @return set of the elements at the specified index of the matching results */ - public static Set searchAndCollect( + public static Collection searchAndCollect( Collection eles, Pattern pattern, int index, Class c) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Match match : searchPlain(eles, pattern)) { @@ -290,7 +286,7 @@ public static Set searchAndCollect( public static Set searchAndCollect( BioPAXElement ele, Pattern pattern, int index, Class c) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Match match : search(ele, pattern)) { @@ -349,12 +345,11 @@ public static void searchInFile(Pattern p, String inFile, String outFile, int se Map> matchMap = Searcher.search(model, p); - System.out.println("matching groups size = " + matchMap.size()); - - List> inters = new LinkedList>(); - Set encountered = new HashSet(); +// System.out.println("matching groups size = " + matchMap.size()); - Set toExise = new HashSet(); + List> inters = new LinkedList<>(); + Set encountered = new HashSet<>(); + Set toExise = new HashSet<>(); int seedCounter = 0; for (BioPAXElement ele : matchMap.keySet()) @@ -444,7 +439,7 @@ private static String getLeadingZeros(int i, int size) * @param model model to excise (bogus parameter, in fact, deprecated) * @param result elements to excise to * @return excised model - * @deprecated use {@link #excise(Set)} instead (parameter:model was not actually used at all) + * @deprecated use {@link #excise(Collection)} instead (parameter:model was not actually used at all) */ private static Model excise(Model model, Set result) { @@ -456,7 +451,7 @@ private static Model excise(Model model, Set result) * @param result elements to excise to * @return excised model */ - private static Model excise(Set result) + private static Model excise(Collection result) { Completer c = new Completer(EM); result = c.complete(result); @@ -471,7 +466,7 @@ private static Model excise(Set result) */ private static Set getInter(Match match) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (BioPAXElement ele : match.getVariables()) { if (ele instanceof Interaction) diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/AND.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/AND.java index 155beaa3b..2b4ead050 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/AND.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/AND.java @@ -48,7 +48,7 @@ public boolean satisfies(Match match, int... ind) @Override public Collection generate(Match match, int... ind) { - Collection gen = new HashSet ( + Collection gen = new HashSet<> ( con[0].generate(match, ind)); for (int i = 1; i < con.length; i++) diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ActivityModificationChangeConstraint.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ActivityModificationChangeConstraint.java index e8743079b..136829be2 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ActivityModificationChangeConstraint.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ActivityModificationChangeConstraint.java @@ -191,7 +191,7 @@ protected Map> extractModifNames(Map mfMap) */ protected Set extractModifNames(Set mfSet) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Object o : mfSet) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConBox.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConBox.java index 9579bdca4..78ea0e787 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConBox.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConBox.java @@ -345,7 +345,7 @@ public static Constraint nameEquals(String name) public static Constraint nameEquals(String... name) { return new Field("Named/name", Field.Operation.INTERSECT, - new HashSet(Arrays.asList(name))); + new HashSet<>(Arrays.asList(name))); } // /** diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintAdapter.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintAdapter.java index 00b7e8f0d..6a7da4ff9 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintAdapter.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintAdapter.java @@ -149,7 +149,7 @@ protected ConversionDirectionType getDirection(Conversion conv, Pathway pathway, if (dir != null) return dir; } - Set dirs = new HashSet(); + Set dirs = new HashSet<>(); Set convSteps = conv.getStepProcessOf(); @@ -179,7 +179,7 @@ protected ConversionDirectionType getDirection(Conversion conv, Pathway pathway, */ protected ConversionDirectionType getDirection(Conversion conv, Pathway pathway) { - Set dirs = new HashSet(); + Set dirs = new HashSet<>(); // find the direction in the pathway step for (PathwayStep step : conv.getStepProcessOf()) @@ -279,7 +279,7 @@ protected Set getConvParticipants(Conversion conv, RelType type) if (dir == ConversionDirectionType.REVERSIBLE) { - HashSet set = new HashSet(conv.getLeft()); + HashSet set = new HashSet<>(conv.getLeft()); set.addAll(conv.getRight()); return set; } @@ -298,7 +298,7 @@ else if (dir == ConversionDirectionType.RIGHT_TO_LEFT) */ protected ConversionDirectionType findDirectionInPathways(Conversion conv) { - Set dirs = new HashSet(); + Set dirs = new HashSet<>(); for (PathwayStep step : conv.getStepProcessOf()) { if (step instanceof BiochemicalPathwayStep) @@ -330,7 +330,7 @@ protected ConversionDirectionType convertStepDirection(StepDirection sdir) */ protected ConversionDirectionType findDirectionInCatalysis(Conversion conv) { - Set dirs = new HashSet(); + Set dirs = new HashSet<>(); for (Control control : conv.getControlledOf()) { ConversionDirectionType dir = getCatalysisDirection(control); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintChain.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintChain.java index 02531ee0d..afa042d7b 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintChain.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConstraintChain.java @@ -56,11 +56,11 @@ public ConstraintChain(Constraint... con) public Collection generate(Match match, int... ind) { - Collection gen = new HashSet ( + Collection gen = new HashSet<> ( con[0].generate(match, ind)); - Set input = new HashSet(); - Set output = new HashSet(gen); + Set input = new HashSet<>(); + Set output = new HashSet<>(gen); int[] tempInd = {0, 1}; for (int i = 1; i < con.length; i++) diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ControlToControllerER.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ControlToControllerER.java index 2c7d83503..82ecdc0f7 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ControlToControllerER.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ControlToControllerER.java @@ -58,12 +58,12 @@ public boolean canGenerate() public Collection generate(Match match, int... ind) { Control ctrl = (Control) match.get(ind[0]); - return new HashSet(getRelatedERs(ctrl)); + return new HashSet<>(getRelatedERs(ctrl)); } public Set getRelatedERs(Control ctrl) { - Set ers = new HashSet(); + Set ers = new HashSet<>(); for (Object o : TO_CONTROLLER.getValueFromBean(ctrl)) { @@ -75,7 +75,7 @@ public Set getRelatedERs(Control ctrl) public Set getRelatedERs(PhysicalEntity pe) { - Set ers = new HashSet(); + Set ers = new HashSet<>(); if (pe instanceof Complex) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConversionSide.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConversionSide.java index fdcfcbe96..5cba98b03 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConversionSide.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ConversionSide.java @@ -106,7 +106,7 @@ else if (conv.getRight().contains(pe1)) else throw new IllegalArgumentException( "The PhysicalEntity has to be a participant of the Conversion."); - if (blacklist == null) return new HashSet(parts); + if (blacklist == null) return new HashSet<>(parts); else { ConversionDirectionType dir = getDirection(conv); @@ -115,7 +115,7 @@ else throw new IllegalArgumentException( (dir == ConversionDirectionType.RIGHT_TO_LEFT && ((relType == RelType.INPUT && parts != conv.getRight()) || (relType == RelType.OUTPUT && parts != conv.getLeft())))) return Collections.emptySet(); - return new HashSet(blacklist.getNonUbiques(parts, relType)); + return new HashSet<>(blacklist.getNonUbiques(parts, relType)); } } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/InterToPartER.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/InterToPartER.java index 858b97626..209a3af5b 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/InterToPartER.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/InterToPartER.java @@ -108,7 +108,7 @@ public Collection generate(Match match, int... ind) { Interaction inter = (Interaction) match.get(ind[0]); - Set taboo = new HashSet(); + Set taboo = new HashSet<>(); for (int i = 1; i < getVariableSize() - 1; i++) { @@ -127,7 +127,7 @@ public Collection generate(Match match, int... ind) */ protected Collection generate(Interaction inter, Set taboo) { - Set simples = new HashSet(); + Set simples = new HashSet<>(); for (Entity part : inter.getParticipant()) { @@ -154,7 +154,7 @@ protected Collection generate(Conversion conv, Direction directio if (!(direction == Direction.BOTHSIDERS || direction == Direction.ONESIDERS)) { - Set simples = new HashSet(); + Set simples = new HashSet<>(); for (Entity part : direction == Direction.ANY ? conv.getParticipant() : direction == Direction.LEFT ? conv.getLeft() : conv.getRight()) @@ -169,8 +169,8 @@ protected Collection generate(Conversion conv, Direction directio } else { - Set leftSimples = new HashSet(); - Set rightSimples = new HashSet(); + Set leftSimples = new HashSet<>(); + Set rightSimples = new HashSet<>(); for (PhysicalEntity pe : conv.getLeft()) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/LinkedPE.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/LinkedPE.java index d9b2d215b..87772c36d 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/LinkedPE.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/LinkedPE.java @@ -102,7 +102,7 @@ public Collection generate(Match match, int... ind) public Set getLinkedElements(PhysicalEntity pe) { - Set set = new HashSet(); + Set set = new HashSet<>(); set.add(pe); enrichWithGenerics(set, set); return set; diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ModificationChangeConstraint.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ModificationChangeConstraint.java index 6f3a89ba2..18d9231c7 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ModificationChangeConstraint.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ModificationChangeConstraint.java @@ -76,7 +76,7 @@ public boolean satisfies(Match match, int... ind) private Set collectTerms(Set... mods) { - Set terms = new HashSet(); + Set terms = new HashSet<>(); collectTerms(mods[0], terms); if (mods.length > 1) collectTerms(mods[1], terms); return terms; diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/OR.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/OR.java index ad7a32e80..b37613963 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/OR.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/OR.java @@ -100,7 +100,7 @@ protected int max(int[] v) @Override public Collection generate(Match match, int... ind) { - Collection gen = new HashSet(); + Collection gen = new HashSet<>(); for (MappedConst mc : con) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/Participant.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/Participant.java index 93078ee95..c9b7fcbc1 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/Participant.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/Participant.java @@ -167,7 +167,7 @@ else if (considerPathway) } else dir = getDirection(cnv); - Set> sides = new HashSet>(); + Set> sides = new HashSet<>(); if (dir == ConversionDirectionType.REVERSIBLE) { @@ -185,7 +185,7 @@ else if ((dir == ConversionDirectionType.LEFT_TO_RIGHT || dir == null)) sides.add(type == RelType.OUTPUT ? cnv.getRight() : cnv.getLeft()); } - Collection result = new HashSet(); + Collection result = new HashSet<>(); if (blacklist == null) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ParticipatesInConv.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ParticipatesInConv.java index a292dc210..a1156d633 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ParticipatesInConv.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/ParticipatesInConv.java @@ -67,7 +67,7 @@ public boolean canGenerate() @Override public Collection generate(Match match, int... ind) { - Collection result = new HashSet(); + Collection result = new HashSet<>(); PhysicalEntity pe = (PhysicalEntity) match.get(ind[0]); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/PathConstraint.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/PathConstraint.java index 4c24b38ea..aa7860aec 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/PathConstraint.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/PathConstraint.java @@ -75,7 +75,7 @@ public Collection generate(Match match, int ... ind) throw new RuntimeException("Constraint cannot generate based on null value"); Set vals = pa.getValueFromBean(ele0); - List list = new ArrayList(vals.size()); + List list = new ArrayList<>(vals.size()); for (Object o : vals) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/RelatedControl.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/RelatedControl.java index d3c99ef12..8bd75bec3 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/RelatedControl.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/RelatedControl.java @@ -88,7 +88,7 @@ public Collection generate(Match match, int... ind) assert rightContains || leftContains : "PE is not a participant."; - Set result = new HashSet(); + Set result = new HashSet<>(); ConversionDirectionType avoidDir = (leftContains && rightContains) ? null : peType == RelType.OUTPUT ? (leftContains ? ConversionDirectionType.LEFT_TO_RIGHT : ConversionDirectionType.RIGHT_TO_LEFT) : diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/XOR.java b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/XOR.java index cac508970..2be100a78 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/XOR.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/constraint/XOR.java @@ -51,7 +51,7 @@ public boolean satisfies(Match match, int... ind) @Override public Collection generate(Match match, int... ind) { - Collection gen = new HashSet ( + Collection gen = new HashSet<> ( con[0].generate(match, ind)); for (int i = 1; i < con.length; i++) @@ -59,7 +59,7 @@ public Collection generate(Match match, int... ind) if (gen.isEmpty()) break; Collection subset = con[i].generate(match, ind); - Set copy = new HashSet(subset); + Set copy = new HashSet<>(subset); copy.removeAll(gen); gen.removeAll(subset); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java b/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java index 1e5880409..90e64ffd2 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java @@ -114,7 +114,7 @@ public void writeResult(Map> matches, OutputStream ou // record mediator ids to map these interactions to detailed data if (!mediators.containsKey(s1s)) mediators.put(s1s, new HashMap>()); - if (!mediators.get(s1s).containsKey(s2s)) mediators.get(s1s).put(s2s, new HashSet()); + if (!mediators.get(s1s).containsKey(s2s)) mediators.get(s1s).put(s2s, new HashSet<>()); List meds = m.get(getMediatorLabels(), getPattern()); for (BioPAXElement med : meds) @@ -142,7 +142,7 @@ private void collect(String s1, String s2, Set modificationFeatures, Map>> map) { if (!map.containsKey(s1)) map.put(s1, new HashMap>()); - if (!map.get(s1).containsKey(s2)) map.get(s1).put(s2, new HashSet()); + if (!map.get(s1).containsKey(s2)) map.get(s1).put(s2, new HashSet<>()); map.get(s1).get(s2).addAll(modificationFeatures); } @@ -325,12 +325,12 @@ public void writeResults(String filename) throws IOException BufferedWriter writer = new BufferedWriter(new FileWriter(filename)); writer.write("Source\tType\tTarget\tSource-modifs\tSource-locs\tGained-modifs\tLost-modifs\tGained-locs\tLost-locs\tMediators"); - Set s1s = new HashSet(gainMods.keySet()); + Set s1s = new HashSet<>(gainMods.keySet()); s1s.addAll(lossMods.keySet()); for (String s1 : s1s) { - Set s2s = new HashSet(); + Set s2s = new HashSet<>(); if (gainMods.containsKey(s1)) s2s.addAll(gainMods.get(s1).keySet()); if (lossMods.containsKey(s1)) s2s.addAll(lossMods.get(s1).keySet()); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator.java index 34ff8a458..d7e3cc534 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator.java @@ -84,12 +84,12 @@ public Blacklist generateBlacklist(Model model) String source = sif.sourceID; String target = sif.targetID; - if (!neighMap.containsKey(source)) neighMap.put(source, new HashSet()); - if (!neighMap.containsKey(target)) neighMap.put(target, new HashSet()); - if (!dwstrMap.containsKey(source)) dwstrMap.put(source, new HashSet()); - if (!dwstrMap.containsKey(target)) dwstrMap.put(target, new HashSet()); - if (!upstrMap.containsKey(source)) upstrMap.put(source, new HashSet()); - if (!upstrMap.containsKey(target)) upstrMap.put(target, new HashSet()); + if (!neighMap.containsKey(source)) neighMap.put(source, new HashSet<>()); + if (!neighMap.containsKey(target)) neighMap.put(target, new HashSet<>()); + if (!dwstrMap.containsKey(source)) dwstrMap.put(source, new HashSet<>()); + if (!dwstrMap.containsKey(target)) dwstrMap.put(target, new HashSet<>()); + if (!upstrMap.containsKey(source)) upstrMap.put(source, new HashSet<>()); + if (!upstrMap.containsKey(target)) upstrMap.put(target, new HashSet<>()); neighMap.get(source).add(target); neighMap.get(target).add(source); @@ -106,7 +106,7 @@ public Blacklist generateBlacklist(Model model) Set upstr = upstrMap.get(name); Set dwstr = dwstrMap.get(name); - Set temp = new HashSet(upstr); + Set temp = new HashSet<>(upstr); upstr.removeAll(dwstr); dwstr.removeAll(temp); } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java index 37a73bbd8..53b2107f8 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java @@ -5,7 +5,6 @@ import org.biopax.paxtools.model.level3.SimplePhysicalEntity; import org.biopax.paxtools.model.level3.SmallMoleculeReference; import org.biopax.paxtools.pattern.util.Blacklist; -import org.biopax.paxtools.pattern.util.ChemicalNameNormalizer; import org.biopax.paxtools.pattern.util.RelType; import java.io.*; @@ -90,21 +89,21 @@ public Blacklist generateBlacklist(Model model) throws IOException // read interactions into maps - Map> upstrMap = new HashMap>(); - Map> dwstrMap = new HashMap>(); - final Map> neighMap = new HashMap>(); + Map> upstrMap = new HashMap<>(); + Map> dwstrMap = new HashMap<>(); + final Map> neighMap = new HashMap<>(); for (SIFInteraction sif : sifs) { String source = sif.sourceID; String target = sif.targetID; - if (!neighMap.containsKey(source)) neighMap.put(source, new HashSet()); - if (!neighMap.containsKey(target)) neighMap.put(target, new HashSet()); - if (!dwstrMap.containsKey(source)) dwstrMap.put(source, new HashSet()); - if (!dwstrMap.containsKey(target)) dwstrMap.put(target, new HashSet()); - if (!upstrMap.containsKey(source)) upstrMap.put(source, new HashSet()); - if (!upstrMap.containsKey(target)) upstrMap.put(target, new HashSet()); + if (!neighMap.containsKey(source)) neighMap.put(source, new HashSet<>()); + if (!neighMap.containsKey(target)) neighMap.put(target, new HashSet<>()); + if (!dwstrMap.containsKey(source)) dwstrMap.put(source, new HashSet<>()); + if (!dwstrMap.containsKey(target)) dwstrMap.put(target, new HashSet<>()); + if (!upstrMap.containsKey(source)) upstrMap.put(source, new HashSet<>()); + if (!upstrMap.containsKey(target)) upstrMap.put(target, new HashSet<>()); neighMap.get(source).add(target); neighMap.get(target).add(source); @@ -121,14 +120,11 @@ public Blacklist generateBlacklist(Model model) throws IOException Set upstr = upstrMap.get(name); Set dwstr = dwstrMap.get(name); - Set temp = new HashSet(upstr); + Set temp = new HashSet<>(upstr); upstr.removeAll(dwstr); dwstr.removeAll(temp); } -// writeTheGuideRankingToTuneTheDecider(model, nameMapping, upstrMap, dwstrMap, neighMap); -// if (true) return null; - Set white = readWhitelist(); Blacklist blacklist = new Blacklist(); @@ -159,19 +155,16 @@ public Blacklist generateBlacklist(Model model) throws IOException return blacklist; } - private void writeTheGuideRankingToTuneTheDecider(Model model, Map nameMapping, Map> upstrMap, Map> dwstrMap, final Map> neighMap) throws IOException + private void writeTheGuideRankingToTuneTheDecider( + Model model, Map nameMapping, + Map> upstrMap, Map> dwstrMap, final Map> neighMap) throws IOException { // Sort to degree - List names = new ArrayList(neighMap.keySet()); - Collections.sort(names, new Comparator() - { - @Override - public int compare(String o1, String o2) - { - return new Integer(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size()); - } - }); + List names = new ArrayList<>(neighMap.keySet()); + Collections.sort(names, (o1, o2) -> new Integer(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size())); SIFSearcher searcher2 = new SIFSearcher(new Fetcher(nameMapping), new ChemicalAffectsThroughControlMiner()); @@ -179,14 +172,14 @@ public int compare(String o1, String o2) // read interactions into maps - final Map> affectMap = new HashMap>(); + final Map> affectMap = new HashMap<>(); for (SIFInteraction sif : sifs2) { String source = sif.sourceID; String target = sif.targetID; - if (!affectMap.containsKey(source)) affectMap.put(source, new HashSet()); + if (!affectMap.containsKey(source)) affectMap.put(source, new HashSet<>()); affectMap.get(source).add(target); } @@ -210,15 +203,15 @@ private void generateNameMappingFileToCurate(Model model) throws IOException // read interactions into maps - final Map> neighMap = new HashMap>(); + final Map> neighMap = new HashMap<>(); for (SIFInteraction sif : sifs) { String source = sif.sourceID; String target = sif.targetID; - if (!neighMap.containsKey(source)) neighMap.put(source, new HashSet()); - if (!neighMap.containsKey(target)) neighMap.put(target, new HashSet()); + if (!neighMap.containsKey(source)) neighMap.put(source, new HashSet<>()); + if (!neighMap.containsKey(target)) neighMap.put(target, new HashSet<>()); neighMap.get(source).add(target); neighMap.get(target).add(source); @@ -226,15 +219,8 @@ private void generateNameMappingFileToCurate(Model model) throws IOException // Sort to degree - List names = new ArrayList(neighMap.keySet()); - Collections.sort(names, new Comparator() - { - @Override - public int compare(String o1, String o2) - { - return new Integer(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size()); - } - }); + List names = new ArrayList<>(neighMap.keySet()); + Collections.sort(names, (o1, o2) -> new Integer(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size())); Set> bag = collectNameSets(model); Map>> nameToSets = getNameToSetsMap(bag); @@ -243,10 +229,9 @@ public int compare(String o1, String o2) // Find and record name mapping String dir = System.getProperty("java.io.tmpdir") + File.separator; - BufferedWriter writer = new BufferedWriter(new FileWriter(dir + MAPPING_FILE)); - List remaining = new ArrayList(); + List remaining = new ArrayList<>(); for (String name : names) { remaining.add(name.toLowerCase()); @@ -257,12 +242,12 @@ public int compare(String o1, String o2) name = name.toLowerCase(); remaining.remove(name); - Map[]> mappings = getMappingsAndBasis( + Map[]> mappings = getMappingsAndBasis( name, remaining, nameToSets, intersectionMap); for (String mapped : mappings.keySet()) { - Set[] s = mappings.get(mapped); + Collection[] s = mappings.get(mapped); writer.write(name + "\t" + mapped + "\t" + s[0] + "\t" + s[1] + "\t" + s[2] + "\n"); } } @@ -275,10 +260,10 @@ public int compare(String o1, String o2) private Set> collectNameSets(Model model) { - Set> bag = new HashSet>(); + Set> bag = new HashSet<>(); for (SmallMoleculeReference smr : model.getObjects(SmallMoleculeReference.class)) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (String name : smr.getName()) { @@ -302,7 +287,7 @@ private Set> collectNameSets(Model model) private void doSomeCleaning(Set set) { - Set rem = new HashSet(); + Set rem = new HashSet<>(); for (String s : set) { if (s.contains("pathway") || s.contains("participant")) rem.add(s); @@ -312,7 +297,7 @@ private void doSomeCleaning(Set set) private void enrichWithModifications(Set set) { - for (String s : new HashSet(set)) + for (String s : new HashSet<>(set)) { if (s.endsWith("-)") || s.endsWith("+)")) { @@ -327,29 +312,29 @@ else if (s.endsWith(" zwitterion")) private Map>> getNameToSetsMap(Set> bag) { - Map>> map = new HashMap>>(); + Map>> map = new HashMap<>(); for (Set set : bag) { for (String name : set) { - if (!map.containsKey(name)) map.put(name, new HashSet>()); + if (!map.containsKey(name)) map.put(name, new HashSet<>()); map.get(name).add(set); } } return map; } - private Set getCommon(Set set1, Set set2) + private Collection getCommon(Collection set1, Collection set2) { - Set comm = new HashSet(set1); + Collection comm = new HashSet<>(set1); comm.retainAll(set2); return comm; } private List getCommon(List list1, Set set2) { - List comm = new ArrayList(); + List comm = new ArrayList<>(); for (String s : list1) { if (set2.contains(s)) comm.add(s); @@ -359,7 +344,7 @@ private List getCommon(List list1, Set set2) private Map, Set>> getIntersectionMap(Set> bag) { - Map, Set>> map = new HashMap, Set>>(); + Map, Set>> map = new HashMap<>(); for (Set set : bag) { @@ -369,7 +354,7 @@ private Map, Set>> getIntersectionMap(Set> b if (!getCommon(set, oth).isEmpty()) { - if (!map.containsKey(set)) map.put(set, new HashSet>()); + if (!map.containsKey(set)) map.put(set, new HashSet<>()); map.get(set).add(oth); } } @@ -377,10 +362,10 @@ private Map, Set>> getIntersectionMap(Set> b return map; } - private Map[]> getMappingsAndBasis(String name, List consider, + private Map[]> getMappingsAndBasis(String name, List consider, Map>> nameToSets, Map, Set>> intersectionMap) { - Map[]> map = new HashMap[]>(); + Map[]> map = new HashMap<>(); for (Set set : nameToSets.get(name)) { @@ -392,7 +377,7 @@ private Map[]> getMappingsAndBasis(String name, List for (String target : common) { - map.put(target, new Set[]{getCommon(set, other), set, other}); + map.put(target, new Collection[]{getCommon(set, other), set, other}); } } } @@ -424,7 +409,7 @@ private Set readWhitelist() throws FileNotFoundException "Not whitelisting anything."); return null; } - Set names = new HashSet(); + Set names = new HashSet<>(); Scanner sc = new Scanner(new File(WHITELIST_FILE)); while (sc.hasNextLine()) { @@ -473,7 +458,7 @@ public Set fetchID(BioPAXElement ele) /** * The class to decide if a molecule is ubique, its score and its context of ubiquity. */ - static interface Decider + interface Decider { /** * Tells if the molecule is ubique in at least one context. @@ -481,7 +466,7 @@ static interface Decider * @param upstrOnly number of upstream neighbors in the used-to-produce network, that are not also at downstream * @param dwstrOnly number of downstream neighbors in the used-to-produce network, that are not also at upstream */ - public boolean isUbique(int neighborSize, int upstrOnly, int dwstrOnly); + boolean isUbique(int neighborSize, int upstrOnly, int dwstrOnly); /** * Gets the ubiquity score of the ubique molecule. This score is used for comparing ubiques @@ -490,7 +475,7 @@ static interface Decider * @param upstrOnly number of upstream neighbors in the used-to-produce network, that are not also at downstream * @param dwstrOnly number of downstream neighbors in the used-to-produce network, that are not also at upstream */ - public int getScore(int neighborSize, int upstrOnly, int dwstrOnly); + int getScore(int neighborSize, int upstrOnly, int dwstrOnly); /** * Gets the context of ubiquity. A molecule can be ubiquitously consumed, or can be @@ -499,9 +484,7 @@ static interface Decider * @param upstrOnly number of upstream neighbors in the used-to-produce network, that are not also at downstream * @param dwstrOnly number of downstream neighbors in the used-to-produce network, that are not also at upstream */ - public RelType getContext(int neighborSize, int upstrOnly, int dwstrOnly); + RelType getContext(int neighborSize, int upstrOnly, int dwstrOnly); } - - } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java index 70e186de0..7a58deaf9 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java @@ -25,7 +25,7 @@ public class CommonIDFetcher implements IDFetcher public Set fetchID(BioPAXElement ele) { - Set set = new HashSet(); + Set set = new HashSet<>(); if (ele instanceof SmallMoleculeReference || ele instanceof SmallMolecule) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java index 9b6dd25e1..2955000a8 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java @@ -23,8 +23,8 @@ public class ConfigurableIDFetcher implements IDFetcher * Constructor. */ public ConfigurableIDFetcher() { - seqDbStartsWithOrEquals = new ArrayList(); - chemDbStartsWithOrEquals = new ArrayList(); + seqDbStartsWithOrEquals = new ArrayList<>(); + chemDbStartsWithOrEquals = new ArrayList<>(); useNameWhenNoDbMatch = false; } @@ -83,7 +83,7 @@ public ConfigurableIDFetcher useNameWhenNoDbMatch(boolean useNameWhenNoDbMatch) public Set fetchID(BioPAXElement ele) { - Set set = new HashSet(); + Set set = new HashSet<>(); if(ele instanceof XReferrable) { //Iterate the db priority list, match/filter all xrefs to collect the IDs of given type, until 'set' is not empty. diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/Dialog.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/Dialog.java index e8668af7b..56f3b9241 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/Dialog.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/Dialog.java @@ -429,7 +429,7 @@ public void keyReleased(KeyEvent keyEvent){} */ private Object[] getAvailablePatterns() { - List minerList = new ArrayList(); + List minerList = new ArrayList<>(); if (miners != null && miners.length > 0) { minerList.addAll(Arrays.asList(miners)); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java index 1174fc002..8b0c6770d 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java @@ -46,7 +46,7 @@ public static boolean write(Set inters, OutputStream out) if (!inters.isEmpty()) { - List interList = new ArrayList(inters); + List interList = new ArrayList<>(inters); Collections.sort(interList); try { OutputStreamWriter writer = new OutputStreamWriter(out); @@ -86,7 +86,7 @@ public static boolean writeInteractions(Set inters, OutputStream if (!inters.isEmpty()) { - List interList = new ArrayList(inters); + List interList = new ArrayList<>(inters); Collections.sort(interList); try { @@ -163,9 +163,9 @@ private static Map> collectEntityRefs(Collection()); + map.put(inter.sourceID, new HashSet<>()); if (!map.containsKey(inter.targetID)) - map.put(inter.targetID, new HashSet()); + map.put(inter.targetID, new HashSet<>()); map.get(inter.sourceID).addAll(inter.sourceERs); map.get(inter.targetID).addAll(inter.targetERs); @@ -175,20 +175,20 @@ private static Map> collectEntityRefs(Collection elements) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (BioPAXElement ele : elements) { String name = ele.getModelInterface().getName(); set.add(name.substring(name.lastIndexOf(".") + 1)); } - List list = new ArrayList(set); + List list = new ArrayList<>(set); Collections.sort(list); return concat(list); } private static String getValue(Set elements, PathAccessor pa) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Object o : pa.getValueFromBeans(elements)) { if(o instanceof RelationshipXref) @@ -203,7 +203,7 @@ private static String getValue(Set elements, PathAccessor pa) set.add(o.toString()); } } - List list = new ArrayList(set); + List list = new ArrayList<>(set); Collections.sort(list); return concat(list); } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java index 4bab9bc07..2594f85c5 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java @@ -272,7 +272,7 @@ public boolean isInhibition(Control ctrl) */ public Set toStringSet(Set set) { - List list = new ArrayList(set); + List list = new ArrayList<>(set); Collections.sort(list, new Comparator() { @@ -303,7 +303,7 @@ public int compare(ModificationFeature o1, ModificationFeature o2) */ private Set getInString(List list) { - Set text = new HashSet(list.size()); + Set text = new HashSet<>(list.size()); for (ModificationFeature mf : list) { @@ -402,7 +402,7 @@ public String getPositionInString(ModificationFeature mf) protected Set getModifications(Match m, String label) { PhysicalEntity pe = (PhysicalEntity) m.get(label, getPattern()); - return toStringSet(new HashSet(FEAT_ACC.getValueFromBean(pe))); + return toStringSet(new HashSet<>(FEAT_ACC.getValueFromBean(pe))); } /** @@ -494,7 +494,7 @@ protected PhysicalEntityChain getChain(Match m, String memLabel, String comLabel protected void removeCommon(Set set1, Set set2) { - Set common = new HashSet(set1); + Set common = new HashSet<>(set1); common.retainAll(set2); set1.removeAll(common); set2.removeAll(common); @@ -586,7 +586,7 @@ protected void writeResultAsSIF(Map> matches, OutputS } // Memory for already written pairs. - Set mem = new HashSet(); + Set mem = new HashSet<>(); String mid = getRelationType() == null ? "\t" : "\trelation\t"; @@ -722,7 +722,7 @@ protected void writeResultDetailed(Map> matches, Outp } // memory for already written lines - Set mem = new HashSet(); + Set mem = new HashSet<>(); // write values @@ -791,7 +791,7 @@ public Set createSIFInteraction(Match m, IDFetcher fetcher) SIFType sifType = ((SIFMiner) this).getSIFType(); - Set set = new HashSet(); + Set set = new HashSet<>(); for (String source : sources) { @@ -801,16 +801,16 @@ public Set createSIFInteraction(Match m, IDFetcher fetcher) else if (sifType.isDirected() || source.compareTo(target) < 0) { set.add(new SIFInteraction(source, target, sourceBpe, targetBpe, sifType, - new HashSet(m.get(getMediatorLabels(), getPattern())), - new HashSet(m.get(getSourcePELabels(), getPattern())), - new HashSet(m.get(getTargetPELabels(), getPattern())))); + new HashSet<>(m.get(getMediatorLabels(), getPattern())), + new HashSet<>(m.get(getSourcePELabels(), getPattern())), + new HashSet<>(m.get(getTargetPELabels(), getPattern())))); } else { set.add(new SIFInteraction(target, source, targetBpe, sourceBpe, sifType, - new HashSet(m.get(getMediatorLabels(), getPattern())), - new HashSet(m.get(getTargetPELabels(), getPattern())), - new HashSet(m.get(getSourcePELabels(), getPattern())))); + new HashSet<>(m.get(getMediatorLabels(), getPattern())), + new HashSet<>(m.get(getTargetPELabels(), getPattern())), + new HashSet<>(m.get(getSourcePELabels(), getPattern())))); } } } @@ -869,7 +869,7 @@ protected Set getIdentifiers(Match m, String label) if (idFetcher != null) return idFetcher.fetchID(el); - Set set = new HashSet(); + Set set = new HashSet<>(); if (el instanceof ProteinReference) { set.add(getGeneSymbol((ProteinReference) el)); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/OutputColumn.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/OutputColumn.java index 0fee13606..ae92c0010 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/OutputColumn.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/OutputColumn.java @@ -81,7 +81,7 @@ public String getColumnValue(SIFInteraction inter) case COMMENTS: return concat(inter.getMediatorComments()); case CUSTOM: { - Set set = new HashSet(); + Set set = new HashSet<>(); for (PathAccessor acc : accessors) { for (Object o : acc.getValueFromBeans(inter.mediators)) @@ -89,7 +89,7 @@ public String getColumnValue(SIFInteraction inter) set.add(o.toString()); } } - List list = new ArrayList(set); + List list = new ArrayList<>(set); Collections.sort(list); return concat(list); } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/RelatedGenesOfInteractionsMiner.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/RelatedGenesOfInteractionsMiner.java index ea6be44c3..65ff1c0fe 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/RelatedGenesOfInteractionsMiner.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/RelatedGenesOfInteractionsMiner.java @@ -56,7 +56,7 @@ public void writeResult(Map> matches, OutputStream ou for (BioPAXElement ele : matches.keySet()) { - Set syms = new HashSet(); + Set syms = new HashSet<>(); for (Match m : matches.get(ele)) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFInteraction.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFInteraction.java index cf95a76c6..7fc8187ce 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFInteraction.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFInteraction.java @@ -30,8 +30,8 @@ public SIFInteraction(String sourceID, String targetID, BioPAXElement sourceER, { this.sourceID = sourceID; this.targetID = targetID; - this.sourceERs = new HashSet(); - this.targetERs = new HashSet(); + this.sourceERs = new HashSet<>(); + this.targetERs = new HashSet<>(); this.sourceERs.add(sourceER); this.targetERs.add(targetER); @@ -114,7 +114,7 @@ public String toString() */ public List getMediatorIDs() { - List ids = new ArrayList(mediators.size()); + List ids = new ArrayList<>(mediators.size()); for (BioPAXElement ele : mediators) { @@ -149,7 +149,7 @@ public List getPublicationIDs(boolean pubmed) Set xrefs = harvestPublicationXrefs(mediators.toArray(new BioPAXElement[mediators.size()])); Set set = pubmed ? harvestPMIDs(xrefs) : harvestPMCIDs(xrefs); - List list = new ArrayList(set); + List list = new ArrayList<>(set); Collections.sort(list); return list; @@ -165,7 +165,7 @@ public List getPublicationIDs(boolean pubmed) */ private Set harvestPublicationXrefs(BioPAXElement... ele) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Object o : xrefAcc.getValueFromBeans(Arrays.asList(ele))) { @@ -205,7 +205,7 @@ private Set harvestPMCIDs(Set xrefs) */ private Set harvestXrefs(Set xrefs, String dbID) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (PublicationXref xref : xrefs) { @@ -236,7 +236,7 @@ private Set harvestXrefs(Set xrefs, String dbID) */ public Set getPathways() { - Set set = new HashSet(); + Set set = new HashSet<>(); for (PathAccessor pAcc : pathwayAcc) { @@ -256,7 +256,7 @@ public Set getPathways() public List getPathwayNames() { Set set = getPathways(); - List names = new ArrayList(); + List names = new ArrayList<>(); for (Pathway p : set) { @@ -274,7 +274,7 @@ public List getPathwayNames() */ public List getPathwayUris() { - List uris = new ArrayList(); + List uris = new ArrayList<>(); for (Pathway p : getPathways()) { String uri = p.getUri(); if (!uris.contains(uri)) uris.add(uri); @@ -291,7 +291,7 @@ public List getPathwayUris() */ public Set getDataSources() { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Object o : dataSourceAcc.getValueFromBeans(mediators)) { @@ -327,7 +327,7 @@ public Set getCellularLocationsOfSource() */ private Set getCellularLocations(Set eles) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Object o : locAcc.getValueFromBeans(eles)) { @@ -343,7 +343,7 @@ private Set getCellularLocations(Set eles) */ public Set getMediatorComments() { - Set comments = new HashSet(); + Set comments = new HashSet<>(); for (BioPAXElement med : mediators) { if (med instanceof Level3Element) comments.addAll(((Level3Element) med).getComment()); @@ -362,8 +362,8 @@ public Set getMediatorComments() public static List getSortedGeneNames(Collection sifInts, SIFType... type) { - Set genes = new HashSet(); - Set types = new HashSet(Arrays.asList(type)); + Set genes = new HashSet<>(); + Set types = new HashSet<>(Arrays.asList(type)); // collect gene names @@ -377,7 +377,7 @@ public static List getSortedGeneNames(Collection sifInts // sort all gene names - List names = new ArrayList(genes); + List names = new ArrayList<>(genes); Collections.sort(names); return names; @@ -392,7 +392,7 @@ public static List getSortedGeneNames(Collection sifInts public static boolean[][] convertToAdjacencyMatrix(Collection sifInts, SIFType... type) { - Set types = new HashSet(Arrays.asList(type)); + Set types = new HashSet<>(Arrays.asList(type)); // collect gene names List names = getSortedGeneNames(sifInts, type); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFSearcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFSearcher.java index bdadd937e..b6785da87 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFSearcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFSearcher.java @@ -70,7 +70,7 @@ public SIFSearcher(SIFMiner... miners) public SIFSearcher(IDFetcher idFetcher, SIFType... types) { this.idFetcher = idFetcher; - this.types = new HashSet(Arrays.asList(types)); + this.types = new HashSet<>(Arrays.asList(types)); if (idFetcher == null) this.idFetcher = new SimpleIDFetcher();//gets URIs } @@ -93,7 +93,7 @@ private void initMiners() { try { - this.miners = new ArrayList(); + this.miners = new ArrayList<>(); for (SIFType type : types) { @@ -177,7 +177,7 @@ public Set searchSIF(final Model model) } } - return new HashSet(map.values()); + return new HashSet<>(map.values()); } /** @@ -216,7 +216,7 @@ public boolean searchSIF(Model model, OutputStream out, SIFToText stt) if (!inters.isEmpty()) { - List interList = new ArrayList(inters); + List interList = new ArrayList<>(inters); Collections.sort(interList); try { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/util/Blacklist.java b/pattern/src/main/java/org/biopax/paxtools/pattern/util/Blacklist.java index 6b81ad9ca..b93a1b86d 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/util/Blacklist.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/util/Blacklist.java @@ -151,7 +151,7 @@ public void write(String filename) */ public void write(OutputStream os) { - List ids = new ArrayList(score.keySet()); + List ids = new ArrayList<>(score.keySet()); final Map score = this.score; Collections.sort(ids, new Comparator() { @@ -221,7 +221,7 @@ private RelType convertContext(String type) */ private Set getLeastUbique(Collection ids) { - Set select = new HashSet(); + Set select = new HashSet<>(); int s = getLeastScore(ids); @@ -426,7 +426,7 @@ public Set getNonUbiques(Set entities, RelType c Collection ubiques = getUbiques(entities, ctx); if (ubiques.isEmpty()) return entities; - Set result = new HashSet(entities); + Set result = new HashSet<>(entities); result.removeAll(ubiques); return result; } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java b/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java index 93f7fc9d0..222b6abea 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java @@ -1,13 +1,10 @@ package org.biopax.paxtools.pattern.util; import org.biopax.paxtools.controller.PathAccessor; -import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.SimplePhysicalEntity; import org.biopax.paxtools.model.level3.SmallMoleculeReference; -import java.io.FileInputStream; -import java.io.FileNotFoundException; import java.util.*; /** @@ -20,19 +17,10 @@ public class ChemicalNameNormalizer { /** - * Mapping from the a small molecule to the one that contains the standard name. + * Mapping from a small molecule to the one that contains the standard name. */ Map map; - public static void main(String[] args) throws FileNotFoundException - { - SimpleIOHandler reader = new SimpleIOHandler(); - Model model = reader.convertFromOWL(new FileInputStream( - "/home/ozgun/Projects/biopax-pattern/All-Data.owl")); - - new ChemicalNameNormalizer(model); - } - /** * Gets the standard name of the small molecule. * @param smr the molecule to check standard name @@ -50,10 +38,9 @@ public String getName(SmallMoleculeReference smr) */ public ChemicalNameNormalizer(Model model) { - map = new HashMap(); - - Set standard = new HashSet(); - Set other = new HashSet(); + map = new HashMap<>(); + Set standard = new HashSet<>(); + Set other = new HashSet<>(); for (SmallMoleculeReference smr : model.getObjects(SmallMoleculeReference.class)) { @@ -67,7 +54,6 @@ public ChemicalNameNormalizer(Model model) Map> smrNames = collectNames(false, standard, other); Map> smNames = collectNames(true, standard, other); - // Unify names of standards Map> standardSelfMatch = @@ -103,9 +89,8 @@ public ChemicalNameNormalizer(Model model) enrichNamesWithMatchings(selfMatch, smrNames); enrichNamesWithMatchings(selfMatch, smNames); - Set missed = new HashSet(); - Map> multiMap = - new HashMap>(); + Set missed = new HashSet<>(); + Map> multiMap = new HashMap<>(); for (SmallMoleculeReference smr : other) { @@ -131,7 +116,6 @@ else if (matching.size() > 1) Set matches = multiMap.get(smr); SmallMoleculeReference rep = selectRepresentative(matches, map); - map.put(smr, rep); for (SmallMoleculeReference match : matches) @@ -139,14 +123,14 @@ else if (matching.size() > 1) if (match == rep) continue; if (map.containsKey(match)) { - if (map.get(match) == rep) continue; - - System.out.println("Already matched " + match.getDisplayName() + " to " + - map.get(match).getDisplayName() + ". This one is " + rep.getDisplayName()); + if (map.get(match) == rep) + continue; +// System.out.println("Already matched " + match.getDisplayName() + " to " + +// map.get(match).getDisplayName() + ". This one is " + rep.getDisplayName()); } else if (map.values().contains(match)) { - System.out.println(match.getDisplayName() + " was mapped from another chem"); +// System.out.println(match.getDisplayName() + " was mapped from another chem"); } else map.put(match, rep); } @@ -163,22 +147,18 @@ else if (map.values().contains(match)) System.out.println("multiCnt = " + multiMap.size()); System.out.println("missCnt = " + missed.size()); System.out.println(); - -// printTopPart("Multi match", multiMap, 50); -// printTopPart("Miss-match", missed, 50); } private Map> collectNames(boolean peLevel, Set... sets) { - Map> map = - new HashMap>(); + Map> map = new HashMap<>(); for (Set set : sets) { for (SmallMoleculeReference smr : set) { - map.put(smr, new HashSet()); + map.put(smr, new HashSet<>()); if (!peLevel) { @@ -218,7 +198,7 @@ else if (dispName.endsWith(" zwitterion")) if (name == null) return Collections.emptySet(); - Set matching = new HashSet(); + Set matching = new HashSet<>(); for (SmallMoleculeReference ref : smrs) { @@ -232,12 +212,12 @@ private Set getMatching(SmallMoleculeReference smr, Set standard, Map> smrNames, Map> smNames) { - Set matching = new HashSet(); + Set matching = new HashSet<>(); for (SmallMoleculeReference std : standard) { if (std.getDisplayName() != null && smr.getDisplayName() != null && - std.getDisplayName().toLowerCase().equals(smr.getDisplayName().toLowerCase())) + std.getDisplayName().equalsIgnoreCase(smr.getDisplayName())) matching.add(std); } @@ -288,8 +268,7 @@ private Map> getSelfMatching Set smrs, Map> smrNames, Map> smNames, boolean normalizeName) { - Map> map = - new HashMap>(); + Map> map = new HashMap<>(); for (SmallMoleculeReference smr : smrs) { @@ -313,7 +292,7 @@ private Map> getSelfMatching private Map getInteractionCounts( Set... smrSets) { - Map cnt = new HashMap(); + Map cnt = new HashMap<>(); for (Set smrSet : smrSets) { @@ -327,63 +306,6 @@ private Map getInteractionCounts( return cnt; } - private List getSortedList(Collection smrs, - final Map cnt) - { - List list = new ArrayList(smrs); - Collections.sort(list, new Comparator() - { - @Override - public int compare(SmallMoleculeReference o1, SmallMoleculeReference o2) - { - return cnt.get(o2).compareTo(cnt.get(o1)); - } - }); - - return list; - } - - private void printTopPart(String listName, Set smrs, int upTo) - { - Map cnt = getInteractionCounts(smrs); - List list = getSortedList(smrs, cnt); - - int i = 0; - - System.out.println(listName + "\n--------------"); - for (SmallMoleculeReference smr : list) - { - System.out.println(cnt.get(smr) + "\t" + smr.getDisplayName()); - - if (++i == upTo) break; - } - System.out.println(); - } - - private void printTopPart(String listName, - Map> smrMap, int upTo) - { - Map cnt = getInteractionCounts(smrMap.keySet()); - List list = getSortedList(smrMap.keySet(), cnt); - - int i = 0; - - System.out.println(listName + "\n--------------"); - for (SmallMoleculeReference smr : list) - { - System.out.print(cnt.get(smr) + "\t" + smr.getDisplayName() + "\t"); - - for (SmallMoleculeReference match : smrMap.get(smr)) - { - System.out.print("\t" + match.getDisplayName()); - } - System.out.println(); - - if (++i == upTo) break; - } - System.out.println(); - } - private void enrichNamesWithMatchings( Map> matchMap, Map> names) @@ -412,33 +334,28 @@ private boolean isGeneric(SmallMoleculeReference smr) private SmallMoleculeReference selectRepresentative(Set smrs, final Map map) { - List list = new ArrayList(smrs); + List list = new ArrayList<>(smrs); final Map cnt = getInteractionCounts(smrs); - Collections.sort(list, new Comparator() - { - @Override - public int compare(SmallMoleculeReference o1, SmallMoleculeReference o2) + Collections.sort(list, (o1, o2) -> { + if (map.containsValue(o1)) { - if (map.containsValue(o1)) - { - if (!map.containsValue(o2)) return -1; - } - else - { - if (map.containsValue(o2)) return 1; - } - - if (!cnt.get(o1).equals(cnt.get(o2))) return cnt.get(o2).compareTo(cnt.get(o1)); + if (!map.containsValue(o2)) return -1; + } + else + { + if (map.containsValue(o2)) return 1; + } - if (o1.getDisplayName().endsWith(")")) - { - if (!o2.getDisplayName().endsWith(")")) return -1; - } - else if (o2.getDisplayName().endsWith(")")) return 1; + if (!cnt.get(o1).equals(cnt.get(o2))) return cnt.get(o2).compareTo(cnt.get(o1)); - return o1.getDisplayName().compareTo(o2.getDisplayName()); + if (o1.getDisplayName().endsWith(")")) + { + if (!o2.getDisplayName().endsWith(")")) return -1; } + else if (o2.getDisplayName().endsWith(")")) return 1; + + return o1.getDisplayName().compareTo(o2.getDisplayName()); }); return list.get(0); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/util/DifferentialModificationUtil.java b/pattern/src/main/java/org/biopax/paxtools/pattern/util/DifferentialModificationUtil.java index fe1444b7c..e5c0ea0fc 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/util/DifferentialModificationUtil.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/util/DifferentialModificationUtil.java @@ -26,13 +26,13 @@ public static Set[] getChangedModifications(PhysicalEntity Set set1 = collectFeatures(before); Set set2 = collectFeatures(after); - Set temp = new HashSet(set1); + Set temp = new HashSet<>(set1); set1.removeAll(set2); set2.removeAll(temp); // Remove common features that can be deemed semantically equivalent - Set furtherRemove = new HashSet(); + Set furtherRemove = new HashSet<>(); for (Modification m1 : set1) { @@ -59,7 +59,7 @@ public static Set collectChangedPhosphorylationSites(PhysicalEntity befo PhysicalEntity after, boolean gained) { Set set = getChangedModifications(before, after)[gained ? 0 : 1]; - Set sites = new HashSet(); + Set sites = new HashSet<>(); for (ModificationFeature mf : set) { String lett = getPhosphoSiteLetter(mf); @@ -77,7 +77,7 @@ public static Set collectChangedPhosphorylationSites(PhysicalEntity befo private static Set collectFeatures(PhysicalEntity pe) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (EntityFeature f : pe.getFeature()) { @@ -91,7 +91,7 @@ private static Set collectFeatures(Set wrappe { if (wrappers.isEmpty()) return Collections.emptySet(); - Set set = new HashSet(); + Set set = new HashSet<>(); for (Modification wrapper : wrappers) { diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/util/PhysicalEntityChain.java b/pattern/src/main/java/org/biopax/paxtools/pattern/util/PhysicalEntityChain.java index abe20f19b..8240693a8 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/util/PhysicalEntityChain.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/util/PhysicalEntityChain.java @@ -128,7 +128,7 @@ protected PhysicalEntity[] fillArray(PhysicalEntity parent, PhysicalEntity targe */ public Set getCellularLocations() { - Set locs = new HashSet(); + Set locs = new HashSet<>(); for (PhysicalEntity pe : pes) { CellularLocationVocabulary voc = pe.getCellularLocation(); @@ -229,7 +229,7 @@ public enum Activity */ public Set getModifications() { - Set set = new HashSet(); + Set set = new HashSet<>(); for (PhysicalEntity pe : pes) { diff --git a/pattern/src/temp/java/org/biopax/paxtools/pattern/PCSiteSIFTest.java b/pattern/src/temp/java/org/biopax/paxtools/pattern/PCSiteSIFTest.java index 533c3dfbc..630bd1d8c 100644 --- a/pattern/src/temp/java/org/biopax/paxtools/pattern/PCSiteSIFTest.java +++ b/pattern/src/temp/java/org/biopax/paxtools/pattern/PCSiteSIFTest.java @@ -26,7 +26,7 @@ private void compare() throws IOException Map names1 = parseFileNames(site1); Map names2 = parseFileNames(site2); - Set dbs = new HashSet(names1.keySet()); + Set dbs = new HashSet<>(names1.keySet()); dbs.retainAll(names2.keySet()); for (String db : dbs) @@ -71,20 +71,20 @@ private void compareTwoSIFFiles(String file1, String file2) throws IOException Map> map1 = parseSIFFIle(file1); Map> map2 = parseSIFFIle(file2); - Set types = new HashSet(map1.keySet()); + Set types = new HashSet<>(map1.keySet()); types.retainAll(map2.keySet()); for (String type : types) { System.out.print(type); - Set set1 = new HashSet(map1.get(type)); - Set set2 = new HashSet(set1); + Set set1 = new HashSet<>(map1.get(type)); + Set set2 = new HashSet<>(set1); set1.removeAll(map2.get(type)); set2.retainAll(map2.get(type)); System.out.print("\t" + set1.size() + "\t" + set2.size()); - Set set3 = new HashSet(map2.get(type)); + Set set3 = new HashSet<>(map2.get(type)); set3.removeAll(set2); System.out.println("\t" + set3.size()); @@ -118,7 +118,7 @@ private Map> parseSIFFIle(String file) throws IOException if (type == null) System.out.println(token[1]); boolean directed = type.isDirected(); - if (!map.containsKey(token[1])) map.put(token[1], new HashSet()); + if (!map.containsKey(token[1])) map.put(token[1], new HashSet<>()); String s = directed || token[0].compareTo(token[2]) < 0 ? token[0] + " " + token[2] : diff --git a/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java b/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java index 48fac4c44..387460800 100644 --- a/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java +++ b/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java @@ -47,7 +47,7 @@ private void compareSIFFIles() throws IOException private Set load(String file) throws FileNotFoundException { - Set set = new HashSet(); + Set set = new HashSet<>(); Scanner sc = new Scanner(new File(file)); while (sc.hasNextLine()) { @@ -116,7 +116,7 @@ private void namesOfPathwaysThatContainReversibleReactions() p.add(new Empty(new PathConstraint("Catalysis/catalysisDirection")), "Cat"); p.add(new Empty(new PathConstraint("Pathway/pathwayComponent:Pathway")), "Pathway"); - List pats = new ArrayList( + List pats = new ArrayList<>( Searcher.searchAndCollect(model, p, 0, Pathway.class)); Collections.sort(pats, new Comparator() @@ -147,7 +147,7 @@ private void extractSignalink() throws IOException { BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/signalink-raw.txt")); - Set set = new HashSet(); + Set set = new HashSet<>(); for (String line = reader.readLine(); line != null; line = reader.readLine()) { String[] token = line.split(";"); @@ -269,8 +269,8 @@ private void printVennIntersections() throws FileNotFoundException for (int i = 1; i < Math.pow(2, file.length); i++) { - Set> intersectSets = new HashSet>(); - Set> subtractSets = new HashSet>(); + Set> intersectSets = new HashSet<>(); + Set> subtractSets = new HashSet<>(); String name = ""; for (int j = 0; j < file.length; j++) @@ -287,7 +287,7 @@ private void printVennIntersections() throws FileNotFoundException } boolean first = true; - Set set = new HashSet(); + Set set = new HashSet<>(); for (Set inset : intersectSets) { if (first) @@ -305,7 +305,7 @@ private void printVennIntersections() throws FileNotFoundException System.out.println(name + "\t" + set.size()); } - Set all = new HashSet(); + Set all = new HashSet<>(); for (Set set : sets) { all.addAll(set); @@ -318,7 +318,7 @@ private void checkOverlap() throws Throwable // Map> map = readSIFFile("/home/ozgun/Projects/chibe/portal-cache/PC.sif"); Map> map = readSIFFile("/home/ozgun/PC.sif"); - List types = new ArrayList(Arrays.asList(SIFEnum.values())); + List types = new ArrayList<>(Arrays.asList(SIFEnum.values())); types.retainAll(map.keySet()); printOverlaps(map, types.subList(0, 8), false); @@ -339,13 +339,13 @@ private void printOverlaps(Map> map, List types, for (SIFType type2 : types) { - Set set = new HashSet(map.get(type)); + Set set = new HashSet<>(map.get(type)); set.retainAll(map.get(type2)); int size = set.size(); if (tryReversing) { - set = new HashSet(map.get(type)); + set = new HashSet<>(map.get(type)); set.retainAll(negatePairs(map.get(type2))); if (set.size() > size) size = set.size(); } @@ -359,7 +359,7 @@ private void printOverlaps(Map> map, List types, private Set negatePairs(Set set) { - Set neg = new HashSet(); + Set neg = new HashSet<>(); for (String pair : set) { String[] tok = pair.split("\t"); @@ -372,7 +372,7 @@ private Set negatePairs(Set set) private Set readPairsFromSIFFile(String file, boolean directed) throws FileNotFoundException { Scanner sc = new Scanner(new File(file)); - Set set = new HashSet(); + Set set = new HashSet<>(); while(sc.hasNextLine()) { @@ -403,7 +403,7 @@ private Map> readSIFFile(String file) throws FileNotFoundEx SIFType type = SIFEnum.typeOf(token[1]); if (type == null) continue; - if (!map.containsKey(type)) map.put(type, new HashSet()); + if (!map.containsKey(type)) map.put(type, new HashSet<>()); map.get(type).add(token[0] + "\t" + token[2]); if (!type.isDirected()) map.get(type).add(token[2] + "\t" + token[0]); @@ -427,7 +427,7 @@ private Map> readSIFFile2(String file) throws FileNotFoundE SIFType type = SIFEnum.typeOf(token[1]); if (type == null) continue; - if (!map.containsKey(type)) map.put(type, new HashSet()); + if (!map.containsKey(type)) map.put(type, new HashSet<>()); map.get(type).add(token[0] + "\t" + type.getTag() + "\t" + token[2]); } @@ -481,7 +481,7 @@ private void compareModels(Model m1, Model m2) private static void compareSIFs() throws FileNotFoundException { - Set set1 = new HashSet(); + Set set1 = new HashSet<>(); Scanner sc = new Scanner(new File("/home/ozgun/Projects/causality/PC/controls-expression-of.txt")); while (sc.hasNextLine()) { @@ -489,7 +489,7 @@ private static void compareSIFs() throws FileNotFoundException set1.add(tok[0] + " " + tok[1]); } - Set set2 = new HashSet(); + Set set2 = new HashSet<>(); sc = new Scanner(new File("/home/ozgun/Projects/chibe/PC/controls-expression-of.txt")); while (sc.hasNextLine()) { diff --git a/pattern/src/temp/java/org/biopax/paxtools/pattern/UbiqueStatHelper.java b/pattern/src/temp/java/org/biopax/paxtools/pattern/UbiqueStatHelper.java index 8d5c85ab5..7e581a24c 100644 --- a/pattern/src/temp/java/org/biopax/paxtools/pattern/UbiqueStatHelper.java +++ b/pattern/src/temp/java/org/biopax/paxtools/pattern/UbiqueStatHelper.java @@ -67,22 +67,22 @@ private void generateStats(String helperSIF, String statFile) throws IOException if (token[1].equals(SIFEnum.USED_TO_PRODUCE.getTag())) { - if (!dwMap.containsKey(token[0])) dwMap.put(token[0], new HashSet()); - if (!upMap.containsKey(token[2])) upMap.put(token[2], new HashSet()); + if (!dwMap.containsKey(token[0])) dwMap.put(token[0], new HashSet<>()); + if (!upMap.containsKey(token[2])) upMap.put(token[2], new HashSet<>()); dwMap.get(token[0]).add(token[2]); upMap.get(token[2]).add(token[0]); } else if (token[1].equals(SIFEnum.CHEMICAL_AFFECTS.getTag())) { - if (!affectMap.containsKey(token[0])) affectMap.put(token[0], new HashSet()); + if (!affectMap.containsKey(token[0])) affectMap.put(token[0], new HashSet<>()); affectMap.get(token[0]).add(token[2]); } } - Set degreeSet = new HashSet(dwMap.keySet()); + Set degreeSet = new HashSet<>(dwMap.keySet()); degreeSet.addAll(upMap.keySet()); - List degreeList = new ArrayList(degreeSet); - List ctrlList = new ArrayList(affectMap.keySet()); + List degreeList = new ArrayList<>(degreeSet); + List ctrlList = new ArrayList<>(affectMap.keySet()); Collections.sort(degreeList, new Comparator() { @@ -128,7 +128,7 @@ private Integer getDegree(String name, Map> upMap, Map> upMap, Map> dwMap) { if (!upMap.containsKey(name)) return 0; - Set up = new HashSet(upMap.get(name)); + Set up = new HashSet<>(upMap.get(name)); if (dwMap.containsKey(name)) up.removeAll(dwMap.get(name)); return up.size(); } @@ -136,7 +136,7 @@ private int getUpOnly(String name, Map> upMap, Map> upMap, Map> dwMap) { if (!dwMap.containsKey(name)) return 0; - Set dw = new HashSet(dwMap.get(name)); + Set dw = new HashSet<>(dwMap.get(name)); if (upMap.containsKey(name)) dw.removeAll(upMap.get(name)); return dw.size(); } diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java b/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java index 4224c2865..4ff1023c1 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java @@ -19,18 +19,16 @@ /** * @author Ozgun Babur */ -//@Ignore public class DBParsers { @Test @Ignore public void extractSignalink() throws IOException { - BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/signalink-raw.txt")); + BufferedReader reader = new BufferedReader(new FileReader( + "/home/ozgun/Desktop/signal-db/signalink-raw.txt")); -// Map refCnt = new HashMap(); - - Set set = new HashSet(); + Set set = new HashSet<>(); for (String line = reader.readLine(); line != null; line = reader.readLine()) { String[] token = line.split(";"); @@ -52,7 +50,7 @@ public void extractSignalink() throws IOException if (type.contains("undirected")) continue; if (!type.contains("directed")) continue; - Set refs = new HashSet(); + Set refs = new HashSet<>(); if (pubs != null) { for (String s : pubs.split("\\|")) @@ -82,9 +80,8 @@ public void extractSignalink() throws IOException reader.close(); -// printOrdered(refCnt, 3); - - BufferedWriter writer = new BufferedWriter(new FileWriter("/home/ozgun/Desktop/signal-db/signalink-extracted-from-raw-nopred.txt")); + BufferedWriter writer = new BufferedWriter(new FileWriter( + "/home/ozgun/Desktop/signal-db/signalink-extracted-from-raw-nopred.txt")); for (String s : set) { @@ -96,7 +93,7 @@ public void extractSignalink() throws IOException System.out.println("set.size() = " + set.size()); } - private static final Set PRED_REF = new HashSet(Arrays.asList(("22110040\t" + + private static final Set PRED_REF = new HashSet<>(Arrays.asList(("22110040\t" + "14681366\t" + "15652477\t" + "22900683\t" + @@ -112,15 +109,8 @@ public void extractSignalink() throws IOException private void printOrdered(final Map map, int min) { - List list = new ArrayList(map.keySet()); - Collections.sort(list, new Comparator() - { - @Override - public int compare(String o1, String o2) - { - return new Integer(map.get(o2)).compareTo(map.get(o1)); - } - }); + List list = new ArrayList<>(map.keySet()); + Collections.sort(list, (o1, o2) -> new Integer(map.get(o2)).compareTo(map.get(o1))); for (String s : list) { @@ -134,9 +124,10 @@ public int compare(String o1, String o2) @Ignore public void extractSignalink2() throws IOException { - BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/signalink-sql-produced.txt")); + BufferedReader reader = new BufferedReader(new FileReader( + "/home/ozgun/Desktop/signal-db/signalink-sql-produced.txt")); - Set set = new HashSet(); + Set set = new HashSet<>(); for (String line = reader.readLine(); line != null; line = reader.readLine()) { String[] token = line.split("\t"); @@ -161,7 +152,8 @@ public void extractSignalink2() throws IOException reader.close(); - BufferedWriter writer = new BufferedWriter(new FileWriter("/home/ozgun/Desktop/signal-db/signalink2.txt")); + BufferedWriter writer = new BufferedWriter(new FileWriter( + "/home/ozgun/Desktop/signal-db/signalink2.txt")); for (String s : set) { @@ -225,7 +217,7 @@ public void printVenn() throws IOException private Set negate(Set normal) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (String s : normal) { String[] tok = s.split("\t"); @@ -236,7 +228,7 @@ private Set negate(Set normal) private int intersect(Set... set) { - Set s = new HashSet(set[0]); + Set s = new HashSet<>(set[0]); for (Set ss : set) { s.retainAll(ss); @@ -283,7 +275,7 @@ private Set read(String file, boolean skipFirstLine) throws IOException { BufferedReader reader = new BufferedReader(new FileReader(file)); - Set set = new HashSet(); + Set set = new HashSet<>(); if (skipFirstLine) reader.readLine(); @@ -301,7 +293,7 @@ private Set read(String file, boolean skipFirstLine) throws IOException private Set readSpike() throws IOException { - Set set = new HashSet(); + Set set = new HashSet<>(); BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/SPIKE-ParsedFromXML.txt")); for (String line = reader.readLine(); line != null; line = reader.readLine()) @@ -321,7 +313,7 @@ public Set readSpikeFromOwl() throws IOException Model model = handler.convertFromOWL(new FileInputStream( "/home/ozgun/Desktop/signal-db/Spike2_LatestSpikeDB.owl")); - Set set = new HashSet(); + Set set = new HashSet<>(); for (Control ctrl : model.getObjects(Control.class)) { @@ -367,7 +359,7 @@ private Set[] parseSpikeControl(String id) private Set collectSymbols(String s) { - Set set = new HashSet(); + Set set = new HashSet<>(); s = s.replaceAll("\\.", " "); s = s.replaceAll(",", " "); @@ -382,8 +374,9 @@ private Set collectSymbols(String s) private Map readSpikeID2Symbol() throws IOException { - Map id2sym = new HashMap(); - BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); + Map id2sym = new HashMap<>(); + BufferedReader reader = new BufferedReader(new FileReader( + "/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); for (String line = reader.readLine(); line != null; line = reader.readLine()) { @@ -405,7 +398,7 @@ private Map readSpikeID2Symbol() throws IOException public Map getEG2HGNC() throws IOException { - Map map = new HashMap(); + Map map = new HashMap<>(); BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/hgnc2eg.txt")); for (String line = reader.readLine(); line != null; line = reader.readLine()) @@ -424,7 +417,8 @@ public Map getEG2HGNC() throws IOException @Ignore public void printLines() throws IOException { - BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); + BufferedReader reader = new BufferedReader(new FileReader( + "/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); int from = 233571; int to = from + 50; @@ -446,7 +440,8 @@ public void printLinesContaining() throws IOException { String query = "1509498"; - BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); + BufferedReader reader = new BufferedReader(new FileReader( + "/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); int i = 0; for (String line = reader.readLine(); line != null; line = reader.readLine()) @@ -462,7 +457,8 @@ public void printLinesContaining() throws IOException @Ignore public void searchFirstOcc() throws IOException { - BufferedReader reader = new BufferedReader(new FileReader("/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); + BufferedReader reader = new BufferedReader(new FileReader( + "/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml")); int i = 0; for (String line = reader.readLine(); line != null; line = reader.readLine()) diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java b/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java index 730871e65..b0a32ea69 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java @@ -22,11 +22,11 @@ public void parse(String inputFile, String outputFile) throws IOException { Map id2gene = new HashMap(); Map id2group = new HashMap(); - Set regs = new HashSet(); + Set regs = new HashSet<>(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); - Set blocks = new HashSet(); + Set blocks = new HashSet<>(); String build = null; int indent = 10; @@ -123,7 +123,7 @@ List getGenes(String id, Map id2gene, Map id2 Group g = id2group.get(id); - List list = new ArrayList(); + List list = new ArrayList<>(); for (String memID : g.members) { @@ -174,7 +174,7 @@ class Group Group(String block) { - members = new ArrayList(); + members = new ArrayList<>(); for (String line : block.split("\n")) { diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java index 095c1b99a..e21905bc2 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java @@ -35,7 +35,7 @@ public void dummyMethod() protected Set collect(List list, int index) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Match match : list) { diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java index 408a519f9..88d75f2ba 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java @@ -30,7 +30,7 @@ public void testGetPathways() { SIFSearcher searcher = new SIFSearcher(SIFEnum.values()); Set inters = searcher.searchSIF(model_urea); - Set pathways = new HashSet(); + Set pathways = new HashSet<>(); for (SIFInteraction inter : inters) { pathways.addAll(inter.getPathways()); @@ -38,7 +38,7 @@ public void testGetPathways() Assert.assertFalse(pathways.isEmpty()); - Set dataSources = new HashSet(); + Set dataSources = new HashSet<>(); for (SIFInteraction inter : inters) { dataSources.addAll(inter.getDataSources()); @@ -52,7 +52,7 @@ public void testGetDataSources() { SIFSearcher searcher = new SIFSearcher(SIFEnum.values()); Set inters = searcher.searchSIF(model_urea); - Set dataSources = new HashSet(); + Set dataSources = new HashSet<>(); for (SIFInteraction inter : inters) { dataSources.addAll(inter.getDataSources()); @@ -79,7 +79,7 @@ public void testSIFMiner() Set sif = s.searchSIF(model_P53); Assert.assertFalse(sif.isEmpty()); - Set pubmedIDs = new HashSet(); + Set pubmedIDs = new HashSet<>(); for (SIFInteraction si : sif) { pubmedIDs.addAll(si.getPublicationIDs(true)); @@ -346,7 +346,7 @@ public static void generate(String inputModelFile, String ubiqueIDFile, String o SimpleIOHandler h = new SimpleIOHandler(); Model model = h.convertFromOWL(new FileInputStream(inputModelFile)); - List sifs = new ArrayList(generate(model, + List sifs = new ArrayList<>(generate(model, new Blacklist(ubiqueIDFile))); Collections.sort(sifs); diff --git a/paxtools-archetype/README.md b/paxtools-archetype/README.md index 464a2a7ba..a12e8d741 100644 --- a/paxtools-archetype/README.md +++ b/paxtools-archetype/README.md @@ -2,7 +2,7 @@ ## Use ## - mvn archetype:generate -DarchetypeRepository=https://oss.sonatype.org/content/groups/public/ -DarchetypeGroupId=org.biopax.paxtools -DarchetypeArtifactId=paxtools-archetype -DarchetypeVersion=5.3.0-SNAPSHOT -DgroupId=YOUR_GROUPID -DartifactId=YOUR_ARTIFACTID -Dversion=0.1-SNAPSHOT + mvn archetype:generate -DarchetypeRepository=https://oss.sonatype.org/content/groups/public/ -DarchetypeGroupId=org.biopax.paxtools -DarchetypeArtifactId=paxtools-archetype -DarchetypeVersion=6.0.0-SNAPSHOT -DgroupId=YOUR_GROUPID -DartifactId=YOUR_ARTIFACTID -Dversion=0.1-SNAPSHOT http://www.biopax.org/paxtools diff --git a/paxtools-archetype/pom.xml b/paxtools-archetype/pom.xml index 9df9e9053..100b947f0 100644 --- a/paxtools-archetype/pom.xml +++ b/paxtools-archetype/pom.xml @@ -5,7 +5,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT paxtools-archetype diff --git a/paxtools-archetype/src/main/resources/archetype-resources/pom.xml b/paxtools-archetype/src/main/resources/archetype-resources/pom.xml index 8db76651f..692391513 100755 --- a/paxtools-archetype/src/main/resources/archetype-resources/pom.xml +++ b/paxtools-archetype/src/main/resources/archetype-resources/pom.xml @@ -13,7 +13,7 @@ maven-compiler-plugin 3.8.1 - 17 + 11 @@ -94,7 +94,7 @@ junit junit - 4.12 + 4.13.2 test diff --git a/paxtools-console/pom.xml b/paxtools-console/pom.xml index 553cc8477..6ff906db7 100644 --- a/paxtools-console/pom.xml +++ b/paxtools-console/pom.xml @@ -3,7 +3,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT paxtools-console jar diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java b/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java index 01be52fc1..c0e49ac20 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java @@ -54,15 +54,13 @@ private PaxtoolsMain() { /* * using arguments: * [-crossSpecies] [-subPathways] [-notPathway] [organisms=9606,mouse,10090,rat,human,..] - * - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... */ public static void toGSEA(String[] argv) throws IOException { //argv[0] is the command name ('toGsea') boolean crossSpecies = false; //cross-check is enabled (i.e., no mixing different species IDs in one row) boolean subPathways = false; //no sub-pathways (i.e., going into sub-pathways is not enabled) boolean notPathways = false; - Set organisms = new HashSet(); + Set organisms = new HashSet<>(); if (argv.length < 4) throw new IllegalArgumentException("Not enough arguments: " + argv); @@ -111,7 +109,7 @@ public static void getNeighbors(String[] argv) throws IOException Model model = io.convertFromOWL(getInputStream(in)); // get elements (entities) - Set elements = new HashSet(); + Set elements = new HashSet<>(); for (Object id : ids) { BioPAXElement e = model.getByID(id.toString()); if (e != null && (e instanceof Entity || e instanceof entity)) { @@ -122,15 +120,14 @@ public static void getNeighbors(String[] argv) throws IOException } // execute the 'nearest neighborhood' query - Set result = QueryExecuter + Collection result = QueryExecuter .runNeighborhood(elements, model, 1, Direction.BOTHSTREAM); // auto-complete/clone the results in a new model // (this also cuts some less important edges, right?..) Completer c = new Completer(io.getEditorMap()); - result = c.complete(result, model); Cloner cln = new Cloner(io.getEditorMap(), io.getFactory()); - model = cln.clone(model, result); // new sub-model + model = cln.clone(c.complete(result)); //a new sub-model if (model != null) { log.info("Elements in the result model: " + model.getObjects().size()); @@ -341,7 +338,7 @@ public static void validate(String[] argv) throws IOException } } - Collection files = new HashSet(); + Collection files = new HashSet<>(); File fileOrDir = new File(input); if (!fileOrDir.canRead()) { System.out.println("Cannot read " + input); @@ -414,10 +411,10 @@ public static void toSifnx(String[] argv) throws IOException { boolean andSif = false; //if extended==false, SIF will be generated as it would be andSif==true boolean mergeInteractions = true; boolean useNameIfNoId = false; - final Collection include = new HashSet(); - final Collection exclude = new HashSet(); + final Collection include = new HashSet<>(); + final Collection exclude = new HashSet<>(); final ConfigurableIDFetcher idFetcher = new ConfigurableIDFetcher(); - final List customFieldList = new ArrayList(); //there may be custom field names (SIF mediators) + final List customFieldList = new ArrayList<>(); //there may be custom field names (SIF mediators) //process arguments if(argv.length > 3) { for(int i=3; i sifTypes = (include.isEmpty()) - ? new HashSet(Arrays.asList(SIFEnum.values())) : include; + ? new HashSet<>(Arrays.asList(SIFEnum.values())) : include; for(SIFType t : exclude) { sifTypes.remove(t); //remove if exists, otherwise - ignore } @@ -685,7 +682,7 @@ private static void mapUriToIds(Model model, PrintStream out) { private static Set identifiers(final PhysicalEntity entity, final String xrefdb, boolean isPrefix, boolean includeEvidence) { - final Set ids = new HashSet(); + final Set ids = new HashSet<>(); final Fetcher fetcher = (includeEvidence) ? new Fetcher(SimpleEditorMap.L3, Fetcher.nextStepFilter) : new Fetcher(SimpleEditorMap.L3, Fetcher.nextStepFilter, Fetcher.evidenceFilter); @@ -711,7 +708,7 @@ private static void summarizePathways(Model model, PrintStream out) throws IOExc final PathAccessor pathwayComponentAccessor = new PathAccessor("Pathway/pathwayComponent"); final PathAccessor pathwayOrderStepProcessAccessor = new PathAccessor("Pathway/pathwayOrder/stepProcess"); - Set pathways = model.getObjects(Pathway.class); + Collection pathways = model.getObjects(Pathway.class); //print column titles out.println("PATHWAY_URI\tDISPLAY_NAME\tDIRECT_SUB_PATHWAY_URIS\tALL_SUB_PATHWAY_URIS"); for(Pathway pathway : pathways) { @@ -757,9 +754,9 @@ private static void summarizeHgncIds(Model model, PrintStream out) { //Analyse SERs (Protein-, Dna* and Rna* references) - HGNC usage, coverage,.. //Calc. the no. non-generic ERs having >1 different HGNC symbols and IDs, or none, etc. - Set haveMultipleHgnc = new HashSet(); - Map numErs = new HashMap(); - Map numProblematicErs = new HashMap(); + Set haveMultipleHgnc = new HashSet<>(); + Map numErs = new HashMap<>(); + Map numProblematicErs = new HashMap<>(); PathAccessor pa = new PathAccessor("EntityReference/entityReferenceOf/dataSource", model.getLevel()); Set problemErs = new TreeSet(); for(EntityReference ser : model.getObjects(EntityReference.class)) { @@ -767,8 +764,8 @@ private static void summarizeHgncIds(Model model, PrintStream out) { if(ser instanceof SmallMoleculeReference || !ser.getMemberEntityReference().isEmpty()) continue; - Set hgncSymbols = new HashSet(); - Set hgncIds = new HashSet(); + Set hgncSymbols = new HashSet<>(); + Set hgncIds = new HashSet<>(); if(ser.getUri().startsWith("http://identifiers.org/hgnc")) { String s = ser.getUri().substring(ser.getUri().lastIndexOf("/")+1); @@ -838,8 +835,8 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { boolean verbose = true; //TODO use another parameter here //Analyse PRs - UniProt ID coverage,.. - Map numErs = new HashMap(); - Map numProblematicErs = new HashMap(); + Map numErs = new HashMap<>(); + Map numProblematicErs = new HashMap<>(); PathAccessor pa = new PathAccessor("EntityReference/entityReferenceOf:Protein/dataSource", model.getLevel()); Set problemErs = new TreeSet(); for(ProteinReference pr : model.getObjects(ProteinReference.class)) { @@ -893,8 +890,8 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { private static void summarizeChebiIds(Model model, PrintStream out) { boolean verbose = true; //TODO use another parameter here //Analyse SMRs - ChEBI usage, coverage,.. - Map numErs = new HashMap(); - Map numProblematicErs = new HashMap(); + Map numErs = new HashMap<>(); + Map numProblematicErs = new HashMap<>(); PathAccessor pa = new PathAccessor("EntityReference/entityReferenceOf:SmallMolecule/dataSource", model.getLevel()); Set problemErs = new TreeSet(); for(SmallMoleculeReference smr : model.getObjects(SmallMoleculeReference.class)) { @@ -960,7 +957,7 @@ public static void summarize(Model model, PrintStream out) throws IOException { for (Class clazz : sortToName(em.getKnownSubClassesOf(BioPAXElement.class))) { - Set set = model.getObjects(clazz); + Collection set = model.getObjects(clazz); int initialSize = set.size(); set = filterToExactClass(set, clazz); String s = clazz.getSimpleName() + " = " + set.size(); @@ -1031,7 +1028,7 @@ else if (returnType.equals(Set.class) && for (String prop : props) { Map cnt = new HashMap(); - List valList = new ArrayList(); + List valList = new ArrayList<>(); PathAccessor acc = new PathAccessor(prop, model.getLevel()); boolean isString = false; @@ -1169,25 +1166,22 @@ public int compare(Class clazz1, Class getOrdering(final Map map) { - List list = new ArrayList(map.keySet()); - Collections.sort(list, new Comparator() - { - public int compare(Object key1, Object key2) - { - int cnt1 = map.get(key1); - int cnt2 = map.get(key2); - - if (cnt1 == cnt2) return key1.toString().compareTo(key2.toString()); - else return cnt2 - cnt1; - } + List list = new ArrayList<>(map.keySet()); + Collections.sort(list, (key1, key2) -> { + int cnt1 = map.get(key1); + int cnt2 = map.get(key2); + if (cnt1 == cnt2) + return key1.toString().compareTo(key2.toString()); + else + return cnt2 - cnt1; }); return list; } - private static Set filterToExactClass(Set classSet, Class clazz) + private static Collection filterToExactClass(Collection classSet, Class clazz) { - Set exact = new HashSet(); + Collection exact = new HashSet<>(); for (BioPAXElement ele : classSet) { if (ele.getModelInterface().equals(clazz)) exact.add(ele); } diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/GOUnificationXREFtoRelationshipXREFConverter.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/GOUnificationXREFtoRelationshipXREFConverter.java index 5adf86e07..4639de50a 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/GOUnificationXREFtoRelationshipXREFConverter.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/GOUnificationXREFtoRelationshipXREFConverter.java @@ -14,6 +14,7 @@ import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.lang.reflect.InvocationTargetException; +import java.util.Collection; import java.util.HashSet; import java.util.Set; @@ -28,60 +29,59 @@ public class GOUnificationXREFtoRelationshipXREFConverter { private static Logger log = LoggerFactory.getLogger(GOUnificationXREFtoRelationshipXREFConverter.class); - + static BioPAXIOHandler reader = new SimpleIOHandler(); - //args - a space seperated list of owl files to be processed - public static void main(String[] args) + //args - a space seperated list of owl files to be processed + public static void main(String[] args) throws IllegalAccessException, InvocationTargetException { - // Process all the args - for (String arg : args) - { - log.info(arg); - if (arg.toLowerCase().endsWith("owl")) - { - try - { - processXrefs(arg); - } - catch (FileNotFoundException e) - { - e.printStackTrace(); - } - } - - } + // Process all the args + for (String arg : args) + { + log.info(arg); + if (arg.toLowerCase().endsWith("owl")) + { + try + { + processXrefs(arg); + } + catch (FileNotFoundException e) + { + e.printStackTrace(); + } + } + + } } - /** - * Main conversion method. Demonstrates how to read and write a BioPAX - * model and accessing its objects. - * @param arg file name to be processed - */ - private static void processXrefs(String arg) throws + /** + * Main conversion method. Demonstrates how to read and write a BioPAX + * model and accessing its objects. + * @param arg file name to be processed + */ + private static void processXrefs(String arg) throws FileNotFoundException, IllegalAccessException, InvocationTargetException { //Read in the model - FileInputStream in = + FileInputStream in = new FileInputStream(new File(arg)); Model level2 = reader.convertFromOWL(in); - //Get all unification xrefs. - Set unis = - level2.getObjects(unificationXref.class); + //Get all unification xrefs. + Collection unis = level2.getObjects(unificationXref.class); //Create another set for avoiding concurrent modifications - Set gos = new HashSet(); + Set gos = new HashSet<>(); - //Process all uni. refs - for (unificationXref uni : unis) + //Process all uni. refs + for (unificationXref uni : unis) { log.trace(uni.getDB()); //Assuming DB is represented as "GO" - if (uni.getDB().equalsIgnoreCase("GO")) + if (uni.getDB().equalsIgnoreCase("GO")) { //this it to avoid concurrent modification. log.info("scheduling " + uni.getUri()); @@ -89,36 +89,36 @@ private static void processXrefs(String arg) throws } } - //Now we have a list of xrefs to be converted. Let's do it. - for (unificationXref go : gos) + //Now we have a list of xrefs to be converted. Let's do it. + for (unificationXref go : gos) { convert(go, level2); } //And finally write out the file. We are done ! - reader.convertToOWL(level2, new FileOutputStream( + reader.convertToOWL(level2, new FileOutputStream( arg.substring(0, arg.lastIndexOf('.')) + "-converted.owl")); } - /** - * This method converts the given unification xref to a relationship xref - * @param uni xref to be converted - * @param level2 model containing the xref - */ - private static void convert(unificationXref uni, Model level2) + /** + * This method converts the given unification xref to a relationship xref + * @param uni xref to be converted + * @param level2 model containing the xref + */ + private static void convert(unificationXref uni, Model level2) { //We can not simply convert a class, so we need to remove the - //uni and insert a new relationship xref + //uni and insert a new relationship xref - //First get all the objects that refers to this uni - Set referrables = - new HashSet(uni.isXREFof()); + //First get all the objects that refers to this uni + Set referrables = + new HashSet<>(uni.isXREFof()); - //Create the new relationship xref in the model. - relationshipXref relationshipXref = - level2.addNew(relationshipXref.class, uni.getUri()); + //Create the new relationship xref in the model. + relationshipXref relationshipXref = + level2.addNew(relationshipXref.class, uni.getUri()); - //Copy the fields from uni + //Copy the fields from uni relationshipXref.setCOMMENT(uni.getCOMMENT()); relationshipXref.setDB(uni.getDB()); relationshipXref.setDB_VERSION(uni.getDB_VERSION()); @@ -127,21 +127,20 @@ private static void convert(unificationXref uni, Model level2) relationshipXref.setRELATIONSHIP_TYPE( "http://www.biopax.org/paxtools/convertedGOUnificationXREF"); - //Create a link to the new xref from all the owners. - for (XReferrable referrable : referrables) + //Create a link to the new xref from all the owners. + for (XReferrable referrable : referrables) { referrable.addXREF(relationshipXref); } - //Remove the references to the old uni - for (XReferrable referrable : referrables) - { - referrable.removeXREF(uni); - } - //Now remove it from the model. - level2.remove(uni); + //Remove the references to the old uni + for (XReferrable referrable : referrables) + { + referrable.removeXREF(uni); + } + //Now remove it from the model. + level2.remove(uni); - //We are done! - } + //We are done! + } } - diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/PathwayGenesExtractor.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/PathwayGenesExtractor.java index 278d5afb9..ac31b10a2 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/PathwayGenesExtractor.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/PathwayGenesExtractor.java @@ -38,9 +38,9 @@ public class PathwayGenesExtractor implements Visitor { public PathwayGenesExtractor(pathway pw) { traverser = new Traverser(SimpleEditorMap.get(BioPAXLevel.L2), this); geneset = new HashMap>(); - subpathways = new HashSet(); - interactions = new HashSet(); - visited = new HashSet(); + subpathways = new HashSet<>(); + interactions = new HashSet<>(); + visited = new HashSet<>(); this.pw = pw; } @@ -66,7 +66,7 @@ public static void main(String[] args) throws FileNotFoundException { PrintWriter out = new PrintWriter(OUT); out.println("rdf:IDs of proteins in the pathway : " + pw.getNAME() + " and its sub-pathways."); - Set glist = new HashSet(); // to keep all IDs + Set glist = new HashSet<>(); // to keep all IDs for(String key : extractor.geneset.keySet()) { glist.addAll(extractor.geneset.get(key)); @@ -125,7 +125,7 @@ public void visit(BioPAXElement domain1, Object range, Model model, PropertyEdit protein p = (protein) bpe; String id = getLocalId(p); - Set refs = new HashSet(); + Set refs = new HashSet<>(); for (xref x : p.getXREF()) { if (x instanceof unificationXref || x instanceof relationshipXref) { refs.add(x.getID()); diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java index 5d5473970..65ebdf736 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java @@ -16,6 +16,7 @@ import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FilenameFilter; +import java.util.Collection; import java.util.Set; @@ -101,7 +102,7 @@ private static void process(String pathname, String name, BioPAXIOHandler reader public static void listProteinUnificationXrefsPerPathway(Model model) { - Set pathways = model.getObjects(pathway.class); + Collection pathways = model.getObjects(pathway.class); for (pathway aPathway : pathways) { //printout aPathway's name @@ -111,7 +112,7 @@ public static void listProteinUnificationXrefsPerPathway(Model model) Model onePathwayModel = BioPAXLevel.L2.getDefaultFactory().createModel(); fetcher.fetch(aPathway, onePathwayModel); //get all proteins in the new level2 - Set proteins = onePathwayModel.getObjects(protein.class); + Collection proteins = onePathwayModel.getObjects(protein.class); //iterate and print names for (protein aProtein : proteins) @@ -157,7 +158,7 @@ public void visit(BioPAXElement domain, Object range, Model model, PropertyEdito Traverser traverser = new Traverser(SimpleEditorMap.L2, visitor); - Set pathways = model.getObjects(pathway.class); + Collection pathways = model.getObjects(pathway.class); for (pathway pathway : pathways) { traverser.traverse(pathway, model); diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/ReactomeEntitySetUnificationXrefFix.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/ReactomeEntitySetUnificationXrefFix.java index 422c976b2..13d3e71ac 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/ReactomeEntitySetUnificationXrefFix.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/ReactomeEntitySetUnificationXrefFix.java @@ -40,7 +40,7 @@ public static void fixReactome(InputStream in, OutputStream out) throws IOExcept { BioPAXIOHandler io = new SimpleIOHandler(); Model level2 = io.convertFromOWL(in); - Set physicalEntitySet = new HashSet(); + Set physicalEntitySet = new HashSet<>(); physicalEntitySet.addAll(level2.getObjects(physicalEntity.class)); for (physicalEntity pe : physicalEntitySet) { @@ -57,7 +57,7 @@ public static void fixReactome(InputStream in, OutputStream out) throws IOExcept } if (entitySet) { - Set unis = new HashSet(); + Set unis = new HashSet<>(); unis.addAll(new ClassFilterSet(pe.getXREF(), unificationXref.class)); for (unificationXref uni : unis) diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java index 488246b19..fe81d1503 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java @@ -16,6 +16,7 @@ import java.io.FileNotFoundException; import java.io.InputStream; import java.io.OutputStream; +import java.util.Collection; import java.util.Collections; import java.util.HashSet; import java.util.Set; @@ -32,12 +33,12 @@ public static void myFirstModel() BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model model = factory.createModel(); Protein protein1 = model.addNew(Protein.class, - "http://biopax.org/tutorial/test1"); + "http://biopax.org/tutorial/test1"); protein1.addName("Tutorial Example Small molecule Transporter 1"); protein1.setDisplayName("TEST1"); BiochemicalReaction rxn1 = model.addNew(BiochemicalReaction.class, - "http://biopax.org/tutorial/rxn1"); + "http://biopax.org/tutorial/rxn1"); rxn1.addLeft(protein1); } @@ -116,7 +117,7 @@ public void visit(BioPAXElement domain, Object range, Model model, { BioPAXElement bpe = (BioPAXElement) range; - if (!targetModel.contains(bpe)) + if (!targetModel.containsID(bpe.getUri())) //avoid IllegalBioPAXArgumentException { targetModel.add(bpe); traverser.traverse(bpe, model); @@ -155,7 +156,7 @@ public static void merge(EditorMap editorMap, Model srcModel2, public Set access1(Complex complex) { - Set xrefs = new HashSet(); + Set xrefs = new HashSet<>(); recursivelyObtainMembers(complex, xrefs); return xrefs; } @@ -211,7 +212,7 @@ private void recursivelyObtainMembers(Complex complex, public void graphQuery(Model model, PhysicalEntity entity3, PhysicalEntity entity2, PhysicalEntity entity1) { - Set sourceSet = new HashSet(); + Collection sourceSet = new HashSet<>(); // Add the related source PhysicalEntity (or children) objects to the // source set @@ -222,12 +223,11 @@ public void graphQuery(Model model, PhysicalEntity entity3, // Direction can be upstream, downstream, or bothstream. Direction direction = Direction.BOTHSTREAM; - - Set result = QueryExecuter.runNeighborhood(sourceSet, model, - limit, direction, null); + Collection result = QueryExecuter.runNeighborhood(sourceSet, model, + limit, direction, null); Completer c = new Completer(SimpleEditorMap.get(BioPAXLevel.L3)); - result = c.complete(result, model); + result = c.complete(result); } @@ -239,7 +239,7 @@ public void simpleTraverse() throws FileNotFoundException Model model = handler.convertFromOWL(fin); // Iterate through all BioPAX Elements and Display RDF ID and Class Name - Set elementSet = model.getObjects(); + Collection elementSet = model.getObjects(); for (BioPAXElement currentElement : elementSet) { String rdfId = currentElement.getUri(); @@ -247,11 +247,11 @@ public void simpleTraverse() throws FileNotFoundException System.out.println("Element: " + rdfId + ": " + className); } // Get Proteins Only - Set proteinSet = model.getObjects(Protein.class); + Collection proteinSet = model.getObjects(Protein.class); for (Protein currentProtein : proteinSet) { System.out.println("Protein: " + currentProtein.getName() + ": " + - currentProtein.getDisplayName()); + currentProtein.getDisplayName()); } // Iterate through all proteins in the model @@ -285,5 +285,4 @@ public void highlightWorkaround() graphQuery(null, null, null, null); } - } diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/UnificationIDtoRDFIDLister.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/UnificationIDtoRDFIDLister.java index 8dd593f1b..44667954b 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/UnificationIDtoRDFIDLister.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/UnificationIDtoRDFIDLister.java @@ -13,7 +13,7 @@ import java.io.FileInputStream; import java.io.FileNotFoundException; import java.lang.reflect.InvocationTargetException; -import java.util.Set; +import java.util.Collection; /** * A basic example that shows how to list all unification xrefs. @@ -59,8 +59,7 @@ private static void processXrefs(String arg) throws new FileInputStream(new File(arg)); Model level2 = handler.convertFromOWL(in); - Set unis = - level2.getObjects(unificationXref.class); + Collection unis = level2.getObjects(unificationXref.class); for (unificationXref uni : unis) { ClassFilterSet referrables = new ClassFilterSet(uni.isXREFof(), diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/UseOfReflection.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/UseOfReflection.java index 3f6ed1893..60d123b55 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/UseOfReflection.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/UseOfReflection.java @@ -33,7 +33,7 @@ public final class UseOfReflection { * @return the BioPAX object property values or empty set */ public static Set getObjectBiopaxPropertyValues(BioPAXElement bpe, String property) { - Set values = new HashSet(); + Set values = new HashSet<>(); // get the BioPAX L3 property editors map EditorMap em = SimpleEditorMap.L3; diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/tutorial-pom-examples.xml b/paxtools-console/src/main/java/org/biopax/paxtools/examples/tutorial-pom-examples.xml index 278ca4a9c..6c81f64b5 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/tutorial-pom-examples.xml +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/tutorial-pom-examples.xml @@ -8,6 +8,6 @@ org.biopax.paxtools paxtools-core - 5.3.0-SNAPSHOT + 6.0.0-SNAPSHOT \ No newline at end of file diff --git a/paxtools-core/pom.xml b/paxtools-core/pom.xml index 04ae8ed41..410c6b5c9 100644 --- a/paxtools-core/pom.xml +++ b/paxtools-core/pom.xml @@ -4,7 +4,7 @@ org.biopax.paxtools paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT paxtools-core @@ -23,6 +23,7 @@ + net.sourceforge.collections collections-generic diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractPropertyEditor.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractPropertyEditor.java index 8551557bf..c1a3ee40c 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractPropertyEditor.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractPropertyEditor.java @@ -422,14 +422,14 @@ protected R parseValueFromString(String value) { if (this.getPrimarySetMethod() != null) { - if (log.isTraceEnabled()) log.trace( - this.getPrimarySetMethod().getName() + " bean:" + bean + " val:" + value); - } else - { + if (log.isTraceEnabled()) { + log.trace(this.getPrimarySetMethod().getName() + " bean:" + bean + " val:" + value); + } + } else { log.error("setMethod is null; " + " bean:" + bean + " (" + bean.getUri() + ") val:" + value); } - // 'null' definitely means 'unknown'for single cardinality props + // 'null' definitely means 'unknown' for single cardinality props if (value == null && !isMultipleCardinality()) value = getUnknown(); // not null for primitive property editors @@ -456,17 +456,18 @@ protected R parseValueFromString(String value) @Override public void setValueToBean(Set values, D bean) { - if (values == null) setValueToBean(((R) null), bean); - + if (values == null) { + setValueToBean(((R) null), bean); + } else if (this.isMultipleCardinality() || values.size() < 2) { - for (R r : values) - { + for (R r : values) { this.setValueToBean(r, bean); } - } else throw new IllegalBioPAXArgumentException( - this.getProperty() + " is single cardinality. Can not set" + "it with a set of size larger than" + - " 1"); + } else { + throw new IllegalBioPAXArgumentException(this.getProperty() + + " is single cardinality; cannot set it with a set of size larger than 1"); + } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractTraverser.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractTraverser.java index 92b3caf77..dc0c2ac80 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractTraverser.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/AbstractTraverser.java @@ -34,7 +34,7 @@ public AbstractTraverser(EditorMap editorMap, { super(editorMap, null, filters); setVisitor(this); - visited = new HashSet(); + visited = new HashSet<>(); } /** diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Cloner.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Cloner.java index 25de5765f..55028143b 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Cloner.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Cloner.java @@ -6,8 +6,8 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.util.Collection; import java.util.HashSet; -import java.util.Set; /** * Specifically "Clones" the BioPAX elements set @@ -31,23 +31,6 @@ public Cloner(EditorMap map, BioPAXFactory factory) this.traverser = new Traverser(map, this); } - /** - * For each element from the 'toBeCloned' list, - * it creates a copy in the new model, setting all - * the data properties; however, object property values - * that refer to BioPAX elements not in 'toBeCloned' list - * are ignored. - * - * @deprecated use {@link #clone(Set)} instead ('source' model was not used in previous versions) - * - * @param source - actually, is never used... can be null all the same - * @param toBeCloned elements to clone - * @return a new model containing the cloned biopax objects - */ - public Model clone(Model source, Set toBeCloned) { - return clone(toBeCloned); - } - /** * For each element from the 'toBeCloned' list, * it creates a copy in the new model, setting all @@ -59,11 +42,11 @@ public Model clone(Model source, Set toBeCloned) { * @param toBeCloned elements to clone * @return a new model containing the cloned biopax objects */ - public Model clone(Set toBeCloned) + public Model clone(Collection toBeCloned) { final Model targetModel = factory.createModel(); - for (BioPAXElement bpe : new HashSet(toBeCloned)) + for (BioPAXElement bpe : new HashSet<>(toBeCloned)) { // create a new empty object using the URI (all the biopax properties are empty; // addNew fails when there are several objects having the same URI) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java index 9a9e24bd3..f48de1fc7 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java @@ -42,21 +42,12 @@ public boolean filterInverse(PropertyEditor editor) } }); - completed = new HashSet(); + completed = new HashSet<>(); skipSubPathways = true; //makes default - skip sub-pathways } - /** - * @deprecated use {@link #complete(Collection)} instead (- model is never explicitly used there) - * @param elements - * @param model - * @return - */ - public Set complete(Collection elements, Model model) { - return complete(elements); - } - public Set complete(Collection elements) + public Collection complete(Collection elements) { completed.clear(); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/EditorMapImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/EditorMapImpl.java index 896387841..df3eca8ad 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/EditorMapImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/EditorMapImpl.java @@ -125,7 +125,7 @@ protected PropertyEditor createAndRegisterBeanEditor(String pName, Class domain, if (editor != null) { Set beanEditorsForProperty = this.propertyToEditorMap.get(pName); if (beanEditorsForProperty == null) { - beanEditorsForProperty = new HashSet(); + beanEditorsForProperty = new HashSet<>(); propertyToEditorMap.put(pName, beanEditorsForProperty); } beanEditorsForProperty.add(editor); @@ -206,7 +206,7 @@ protected void registerModelClass(String localName) { HashMap peMap = new HashMap(); classToEditorMap.put(domain, peMap); - classToInverseEditorMap.put(domain, new HashSet()); + classToInverseEditorMap.put(domain, new HashSet<>()); classToEditorSet.put(domain, new ValueSet(peMap.values())); } catch (IllegalBioPAXArgumentException e) { if (log.isDebugEnabled()) { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Fetcher.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Fetcher.java index 63ecb6180..7078094bb 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Fetcher.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Fetcher.java @@ -15,17 +15,17 @@ * its dependent elements) and to add this element into a model * using the visitor and traverse functions. * - * Must be thread safe if the property filters and {@link EditorMap} + * Must be thread safe if the property filters and {@link EditorMap} * passed to the constructor are safe. - * + * * @see org.biopax.paxtools.controller.Visitor * @see org.biopax.paxtools.controller.Traverser * */ public class Fetcher { - + private final EditorMap editorMap; - private final Filter[] filters; + private final Filter[] filters; private boolean skipSubPathways; @@ -40,54 +40,39 @@ public class Fetcher { * to find all proteins or xrefs within a pathway and its sub-pathways, etc. */ @SuppressWarnings("rawtypes") - public static final Filter nextStepFilter = new Filter() - { - public boolean filter(PropertyEditor editor) - { - return !editor.getProperty().equals("nextStep") && !editor.getProperty().equals("NEXT-STEP"); - } - }; - + public static final Filter nextStepFilter = + editor -> !editor.getProperty().equals("nextStep") && !editor.getProperty().equals("NEXT-STEP"); + /** * A property filter to ignore 'evidence' ('EVIDENCE' in L2) property * (it can eventually lead to other organism, experimental entities) */ @SuppressWarnings("rawtypes") - public static final Filter evidenceFilter = new Filter() - { - public boolean filter(PropertyEditor editor) - { - return !editor.getProperty().equals("evidence") && !editor.getProperty().equals("EVIDENCE"); - } - }; + public static final Filter evidenceFilter = + editor -> !editor.getProperty().equals("evidence") && !editor.getProperty().equals("EVIDENCE"); /** * A property filter to visit only biopax object type properties. */ - public static final Filter objectPropertiesOnlyFilter = new Filter() - { - public boolean filter(PropertyEditor editor) - { - return (editor instanceof ObjectPropertyEditor); - } - }; - - - /** - * Constructor. - * - * @param editorMap BioPAX property editors map implementation - * @param filters optional, biopax object property filters - * to skip traversing/visiting into some object property values + public static final Filter objectPropertiesOnlyFilter = + editor -> (editor instanceof ObjectPropertyEditor); + + + /** + * Constructor. + * + * @param editorMap BioPAX property editors map implementation + * @param filters optional, biopax object property filters + * to skip traversing/visiting into some object property values * (the default 'object properties only' filter to is always enabled). - */ + */ public Fetcher(EditorMap editorMap, Filter... filters) { - this.editorMap = editorMap; - this.filters = (Filter[])ArrayUtils.add(filters, objectPropertiesOnlyFilter); + this.editorMap = editorMap; + this.filters = ArrayUtils.add(filters, objectPropertiesOnlyFilter); this.skipSubPathways = false; - } + } /** @@ -107,96 +92,94 @@ public boolean isSkipSubPathways() { } /** - * Adds the element and all its children + * Adds the element and all its children * (found via traversing into object properties that * pass all the filters defined in the Constructor, and * also taking #isSkipSubPathways into account) * to the target model. - * - * This method fails if there are different child objects - * with the same ID, because normally a good (self-consistent) - * model does not contain duplicate BioPAX elements. Consider - * using {@link #fetch(BioPAXElement)} method instead if you - * want to get all the child elements anyway. - * - * @param element the BioPAX element to be added into the model - * @param model model into which elements will be added - */ - public void fetch(final BioPAXElement element, final Model model) + * + * This method fails if there are different child objects + * with the same ID, because normally a good (self-consistent) + * model does not contain duplicate BioPAX elements. Consider + * using {@link #fetch(BioPAXElement)} method instead if you + * want to get all the child elements anyway. + * + * @param element the BioPAX element to be added into the model + * @param model model into which elements will be added + */ + public void fetch(final BioPAXElement element, final Model model) { - if(!model.containsID(element.getUri())) - model.add(element); - - Set children = fetch(element); - - for(BioPAXElement e : children) { + if(!model.containsID(element.getUri())) + model.add(element); + + Set children = fetch(element); + + for(BioPAXElement e : children) { if (!model.containsID(e.getUri())) { model.add(e); } else if (!model.contains(e)) { throw new AssertionError("fetch(bioPAXElement, model): found different child objects " + - "with the same URI: " + e.getUri() + - "(replace/merge, or use fetch(bioPAXElement) instead!)"); + "with the same URI: " + e.getUri() + + "(replace/merge, or use fetch(bioPAXElement) instead!)"); } } } - - - /** - * Recursively finds and collects all child objects, + + + /** + * Recursively finds and collects all child objects, * while escaping possible infinite loops. - * - * This method can eventually return - * different objects with the same URI if these - * are present among child elements. - * - * @param element to traverse into - * @return a set of child biopax objects - */ - public Set fetch(final BioPAXElement element) { - return fetch(element, BioPAXElement.class); - } - - - /** - * Recursively collects unique child objects from + * + * This method can eventually return + * different objects with the same URI if these + * are present among child elements. + * + * @param element to traverse into + * @return a set of child biopax objects + */ + public Set fetch(final BioPAXElement element) { + return fetch(element, BioPAXElement.class); + } + + + /** + * Recursively collects unique child objects from * BioPAX object type properties that pass * all the filters (as set via Constructor). * * The #isSkipSubPathways flag is ignored. - * - * Note: this method might return different objects with the same URI if such - * are present among the child elements for some reason (for a self-integral BioPAX Model, this should not happen). - * - * @param bpe biopax object to traverse into properties of - * @param depth positive int.; 1 means - get only direct children, 2 - include children of children, etc.; - * @return set of child objects + * + * Note: this method might return different objects with the same URI if such + * are present among the child elements for some reason (for a self-integral BioPAX Model, this should not happen). + * + * @param bpe biopax object to traverse into properties of + * @param depth positive int.; 1 means - get only direct children, 2 - include children of children, etc.; + * @return set of child objects * @throws IllegalArgumentException when depth is less or equals 0 - */ - public Set fetch(final BioPAXElement bpe, int depth) + */ + public Set fetch(final BioPAXElement bpe, int depth) { //a sanity check if(depth <= 0) { throw new IllegalArgumentException("fetch(..), not a positive 'depth':" + depth); } - final Set children = new HashSet(); + final Set children = new HashSet<>(); - //create a simple traverser to collect direct child elements + //create a simple traverser to collect direct child elements: Traverser traverser = new Traverser(editorMap, - new Visitor() { - @Override - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) { - children.add((BioPAXElement) range); - } - }, filters); + (domain, range, model, editor) -> children.add((BioPAXElement) range), + filters + ); + //run traverser.traverse(bpe, null); if(!children.isEmpty() && --depth > 0) { - for (BioPAXElement element : new HashSet(children)) { - if(skipSubPathways && (element instanceof Pathway)) + for (BioPAXElement element : new HashSet<>(children)) { + if(skipSubPathways && (element instanceof Pathway)) { continue; - + } Set nextLevelElements = fetch(element, depth); //recursion goes on children.addAll(nextLevelElements); } @@ -208,36 +191,36 @@ public void visit(BioPAXElement domain, Object range, Model model, PropertyEdito return children; } - - /** - * Goes over object type biopax properties to collect nested objects + + /** + * Goes over object type biopax properties to collect nested objects * (using only properties that pass all the filters set in Constructor, * and taking #isSkipSubPathways into account) * of the given biopax element, its children, etc. * (it also escapes any infinite semantic loops in the biopax model) * It saves only biopax objects of the given type, incl. sub-types. - * - * Note: this method can eventually return - * different objects with the same URI if these - * are present among child elements. - * - * @param element to fetch child objects from - * @param filterByType biopax type filter - * @param biopax type - * @return set of biopax objects - */ - public Set fetch(final BioPAXElement element, final Class filterByType) + * + * Note: this method can eventually return + * different objects with the same URI if these + * are present among child elements. + * + * @param element to fetch child objects from + * @param filterByType biopax type filter + * @param biopax type + * @return set of biopax objects + */ + public Set fetch(final BioPAXElement element, final Class filterByType) { - final Set children = new HashSet(); + final Set children = new HashSet<>(); AbstractTraverser traverser = new AbstractTraverser(editorMap, filters) { - /* - * Adds the BioPAX element into the model and traverses the element's properties - * to collect all dependent/nested elements. - */ - protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) - { - //by design (see Constructor, filters), it'll visit only object properties. + /* + * Adds the BioPAX element into the model and traverses the element's properties + * to collect all dependent/nested elements. + */ + protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) + { + //by design (see Constructor, filters), it'll visit only object properties. BioPAXElement bpe = (BioPAXElement) range; if(filterByType.isInstance(bpe)) { @@ -247,49 +230,49 @@ protected void visit(Object range, BioPAXElement domain, Model model, PropertyEd if(!(skipSubPathways && (bpe instanceof Pathway))) traverse(bpe, null); //(does nothing when bpe has been previously visited) } - }; + }; + + traverser.traverse(element, null); - traverser.traverse(element, null); - - return children; + return children; } - - - /** - * Iterates over child objects of the given biopax element, - * using BioPAX object-type properties, until the element - * with specified URI and class (including its sub-classes). - * is found. - * - * @param root biopax element to process - * @param uri URI to match - * @param type class to match - * - * @return true if the match found; false - otherwise - */ - public boolean subgraphContains(final BioPAXElement root, final String uri, - final Class type) { - - final AtomicBoolean found = new AtomicBoolean(false); - - Traverser traverser = new AbstractTraverser(editorMap, filters) { - - @Override - protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) - { - if (range instanceof BioPAXElement && !found.get()) - { - if( ((BioPAXElement) range).getUri().equals(uri) ) - found.set(true); //set global flag; done. - else - if(!(skipSubPathways && (range instanceof Pathway))) - traverse((BioPAXElement)range, model); - } - } - }; - - traverser.traverse(root, null); - - return found.get(); + + + /** + * Iterates over child objects of the given biopax element, + * using BioPAX object-type properties, until the element + * with specified URI and class (including its sub-classes). + * is found. + * + * @param root biopax element to process + * @param uri URI to match + * @param type class to match + * + * @return true if the match found; false - otherwise + */ + public boolean subgraphContains(final BioPAXElement root, final String uri, + final Class type) { + + final AtomicBoolean found = new AtomicBoolean(false); + + Traverser traverser = new AbstractTraverser(editorMap, filters) { + + @Override + protected void visit(Object range, BioPAXElement domain, Model model, PropertyEditor editor) + { + if (range instanceof BioPAXElement && !found.get()) + { + if( ((BioPAXElement) range).getUri().equals(uri) ) + found.set(true); //set global flag; done. + else + if(!(skipSubPathways && (range instanceof Pathway))) + traverse((BioPAXElement)range, model); + } + } + }; + + traverser.traverse(root, null); + + return found.get(); } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java index 2946463d8..bfdd2bb6b 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java @@ -21,8 +21,8 @@ public class IdFetcher * Constructor. */ public IdFetcher() { - seqDbStartsWithOrEquals = new ArrayList(); - chemDbStartsWithOrEquals = new ArrayList(); + seqDbStartsWithOrEquals = new ArrayList<>(); + chemDbStartsWithOrEquals = new ArrayList<>(); useNameWhenNoDbMatch = false; } @@ -81,7 +81,7 @@ public IdFetcher useNameWhenNoDbMatch(boolean useNameWhenNoDbMatch) { public Set fetchID(BioPAXElement ele) { - Set set = new HashSet(); + Set set = new HashSet<>(); if(ele instanceof XReferrable) { //Iterate the db priority list, match/filter all xrefs to collect the IDs of given type, until 'set' is not empty. diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Integrator.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Integrator.java index cce17349a..c72dc0e69 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Integrator.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Integrator.java @@ -66,7 +66,7 @@ public class Integrator { {"Chemical Entities of Biological Interest", "ChEBI"} }; - private Set> relatedTerms = new HashSet>(); + private Set> relatedTerms = new HashSet<>(); private String[][] termLists = { {"active", "active1", "active2", "phosphorylation", "phosphate group", "phosphorylation site"}, @@ -290,7 +290,7 @@ public List integrate(List alternativeScores) } if(this.similarConversions == null) - this.similarConversions = new ArrayList(); + this.similarConversions = new ArrayList<>(); /* Original score matrixes won't be modified for a later use * Instead, we are going to copy them, and modify their copies. @@ -309,7 +309,7 @@ public List integrate(List alternativeScores) log.info("PEP scores copied."); similarConversions = (alternativeScores == null) - ? new ArrayList(this.similarConversions) + ? new ArrayList<>(this.similarConversions) : alternativeScores; log.info("Conversion scores copied."); @@ -342,8 +342,8 @@ public List integrate(List alternativeScores) } private void equalizeEntities(List similarConversions) { - Set doNotModifySet = new HashSet(); - Set containsSelfRemoved = new HashSet(); + Set doNotModifySet = new HashSet<>(); + Set containsSelfRemoved = new HashSet<>(); for(ConversionScore convScore: similarConversions) { // Since we sorted the list, we are safe to break @@ -442,7 +442,7 @@ private boolean equals(BioPAXElement a, BioPAXElement b) { private void equalizePEP(physicalEntityParticipant controller1, physicalEntityParticipant controller2) { // There is a special case for PEPs: we also need to update equivalent PEPs' fields - Set tempEqvPeps = new HashSet(); + Set tempEqvPeps = new HashSet<>(); tempEqvPeps.addAll(getEquivalentsOfPEP(controller1)); tempEqvPeps.addAll(getEquivalentsOfPEP(controller2)); for(physicalEntityParticipant eqPep : tempEqvPeps) @@ -455,7 +455,7 @@ private void equalizePEP(physicalEntityParticipant controller1, physicalEntityPa } private Set getEquivalentsOfPEP(physicalEntityParticipant onePep) { - Set eqGrp = new HashSet(); + Set eqGrp = new HashSet<>(); for(physicalEntityParticipant aPep : onePep.getPHYSICAL_ENTITY().isPHYSICAL_ENTITYof() ) { if(aPep.isInEquivalentState(onePep)) eqGrp.add(aPep); @@ -499,7 +499,7 @@ private void mapConversions(Collection similarConversions, Map> pepScoreMatrix) { // To get rid of Concurrent modification :| - Set toBeUpdated = new HashSet(); + Set toBeUpdated = new HashSet<>(); for(ConversionScore convScore : similarConversions) { // Check if the score is equal to or higher than the threshold @@ -531,10 +531,12 @@ private void mapConversions(Collection similarConversions, } - private List createConversionScoreMap(Map> pepScoreMatrix, - Set convSet1, Set convSet2) { - List similarConversions = new ArrayList(); + private List createConversionScoreMap( + Map> pepScoreMatrix, + Collection convSet1, Collection convSet2) + { + List similarConversions = new ArrayList<>(); double totalSize = convSet1.size() * convSet2.size(); double convCnt = 0; @@ -675,7 +677,7 @@ private boolean isSeqParTermsSimilar(physicalEntityParticipant fPep, physicalEntityParticipant sPep) { if( relatedTerms.isEmpty() ) { for( String[] termL : termLists ) { - Set termSet = new HashSet(); + Set termSet = new HashSet<>(); termSet.addAll(Arrays.asList(termL)); relatedTerms.add(termSet); } @@ -935,7 +937,7 @@ private void normalizeCellularLocations(Model model) { if( mostlyUsed == null ) return; - ArrayList pepList = new ArrayList(); + ArrayList pepList = new ArrayList<>(); pepList.addAll( model.getObjects(physicalEntityParticipant.class) ); for(BioPAXElement pep : pepList) { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Merger.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Merger.java index 994319a8b..a6f6dbb97 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Merger.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Merger.java @@ -27,10 +27,10 @@ public class Merger implements Visitor // Keep track of merged elements private final HashSet mergedElements = - new HashSet(); + new HashSet<>(); // Keep track of new elements - private final HashSet addedElements = new HashSet(); + private final HashSet addedElements = new HashSet<>(); // --------------------------- CONSTRUCTORS --------------------------- @@ -119,7 +119,7 @@ public HashSet getAddedElements() addedElements.clear(); // Fill equivalence map with objects from target model - Set targetElements = target.getObjects(); + Collection targetElements = target.getObjects(); for (BioPAXElement t_bpe : targetElements) { this.addIntoEquivalanceMap(t_bpe); @@ -128,7 +128,7 @@ public HashSet getAddedElements() // Try to insert every biopax element in every source one by one for (Model source : sources) { - Set sourceElements = source.getObjects(); + Collection sourceElements = source.getObjects(); for (BioPAXElement bpe : sourceElements) { insert(target, bpe); @@ -137,8 +137,10 @@ public HashSet getAddedElements() } /** - * Inserts a BioPAX element into the target model if it does not contain an equivalent; - * but if does, than it updates the equivalent using this element's values. + * Insert the BioPAX element into the target model unless it's there already. + * But if target model has an "equal" object (same URI, type), + * update that object with this element's values not replacing the existing object + * (this can copy new property values, such as xrefs, comments, etc.) * * @param target model into which bpe will be inserted * @param bpe BioPAX element to be inserted into target @@ -146,23 +148,16 @@ public HashSet getAddedElements() private void insert(Model target, BioPAXElement bpe) { // do nothing if you already inserted this - if (!target.contains(bpe)) + if (!target.contains(bpe)) //get by URI and also compare objects using '==' { - //if there is an identical (in fact, "equal") object + //but if there is another object with same URI BioPAXElement ibpe = target.getByID(bpe.getUri()); - if (ibpe != null && ibpe.equals(bpe)) - /* - ibpe.equals(bpe) can be 'false' here, because, - * even though the above !target.contains(bpe) is true, - * it probably compared objects using '==' operator - * (see the ModelImpl for details) - */ - { + if (bpe.equals(ibpe)) { updateObjectFields(bpe, ibpe, target); // We have a merged element, add it into the tracker mergedElements.add(ibpe); } - else - { + else { target.add(bpe); this.addIntoEquivalanceMap(bpe); traverser.traverse(bpe, target); @@ -206,21 +201,10 @@ private BioPAXElement getIdentical(BioPAXElement bpe) private void updateObjectFields(BioPAXElement update, BioPAXElement existing, Model target) { - Set editors = - map.getEditorsOf(update); - for (PropertyEditor editor : editors) - { + Set editors = map.getEditorsOf(update); + for (PropertyEditor editor : editors) { updateObjectFieldsForEditor(editor, update, existing, target); } - -// if (!update.getUri().equals(existing.getUri())) -// { -//TODO addNew a unification xref -// if(existing instanceof XReferrable) -// { -// ((XReferrable) existing).addXref(fa); -// } -// } } /** @@ -305,7 +289,7 @@ private void addIntoEquivalanceMap(BioPAXElement bpe) List list = equivalenceMap.get(key); if (list == null) { - list = new ArrayList(); + list = new ArrayList<>(); equivalenceMap.put(key, list); } list.add(bpe); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java index 0673a9496..30c8300e5 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java @@ -50,7 +50,7 @@ public final class ModelUtils private final static BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); private final static EditorMap em = SimpleEditorMap.L3; - private final static BioPAXIOHandler io = new SimpleIOHandler(BioPAXLevel.L3); + private final static SimpleIOHandler io = new SimpleIOHandler(BioPAXLevel.L3); /** @@ -62,9 +62,8 @@ public final class ModelUtils } catch (NoSuchAlgorithmException e) { throw new RuntimeException("Cannot instantiate MD5 MessageDigest!", e); } - - ((SimpleIOHandler) io).mergeDuplicates(true); - ((SimpleIOHandler) io).normalizeNameSpaces(false); + io.mergeDuplicates(true); + io.normalizeNameSpaces(false); } @@ -93,47 +92,39 @@ public final class ModelUtils public static void replace(Model model, final Map subs) { // update properties - Visitor visitor = new Visitor() - { - @Override - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) + Visitor visitor = (domain, range, bpModel, propertyEditor) -> { + if (propertyEditor instanceof ObjectPropertyEditor && range != null && subs.containsKey(range)) { - if (editor instanceof ObjectPropertyEditor && range != null && subs.containsKey(range)) + ObjectPropertyEditor editor = (ObjectPropertyEditor) propertyEditor; + BioPAXElement value = (BioPAXElement) range; + // 'value' is to be replaced with the 'replacement' + BioPAXElement replacement = subs.get(range); //can get null (ok) + + // normal biopax property - + if (replacement != null && !editor.getRange().isInstance(replacement)) { - BioPAXElement value = (BioPAXElement) range; - // 'value' is to be replaced with the 'replacement' - BioPAXElement replacement = subs.get(range); //can get null (ok) - - // normal biopax property - - if (replacement != null && !editor.getRange().isInstance(replacement)) - { - throw new IllegalBioPAXArgumentException( - "Incompatible type! Attempted to replace " - + value.getUri() + " (" + value.getModelInterface().getSimpleName() - + ") with " + replacement.getUri() + " (" - + replacement.getModelInterface().getSimpleName() + "); " - + "property: " + editor.getProperty() - + " of bean: " + domain.getUri() + " (" - + domain.getModelInterface().getSimpleName() + ")"); - } + throw new IllegalBioPAXArgumentException( + "Incompatible type! Attempted to replace " + + value.getUri() + " (" + value.getModelInterface().getSimpleName() + + ") with " + replacement.getUri() + " (" + + replacement.getModelInterface().getSimpleName() + "); " + + "property: " + editor.getProperty() + + " of bean: " + domain.getUri() + " (" + + domain.getModelInterface().getSimpleName() + ")"); + } - if (replacement != value) - { - editor.removeValueFromBean(value, domain); - editor.setValueToBean(replacement, domain); - } else { - LOG.debug("replace: skipped the identical: " + replacement.getUri()); - } + if (replacement != value) + { + editor.removeValueFromBean(value, domain); + editor.setValueToBean(replacement, domain); + } else { + LOG.debug("replace: skipped the identical: " + replacement.getUri()); } } }; Traverser traverser = new Traverser(em, visitor); - for (BioPAXElement bpe : new HashSet(model.getObjects())) - { - // update object properties and clear inverse properties using 'subs' map - traverser.traverse(bpe, null); //model is not needed - } + model.getObjects().parallelStream().forEach(bpe -> traverser.traverse(bpe, null));//model is not used by traveser } @@ -151,29 +142,18 @@ public void visit(BioPAXElement domain, Object range, Model model, PropertyEdito public static Set getRootElements(final Model model, final Class filterClass) { // copy all such elements (initially, we think all are roots...) - final Set result = new HashSet(model.getObjects(filterClass)); - - //"shallow" traverser (direct object properties only - Visitor.visit does not call traverse again) - @SuppressWarnings("unchecked") - Traverser traverser = new Traverser(em, - new Visitor() { - @Override - public void visit(BioPAXElement parent, Object value, Model model, - PropertyEditor editor) - { - if (filterClass.isInstance(value)) result.remove(value); - } - }, - new Filter() { - @Override - public boolean filter(PropertyEditor pe) { - return (pe instanceof ObjectPropertyEditor); - } - }); - - // but we run from every element (all types) - for(BioPAXElement e : model.getObjects()) - traverser.traverse(e, null); + final Set result = new HashSet<>(model.getObjects(filterClass)); + + //define a "shallow" (non-recursive) object property traverser + Traverser traverser = new Traverser( + em, // editor map + (bpe, value, m, e) -> { // visitor.visit + if (filterClass.isInstance(value)) result.remove(value); + }, + pe -> (pe instanceof ObjectPropertyEditor) // filter + ); + + model.getObjects().parallelStream().forEach(e -> traverser.traverse(e, null)); return result; } @@ -200,7 +180,7 @@ public boolean filter(PropertyEditor pe) { */ public static Set removeObjectsIfDangling(Model model, Class clazz) { - final Set removed = new HashSet(); + final Set removed = new HashSet<>(); // 'equals' below is used intentionally (isAssignableFrom() would be incorrect) if(Entity.class.equals(clazz)) { @@ -273,13 +253,9 @@ public static Model getDirectChildren(BioPAXElement bpe) { Model m = factory.createModel(); - Traverser traverser = new Traverser(em, new Visitor() { - @Override - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) - { - if (range instanceof BioPAXElement && !model.containsID(((BioPAXElement) range).getUri())) - model.add((BioPAXElement) range); - } + Traverser traverser = new Traverser(em, (domain, range, model, editor) -> { + if (range instanceof BioPAXElement && !model.containsID(((BioPAXElement) range).getUri())) + model.add((BioPAXElement) range); }); traverser.traverse(bpe, m); @@ -320,14 +296,12 @@ public static Model getAllChildren(BioPAXElement bpe, */ public static Set getDirectChildrenAsSet(BioPAXElement bpe) { - final Set toReturn = new HashSet(); + final Set toReturn = new HashSet<>(); - Traverser traverser = new Traverser(em, new Visitor() { - @Override - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) { - if (range instanceof BioPAXElement) { - toReturn.add((BioPAXElement) range); - } + Traverser traverser = new Traverser(em, + (domain, range, model, editor) -> { // Visitor impl. + if (range instanceof BioPAXElement) { + toReturn.add((BioPAXElement) range); } } ); @@ -346,7 +320,7 @@ public void visit(BioPAXElement domain, Object range, Model model, PropertyEdito */ public static Map, Integer> generateClassMetrics(Model model) { - Map, Integer> metrics = new HashMap, Integer>(); + Map, Integer> metrics = new HashMap<>(); for (BioPAXElement bpe : model.getObjects()) { Integer count = metrics.get(bpe.getModelInterface()); @@ -393,7 +367,6 @@ public static T getObject(Model model, String uri, Cla * used for many purposes, such as generating * new unique URIs, database primary keys, etc. * - * * @param id some identifier, e.g., URI * @return the 32-byte digest string */ @@ -403,7 +376,7 @@ public static String md5hex(String id) StringBuffer sb = new StringBuffer(); for (byte b : digest) { - sb.append(Integer.toHexString((int) (b & 0xff) | 0x100).substring(1, 3)); + sb.append(Integer.toHexString((b & 0xff) | 0x100), 1, 3); } String hex = sb.toString(); return hex; @@ -419,20 +392,14 @@ public static String md5hex(String id) */ public static void fixDanglingObjectProperties(BioPAXElement bpe, Model model) { - final Visitor visitor = new Visitor() - { - @Override - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) + Visitor visitor = (domain, range, m, editor) -> { + if (editor instanceof ObjectPropertyEditor) { - if (editor instanceof ObjectPropertyEditor) - { - BioPAXElement value = (BioPAXElement) range; - if (value != null && !model.containsID(value.getUri())) - editor.removeValueFromBean(value, domain); - } + BioPAXElement value = (BioPAXElement) range; + if (value != null && !m.containsID(value.getUri())) + ((ObjectPropertyEditor)editor).removeValueFromBean(value, domain); } }; - Traverser traverser = new Traverser(em, visitor); traverser.traverse(bpe, model); } @@ -446,26 +413,21 @@ public void visit(BioPAXElement domain, Object range, Model model, PropertyEdito */ public static void fixDanglingInverseProperties(BioPAXElement bpe, Model model) { - final Visitor visitor = new Visitor() - { - @Override - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) - { - BioPAXElement value = (BioPAXElement) range; - if (value != null && !model.containsID(value.getUri())) - editor.removeValueFromBean(domain, value); //right order! - } + final Visitor visitor = (domain, range, m, editor) -> { + BioPAXElement value = (BioPAXElement) range; + if (value != null && !m.containsID(value.getUri())) + ((ObjectPropertyEditor)editor).removeValueFromBean(domain, value); //in this order! }; TraverserBilinked traverser = new TraverserBilinked(em, visitor); - traverser.setInverseOnly(true); + traverser.setInverseOnly(true); //do only inverse properties (e.g. "entityReferenceOf", object property editors) traverser.traverse(bpe, model); } // Moved from FeatureUtils; provides operations for comparing features of physical entities. - static enum FeatureType + enum FeatureType { FEATURE, NOT_FEATURE, @@ -485,7 +447,7 @@ public static Set getFeatureIntersection(PhysicalEntity first, Fe public static Set getFeatureSetByType(PhysicalEntity pe, FeatureType type) { - Set modifiableSet = new HashSet(); + Set modifiableSet = new HashSet<>(); switch (type) { @@ -639,14 +601,14 @@ public static void fixControlled(Model model, Control control) { } /** - * In all interactions and complexes, replace generic physical entities (having members) + * In all interactions and complexes, replace generic physical entities (have members) * with their corresponding members; clone the parent object, if needed, for each member. * * @param model biopax model * @param generic physical entity (PE) that has member PEs */ public static void normalizeGeneric(Model model, PhysicalEntity generic) { - //TODO: implement? + //TODO: implement?.. } /** @@ -663,13 +625,13 @@ public static void normalizeGeneric(Model model, PhysicalEntity generic) { */ public static void normalizeGenerics(Model model) { - final Set simplePEsToDo = new HashSet(); + final Set simplePEsToDo = new HashSet<>(); for (SimplePhysicalEntity spe : model.getObjects(SimplePhysicalEntity.class)) if (spe.getEntityReference() == null && !spe.getMemberPhysicalEntity().isEmpty()) simplePEsToDo.add(spe); - final Map,EntityReference> memberMap = new HashMap,EntityReference>(); + final Map,EntityReference> memberMap = new HashMap<>(); for (SimplePhysicalEntity pe : simplePEsToDo) { try { @@ -679,7 +641,7 @@ public static void normalizeGenerics(Model model) LOG.error("createGenericEntityRef failed at " + pe.getUri(), e); } } - //TODO: unlink and remove all pe.memberPhysicalEntity for each pe in simplePEsToDo? + //TODO: unlink and remove all pe.memberPhysicalEntity for each pe in simplePEs? } private static void createGenericEntityRef(Model model, SimplePhysicalEntity spe, @@ -715,8 +677,7 @@ private static void createGenericEntityRef(Model model, SimplePhysicalEntity spe copySimplePointers(model, spe, er); //remove unification xrefs from the pe - for(UnificationXref ux : new HashSet( - new ClassFilterSet(spe.getXref(), UnificationXref.class))) + for(UnificationXref ux : new HashSet<>(new ClassFilterSet<>(spe.getXref(), UnificationXref.class))) { spe.removeXref(ux); } @@ -770,13 +731,13 @@ else if (pe instanceof RnaRegion) //generate a new URI in the same namespace (xml:base) String syntheticId = model.getXmlBase() + type.getSimpleName() + "_"+ md5hex(pe.getUri()); //create a new ER object using the auto-detected above type: - EntityReference er = (EntityReference) model.addNew(type, syntheticId); + EntityReference er = model.addNew(type, syntheticId); - // copy names and xrefs (making orig. UnificationXrefs become RelatioshipXrefs) + // copy names and xrefs (making orig. UnificationXrefs become RelationshipXrefs) copySimplePointers(model, pe, er); //remove unification xrefs from the original pe - for(UnificationXref ux : new HashSet(new ClassFilterSet(pe.getXref(),UnificationXref.class))) + for(UnificationXref ux : new HashSet<>(new ClassFilterSet<>(pe.getXref(),UnificationXref.class))) pe.removeXref(ux); er.addComment("auto-generated by Paxtools"); @@ -864,7 +825,7 @@ public static void replaceEquivalentFeatures(Model model) EquivalenceGrouper equivalents = new EquivalenceGrouper(); HashMap mapped = new HashMap(); - HashSet scheduled = new HashSet(); + HashSet scheduled = new HashSet<>(); for (EntityFeature ef : model.getObjects(EntityFeature.class)) { @@ -891,7 +852,7 @@ public static void replaceEquivalentFeatures(Model model) } for (PhysicalEntity physicalEntity : model.getObjects(PhysicalEntity.class)) { - Set features = new HashSet(physicalEntity.getFeature()); + Set features = new HashSet<>(physicalEntity.getFeature()); for (EntityFeature feature : features) { EntityFeature that = mapped.get(feature); @@ -957,12 +918,12 @@ public static Set getKeywords(BioPAXElement biopaxElement, int depth, LOG.debug("getKeywords called: " + biopaxElement.getUri()); EditorMap em = SimpleEditorMap.L3; - Set ss = new HashSet(); + Set ss = new HashSet<>(); //if depth>0, fetch child biopax objects (ignoring PathwayStep.nextStep property) Set elms = (depth > 0) ? new Fetcher(em, Fetcher.nextStepFilter).fetch(biopaxElement, depth) - : new HashSet(); + : new HashSet<>(); //add this one elms.add(biopaxElement); @@ -1019,7 +980,7 @@ private static boolean filter(T pe, Filter... prop * @return organism names */ public static Set getOrganisms(BioPAXElement biopaxElement) { - final Set biosources = new HashSet(); + final Set biosources = new HashSet<>(); //shortcut if(biopaxElement == null) return biosources; @@ -1078,7 +1039,7 @@ public static Set getOrganisms(BioPAXElement biopaxElement) { */ public static Set getDatasources(BioPAXElement biopaxElement) { - final Set datasources = new HashSet(); + final Set datasources = new HashSet<>(); //shortcut if(biopaxElement == null) @@ -1116,7 +1077,7 @@ public static Set getDatasources(BioPAXElement biopaxElement) { * @return inferred parent pathways */ public static Set getParentPathways(BioPAXElement biopaxElement) { - final Set visited = new HashSet(); + final Set visited = new HashSet<>(); return getParentPathwaysRecursively(biopaxElement, visited); } @@ -1124,7 +1085,7 @@ public static Set getParentPathways(BioPAXElement biopaxElement) { private static Set getParentPathwaysRecursively( final BioPAXElement biopaxElement, final Set visited) { - final Set pathways = new HashSet(); + final Set pathways = new HashSet<>(); //shortcut, when bpe is null or already processed if(biopaxElement == null || !visited.add(biopaxElement)) { @@ -1187,7 +1148,6 @@ public static void mergeEquivalentInteractions(Model model) if (group.size() > 1) { HashMap subs = new HashMap();//to replace in the model -// HashSet tobeRemoved = new HashSet(); Conversion primus = null; for (Conversion conversion : group) { @@ -1198,26 +1158,6 @@ public static void mergeEquivalentInteractions(Model model) { copySimplePointers(model, conversion, primus); subs.put(conversion, primus); - -// Set controlledOf = conversion.getControlledOf(); -// for (Control control : controlledOf) -// { -// if (!control.getControlled().contains(primus)) -// { -// control.addControlled(primus); -// } -// } -// Set owners = conversion.getPathwayComponentOf(); -// for (Pathway pathway : owners) -// { -// if(!pathway.getPathwayComponent().contains(primus)) -// { -// pathway.addPathwayComponent(primus); -// } -// -// } -// -// tobeRemoved.add(conversion); } } @@ -1225,7 +1165,6 @@ public static void mergeEquivalentInteractions(Model model) for (Conversion conversion : subs.keySet()) { -// cleanAllInverse(conversion); model.remove(conversion); } } @@ -1362,7 +1301,7 @@ public static void updateUri(Model model, BioPAXElement el, String newUri) { */ public static void breakPathwayComponentCycle(final Model model) { for(Pathway pathway : model.getObjects(Pathway.class)) - breakPathwayComponentCycle(new HashSet(), pathway, pathway); + breakPathwayComponentCycle(new HashSet<>(), pathway, pathway); } //Recursively, though, avoiding infinite loops (KEGG pathways can cause it), diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/PathAccessor.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/PathAccessor.java index 652692e51..45b8db18e 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/PathAccessor.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/PathAccessor.java @@ -196,7 +196,7 @@ private Class getClass(String domainstr) public Set getValueFromBean(BioPAXElement bean) throws IllegalBioPAXArgumentException { - Set bpes = new HashSet(); + Set bpes = new HashSet<>(); bpes.add(bean); return getValueFromBeans(bpes); } @@ -209,7 +209,7 @@ public Set getValueFromBeans(Collection beans) throws I { PropertyAccessor accessor = accessors.get(i); if (log.isTraceEnabled()) log.trace(String.valueOf(accessor)); - HashSet nextBpes = new HashSet(); + HashSet nextBpes = new HashSet<>(); for (BioPAXElement bpe : bpes) { if (log.isTraceEnabled()) log.trace("\t" + bpe); @@ -251,7 +251,7 @@ public Set getValueFromBeans(Collection beans) throws I */ public Set getValueFromModel(Model model) { - Set domains = new HashSet(model.getObjects(this.getDomain())); + Set domains = new HashSet<>(model.getObjects(this.getDomain())); return getValueFromBeans(domains); } @@ -272,9 +272,10 @@ private PropertyAccessor getStepAccessor(BioPAXLevel l { if (ope.property.equals(forwardName)) { - if (simple == null) simple = ope.getInverseAccessor();//TODO why not simply break, after assignment, instead using 'if'? + if (simple == null) { + simple = ope.getInverseAccessor(); + } } - } } else { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/PropertyAccessorAdapter.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/PropertyAccessorAdapter.java index 1798d7bca..b7373ab46 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/PropertyAccessorAdapter.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/PropertyAccessorAdapter.java @@ -66,7 +66,7 @@ public boolean isMultipleCardinality() @Override public Set getValueFromBeans(Collection beans) throws IllegalBioPAXArgumentException { - Set aggregate = new HashSet(); + Set aggregate = new HashSet<>(); for (D bean : beans) { aggregate.addAll(this.getValueFromBean(bean)); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/SimpleMerger.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/SimpleMerger.java index 7648b98c5..c00559291 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/SimpleMerger.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/SimpleMerger.java @@ -113,7 +113,7 @@ public void merge(Model target, Collection elements) // Auto-complete source 'elements' by discovering all the implicit elements there // copy all elements, as the collection can be immutable or unsafe to add elements to - final Set sources = new HashSet(elements); + final Set sources = new HashSet<>(elements); for(BioPAXElement se : elements) { sources.addAll(fetcher.fetch(se)); } @@ -145,7 +145,7 @@ public void merge(Model target, Collection elements) else if(bpe.getModelInterface() != target.getByID(uri).getModelInterface()) { // source object/model(s) have to be fixed (URI conflicts resolved) before merging by URI throw new RuntimeException(String.format( - "URI:%s of %s (to merge) is also URI of %s in target model (different class)", + "URI:%s of %s (to merge) is also the URI of %s in the target model but different biopax type", uri, bpe.getModelInterface().getSimpleName(), target.getByID(uri).getModelInterface().getSimpleName())); } @@ -197,7 +197,7 @@ private void updateObjectFields(BioPAXElement source, Model target) if (editor instanceof ObjectPropertyEditor) { //copy prop. values (to avoid concurrent modification exception) - Set values = new HashSet((Set) editor.getValueFromBean(source)); + Collection values = new HashSet<>(editor.getValueFromBean(source)); if(keep == source) //i.e., it has been just added to the target, - simply update properties { for (BioPAXElement value : values) { @@ -217,7 +217,7 @@ private void updateObjectFields(BioPAXElement source, Model target) else // - primitive, enum, or string property editor (e.g., comment, name), and - if (mergePropOf != null && mergePropOf.filter(source) && editor.isMultipleCardinality()) { - Set values = new HashSet((Set) editor.getValueFromBean(source)); + Set values = new HashSet<>(editor.getValueFromBean(source)); for (Object value : values) { mergeToTarget(keep, target, editor, value); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/TransitivePropertyAccessor.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/TransitivePropertyAccessor.java index 3e118aade..543786787 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/TransitivePropertyAccessor.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/TransitivePropertyAccessor.java @@ -28,7 +28,7 @@ private TransitivePropertyAccessor(PropertyAccessor accessor) @Override public Set getValueFromBean(D bean) throws IllegalBioPAXArgumentException { - Set values = new HashSet(); + Set values = new HashSet<>(); transitiveGet(bean, values); return values; diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Traverser.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Traverser.java index a9e531730..d2eef97fc 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Traverser.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Traverser.java @@ -85,7 +85,7 @@ public void traverse(D element, Model model) protected void traverseElements(BioPAXElement element, Model model, PropertyEditor editor, Set valueSet) { - for (Object value : new HashSet(valueSet)) + for (Object value : new HashSet<>(valueSet)) { visitor.visit(element, value, model, editor); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/TraverserBilinked.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/TraverserBilinked.java index 0c1f46df5..b8dd5483b 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/TraverserBilinked.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/TraverserBilinked.java @@ -45,11 +45,11 @@ public void setInverseOnly(boolean isInverseOnly) { @Override public void traverse(BioPAXElement element, Model model) { - if(!isInverseOnly) + if(!isInverseOnly) { super.traverse(element, model); + } // Now traverse the inverse links - Set editors = editorMap.getInverseEditorsOf(element); if(editors == null) @@ -61,12 +61,13 @@ public void traverse(BioPAXElement element, Model model) { if (filterInverse(editor)) { - Set valueSet = new HashSet(editor.getInverseAccessor().getValueFromBean(element)); - if (!valueSet.isEmpty()) for (BioPAXElement value : valueSet) - { - if(value != null) { - //TODO how visitor knows whether it's called from inverse or normal property (e.g., to modify a value)? - visitor.visit(element, value, model, editor); + Set valueSet = new HashSet<>(editor.getInverseAccessor().getValueFromBean(element)); + if (!valueSet.isEmpty()) { + for (BioPAXElement value : valueSet) { + if (value != null) { + //TODO how visitor knows whether it's called from inverse or normal property (e.g., to modify a value)? + visitor.visit(element, value, model, editor); + } } } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/UnionPropertyAccessor.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/UnionPropertyAccessor.java index 83a1a46ac..fbf7e02de 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/UnionPropertyAccessor.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/UnionPropertyAccessor.java @@ -29,7 +29,7 @@ public UnionPropertyAccessor(Set> uni @Override public Set getValueFromBean(D bean) throws IllegalBioPAXArgumentException { - CompositeSet valueFromBean =new CompositeSet(); + CompositeSet valueFromBean = new CompositeSet(); for (PropertyAccessor atomicAccessor : union) { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/converter/LevelUpgrader.java b/paxtools-core/src/main/java/org/biopax/paxtools/converter/LevelUpgrader.java index 5ace81489..72e2def77 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/converter/LevelUpgrader.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/converter/LevelUpgrader.java @@ -574,7 +574,7 @@ protected Object getMatchingEnum(Object o) private List> getPepsGrouped(physicalEntity pe) { - List> list = new ArrayList>(); + List> list = new ArrayList<>(); for (physicalEntityParticipant pep : pe.isPHYSICAL_ENTITYof()) { @@ -594,7 +594,7 @@ private List> getPepsGrouped(physicalEntity pe) if (!added) { - Set group = new HashSet(); + Set group = new HashSet<>(); group.add(pep); list.add(group); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java index 3c5d1ef0c..61c44ef89 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java @@ -1,85 +1,94 @@ package org.biopax.paxtools.impl; +import org.apache.commons.lang3.builder.EqualsBuilder; +import org.apache.commons.lang3.builder.HashCodeBuilder; import org.biopax.paxtools.model.BioPAXElement; -import org.biopax.paxtools.util.BPCollections; +import java.util.Collections; +import java.util.HashMap; import java.util.Map; public abstract class BioPAXElementImpl implements BioPAXElement { private String uri; - + // anything extra can be stored in this map (not to persist in a DB usually) private Map annotations; - + public BioPAXElementImpl() { - this.annotations = BPCollections.I.createMap(); + this.annotations = Collections.emptyMap(); //lazy-replace later on with a new writable map + } + + public boolean isEquivalent(BioPAXElement element) + { + return this.equals(element) || this.semanticallyEquivalent(element); + } + + protected boolean semanticallyEquivalent(BioPAXElement element) + { + return false; } - public boolean isEquivalent(BioPAXElement element) - { - return this.equals(element) || this.semanticallyEquivalent(element); - } - - protected boolean semanticallyEquivalent(BioPAXElement element) - { - return false; - } - - public int equivalenceCode() - { - return uri.hashCode(); - } - - public String getUri() - { - return uri; - } - - /** - * Private setter for the element's absolute URI. - * - * Normally, URI should never be modified - * after the object is created unless you know - * what you're doing (and can use Java Reflection). - * - * @param uri new absolute URI - */ - @SuppressWarnings("unused") + public int equivalenceCode() + { + return uri.hashCode(); + } + + public String getUri() + { + return uri; + } + + /** + * Private setter for the element's absolute URI. + * + * Normally, URI should never be modified + * after the object is created unless you know + * what you're doing (and can use Java Reflection). + * + * @param uri new absolute URI + */ + @SuppressWarnings("unused") private void setUri(String uri) - { - if(uri == null) - throw new IllegalArgumentException(); - - this.uri = uri; - } - - - public String toString() - { - return uri; - } - - - public Map getAnnotations() { - return annotations; + { + if(uri == null) + throw new IllegalArgumentException(); + + this.uri = uri; + } + + + public String toString() + { + return uri; + } + + + public Map getAnnotations() { + synchronized (annotations) { + if(annotations.isEmpty()) { + annotations = new HashMap<>(); + } + return annotations; + } } - - + + /** * true if and only if the other obj has the same biopax type * (same {@link #getModelInterface()}, not a subclass) and * same URI. Other properties are not considered. - * */ @Override public boolean equals(Object obj) { - return (obj instanceof BioPAXElement) - && this.getModelInterface() == ((BioPAXElement) obj).getModelInterface() - && this.uri.equals(((BioPAXElement) obj).getUri()); + return (obj instanceof BioPAXElement) && + new EqualsBuilder() + .append(getModelInterface(),((BioPAXElement) obj).getModelInterface()) + .append(uri,((BioPAXElement) obj).getUri()) + .build(); } - - + + /** * This method is consistent with the * overridden {@link #equals(Object)} method @@ -87,8 +96,10 @@ public boolean equals(Object obj) { */ @Override public int hashCode() { - return (getModelInterface() + uri).hashCode(); + return new HashCodeBuilder() + .append(getModelInterface()) + .append(uri) + .hashCode(); } } - diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java index 6e4261cfb..46da19787 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java @@ -161,7 +161,7 @@ private Object getStrings(BioPAXElement bpe, boolean multiple) { if (multiple) { - ArrayList list = new ArrayList(4); + ArrayList list = new ArrayList<>(4); for (String str : strings) { list.add(bpe.getUri() + str); @@ -172,7 +172,7 @@ private Object getStrings(BioPAXElement bpe, boolean multiple) private HashSet createRestrictedMock(ObjectPropertyEditor propertyEditor, BioPAXElement bpe, int k) { - HashSet hashSet = new HashSet(); + HashSet hashSet = new HashSet<>(); Set> rRanges = propertyEditor.getRestrictedRangesFor(bpe.getModelInterface()); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java index ad4316b63..2afe5826b 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java @@ -22,64 +22,75 @@ public class ModelImpl implements Model private static final long serialVersionUID = -2087521863213381434L; protected final Map idMap; - private final Map nameSpacePrefixMap; + private final Map nameSpacePrefixMap; private BioPAXLevel level; private transient BioPAXFactory factory; - private final transient Set exposedObjectSet; - private boolean addDependencies = false; - private String xmlBase; - private String uri; - private String name; + private boolean addDependencies = false; + private String xmlBase; + private String uri; + private String name; // --------------------------- CONSTRUCTORS --------------------------- - protected ModelImpl() { - idMap = BPCollections.I.createMap(); - nameSpacePrefixMap = new HashMap(); - this.exposedObjectSet = new UnmodifiableImplicitSet(idMap.values()); + protected ModelImpl() { + idMap = BPCollections.I.createMap(100); + nameSpacePrefixMap = new HashMap<>(5); } - protected ModelImpl(BioPAXLevel level) - { - this(level.getDefaultFactory()); + protected ModelImpl(int initialCapacity) { + idMap = BPCollections.I.createMap(initialCapacity); + nameSpacePrefixMap = new HashMap<>(5); } - public ModelImpl(BioPAXFactory factory) + protected ModelImpl(BioPAXLevel level) { + this(level.getDefaultFactory()); + } + + public ModelImpl(BioPAXFactory factory) { this(); this.factory = factory; this.level = factory.getLevel(); - } + } + + public ModelImpl(BioPAXFactory factory, int initialCapacity) { + this(initialCapacity); + this.factory = factory; + this.level = factory.getLevel(); + } // --------------------- GETTER / SETTER METHODS --------------------- - public synchronized boolean containsID(String id) { - return this.idMap.containsKey(id); - } + public synchronized boolean containsID(String id) { + return this.idMap.containsKey(id); + } + - - public synchronized BioPAXElement getByID(String id) { - BioPAXElement ret = this.idMap.get(id); - if(ret != null) { - assert ret.getUri().equals(id); - } - return ret; - } + public synchronized BioPAXElement getByID(String id) { + if(id == null) { + return null; + } + BioPAXElement ret = idMap.get(id); + if(ret != null) { + assert ret.getUri().equals(id); + } + return ret; + } - public Map getNameSpacePrefixMap() + public Map getNameSpacePrefixMap() { return nameSpacePrefixMap; } - - private synchronized void setNameSpacePrefixMap(Map nameSpacePrefixMap) { + + private synchronized void setNameSpacePrefixMap(Map nameSpacePrefixMap) { this.nameSpacePrefixMap.clear(); this.nameSpacePrefixMap.putAll(nameSpacePrefixMap); } - - public void setFactory(BioPAXFactory factory) + + public void setFactory(BioPAXFactory factory) { this.factory = factory; this.level = factory.getLevel(); @@ -89,50 +100,52 @@ public void setFactory(BioPAXFactory factory) // --------------------- Interface Model --------------------- -// --------------------- ACCESORS and MUTATORS--------------------- +// --------------------- ACCESSORS and MUTATORS--------------------- - public synchronized Set getObjects() + public synchronized Collection getObjects() { - return exposedObjectSet; + return new UnmodifiableImplicitSet(idMap.values()); } - public synchronized Set getObjects(Class filterBy) + public synchronized Collection getObjects(Class filterBy) { - return new ClassFilterSet(exposedObjectSet, filterBy); + return new ClassFilterSet<>(getObjects(), filterBy); } - synchronized void synchronizedsetObjects(Set objects) { - idMap.clear(); - for(BioPAXElement bpe : objects) { - add(bpe); - } - } + //a setter for persistence, serialize or tests + synchronized void setObjects(Collection objects) { + idMap.clear(); + for(BioPAXElement bpe : objects) { + add(bpe); + } + } - - public synchronized void remove(BioPAXElement aBioPAXElement) - { - if(this.contains(aBioPAXElement)) - this.idMap.remove(aBioPAXElement.getUri()); + public synchronized void remove(BioPAXElement aBioPAXElement) { + idMap.remove(aBioPAXElement.getUri()); } - + public synchronized T addNew(Class c, String id) { - T paxElement = factory.create(c, id); - this.add(paxElement); - return paxElement; + T e = factory.create(c, id); + this.add(e); + return e; } /** - * This method returns true if given element - * is the same object ("==") as the object stored in the model - * usually (for self-consistent models) but not necessarily under the element's ID. - * + * This method returns true iif given biopax object + * is the same object ("==") as the one stored in the model + * under the same key (URI). + * + * This method is a useful alternative or addition to {@link #containsID(String)} + * to use in unit tests/assertions or when handling several Models and different + * biopax objects can have same URI at some point. + * * @param aBioPAXElement BioPAX object (individual) * @return true/false - whether this model contains the object or not */ public synchronized boolean contains(BioPAXElement aBioPAXElement) { - return this.idMap.get(aBioPAXElement.getUri()) == aBioPAXElement; + return idMap.get(aBioPAXElement.getUri()) == aBioPAXElement; } // -------------------------- OTHER METHODS -------------------------- @@ -155,59 +168,47 @@ public void setName(String modelName) { public synchronized void add(BioPAXElement aBioPAXElement) { - String rdfId = aBioPAXElement.getUri(); - if(!this.level.hasElement(aBioPAXElement)) - { - throw new IllegalBioPAXArgumentException( - "Given object is of wrong level"); - } - - if (rdfId == null) - { + String uri = aBioPAXElement.getUri(); + if (uri == null) { throw new IllegalBioPAXArgumentException( - "null ID: every object must have an RDF ID"); + "BioPAX object URI is null: " + aBioPAXElement); } - else if (this.idMap.containsKey(rdfId)) - { + else if(!level.hasElement(aBioPAXElement)) { throw new IllegalBioPAXArgumentException( - "I already have an object with the same ID: " + rdfId + - ". Try removing it first"); + "Given object is of wrong level"); } - else if (this.contains(aBioPAXElement)) - { + else if (idMap.containsKey(uri)) { throw new IllegalBioPAXArgumentException( - "duplicate element:" + aBioPAXElement); + "I already have an object with the same ID: " + uri + + ". Try removing it first"); } - else - { - this.idMap.put(rdfId, aBioPAXElement); + else { + idMap.put(uri, aBioPAXElement); } } - - public BioPAXLevel getLevel() + public BioPAXLevel getLevel() { return level; } // used by hibernate - synchronized void setLevel(BioPAXLevel level) { + synchronized void setLevel(BioPAXLevel level) { this.level = level; this.factory = level.getDefaultFactory(); } - - public void setAddDependencies(boolean value) { - this.addDependencies = value; - } - - public boolean isAddDependencies() { - return addDependencies; - } + public void setAddDependencies(boolean value) { + this.addDependencies = value; + } + + public boolean isAddDependencies() { + return addDependencies; + } + + private class UnmodifiableImplicitSet implements Set { - private class UnmodifiableImplicitSet implements Set - { private final Collection elements; public UnmodifiableImplicitSet( @@ -244,7 +245,7 @@ public Object[] toArray() public T[] toArray(T[] a) { - return elements.toArray(a); + return elements.toArray(a); } public boolean add(BioPAXElement bioPAXElement) @@ -283,31 +284,31 @@ public void clear() } } - /** - * It does not automatically replace or clean up the old - * element's object properties, therefore, some child - * elements may become "dangling" if they were used by - * the replaced element only. - * - * Can also clear object properties (- replace with null). - */ - public synchronized void replace(final BioPAXElement existing, final BioPAXElement replacement) + /** + * It does not automatically replace or clean up the old + * element's object properties, therefore, some child + * elements may become "dangling" if they were used by + * the replaced element only. + * + * Can also clear object properties (- replace with null). + */ + public synchronized void replace(final BioPAXElement existing, final BioPAXElement replacement) { - ModelUtils.replace(this, Collections.singletonMap(existing, replacement)); - remove(existing); - if(replacement != null) - add(replacement); + ModelUtils.replace(this, Collections.singletonMap(existing, replacement)); + remove(existing); + if(replacement != null) + add(replacement); } - - + + /** * This is default implementation that uses the * id-based merging ({@link SimpleMerger#merge(Model, Model...)}) - * + * * NOTE: some applications, such as those dealing with persistence/transactions * or advanced BioPAX alignment/comparison algorithms (like the Patch), * may have to implement and use a more specific method instead. - * + * * @see SimpleMerger * @see Model#merge(Model) */ @@ -320,15 +321,15 @@ public synchronized void merge(Model source) { merger.merge(this, source); } - + /** - * + * * This implementation "repairs" the model * without unnecessarily copying objects: - * - recursively adds lost "children" (not null object property values - * for which {@link Model#contains(BioPAXElement)} returns False) - * - updates object properties (should refer to model's elements) - * + * - recursively adds lost "children" (not null object property values + * for which {@link Model#contains(BioPAXElement)} returns False) + * - updates object properties (should refer to model's elements) + * */ @Override public synchronized void repair() { @@ -345,4 +346,9 @@ public void setXmlBase(String base) { public String getXmlBase() { return this.xmlBase; } + + @Override + public int size() { + return idMap.size(); + } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/BioPAXLevel2ElementImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/BioPAXLevel2ElementImpl.java index 5726f506a..0277a898f 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/BioPAXLevel2ElementImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/BioPAXLevel2ElementImpl.java @@ -19,7 +19,7 @@ abstract class BioPAXLevel2ElementImpl extends BioPAXElementImpl BioPAXLevel2ElementImpl() { - this.COMMENT = new HashSet(); + this.COMMENT = new HashSet<>(); } public Set getCOMMENT() diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/ReferenceHelper.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/ReferenceHelper.java index 30d92943a..9d5d1dca5 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/ReferenceHelper.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/ReferenceHelper.java @@ -34,7 +34,7 @@ class ReferenceHelper implements Serializable ReferenceHelper(XReferrable owner) { this.owner = owner; - this.XREF = new HashSet(); + this.XREF = new HashSet<>(); } // -------------------------- OTHER METHODS -------------------------- @@ -64,7 +64,7 @@ void setXREF(Set XREF) xref.isXREFof().remove(this.owner); } - this.XREF = XREF == null ? new HashSet() : XREF; + this.XREF = XREF == null ? new HashSet<>() : XREF; for (xref xref : this.XREF) { xref.isXREFof().add(owner); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/biochemicalReactionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/biochemicalReactionImpl.java index d470a32be..0f566aee3 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/biochemicalReactionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/biochemicalReactionImpl.java @@ -29,11 +29,11 @@ class biochemicalReactionImpl extends conversionImpl public biochemicalReactionImpl() { - this.DELTA_G = new HashSet(); - this.DELTA_H = new HashSet(); - this.DELTA_S = new HashSet(); - this.EC_NUMBER = new HashSet(); - this.KEQ = new HashSet(); + this.DELTA_G = new HashSet<>(); + this.DELTA_H = new HashSet<>(); + this.DELTA_S = new HashSet<>(); + this.EC_NUMBER = new HashSet<>(); + this.KEQ = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ @@ -107,7 +107,7 @@ public void addDELTA_S(double DELTA_S) public void removeDELTA_S(double DELTA_S) { - this.DELTA_S.remove(new Double(DELTA_S)); + this.DELTA_S.remove(Double.valueOf(DELTA_S)); } public void addEC_NUMBER(String EC_NUMBER) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/catalysisImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/catalysisImpl.java index 65fc5f265..aa3d971c0 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/catalysisImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/catalysisImpl.java @@ -22,7 +22,7 @@ class catalysisImpl extends controlImpl implements catalysis public catalysisImpl() { - this.COFACTOR = new HashSet(); + this.COFACTOR = new HashSet<>(); updatePARTICIPANTS(null, COFACTOR); } @@ -61,7 +61,7 @@ public void setCOFACTOR(Set COFACTOR) { if (COFACTOR == null) { - COFACTOR = new HashSet(); + COFACTOR = new HashSet<>(); } updatePARTICIPANTS(this.COFACTOR, this.COFACTOR = COFACTOR); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/complexImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/complexImpl.java index e6dc3dbaf..378f34151 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/complexImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/complexImpl.java @@ -22,7 +22,7 @@ class complexImpl extends physicalEntityImpl implements complex public complexImpl() { - this.COMPONENTS = new HashSet(); + this.COMPONENTS = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/controlImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/controlImpl.java index 80bae2db3..aed9803e3 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/controlImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/controlImpl.java @@ -25,8 +25,8 @@ class controlImpl extends physicalInteractionAdapter public controlImpl() { - this.CONTROLLER = new HashSet(); - this.CONTROLLED = new HashSet(); + this.CONTROLLER = new HashSet<>(); + this.CONTROLLED = new HashSet<>(); updatePARTICIPANTS(null, CONTROLLER); updatePARTICIPANTS(null, CONTROLLED); } @@ -63,7 +63,7 @@ public void setCONTROLLED(Set CONTROLLED) if (CONTROLLED == null) { - CONTROLLED = new HashSet(); + CONTROLLED = new HashSet<>(); } for (process aProcess : CONTROLLED) { @@ -108,7 +108,7 @@ public void setCONTROLLER(Set CONTROLLER) { if (CONTROLLER == null) { - CONTROLLER = new HashSet(); + CONTROLLER = new HashSet<>(); } updatePARTICIPANTS(this.CONTROLLER, this.CONTROLLER = CONTROLLER); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/conversionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/conversionImpl.java index 6f6aa128d..948aa0b65 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/conversionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/conversionImpl.java @@ -25,8 +25,8 @@ class conversionImpl extends physicalInteractionAdapter public conversionImpl() { - this.LEFT = new HashSet(); - this.RIGHT = new HashSet(); + this.LEFT = new HashSet<>(); + this.RIGHT = new HashSet<>(); updatePARTICIPANTS(null, LEFT); updatePARTICIPANTS(null, RIGHT); } @@ -65,7 +65,7 @@ public void setRIGHT(Set RIGHT) { if (RIGHT == null) { - RIGHT = new HashSet(); + RIGHT = new HashSet<>(); } updatePARTICIPANTS(this.RIGHT, this.RIGHT = RIGHT); } @@ -92,7 +92,7 @@ public void setLEFT(Set LEFT) { if (LEFT == null) { - LEFT = new HashSet(); + LEFT = new HashSet<>(); } updatePARTICIPANTS(this.LEFT, this.LEFT = LEFT); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/dataSourceImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/dataSourceImpl.java index a20fd40f9..89963e6e9 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/dataSourceImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/dataSourceImpl.java @@ -20,7 +20,7 @@ class dataSourceImpl extends BioPAXLevel2ElementImpl implements dataSource public dataSourceImpl() { - this.NAME = new HashSet(); + this.NAME = new HashSet<>(); this.referenceHelper = new ReferenceHelper(this); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/entityImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/entityImpl.java index 6a4755f30..32a5c63a0 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/entityImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/entityImpl.java @@ -46,11 +46,11 @@ abstract class entityImpl extends BioPAXLevel2ElementImpl implements entity public entityImpl() { - this.AVAILABILITY = new HashSet(); - this.DATA_SOURCE = new HashSet(); - this.SYNONYMS = new HashSet(); + this.AVAILABILITY = new HashSet<>(); + this.DATA_SOURCE = new HashSet<>(); + this.SYNONYMS = new HashSet<>(); this.referenceHelper = new ReferenceHelper(this); - this.PARTICIPANTof = new HashSet(); + this.PARTICIPANTof = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/evidenceImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/evidenceImpl.java index 33175d812..f56a2ead5 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/evidenceImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/evidenceImpl.java @@ -21,9 +21,9 @@ class evidenceImpl extends BioPAXLevel2ElementImpl implements evidence public evidenceImpl() { - this.CONFIDENCE = new HashSet(); - this.EVIDENCE_CODE = new HashSet(); - this.EXPERIMENTAL_FORM = new HashSet(); + this.CONFIDENCE = new HashSet<>(); + this.EVIDENCE_CODE = new HashSet<>(); + this.EXPERIMENTAL_FORM = new HashSet<>(); this.referenceHelper = new ReferenceHelper(this); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/experimentalFormImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/experimentalFormImpl.java index ba01e6535..ce3792397 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/experimentalFormImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/experimentalFormImpl.java @@ -23,7 +23,7 @@ class experimentalFormImpl extends BioPAXLevel2ElementImpl public experimentalFormImpl() { - this.EXPERIMENTAL_FORM_TYPE = new HashSet(); + this.EXPERIMENTAL_FORM_TYPE = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionAdapter.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionAdapter.java index cb338f6a3..02ba888b1 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionAdapter.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionAdapter.java @@ -38,24 +38,9 @@ public Set getPARTICIPANTS() // -------------------------- OTHER METHODS -------------------------- - //TODO - boolean compareParticipantSets( - Set set1, - Set set2) - { - if (set1.size() == set2.size()) - { - for (InteractionParticipant ip : set1) - { -//TODO - } - } - return false; - } protected boolean semanticallyEquivalent(BioPAXElement element) { - final interaction that = (interaction) element; - return compareParticipantSets(this.PARTICIPANTS, that.getPARTICIPANTS()); + return false; } public int equivalenceCode() diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionImpl.java index 79ec533c6..3f16430a7 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/interactionImpl.java @@ -20,7 +20,7 @@ class interactionImpl extends interactionAdapter public interactionImpl() { - this.PARTICIPANTS = new HashSet(); + this.PARTICIPANTS = new HashSet<>(); updatePARTICIPANTS(null, PARTICIPANTS); } @@ -50,7 +50,7 @@ public void setPARTICIPANTS(Set PARTICIPANTS) { if (PARTICIPANTS == null) { - PARTICIPANTS = new HashSet(); + PARTICIPANTS = new HashSet<>(); } updatePARTICIPANTS(this.PARTICIPANTS, this.PARTICIPANTS = PARTICIPANTS); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/openControlledVocabularyImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/openControlledVocabularyImpl.java index f575b6238..6bdea3798 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/openControlledVocabularyImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/openControlledVocabularyImpl.java @@ -21,7 +21,7 @@ class openControlledVocabularyImpl extends BioPAXLevel2ElementImpl public openControlledVocabularyImpl() { - this.TERM = new HashSet(); + this.TERM = new HashSet<>(); this.referenceHelper = new ReferenceHelper(this); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayImpl.java index 00a26fc99..055d95170 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayImpl.java @@ -21,7 +21,7 @@ class pathwayImpl extends processImpl implements pathway public pathwayImpl() { - this.PATHWAY_COMPONENTS = new HashSet(); + this.PATHWAY_COMPONENTS = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ @@ -57,7 +57,7 @@ public void setPATHWAY_COMPONENTS(Set PATHWAY_COMPONENTS) } } this.PATHWAY_COMPONENTS = PATHWAY_COMPONENTS != null ? - PATHWAY_COMPONENTS : new HashSet(); + PATHWAY_COMPONENTS : new HashSet<>(); for (pathwayComponent pathwayComponent : this.PATHWAY_COMPONENTS) { pathwayComponent.isPATHWAY_COMPONENTSof().add(this); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayStepImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayStepImpl.java index 77d268797..296a28dca 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayStepImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/pathwayStepImpl.java @@ -23,10 +23,10 @@ class pathwayStepImpl extends BioPAXLevel2ElementImpl implements pathwayStep public pathwayStepImpl() { - this.NEXT_STEP = new HashSet(); - this.NEXT_STEPof = new HashSet(); - this.PATHWAY_COMPONENTSof = new HashSet(); - this.STEP_INTERACTIONS = new HashSet(); + this.NEXT_STEP = new HashSet<>(); + this.NEXT_STEPof = new HashSet<>(); + this.PATHWAY_COMPONENTSof = new HashSet<>(); + this.STEP_INTERACTIONS = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityImpl.java index f8ed7b7e7..655ed4fed 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityImpl.java @@ -19,7 +19,7 @@ class physicalEntityImpl extends entityImpl implements physicalEntity public physicalEntityImpl() { - this.PHYSICAL_ENTITYof = new HashSet(); + this.PHYSICAL_ENTITYof = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ @@ -41,7 +41,7 @@ public Set isPHYSICAL_ENTITYof() public Set getAllInteractions() { - HashSet allInteractions = new HashSet( + HashSet allInteractions = new HashSet<>( this.isPARTICIPANTSof()); Set peps = this.isPHYSICAL_ENTITYof(); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityParticipantImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityParticipantImpl.java index 7c89eabed..a06da7309 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityParticipantImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalEntityParticipantImpl.java @@ -17,7 +17,7 @@ class physicalEntityParticipantImpl extends BioPAXLevel2ElementImpl private openControlledVocabulary CELLULAR_LOCATION; private double STOICHIOMETRIC_COEFFICIENT = BioPAXElement.UNKNOWN_DOUBLE; private physicalEntity PHYSICAL_ENTITY; - private Set PARTICIPANTSof = new HashSet(); + private Set PARTICIPANTSof = new HashSet<>(); private complex COMPONENTSof; diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionAdapter.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionAdapter.java index af2153885..73989fe26 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionAdapter.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionAdapter.java @@ -20,7 +20,7 @@ abstract class physicalInteractionAdapter extends interactionAdapter physicalInteractionAdapter() { - this.INTERACTION_TYPE = new HashSet(); + this.INTERACTION_TYPE = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionImpl.java index 806322c10..f0c038ad4 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/physicalInteractionImpl.java @@ -20,7 +20,7 @@ class physicalInteractionImpl extends physicalInteractionAdapter public physicalInteractionImpl() { - this.PARTICIPANTS = new HashSet(); + this.PARTICIPANTS = new HashSet<>(); this.updatePARTICIPANTS(null, PARTICIPANTS); } @@ -48,7 +48,7 @@ public void setPARTICIPANTS(Set PARTICIPANTS) { if (PARTICIPANTS == null) { - PARTICIPANTS = new HashSet(); + PARTICIPANTS = new HashSet<>(); } updatePARTICIPANTS(this.PARTICIPANTS, this.PARTICIPANTS = PARTICIPANTS); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/processImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/processImpl.java index 6687e4bdc..188a79dc9 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/processImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/processImpl.java @@ -20,10 +20,10 @@ abstract class processImpl extends entityImpl implements process processImpl() { - this.EVIDENCE = new HashSet(); - this.CONTROLLEDof = new HashSet(); - this.STEP_INTERACTIONSOf = new HashSet(); - this.PATHWAY_COMPONENTSof = new HashSet(); + this.EVIDENCE = new HashSet<>(); + this.CONTROLLEDof = new HashSet<>(); + this.STEP_INTERACTIONSOf = new HashSet<>(); + this.PATHWAY_COMPONENTSof = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/publicationXrefImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/publicationXrefImpl.java index a7c74de63..393b55b81 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/publicationXrefImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/publicationXrefImpl.java @@ -23,9 +23,9 @@ class publicationXrefImpl extends xrefImpl implements publicationXref public publicationXrefImpl() { super(); - this.AUTHORS = new HashSet(); - this.SOURCE = new HashSet(); - this.URL = new HashSet(); + this.AUTHORS = new HashSet<>(); + this.SOURCE = new HashSet<>(); + this.URL = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceFeatureImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceFeatureImpl.java index 73b8df0d5..558f89346 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceFeatureImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceFeatureImpl.java @@ -25,8 +25,8 @@ class sequenceFeatureImpl extends BioPAXLevel2ElementImpl public sequenceFeatureImpl() { - this.FEATURE_LOCATION = new HashSet(); - this.SYNONYMS = new HashSet(); + this.FEATURE_LOCATION = new HashSet<>(); + this.SYNONYMS = new HashSet<>(); this.referenceHelper = new ReferenceHelper(this); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceParticipantImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceParticipantImpl.java index 45a408f5f..0e6b9ca50 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceParticipantImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/sequenceParticipantImpl.java @@ -22,7 +22,7 @@ class sequenceParticipantImpl extends physicalEntityParticipantImpl public sequenceParticipantImpl() { - this.SEQUENCE_FEATURE_LIST = new HashSet(); + this.SEQUENCE_FEATURE_LIST = new HashSet<>(); } public Class getModelInterface() diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/smallMoleculeImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/smallMoleculeImpl.java index da98e2d86..ceef7fa02 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/smallMoleculeImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/smallMoleculeImpl.java @@ -24,7 +24,7 @@ class smallMoleculeImpl extends physicalEntityImpl public smallMoleculeImpl() { - this.STRUCTURE = new HashSet(); + this.STRUCTURE = new HashSet<>(); } // ------------------------ INTERFACE METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/xrefImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/xrefImpl.java index 7025e34e8..89b0ca4c5 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/xrefImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level2/xrefImpl.java @@ -26,7 +26,7 @@ abstract class xrefImpl extends BioPAXLevel2ElementImpl implements xref public xrefImpl() { - this.XREFof = new HashSet(); + this.XREFof = new HashSet<>(); } // ------------------------ CANONICAL METHODS ------------------------ diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalReactionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalReactionImpl.java index 90c01ccd1..39e5cdc99 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalReactionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalReactionImpl.java @@ -93,7 +93,7 @@ public void addDeltaS(float deltaS) public void removeDeltaS(float deltaS) { - this.deltaS.remove(new Float(deltaS)); + this.deltaS.remove(Float.valueOf(deltaS)); } public Set getECNumber() diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ControlImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ControlImpl.java index d00cc9626..d040f2501 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ControlImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ControlImpl.java @@ -10,8 +10,7 @@ import java.util.Set; -public class ControlImpl extends InteractionImpl - implements Control +public class ControlImpl extends InteractionImpl implements Control { // ------------------------------ FIELDS ------------------------------ @@ -59,9 +58,9 @@ public void addControlled(Process process) { if (process != null) { if (!checkControlled(process)) { - throw new IllegalBioPAXArgumentException("Illegal argument. Attempting to set " - + process.getUri() + " to " + this.getUri()); - } else { //TODO: in paxtools v6, disallow multiple values (OWL functional property)... + throw new IllegalBioPAXArgumentException("addControlled: cannot add Process " + + process.getUri() + " to Control " + this.getUri()); + } else { //TODO: in Paxtools v6, disallow multiple values (it's a OWL functional property)? controlled.add(process); process.getControlledOf().add(this); super.addParticipant(process); @@ -80,7 +79,7 @@ public void removeControlled(Process controlled) public Set getController() { - Set controller = new HashSet(this.getPeController()); + Set controller = new HashSet<>(this.getPeController()); controller.addAll(getPathwayController()); return Collections.unmodifiableSet(controller); } @@ -107,9 +106,9 @@ public void removeController(Controller controller) pathwayController.remove(controller); } else if(controller instanceof PhysicalEntity) { peController.remove(controller); - } else { //hardly ever possible, anyway - - throw new IllegalBioPAXArgumentException("removeController: argument " + controller.getUri() - + " is neither Pathway nor PE - " + controller.getModelInterface().getSimpleName()); + } else { //hardly ever possible + throw new IllegalBioPAXArgumentException("removeController: argument " + + controller.getUri() + " is neither Pathway nor PE"); } } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java index 047d8dada..e45692939 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java @@ -51,16 +51,18 @@ public Set getRight() public void addRight(PhysicalEntity right) { if(right != null) { - this.right.add(right); - super.addParticipant(right); + if(this.right.add(right)) { + super.addParticipant(right); + } } } public void removeRight(PhysicalEntity right) { if(right != null) { - super.removeParticipant(right); - this.right.remove(right); + if(this.right.remove(right)) { + super.removeParticipant(right); + } } } @@ -72,19 +74,20 @@ public Set getLeft() public void addLeft(PhysicalEntity left) { if(left != null) { - this.left.add(left); - super.addParticipant(left); + if(this.left.add(left)) { + super.addParticipant(left); + } } } public void removeLeft(PhysicalEntity left) { if(left != null) { - super.removeParticipant(left); - this.left.remove(left); + if(this.left.remove(left)) { + super.removeParticipant(left); + } } } - public Boolean getSpontaneous() { @@ -150,7 +153,6 @@ else if(SetEquivalenceChecker.isEquivalent(this.getLeft(), that.getRight())) public int equivalenceCode() { return getEqCodeForSet(this.getLeft())*getEqCodeForSet(this.getRight()); - } private int getEqCodeForSet(Set peSet) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java index a2fd3eed4..52863e4bd 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java @@ -4,8 +4,6 @@ import org.biopax.paxtools.model.level3.Interaction; import org.biopax.paxtools.model.level3.InteractionVocabulary; import org.biopax.paxtools.util.BPCollections; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import java.util.Set; @@ -15,7 +13,6 @@ public class InteractionImpl extends ProcessImpl implements Interaction private Set participant; private Set interactionType; - private final Logger log = LoggerFactory.getLogger(InteractionImpl.class); // --------------------------- CONSTRUCTORS --------------------------- @@ -41,21 +38,21 @@ public Class getModelInterface() public Set getInteractionType() { - return interactionType; + return interactionType; } - public void addInteractionType( - InteractionVocabulary newinteractionType) + public void addInteractionType(InteractionVocabulary newinteractionType) { - if(newinteractionType != null) + if(newinteractionType != null) { this.interactionType.add(newinteractionType); + } } - public void removeInteractionType( - InteractionVocabulary oldinteractionType) + public void removeInteractionType(InteractionVocabulary oldinteractionType) { - if(oldinteractionType != null) + if(oldinteractionType != null) { this.interactionType.remove(oldinteractionType); + } } public Set getParticipant() @@ -63,24 +60,27 @@ public Set getParticipant() return participant; } + //this was originally added mainly for JPA protected void setParticipant(Set participant) { - this.participant = participant; - } + this.participant = participant; + } public void addParticipant(Entity aParticipant) { if (aParticipant != null) { - this.participant.add(aParticipant); - aParticipant.getParticipantOf().add(this); + if(this.participant.add(aParticipant)) { + aParticipant.getParticipantOf().add(this); + } } - } + } public void removeParticipant(Entity aParticipant) { if (aParticipant != null) { - this.participant.remove(aParticipant); - aParticipant.getParticipantOf().remove(this); + if(this.participant.remove(aParticipant)) { + aParticipant.getParticipantOf().remove(this); + } } } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/MolecularInteractionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/MolecularInteractionImpl.java index a3b61e1c2..b5e5c8a44 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/MolecularInteractionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/MolecularInteractionImpl.java @@ -6,29 +6,27 @@ import org.biopax.paxtools.util.IllegalBioPAXArgumentException; -public class MolecularInteractionImpl extends InteractionImpl - implements MolecularInteraction +public class MolecularInteractionImpl extends InteractionImpl + implements MolecularInteraction { public MolecularInteractionImpl() { } - public Class getModelInterface() - { - return MolecularInteraction.class; - } + public Class getModelInterface() + { + return MolecularInteraction.class; + } - public void addParticipant(Entity participant) - { + public void addParticipant(Entity participant) + { if (participant != null) { if (participant instanceof PhysicalEntity) { super.addParticipant(participant); } else { throw new IllegalBioPAXArgumentException( - "Participants of a molecular interaction should be" - + "of type PhysicalEntity. Parameter " - + participant + "is of type " - + participant.getClass()); + "Participants of a molecular interaction should be " + + "of type PhysicalEntity but " + participant + " is not."); } } - } + } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java index 85ef3dc1e..2881cd448 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java @@ -10,71 +10,73 @@ public class TemplateReactionImpl extends InteractionImpl implements TemplateReaction { - private Set product; - private NucleicAcid template; - private TemplateDirectionType templateDirection; + private Set product; + private NucleicAcid template; + private TemplateDirectionType templateDirection; - public TemplateReactionImpl() - { - this.product = BPCollections.I.createSafeSet(); - } - - public Class getModelInterface() - { - return TemplateReaction.class; - } + public TemplateReactionImpl() + { + this.product = BPCollections.I.createSafeSet(); + } - public Set getProduct() - { - return product; - } + public Class getModelInterface() + { + return TemplateReaction.class; + } - protected void setProduct(Set product) - { - this.product = product; - } + public Set getProduct() + { + return product; + } - public void addProduct(PhysicalEntity product) - { - if(product != null) { - this.product.add(product); - super.addParticipant(product); - } + protected void setProduct(Set product) + { + this.product = product; + } + + public void addProduct(PhysicalEntity product) + { + if(product != null) { + if(this.product.add(product)) { + super.addParticipant(product); + } } + } - public void removeProduct(PhysicalEntity product) - { - if(product != null) { - super.removeParticipant(product); - this.product.remove(product); - } + public void removeProduct(PhysicalEntity product) + { + if(product != null) { + if (this.product.remove(product)) { + super.removeParticipant(product); + } } + } - public NucleicAcid getTemplate() - { - return this.template; - } + public NucleicAcid getTemplate() + { + return this.template; + } - public void setTemplate(NucleicAcid template) - { - if(this.template!= null) - { - super.removeParticipant(this.template); - } - if(template != null) { - this.template=template; - super.addParticipant(template); - } + public void setTemplate(NucleicAcid template) + { + if(this.template != null) { + super.removeParticipant(this.template); + } + if(template != null) { + super.addParticipant(template); } + this.template = template; //can be null + } - public TemplateDirectionType getTemplateDirection() - { - return templateDirection; - } + public TemplateDirectionType getTemplateDirection() + { + return templateDirection; + } - public void setTemplateDirection(TemplateDirectionType templateDirection) - { - this.templateDirection = templateDirection; - } + public void setTemplateDirection(TemplateDirectionType templateDirection) + { + this.templateDirection = templateDirection; + } +//TODO: override add/remove participant to block direct use (allow only via add/remove "template", "product")? } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java b/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java index ca168a705..c7a9ee75d 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java @@ -610,7 +610,7 @@ private void writeObjects(Writer out, Model model) throws IOException { writeHeader(out); - Set bioPAXElements = model.getObjects(); + Collection bioPAXElements = model.getObjects(); for (BioPAXElement bean : bioPAXElements) { writeObject(out, bean); @@ -714,9 +714,10 @@ private void writeIDLine(Writer out, BioPAXElement bpe, String name) throws IOEx private void initializeExporter(Model model) { base = model.getXmlBase(); - namespaces = new HashMap(model.getNameSpacePrefixMap()); + namespaces = new HashMap<>(model.getNameSpacePrefixMap()); normalizeNameSpaces(); // - for this reader/exporter tool + // also save the changes to the model? if (normalizeNameSpaces) { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXElement.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXElement.java index 6b6476600..7ec5e7a83 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXElement.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXElement.java @@ -14,21 +14,21 @@ public interface BioPAXElement extends Serializable, Cloneable * Constant for representing unknown doubles. This is required * as by default java would assign 0. */ - public static final Double UNKNOWN_DOUBLE = Double.MIN_VALUE; + Double UNKNOWN_DOUBLE = Double.MIN_VALUE; /** * Constant for representing unknown floats. This is required * as by default java would assign 0. */ - public static final Float UNKNOWN_FLOAT = Float.MIN_VALUE; + Float UNKNOWN_FLOAT = Float.MIN_VALUE; /** * Constant for representing unknown integers. This is required * as by default java would assign 0. */ - public static final Integer UNKNOWN_INT = Integer.MIN_VALUE; - - + Integer UNKNOWN_INT = Integer.MIN_VALUE; + + /** * This method returns the actual model interface that a class implements. * @return an interface from {@link org.biopax.paxtools.model} package @@ -41,7 +41,7 @@ public interface BioPAXElement extends Serializable, Cloneable * BioPAX data providers are responsible * for generating globally unique and standard URIs * for their BioPAX elements. - * + * * @return unique URI for this object. */ String getUri(); @@ -76,9 +76,8 @@ public interface BioPAXElement extends Serializable, Cloneable * store additional application-specific information * about the BioPAX element, such as statistics, * inferred fields, etc. - * + * * @return additional (not BioPAX standard) annotations */ - public Map getAnnotations(); - + Map getAnnotations(); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java index 6d2b29000..99b2490fd 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java @@ -1,9 +1,8 @@ package org.biopax.paxtools.model; - import java.io.Serializable; +import java.util.Collection; import java.util.Map; -import java.util.Set; /** * A model acts as a container for BioPAX elements. @@ -74,29 +73,28 @@ public interface Model extends Serializable * @see #containsID(String) * * @param aBioPAXElement to be checked - * @return true if the parameter is in the object set + * @return true if the parameter is in the model (objects) */ boolean contains(BioPAXElement aBioPAXElement); /** - * This method returns the biopax element with the given id, + * This method returns the biopax element with the given URI, * returns null if the object with the given id does not exist * in this model. - * @param id of the object to be retrieved. - * @return biopax element with the given id. + * @param id URI of the object to be retrieved. + * @return biopax element with the given URI. */ BioPAXElement getByID(String id); /** - * This method checks for the biopax element with the given id, + * This method checks for the biopax element with the given URI, * returns true if the object with the given id exists. * in this model. - * @param id of the object to be retrieved. - * @return biopax element with the given id. + * @param id URI of the object to be retrieved. + * @return biopax element with the given URI. */ boolean containsID(String id); - /** * This method returns a map of name space prefixes. * This map can be modified. @@ -104,24 +102,24 @@ public interface Model extends Serializable */ Map getNameSpacePrefixMap(); -// --------------------- ACCESORS and MUTATORS--------------------- +// --------------------- ACCESSORS and MUTATORS--------------------- /** - * This method returns a set of objects in the model. - * Contents of this set can not be modified. - * @return an unmodifiable set of objects. + * This method returns the objects in the model + * (This collection should not be modified.) + * @return objects (the collection should not be modified). */ - Set getObjects(); + Collection getObjects(); /** - * This method returns a set of objects in the model of the given class. - * Contents of this set should not be modified. + * This method returns the objects of the given class in the model + * (The collection should not be modified.) * * @param a BioPAX type * @param filterBy class to be used as a filter. - * @return an unmodifiable set of objects of the given class. + * @return objects of the given class. */ - Set getObjects(Class filterBy); + Collection getObjects(Class filterBy); /** * This method removes the given BioPAX Element from the model. @@ -223,4 +221,6 @@ public interface Model extends Serializable * @return xml:base value */ String getXmlBase(); + + int size(); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/level2/InteractionHelper.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/level2/InteractionHelper.java index 573490b51..7157d9abe 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/level2/InteractionHelper.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/level2/InteractionHelper.java @@ -16,8 +16,8 @@ public static openControlledVocabulary inferLocation( // I will use two array lists instead - ArrayList ocvs = new ArrayList(5); - ArrayList counts = new ArrayList(5); + ArrayList ocvs = new ArrayList<>(5); + ArrayList counts = new ArrayList<>(5); Set ips = interaction.getPARTICIPANTS(); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/TemplateReaction.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/TemplateReaction.java index ed1cf5dec..8b27a1368 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/TemplateReaction.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/TemplateReaction.java @@ -2,28 +2,23 @@ import java.util.Set; -/** - */ public interface TemplateReaction extends Interaction { // Property Product - public Set getProduct(); + Set getProduct(); void addProduct(PhysicalEntity product); void removeProduct(PhysicalEntity product); - // Property template - public NucleicAcid getTemplate(); - - public void setTemplate(NucleicAcid template); - + NucleicAcid getTemplate(); - public TemplateDirectionType getTemplateDirection(); + void setTemplate(NucleicAcid template); - public void setTemplateDirection(TemplateDirectionType templateD1nmirection); + TemplateDirectionType getTemplateDirection(); + void setTemplateDirection(TemplateDirectionType templateD1nmirection); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java index e89dda554..e62f3fa28 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java @@ -4,9 +4,9 @@ import org.slf4j.LoggerFactory; import java.util.AbstractSet; +import java.util.Collection; import java.util.Iterator; import java.util.NoSuchElementException; -import java.util.Set; /** * Base class for implementing various filter sets. @@ -20,13 +20,12 @@ public abstract class AbstractFilterSet extends AbstractSet implements int size = -1; - protected final Set baseSet; + protected final Collection baseSet; - public AbstractFilterSet(Set baseSet) + public AbstractFilterSet(Collection baseSet) { this.baseSet = baseSet; - } /** @@ -51,7 +50,6 @@ public int size() @Override public boolean contains(Object o) { - return baseSet.contains(o) && filter(((F) o)); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java index bac01f747..38d6b1e75 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java @@ -4,20 +4,36 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Map; -import java.util.Set; +import java.util.*; public enum BPCollections { - I; + I; // singleton + + /** + * This interface is responsible for setting the class + * and initialize and load factor for all sets and maps + * used in all model objects for performance purposes. + */ + public interface CollectionProvider + { + Set createSet(); + + Map createMap(); + + Map createMap(int initSz); + + Collection createCollection(); + + Collection createCollection(int initSz); + } private CollectionProvider cProvider; private final Logger log = LoggerFactory.getLogger(BPCollections.class); + BPCollections() { String prop = System.getProperty("paxtools.CollectionProvider"); @@ -31,7 +47,7 @@ public enum BPCollections cProvider = cProviderClass.getDeclaredConstructor().newInstance(); log.info("CollectionProvider " + prop + " was successfully activated."); } - catch (Exception e) // catch (IllegalAccessException | ClassNotFoundException | InstantiationException e) + catch (Exception e) { log.warn("Could not initialize the specified collector provider:" + prop + " . Falling back to default " + @@ -41,33 +57,32 @@ public enum BPCollections } if (cProvider == null) { + //Use the default CollectionProvider implementation (HashMap, HashSet, ArrayList) cProvider = new CollectionProvider() { - @Override public Set createSet() { - return new HashSet(); + return new HashSet<>(); } - @Override public Map createMap() { - return new HashMap(); + return new HashMap<>(); + } + + public Map createMap(int initSz) { + return new HashMap<>(initSz); + } + + public Collection createCollection(int initSz) { + return new ArrayList<>(initSz); + } + + public Collection createCollection() { + return new ArrayList<>(); } }; - log.info("Using the default CollectionProvider (creates HashMap, HashSet)."); + log.info("Using the default CollectionProvider."); } - } - /** - * This interface is responsible for setting the class - * and initialize and load factor for all sets and maps - * used in all model objects for performance purposes. - */ - public interface CollectionProvider - { - Set createSet(); - - Map createMap(); - } /** * Sets a specific {@link CollectionProvider} (for @@ -100,4 +115,30 @@ public Map createMap() { return cProvider.createMap(); } + + public Map createMap(int initSize) + { + return cProvider.createMap(initSize); + } + + public Collection createCollection() + { + return cProvider.createCollection(); + } + + public Collection createCollection(int initSize) + { + return cProvider.createCollection(initSize); + } + + public Collection createSafeCollection() + { + return new BiopaxSafeCollection<>(); + } + + public Collection createSafeCollection(int initSz) + { + return new BiopaxSafeCollection<>(initSz); + } + } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java new file mode 100644 index 000000000..b72fa60c6 --- /dev/null +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java @@ -0,0 +1,74 @@ +package org.biopax.paxtools.util; + +import org.biopax.paxtools.model.BioPAXElement; + +import java.util.*; + +/** + * A thread-safe, not necessarily ordered, collection of unique BioPAX elements + * to be used mostly with add and iterator methods, + * rarely - remove or clear, and never insert or get. + */ +public class BiopaxSafeCollection extends AbstractCollection +{ + //initial map is to be reset to a modifiable instance on first write + private final static Collection empty = Collections.emptyList(); + + private Collection c_; + private int l_; + + public BiopaxSafeCollection() { + c_ = empty; + l_ = 10; + } + + @Override + public Iterator iterator() { + return c_.iterator(); + } + + public BiopaxSafeCollection(int initialCapacity) { + c_ = empty; + l_ = initialCapacity; + } + + public int size() { + synchronized (c_) { + return c_.size(); + } + } + + @Override + public boolean add(E bpe) + { + if(bpe == null) { + return false; + } + + synchronized (c_) { + if(c_ == empty) { //replace the unmodifiable empty list + this.c_ = BPCollections.I.createCollection(l_); + } + } + + synchronized (c_) { + if(!c_.contains(bpe)) { + c_.add(bpe); + return true; + } + return false; + } + } + + @Override + public boolean contains(Object o) { + if (c_ == empty || !(o instanceof BioPAXElement) || ((E)o).getUri() == null) { + return false; + } + + synchronized (c_) { + return super.contains(o); //~O(N); uses iterator() and E.equals() (compares BioPAX URI and interface) + } + } + +} diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java index 1bd00be61..7f185c39c 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java @@ -1,8 +1,6 @@ package org.biopax.paxtools.util; import org.biopax.paxtools.model.BioPAXElement; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import java.util.*; @@ -17,10 +15,8 @@ */ public class BiopaxSafeSet extends AbstractSet { - private final static Logger LOG = LoggerFactory.getLogger(BiopaxSafeSet.class); - //initial map is to be reset to a modifiable instance on first write - private final static Map empty = Collections.unmodifiableMap(Collections.emptyMap()); + private final static Map empty = Collections.emptyMap(); private Map map; @@ -41,11 +37,22 @@ public int size() return map.size(); } } - + + + /** + * Adds a new element to the collection unless it is null, or URI is null, + * or already contains an element with the same URI. + * @param bpe + * @return + */ @Override public boolean add(E bpe) { - synchronized (map) { + if(bpe == null || bpe.getUri() == null) { + return false; + } + + synchronized (map) { if(map.isEmpty()) { //new real map instead of initial fake (empty) one this.map = BPCollections.I.createMap(); @@ -53,47 +60,26 @@ public boolean add(E bpe) } String uri = bpe.getUri(); - synchronized (map) { //sync on the new map instance - if (!map.containsKey(uri)) { + if (!map.containsKey(uri)) { //prevent replacing existing objects with the same URI map.put(uri, bpe); return true; } else { - // do not throw an ex., because duplicate attempts occur naturally - // (e.g., same PE on both left and right sides of a reaction - // causes same participant/participantOf is touched twice) - LOG.debug("ignored duplicate:" + uri); + // do not throw an ex., because duplicate attempts may occur naturally return false; } } } - + @Override public boolean contains(Object o) { - if(map==empty) + if(map == empty || !(o instanceof BioPAXElement) || ((E)o).getUri() == null) { return false; - - synchronized (map) {//to sync due to two operations - return super.contains(o) - && ( get(((E)o).getUri()) == o ); } - } - - - /** - * Gets a BioPAX element by URI. - * - * @param uri absolute URI of a BioPAX individual - * @return BioPAX object or null - */ - public E get(String uri) { - - if(map==empty) - return null; synchronized (map) { - return map.get(uri); + return map.get(((E)o).getUri()) == o; } } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/ClassFilterSet.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/ClassFilterSet.java index 8bac30b78..c705558f5 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/ClassFilterSet.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/ClassFilterSet.java @@ -1,6 +1,6 @@ package org.biopax.paxtools.util; -import java.util.Set; +import java.util.Collection; /** @@ -16,11 +16,10 @@ public class ClassFilterSet extends AbstractFilterSet // --------------------------- CONSTRUCTORS --------------------------- - public ClassFilterSet(Set baseSet,Class filterClass) + public ClassFilterSet(Collection baseSet, Class filterClass) { super(baseSet); this.filterClass = filterClass; - } /** diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java index 1f6230f9c..5af590db8 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java @@ -1,9 +1,8 @@ package org.biopax.paxtools.util; import org.biopax.paxtools.model.BioPAXElement; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; +import java.util.Collection; import java.util.HashSet; import java.util.LinkedList; import java.util.List; @@ -26,22 +25,20 @@ */ public class EquivalenceGrouper { - HashSet> buckets; + Set> buckets; - private static final Logger log = LoggerFactory.getLogger(EquivalenceGrouper.class); - - public EquivalenceGrouper(Set bpes) + public EquivalenceGrouper(Collection bpes) { this(); addAll(bpes); } - public HashSet> getBuckets() + public Set> getBuckets() { return buckets; } - void addAll(Set bpes) + void addAll(Collection bpes) { for (T bpe : bpes) { @@ -93,7 +90,7 @@ public boolean equals(Object other) public EquivalenceGrouper() { - this.buckets = new HashSet>(); + this.buckets = new HashSet<>(); } public void add(T bpe) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java index 4b8cd62c5..664fb785d 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java @@ -79,7 +79,7 @@ public static Set findEquivalentIntersection(Set set2) { - Set value = new HashSet(); + Set value = new HashSet<>(); if (set1 != null && !set1.isEmpty() && set2 != null && !set2.isEmpty()) { diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java index 2ed62d1bd..4b6ec7eb5 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java @@ -23,7 +23,7 @@ public void TestCommandManager() BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model model = factory.createModel(); CommandManager manager = new CommandManager(model); - Set objects = new HashSet(); + Set objects = new HashSet<>(); Protein protein = factory.create(Protein.class, "1"); objects.add(protein); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java index fd360fba5..d44da305a 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java @@ -9,6 +9,7 @@ import org.junit.Before; import org.junit.Test; +import java.util.Collection; import java.util.Collections; import java.util.Set; @@ -44,17 +45,17 @@ public void init() { @Test - public void testCompleteAndClone() throws Exception + public void testCompleteAndClone() { Completer completer = new Completer(SimpleEditorMap.L3); - Set completed = completer.complete(Collections.singleton(model.getByID(pwUri))); + Collection completed = completer.complete(Collections.singleton(model.getByID(pwUri))); assertTrue(completed.size()>1); //PathwayStep1 should not be there if @AutoComplete(forward=false) has any effect on getNextStep() - Set steps = new ClassFilterSet(completed,PathwayStep.class); + Set steps = new ClassFilterSet<>(completed,PathwayStep.class); assertEquals(1, steps.size()); //There should be only one BiochemicalReaction that belongs to PathwayStep0 - Set rxs = new ClassFilterSet(completed,Conversion.class); + Set rxs = new ClassFilterSet<>(completed,Conversion.class); assertEquals(1, rxs.size()); } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java index 155672693..ef7a68688 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java @@ -88,7 +88,7 @@ public void testPaths() assertTrue(mwAccessor.isUnknown(values)); accessor = new PathAccessor("Protein/entityReference", BioPAXLevel.L3); - Collection beans = new ArrayList(); + Collection beans = new ArrayList<>(); beans.add(p[0]); beans.add(sm[0]); values = accessor.getValueFromBeans(beans); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java index cde1035b1..d56e311b2 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java @@ -4,13 +4,11 @@ import java.util.Set; import org.biopax.paxtools.model.*; -import org.biopax.paxtools.model.level3.Protein; import org.biopax.paxtools.model.level3.RelationshipXref; import org.biopax.paxtools.model.level3.UnificationXref; -import org.biopax.paxtools.model.level3.XReferrable; + import org.biopax.paxtools.model.level3.Xref; import org.biopax.paxtools.util.BiopaxSafeSet; -import org.junit.Ignore; import org.junit.Test; import static org.junit.Assert.*; @@ -25,56 +23,42 @@ public final void testEquals() { UnificationXref x1 = factory.create(UnificationXref.class, "x1"); x1.setDb("MI"); x1.setId("MI:0492"); - + // another xref - different ID, different properties - UnificationXref x2 = factory.create(UnificationXref.class, "x2"); + UnificationXref x2 = factory.create(UnificationXref.class, "x2"); x2.setDb("MI"); x2.setId("MI:0493"); - + // - same ID (x1), different property value - UnificationXref x3 = factory.create(UnificationXref.class, "x1"); + UnificationXref x3 = factory.create(UnificationXref.class, "x1"); x3.setDb("MI"); x3.setId("MI:0493"); - + // - a copy of x1 (a different java object) - UnificationXref x4 = factory.create(UnificationXref.class, "x1"); + UnificationXref x4 = factory.create(UnificationXref.class, "x1"); x4.setDb("MI"); x4.setId("MI:0492"); - + // - different ID, same properties (as of x1) - UnificationXref x5 = factory.create(UnificationXref.class, "x5"); + UnificationXref x5 = factory.create(UnificationXref.class, "x5"); x5.setDb("MI"); x5.setId("MI:0492"); - - - UnificationXref x6 = null; - UnificationXref x7 = null; - assertTrue(x6 == x7); - - x6 = x1; - assertFalse(x6 == x7); - assertTrue(x1 == x6); // same reference (address) - assertTrue(x1.equals(x6)); // - for sure - - x7 = x1; - assertTrue(x6 == x7); - assertTrue(x6.equals(x7)); - assertTrue(x1.equals(x7)); - assertTrue(x1.equals(x6)); - - assertFalse(x1 == x3); - assertTrue(x1.equals(x3)); //same type and URI (prop. are ignored) - assertTrue(x1.isEquivalent(x3)); // not the same db/id, same URI - equivalent because equals (above) - - assertFalse(x1 == x4); - assertTrue(x1.equals(x4)); //same type and URI - assertTrue(x1.isEquivalent(x4)); // x4 is a copy of x1 - - assertTrue(x1.isEquivalent(x5)); // x5 has different rdfId but same db/id + + UnificationXref x7 = x1; + UnificationXref x6 = x1; + + assertTrue(x6 == x7); + assertTrue(x6.equals(x7)); + assertFalse(x1 == x3); + assertTrue(x1.equals(x3)); //same type and URI (prop. are ignored) + assertTrue(x1.isEquivalent(x3)); // not the same db,id but same URI - equivalent because of equals (above) + assertFalse(x1 == x4); + assertTrue(x1.equals(x4)); //same type and URI + assertTrue(x1.isEquivalent(x4)); // x4 is a copy of x1 + assertTrue(x1.isEquivalent(x5)); // x5 has different rdfId but same db/id } - - + // we override 'equals' and 'hashCode' methods in BioPAXElementImpl (base class); // the must PASS @Test @@ -84,33 +68,33 @@ public final void testCollectionOfBiopaxElementsCustom() { UnificationXref x1 = factory.create(UnificationXref.class, "x1"); x1.setDb("foo"); x1.setId("foo"); - UnificationXref x2 = factory.create(UnificationXref.class, "x1"); + UnificationXref x2 = factory.create(UnificationXref.class, "x1"); x2.setDb("bar"); x2.setId("bar"); - - Set col = new HashSet(); + + Set col = new HashSet<>(); col.add(x1); assertTrue(col.contains(x1)); assertTrue(col.contains(x2)); // different xref, same URI and type! col.add(x2); //silently ignored assertTrue(col.size() == 1); - + col.remove(x2); //actually removes x1 (equal object) assertTrue(col.isEmpty()); - + //add back col.add(x2); Xref x3 = factory.create(RelationshipXref.class, "x1"); // x3 is of different xref type than x1 - assertFalse(col.contains(x3)); - + assertFalse(col.contains(x3)); + Xref x4 = factory.create(UnificationXref.class, "x1"); // same xref class, properties, same URI as x1 - equals x1 - - assertTrue(col.contains(x4)); + assertTrue(col.contains(x4)); } - - + + @Test public final void testBiopaxSafeSet() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); @@ -118,38 +102,36 @@ public final void testBiopaxSafeSet() { UnificationXref x1 = factory.create(UnificationXref.class, "x1"); x1.setDb("foo"); x1.setId("foo"); - //another xref, same URI - UnificationXref x2 = factory.create(UnificationXref.class, "x1"); + + //another xref using the same URI + UnificationXref x2 = factory.create(UnificationXref.class, "x1"); x2.setDb("bar"); x2.setId("bar"); - - Set col = new BiopaxSafeSet(); + + Set col = new BiopaxSafeSet<>(); + col.add(x1); assertTrue(col.contains(x1)); - assertEquals(x1, ((BiopaxSafeSet)col).get("x1")); - - // BiopaxSafeSet overrides 'contains' assertFalse(col.contains(x2)); - col.add(x2); //duplicate URI is ignored (warning is logged) - assertTrue(col.size() == 1); - + + col.add(x2); //duplicate URI object is ignored + assertFalse(col.contains(x2)); + x2 = factory.create(UnificationXref.class, "x2"); x2.setDb("bar"); x2.setId("bar"); col.add(x2); assertTrue(col.size() == 2); - + Set col1 = new BiopaxSafeSet(); col1.addAll(col); assertTrue(col1.size() == 2); assertTrue(col1.contains(x1)); assertTrue(col1.contains(x2)); - + col1.remove(x2); assertTrue(col1.size() == 1); assertTrue(col1.contains(x1)); assertFalse(col1.contains(x2)); - assertEquals("foo", ((BiopaxSafeSet)col1).get("x1").getDb()); - } } diff --git a/paxtools-query/pom.xml b/paxtools-query/pom.xml index 0aea78f2d..6d4579f27 100644 --- a/paxtools-query/pom.xml +++ b/paxtools-query/pom.xml @@ -2,7 +2,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT 4.0.0 @@ -20,7 +20,7 @@ HEAD - + org.biopax.paxtools paxtools-core diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java index 21a4ff6c6..4620ac3b6 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java @@ -32,8 +32,8 @@ public class QueryExecuter * @param filters for filtering graph elements * @return BioPAX elements in the result set */ - public static Set runNeighborhood( - Set sourceSet, + public static Collection runNeighborhood( + Collection sourceSet, Model model, int limit, Direction direction, @@ -55,12 +55,13 @@ public static Set runNeighborhood( } else return Collections.emptySet(); - Set source = prepareSingleNodeSet(sourceSet, graph); + Collection source = prepareSingleNodeSet(sourceSet, graph); if (sourceSet.isEmpty()) return Collections.emptySet(); NeighborhoodQuery query = new NeighborhoodQuery(source, direction, limit); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); + return convertQueryResult(resultWrappers, graph, true); } @@ -74,8 +75,8 @@ public static Set runNeighborhood( * @param filters for filtering graph elements * @return BioPAX elements in the result set */ - public static Set runNeighborhoodMultiSet( - Set> sourceSets, + public static Collection runNeighborhoodMultiSet( + Collection> sourceSets, Model model, int limit, Direction direction, @@ -97,12 +98,12 @@ public static Set runNeighborhoodMultiSet( } else return Collections.emptySet(); - Set source = prepareSingleNodeSetFromSets(sourceSets, graph); + Collection source = prepareSingleNodeSetFromSets(sourceSets, graph); if (sourceSets.isEmpty()) return Collections.emptySet(); NeighborhoodQuery query = new NeighborhoodQuery(source, direction, limit); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -115,7 +116,7 @@ public static Set runNeighborhoodMultiSet( * @param filters optional filters - for filtering graph elements * @return BioPAX elements in the result */ - public static Set runPathsBetween(Set sourceSet, Model model, + public static Collection runPathsBetween(Collection sourceSet, Model model, int limit, Filter... filters) { Graph graph; @@ -131,7 +132,8 @@ public static Set runPathsBetween(Set sourceSet, M if (sourceWrappers.size() < 2) return Collections.emptySet(); PathsBetweenQuery query = new PathsBetweenQuery(sourceWrappers, limit); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); + return convertQueryResult(resultWrappers, graph, true); } @@ -144,7 +146,8 @@ public static Set runPathsBetween(Set sourceSet, M * @param filters optional filters - for filtering graph elements * @return BioPAX elements in the result */ - public static Set runPathsBetweenMultiSet(Set> sourceSets, Model model, + public static Collection runPathsBetweenMultiSet( + Collection> sourceSets, Model model, int limit, Filter... filters) { Graph graph; @@ -160,7 +163,7 @@ public static Set runPathsBetweenMultiSet(Set> if (sourceWrappers.size() < 2) return Collections.emptySet(); PathsBetweenQuery query = new PathsBetweenQuery(sourceWrappers, limit); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -173,8 +176,8 @@ public static Set runPathsBetweenMultiSet(Set> * @return BioPAX elements in the result * @deprecated Use runPathsBetween instead */ - public static Set runGOI( - Set sourceSet, + public static Collection runGOI( + Collection sourceSet, Model model, int limit, Filter... filters) @@ -192,9 +195,9 @@ public static Set runGOI( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Set runPathsFromTo( - Set sourceSet, - Set targetSet, + public static Collection runPathsFromTo( + Collection sourceSet, + Collection targetSet, Model model, LimitType limitType, int limit, @@ -208,11 +211,12 @@ public static Set runPathsFromTo( } else return Collections.emptySet(); - Set source = prepareSingleNodeSet(sourceSet, graph); - Set target = prepareSingleNodeSet(targetSet, graph); + Collection source = prepareSingleNodeSet(sourceSet, graph); + Collection target = prepareSingleNodeSet(targetSet, graph); PathsFromToQuery query = new PathsFromToQuery(source, target, limitType, limit, true); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); + return convertQueryResult(resultWrappers, graph, true); } @@ -226,9 +230,9 @@ public static Set runPathsFromTo( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Set runPathsFromToMultiSet( - Set> sourceSets, - Set> targetSets, + public static Collection runPathsFromToMultiSet( + Collection> sourceSets, + Collection> targetSets, Model model, LimitType limitType, int limit, @@ -242,11 +246,12 @@ public static Set runPathsFromToMultiSet( } else return Collections.emptySet(); - Set source = prepareSingleNodeSetFromSets(sourceSets, graph); - Set target = prepareSingleNodeSetFromSets(targetSets, graph); + Collection source = prepareSingleNodeSetFromSets(sourceSets, graph); + Collection target = prepareSingleNodeSetFromSets(targetSets, graph); PathsFromToQuery query = new PathsFromToQuery(source, target, limitType, limit, true); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); + return convertQueryResult(resultWrappers, graph, true); } @@ -259,8 +264,8 @@ public static Set runPathsFromToMultiSet( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Set runCommonStream( - Set sourceSet, + public static Collection runCommonStream( + Collection sourceSet, Model model, Direction direction, int limit, @@ -280,7 +285,8 @@ public static Set runCommonStream( CommonStreamQuery query = new CommonStreamQuery(source, direction, limit); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); + return convertQueryResult(resultWrappers, graph, false); } @@ -293,8 +299,8 @@ public static Set runCommonStream( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Set runCommonStreamMultiSet( - Set> sourceSets, + public static Collection runCommonStreamMultiSet( + Collection> sourceSets, Model model, Direction direction, int limit, @@ -314,7 +320,8 @@ public static Set runCommonStreamMultiSet( CommonStreamQuery query = new CommonStreamQuery(source, direction, limit); - Set resultWrappers = query.run(); + Collection resultWrappers = query.run(); + return convertQueryResult(resultWrappers, graph, false); } @@ -328,8 +335,8 @@ public static Set runCommonStreamMultiSet( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Set runCommonStreamWithPOI( - Set sourceSet, + public static Collection runCommonStreamWithPOI( + Collection sourceSet, Model model, Direction direction, int limit, @@ -360,8 +367,8 @@ public static Set runCommonStreamWithPOI( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Set runCommonStreamWithPOIMultiSet( - Set> sourceSets, + public static Collection runCommonStreamWithPOIMultiSet( + Collection> sourceSets, Model model, Direction direction, int limit, @@ -382,21 +389,21 @@ public static Set runCommonStreamWithPOIMultiSet( return runCommonStreamWithPOIContinued(nodes, direction, limit, graph); } - private static Set runCommonStreamWithPOIContinued(Collection> sourceSets, + private static Collection runCommonStreamWithPOIContinued(Collection> sourceSets, Direction direction, int limit, Graph graph) { // Run a common stream query CommonStreamQuery commStream = new CommonStreamQuery(sourceSets, direction, limit); - Set resultWrappers = commStream.run(); + Collection resultWrappers = commStream.run(); // Stop if they have no common stream. if (resultWrappers.isEmpty()) return Collections.emptySet(); // Extract nodes from the result - Set target = new HashSet(); + Collection target = new HashSet<>(); for (GraphObject go : resultWrappers) { @@ -405,8 +412,8 @@ private static Set runCommonStreamWithPOIContinued(Collection source = new HashSet(); - for (Set set : sourceSets) + Collection source = new HashSet<>(); + for (Collection set : sourceSets) { source.addAll(set); } @@ -425,6 +432,7 @@ private static Set runCommonStreamWithPOIContinued(Collection runCommonStreamWithPOIContinued(Collection convertQueryResult( - Set resultWrappers, Graph graph, boolean removeDisconnected) + private static Collection convertQueryResult( + Collection resultWrappers, Graph graph, boolean removeDisconnected) { - Set result = graph.getWrappedSet(resultWrappers); + Collection result = graph.getWrappedSet(resultWrappers); - Set set = new HashSet(); + Collection set = new HashSet<>(); for (Object o : result) { set.add((BioPAXElement) o); @@ -449,7 +457,7 @@ private static Set convertQueryResult( // remove disconnected simple physical entities if (removeDisconnected) { - Set remove = new HashSet(); + Collection remove = new HashSet<>(); for (BioPAXElement ele : set) { @@ -465,7 +473,7 @@ private static Set convertQueryResult( return set; } - private static boolean isDisconnected(SimplePhysicalEntity spe, Set resultSet) + private static boolean isDisconnected(SimplePhysicalEntity spe, Collection resultSet) { for (Interaction inter : spe.getParticipantOf()) { @@ -496,12 +504,12 @@ private static boolean isDisconnected(SimplePhysicalEntity spe, Set prepareSingleNodeSet(Set elements, Graph graph) + public static Set prepareSingleNodeSet(Collection elements, Graph graph) { - Map> map = getRelatedPhysicalEntityMap(elements); + Map> map = getRelatedPhysicalEntityMap(elements); - Set pes = new HashSet(); - for (Set valueSet : map.values()) + Collection pes = new HashSet<>(); + for (Collection valueSet : map.values()) { pes.addAll(valueSet); } @@ -522,10 +530,10 @@ public static Set prepareSingleNodeSet(Set elements, Graph * @param graph Owner graph * @return Related wrappers in a set */ - public static Set prepareSingleNodeSetFromSets(Set> sets, Graph graph) + public static Collection prepareSingleNodeSetFromSets(Collection> sets, Graph graph) { - Set elements = new HashSet(); - for (Set set : sets) + Collection elements = new HashSet<>(); + for (Collection set : sets) { elements.addAll(set); } @@ -540,22 +548,21 @@ public static Set prepareSingleNodeSetFromSets(Set> set * @param graph Owner graph * @return Related wrappers in individual sets */ - private static Collection> prepareNodeSets(Set elements, Graph graph) + private static Collection> prepareNodeSets(Collection elements, Graph graph) { - Collection> sets = new HashSet>(); + Collection> sets = new HashSet<>(); - Map> map = getRelatedPhysicalEntityMap(elements); + Map> map = getRelatedPhysicalEntityMap(elements); - for (Set pes : map.values()) + for (Collection pes : map.values()) { Set set = graph.getWrapperSet(pes); - if (!set.isEmpty()) sets.add(set); } // Add interactions in the seed as single node set - Set inters = getSeedInteractions(elements, graph); + Collection inters = getSeedInteractions(elements, graph); for (Node node : inters) { sets.add(Collections.singleton(node)); @@ -572,11 +579,11 @@ private static Collection> prepareNodeSets(Set elements * @param graph Owner graph * @return Related wrappers in individual sets */ - private static Collection> prepareNodeSetsFromSets(Set> sets, Graph graph) + private static Collection> prepareNodeSetsFromSets(Collection> sets, Graph graph) { - Collection> result = new HashSet>(); + Collection> result = new HashSet<>(); - for (Set set : sets) + for (Collection set : sets) { Set nodes = prepareSingleNodeSet(set, graph); if (!nodes.isEmpty()) result.add(nodes); @@ -591,16 +598,15 @@ private static Collection> prepareNodeSetsFromSets(Set> getRelatedPhysicalEntityMap( + public static Map> getRelatedPhysicalEntityMap( Collection elements) { replaceXrefsWithRelatedER(elements); - Map> map = new HashMap>(); + Map> map = new HashMap<>(); for (BioPAXElement ele : elements) { - Set ents = getRelatedPhysicalEntities(ele, null); - + Collection ents = getRelatedPhysicalEntities(ele, null); if (!ents.isEmpty()) { map.put(ele, ents); @@ -617,8 +623,8 @@ public static Map> getRelatedPhysicalEntityMa protected static void replaceXrefsWithRelatedER( Collection elements) { - Set ers = new HashSet(); - Set xrefs = new HashSet(); + Collection ers = new HashSet<>(); + Collection xrefs = new HashSet<>(); for (BioPAXElement element : elements) { if (element instanceof Xref) @@ -648,10 +654,10 @@ protected static void replaceXrefsWithRelatedER( * @param pes Result set. If not supplied, a new set will be initialized. * @return Related PhysicalEntity objects */ - public static Set getRelatedPhysicalEntities(BioPAXElement element, - Set pes) + public static Collection getRelatedPhysicalEntities(BioPAXElement element, + Collection pes) { - if (pes == null) pes = new HashSet(); + if (pes == null) pes = new HashSet<>(); if (element instanceof PhysicalEntity) { @@ -702,7 +708,7 @@ else if (element instanceof EntityReference) * @param pe The PhysicalEntity to add its equivalents and complexes * @param pes Set to collect equivalents and complexes */ - private static void addEquivalentsComplexes(PhysicalEntity pe, Set pes) + private static void addEquivalentsComplexes(PhysicalEntity pe, Collection pes) { addEquivalentsComplexes(pe, true, pes); @@ -720,9 +726,9 @@ private static void addEquivalentsComplexes(PhysicalEntity pe, Set pes) + Collection pes) { - Set set = outer ? + Collection set = outer ? pe.getMemberPhysicalEntityOf() : pe.getMemberPhysicalEntity(); for (PhysicalEntity related : set) @@ -745,7 +751,7 @@ private static void addEquivalentsComplexes(PhysicalEntity pe, boolean outer, */ public static Set getSeedInteractions(Collection elements, Graph graph) { - Set nodes = new HashSet(); + Set nodes = new HashSet<>(); for (BioPAXElement ele : elements) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java index f2d673d1d..310794c7d 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java @@ -6,10 +6,10 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.util.Collection; import java.util.HashMap; import java.util.LinkedList; import java.util.Map; -import java.util.Set; /** * Implements breadth-first search. Takes a set of source nodes, distance limit and labels nodes @@ -35,12 +35,12 @@ public class BFS /** * BFS starts from source nodes. They get the label 0. */ - protected Set sourceSet; + protected Collection sourceSet; /** * BFS will not further traverse neighbors of any node in the stopSet. */ - protected Set stopSet; + protected Collection stopSet; /** * Whether the direction is FORWARD, it is REVERSE otherwise. @@ -64,7 +64,7 @@ public class BFS * @param direction Direction of the traversal * @param limit Distance limit */ - public BFS(Set sourceSet, Set stopSet, Direction direction, int limit) + public BFS(Collection sourceSet, Collection stopSet, Direction direction, int limit) { if (direction != Direction.UPSTREAM && direction != Direction.DOWNSTREAM) throw new IllegalArgumentException("Direction has to be either upstream or downstream"); @@ -78,9 +78,7 @@ public BFS(Set sourceSet, Set stopSet, Direction direction, int limi /** * Empty constructor for other possible uses. */ - public BFS() - { - } + public BFS() {} /** * Executes the algorithm. @@ -130,9 +128,9 @@ protected void initMaps() { // Initialize label, maps and queue - dist = new HashMap(); - colors = new HashMap(); - queue = new LinkedList(); + dist = new HashMap<>(); + colors = new HashMap<>(); + queue = new LinkedList<>(); } /** @@ -149,8 +147,6 @@ protected void processNode(Node current) return; } -// System.out.println("processing = " + current); - // Process edges towards the direction for (Edge edge : direction == Direction.DOWNSTREAM ? @@ -213,7 +209,6 @@ protected void processNode(Node current) } } - labelEquivRecursive(neigh, UPWARD, getLabel(neigh), further, !neigh.isBreadthNode()); labelEquivRecursive(neigh, DOWNWARD, getLabel(neigh), further, !neigh.isBreadthNode()); } @@ -264,7 +259,7 @@ protected void labelEquivRecursive(Node node, boolean up, int dist, * @param set Node set * @return true if an equivalent is in the set */ - protected boolean isEquivalentInTheSet(Node node, Set set) + protected boolean isEquivalentInTheSet(Node node, Collection set) { return set.contains(node) || isEquivalentInTheSet(node, UPWARD, set) || isEquivalentInTheSet(node, DOWNWARD, set); @@ -277,7 +272,7 @@ protected boolean isEquivalentInTheSet(Node node, Set set) * @param set Node set * @return true if an equivalent is in the set */ - protected boolean isEquivalentInTheSet(Node node, boolean direction, Set set) + protected boolean isEquivalentInTheSet(Node node, boolean direction, Collection set) { for (Node eq : direction == UPWARD ? node.getUpperEquivalent() : node.getLowerEquivalent()) { @@ -341,7 +336,6 @@ public int getLabel(GraphObject go) */ protected void setLabel(GraphObject go, int label) { -// System.out.println("Labeling(" + label + "): " + go); dist.put(go, label); } diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java index 29b63ae94..d93c360d1 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java @@ -40,7 +40,7 @@ public class CommonStreamQuery * represents whether the particular graph object is in the boundaries * of BFS. */ - Map reachedCount = new HashMap(); + Map reachedCount = new HashMap<>(); /** * Constructor for Common Stream with Selected Nodes. @@ -53,12 +53,12 @@ public CommonStreamQuery(Set sourceNodeSet, Direction direction, int limit if (direction != Direction.UPSTREAM && direction != Direction.DOWNSTREAM) throw new IllegalArgumentException("Direction has to be either upstream or downstream"); - this.sourceSet = new LinkedHashSet>(); + this.sourceSet = new LinkedHashSet<>(); //Each set contains only one selected Node for (Node node : sourceNodeSet) { - Set sourceNode = new HashSet(); + Set sourceNode = new HashSet<>(); sourceNode.add(node); sourceSet.add(sourceNode); } @@ -87,22 +87,22 @@ public CommonStreamQuery(Collection> sourceStateSet, Direction directi * Method to run the query. * @return Common stream */ - public Set run() + public Collection run() { /** * Candidate contains all the graph objects that are the results of BFS. * Eliminating nodes from candidate according to the reached counts * will yield result. */ - Map candidate = new HashMap(); - Set result = new HashSet(); + Map candidate = new HashMap<>(); + Set result = new HashSet<>(); //for each set of states of entity, run BFS separately - for (Set source : sourceSet) + for (Collection source : sourceSet) { //run BFS for set of states of each entity - BFS bfs = new BFS (source, null, direction, limit); - Map BFSResult = new HashMap(); + BFS bfs = new BFS (source, null, direction, limit); + Map BFSResult = new HashMap<>(); BFSResult.putAll(bfs.run()); /** diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java index c06c60f77..a3747f347 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java @@ -6,7 +6,6 @@ import java.util.ArrayList; import java.util.Collection; -import java.util.Set; /** * When an algorithm searches for a paths between multiple source nodes, or from a source to a @@ -21,12 +20,12 @@ public class CycleBreaker extends BFS /** * The result set to search for cycles. */ - Set result; + Collection result; /** * Source and (if exists) target nodes. */ - Set ST; + Collection ST; /** * Constructor with the objects in the result, source and target nodes, and search limit. @@ -34,7 +33,7 @@ public class CycleBreaker extends BFS * @param ST Source and target nodes * @param limit Search limit */ - public CycleBreaker(Set result, Set ST, int limit) + public CycleBreaker(Collection result, Collection ST, int limit) { this.result = result; this.ST = ST; @@ -46,7 +45,7 @@ public CycleBreaker(Set result, Set ST, int limit) */ public void breakCycles() { - for (GraphObject go : new ArrayList(result)) + for (GraphObject go : new ArrayList<>(result)) { if (go instanceof Node) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java index 25237b31e..60fbf0bf3 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java @@ -3,6 +3,7 @@ import org.biopax.paxtools.query.model.GraphObject; import org.biopax.paxtools.query.model.Node; +import java.util.Collection; import java.util.HashSet; import java.util.Map; import java.util.Set; @@ -17,7 +18,7 @@ public class NeighborhoodQuery /** * Set of source nodes. */ - private Set sourceNodes; + private Collection sourceNodes; /** * Booleans to determine the directin of search. @@ -35,7 +36,7 @@ public class NeighborhoodQuery * @param direction Direction of the search * @param limit Distance limit */ - public NeighborhoodQuery(Set sourceNodes, Direction direction, int limit) + public NeighborhoodQuery(Collection sourceNodes, Direction direction, int limit) { if (direction == Direction.UNDIRECTED) throw new IllegalArgumentException("Direction cannot be undirected, " + @@ -50,10 +51,10 @@ public NeighborhoodQuery(Set sourceNodes, Direction direction, int limit) * Executes the query. * @return Neighborhood */ - public Set run() + public Collection run() { // result set of neighborhood query - Set queryResult = new HashSet(); + Collection queryResult = new HashSet<>(); // if upstream is selected if (direction == Direction.UPSTREAM || direction == Direction.BOTHSTREAM) diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java index c4ab741e8..b28470494 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java @@ -37,22 +37,21 @@ public PathsBetweenQuery(Collection> sourceSet, int limit) this.limit = limit; } - public Set run() + public Collection run() { /** * Distance labels of graph objects. Note that each source set may have a distinct label for * the object. */ - Map, Integer>> fwdObj = new HashMap, Integer>>(); - Map, Integer>> revObj = new HashMap, Integer>>(); + Map, Integer>> fwdObj = new HashMap<>(); + Map, Integer>> revObj = new HashMap<>(); - Set result = new HashSet(); + Collection result = new HashSet<>(); for (Set set : sourceSet) { BFS bfsFwd = new BFS(set, null, Direction.DOWNSTREAM, limit); BFS bfsRev = new BFS(set, null, Direction.UPSTREAM, limit); - recordLabels(fwdObj, set, bfsFwd.run()); recordLabels(revObj, set, bfsRev.run()); } @@ -72,7 +71,7 @@ public Set run() } } - Set sources = new HashSet(); + Set sources = new HashSet<>(); for (Set set : sourceSet) { sources.addAll(set); @@ -92,8 +91,9 @@ private void recordLabels(Map, Integer>> labels, Set< { for (GraphObject go : bfsResult.keySet()) { - if (!labels.containsKey(go)) labels.put(go, new HashMap, Integer>()); - + if (!labels.containsKey(go)) { + labels.put(go, new HashMap<>()); + } labels.get(go).put(set, bfsResult.get(go)); } } diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java index 647c4ec63..50bb1b9e0 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java @@ -4,10 +4,10 @@ import org.biopax.paxtools.query.model.GraphObject; import org.biopax.paxtools.query.model.Node; +import java.util.Collection; import java.util.HashMap; import java.util.HashSet; import java.util.Map; -import java.util.Set; /** * Finds the paths from a specified source set of states or entities to a @@ -25,12 +25,12 @@ public class PathsFromToQuery /** * The set of nodes from which the paths of interests should start. */ - private Set sourceSet; + private Collection sourceSet; /** * The set of nodes to which the paths of interests should arrive. */ - private Set targetSet; + private Collection targetSet; /** * True if length limit is used, false if shortes+k is used. @@ -66,11 +66,11 @@ public class PathsFromToQuery * @param stopDistance search limit * @param strict whether we want to extend and result path towards other source and targets */ - public PathsFromToQuery(Set sourceSet, - Set targetSet, - LimitType limitType, - int stopDistance, - boolean strict) + public PathsFromToQuery(Collection sourceSet, + Collection targetSet, + LimitType limitType, + int stopDistance, + boolean strict) { assert limitType != null : "limitType should be specified"; @@ -85,7 +85,7 @@ public PathsFromToQuery(Set sourceSet, * Executes the algorithm. * @return paths from sources to targets */ - public Set run() + public Collection run() { /** * Candidate contains all the graph objects that are the results of BFS. @@ -93,7 +93,7 @@ public Set run() * yield result. */ Map candidate = new HashMap(); - Set result = new HashSet(); + Collection result = new HashSet<>(); BFS bfsFwd = null; BFS bfsRev = null; @@ -176,7 +176,7 @@ else if (limitType == LimitType.SHORTEST_PLUS_K && strict) } } - Set ST = new HashSet(sourceSet); + Collection ST = new HashSet<>(sourceSet); ST.addAll(targetSet); CycleBreaker breaker = new CycleBreaker(result, ST, limit); diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java index a9a4d0411..769637e01 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java @@ -4,8 +4,8 @@ import org.biopax.paxtools.query.model.GraphObject; import org.biopax.paxtools.query.model.Node; +import java.util.Collection; import java.util.HashSet; -import java.util.Set; /** * This algorithm is used internally by PathsBetween and PathsFromTo algorithms. It detects objects @@ -16,12 +16,12 @@ */ public class Prune { - private Set result; + private Collection result; /** * Source and targets merged. */ - private Set ST; + private Collection ST; /** @@ -30,7 +30,7 @@ public class Prune * @param result The result set * @param ST Source and target nodes */ - public Prune(Set result, Set ST) + public Prune(Collection result, Collection ST) { this.result = result; this.ST = ST; @@ -40,9 +40,9 @@ public Prune(Set result, Set ST) * Executes the algorithm. * @return the pruned graph */ - public Set run() + public Collection run() { - for (GraphObject go : new HashSet(result)) + for (GraphObject go : new HashSet<>(result)) { if (go instanceof Node) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractGraph.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractGraph.java index f4912ccec..741e5afb6 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractGraph.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractGraph.java @@ -20,7 +20,7 @@ public abstract class AbstractGraph implements Graph */ protected AbstractGraph() { - this.objectMap = new HashMap(); + this.objectMap = new HashMap<>(); } /** diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractNode.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractNode.java index 87759e266..923a507b1 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractNode.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/AbstractNode.java @@ -67,8 +67,8 @@ public abstract class AbstractNode implements Node protected AbstractNode(Graph graph) { this.graph = graph; - this.upstream = new HashSet(); - this.downstream = new HashSet(); + this.upstream = new HashSet<>(); + this.downstream = new HashSet<>(); this.upstreamInited = false; this.downstreamInited = false; } @@ -96,7 +96,7 @@ public Set getBanned() */ public void initBanned() { - if (banned == null) banned = new HashSet(); + if (banned == null) banned = new HashSet<>(); } /** diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java index 9c2ad693e..7c281bbca 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java @@ -1,5 +1,6 @@ package org.biopax.paxtools.query.model; +import java.util.Collection; import java.util.Map; import java.util.Set; @@ -22,21 +23,21 @@ public interface Graph * @param objects Wrapped objects * @return Related wrappers */ - Set getWrapperSet(Set objects); + Set getWrapperSet(Collection objects); /** * Gets a map from objects to their wrappers. * @param objects Wrapped objects * @return Object-to-wrapper map */ - Map getWrapperMap(Set objects); + Map getWrapperMap(Collection objects); /** * Gets the wrapped objects of the given wrapper set. * @param wrappers Wrappers * @return Wrapped objects */ - Set getWrappedSet(Set wrappers); + Collection getWrappedSet(Collection wrappers); /** * Should clear any analysis specific labeling on the graph. diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java index f4da161a2..b8a82c964 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java @@ -128,9 +128,9 @@ public String getKey(Object wrapped) * @param objects Wrapped objects * @return wrappers */ - public Set getWrapperSet(Set objects) + public Set getWrapperSet(Collection objects) { - Set wrapped = new HashSet(); + Set wrapped = new HashSet<>(); for (Object object : objects) { @@ -148,7 +148,7 @@ public Set getWrapperSet(Set objects) * @param objects Wrapped objects * @return object-to-wrapper map */ - public Map getWrapperMap(Set objects) + public Map getWrapperMap(Collection objects) { Map map = new HashMap(); @@ -168,9 +168,9 @@ public Map getWrapperMap(Set objects) * @param wrappers Wrappers * @return Wrapped objects */ - public Set getWrappedSet(Set wrappers) + public Set getWrappedSet(Collection wrappers) { - Set objects = new HashSet(); + Set objects = new HashSet<>(); for (GraphObject wrapper : wrappers) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/PhysicalEntityWrapper.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/PhysicalEntityWrapper.java index 89ace458c..a7c2349b5 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/PhysicalEntityWrapper.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/PhysicalEntityWrapper.java @@ -143,7 +143,7 @@ public void initDownstream() */ protected Set getUpstreamConversions(Collection inters) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Interaction inter : inters) { @@ -173,7 +173,7 @@ protected Set getUpstreamConversions(Collection inters) */ protected Set getDownstreamInteractions(Collection inters) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Interaction inter : inters) { @@ -207,7 +207,7 @@ else if (inter instanceof Control) */ private Set getRelatedConversions(Collection inters) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (Interaction inter : inters) { @@ -278,7 +278,7 @@ public Collection getLowerEquivalent() */ protected void initUpperEquivalent() { - this.upperEquivalent = new HashSet(); + this.upperEquivalent = new HashSet<>(); for (PhysicalEntity eq : pe.getMemberPhysicalEntityOf()) { @@ -294,7 +294,7 @@ protected void initUpperEquivalent() */ protected void initLowerEquivalent() { - this.lowerEquivalent = new HashSet(); + this.lowerEquivalent = new HashSet<>(); for (PhysicalEntity eq : pe.getMemberPhysicalEntity()) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/StringFieldFilter.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/StringFieldFilter.java index ab875d675..8761b77a3 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/StringFieldFilter.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/StringFieldFilter.java @@ -43,7 +43,7 @@ protected StringFieldFilter(boolean emptyOK, String[] valid) if(valid == null || valid.length == 0) { validValues = Collections.EMPTY_SET; } else { - validValues = new HashSet(); + validValues = new HashSet<>(); //copy all the filter values, making them lower-case (will then match ignoring case) for(String val : valid) if(val != null && !val.isEmpty()) diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java index c37ae6388..6307b29f8 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java @@ -125,9 +125,9 @@ public String getKey(Object wrapped) * @param objects Wrapped objects * @return wrappers */ - public Set getWrapperSet(Set objects) + public Set getWrapperSet(Collection objects) { - Set wrapped = new HashSet(); + Set wrapped = new HashSet<>(); for (Object object : objects) { @@ -145,7 +145,7 @@ public Set getWrapperSet(Set objects) * @param objects Wrapped objects * @return object-to-wrapper map */ - public Map getWrapperMap(Set objects) + public Map getWrapperMap(Collection objects) { Map map = new HashMap(); @@ -165,9 +165,9 @@ public Map getWrapperMap(Set objects) * @param wrappers Wrappers * @return Wrapped objects */ - public Set getWrappedSet(Set wrappers) + public Set getWrappedSet(Collection wrappers) { - Set objects = new HashSet(); + Set objects = new HashSet<>(); for (GraphObject wrapper : wrappers) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/PhysicalEntityWrapper.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/PhysicalEntityWrapper.java index 9cafa5f2d..e7a907e56 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/PhysicalEntityWrapper.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/PhysicalEntityWrapper.java @@ -134,7 +134,7 @@ public Collection getLowerEquivalent() */ protected void initUpperEquivalent() { - this.upperEquivalent = new HashSet(); + this.upperEquivalent = new HashSet<>(); for (PhysicalEntity eq : pe.getMemberPhysicalEntityOf()) { @@ -150,7 +150,7 @@ protected void initUpperEquivalent() */ protected void initLowerEquivalent() { - this.lowerEquivalent = new HashSet(); + this.lowerEquivalent = new HashSet<>(); for (PhysicalEntity eq : pe.getMemberPhysicalEntity()) { diff --git a/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java b/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java index 96b600947..4e8a84994 100644 --- a/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java +++ b/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java @@ -22,6 +22,7 @@ import java.io.IOException; import java.io.InputStream; import java.util.Arrays; +import java.util.Collection; import java.util.HashSet; import java.util.Set; @@ -41,13 +42,13 @@ public void testQueries() throws Throwable Model model = handler.convertFromOWL(QueryTest.class.getResourceAsStream( "raf_map_kinase_cascade_reactome.owl")); - Set source = findElements(model, + Collection source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606"); //MEK2 - Set target = findElements(model, + Collection target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606"); //ERK1 - Set result = QueryExecuter.runNeighborhood( + Collection result = QueryExecuter.runNeighborhood( source, model, 1, Direction.BOTHSTREAM); assertTrue(result.size() > 0); @@ -93,27 +94,22 @@ public void testQueries() throws Throwable assertFalse(result.contains(check)); result = QueryExecuter.runNeighborhood(source, model, 3, Direction.UNDIRECTED); assertTrue(result.contains(check)); - - -// Model clonedModel = excise(model, result); -// handler.convertToOWL(clonedModel, new FileOutputStream( -// getClass().getResource("").getFile() + File.separator + "temp.owl")); } - private Model excise(Model model, Set result) + private Model excise(Collection result) { Completer c = new Completer(SimpleEditorMap.L3); - result = c.complete(result, model); + result = c.complete(result); Cloner cln = new Cloner(SimpleEditorMap.L3, BioPAXLevel.L3.getDefaultFactory()); - return cln.clone(model, result); + return cln.clone(result); } - protected static Set findElements(Model model, String... ids) + protected static Collection findElements(Model model, String... ids) { - Set set = new HashSet(); + Collection set = new HashSet<>(); for (String id : ids) { @@ -144,12 +140,11 @@ public void testQueryPerformance() throws IOException BioPAXElement s1 = model.getByID("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN6022_1_9606"); BioPAXElement t1 = model.getByID("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN6020_1_9606"); - Set source = new HashSet(); -// Set target = new HashSet(); + Collection source = new HashSet<>(); source.add(s1); source.add(t1); - Set result = QueryExecuter.runCommonStreamWithPOI( + Collection result = QueryExecuter.runCommonStreamWithPOI( source, model, Direction.DOWNSTREAM, 3, null); secs = (System.currentTimeMillis() - time); @@ -157,7 +152,7 @@ public void testQueryPerformance() throws IOException System.out.println("result.size() = " + result.size()); System.out.println("milisecs = " + secs); - Model ex = excise(model, result); + Model ex = excise(result); handler.convertToOWL(ex, new FileOutputStream("QueryResult.owl")); } @@ -167,15 +162,15 @@ public void testFilters() Model model = handler.convertFromOWL(this.getClass().getResourceAsStream( "raf_map_kinase_cascade_reactome.owl")); - Set source = findElements(model, + Collection source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606"); //MEK2 - Set target = findElements(model, + Collection target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606"); //ERK1 // test organism filter Filter f = new OrganismFilter(new String[]{"Homo sapiens"}); - Set result = QueryExecuter.runPathsFromTo( + Collection result = QueryExecuter.runPathsFromTo( source, target, model, LimitType.NORMAL, 2, f); assertTrue(!result.isEmpty()); @@ -213,14 +208,14 @@ public void testFilters() target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#SMALLMOLECULE6_1_9606"); //ADP - Set ubiqueIDs = new HashSet(Arrays.asList("Some ID", "Another ID")); + Set ubiqueIDs = Set.of("Some ID", "Another ID"); result = QueryExecuter.runPathsFromTo(source, target, model, LimitType.NORMAL, 1, new UbiqueFilter(ubiqueIDs)); assertTrue(!result.isEmpty()); - ubiqueIDs = new HashSet(Arrays.asList( + ubiqueIDs = new HashSet<>(Arrays.asList( "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#SMALLMOLECULE5_1_9606")); result = QueryExecuter.runPathsFromTo(source, target, model, LimitType.NORMAL, 1, diff --git a/paxtools-search/pom.xml b/paxtools-search/pom.xml index b2173efb5..2ac50b627 100644 --- a/paxtools-search/pom.xml +++ b/paxtools-search/pom.xml @@ -5,7 +5,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT paxtools-search @@ -19,7 +19,7 @@ - 4.10.2 + 7.5.0 diff --git a/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java b/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java index 04eb3a16c..5c74195eb 100644 --- a/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java +++ b/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java @@ -1,14 +1,11 @@ package org.biopax.paxtools.search; -import java.io.File; import java.io.IOException; import java.io.StringReader; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashSet; -import java.util.List; -import java.util.Set; -import java.util.TreeSet; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.TimeUnit; @@ -18,15 +15,15 @@ import org.apache.commons.lang3.StringUtils; import org.apache.lucene.analysis.Analyzer; import org.apache.lucene.analysis.TokenStream; +import org.apache.lucene.analysis.core.KeywordAnalyzer; +import org.apache.lucene.analysis.miscellaneous.PerFieldAnalyzerWrapper; import org.apache.lucene.analysis.standard.StandardAnalyzer; import org.apache.lucene.analysis.tokenattributes.CharTermAttribute; import org.apache.lucene.document.Document; import org.apache.lucene.document.Field; -import org.apache.lucene.document.IntField; import org.apache.lucene.document.StoredField; import org.apache.lucene.document.StringField; import org.apache.lucene.document.TextField; -import org.apache.lucene.index.CorruptIndexException; import org.apache.lucene.index.IndexWriter; import org.apache.lucene.index.IndexWriterConfig; import org.apache.lucene.index.Term; @@ -34,11 +31,8 @@ import org.apache.lucene.queryparser.classic.ParseException; import org.apache.lucene.queryparser.classic.QueryParser; import org.apache.lucene.search.BooleanQuery; -import org.apache.lucene.search.CachingWrapperFilter; -import org.apache.lucene.search.Filter; import org.apache.lucene.search.IndexSearcher; import org.apache.lucene.search.Query; -import org.apache.lucene.search.QueryWrapperFilter; import org.apache.lucene.search.ScoreDoc; import org.apache.lucene.search.SearcherFactory; import org.apache.lucene.search.SearcherManager; @@ -52,7 +46,6 @@ import org.apache.lucene.search.highlight.SimpleSpanFragmenter; import org.apache.lucene.store.FSDirectory; import org.apache.lucene.store.MMapDirectory; -import org.apache.lucene.util.Version; import org.biopax.paxtools.controller.DataPropertyEditor; import org.biopax.paxtools.controller.Fetcher; import org.biopax.paxtools.controller.ModelUtils; @@ -69,13 +62,11 @@ /** * A full-text searcher/indexer for BioPAX L3 models. * - * TODO: upgrade to the latest Lucene API and copy some changes from cPath2 project. - * * @author rodche */ public class SearchEngine implements Indexer, Searcher { private static final Logger LOG = LoggerFactory.getLogger(SearchEngine.class); - + // search fields public static final String FIELD_URI = "uri"; public static final String FIELD_KEYWORD = "keyword"; //anything, e.g., names, terms, comments, incl. - from child elements @@ -84,32 +75,31 @@ public class SearchEngine implements Indexer, Searcher { public static final String FIELD_PATHWAY = "pathway"; //parent/owner pathways; to be inferred from the whole biopax model public static final String FIELD_N_PARTICIPANTS = "participants"; // num. of PEs or Genes in a process or Complex public static final String FIELD_N_PROCESSES = "processes"; // is same as 'size' used to be before cPath2 v7 - public static final String FIELD_N = "n"; // also num. of processes, but indexed to use in range queries, e.g., n:>3 // Full-text search/filter fields (case sensitive) - //index organism names, cell/tissue type (term), taxonomy id, but only store BioSource URIs public static final String FIELD_ORGANISM = "organism"; //index data source names, but only URIs are stored in the index public static final String FIELD_DATASOURCE = "datasource"; public static final String FIELD_TYPE = "type"; - + //Default fields to use with the MultiFieldQueryParser; //one can still search in other fields directly, e.g., //pathway:some_keywords datasource:"pid", etc. - public final static String[] DEFAULT_FIELDS = - { + public final static String[] DEFAULT_FIELDS = + { FIELD_KEYWORD, //includes all data type properties (names, terms, comments), // also from child elements up to given depth (3), also includes pathway names (inferred) FIELD_NAME, // standardName, displayName, other names FIELD_XREFID, //xref.id (also direct child's xref.id, i.e., can find both xref and its owners using a xrefid: query string) - }; - + }; + /** * A Key for the value in a * BioPAX element's annotations map * where additional information about * corresponding search hit will be stored. */ - public enum HitAnnotation + public enum HitAnnotation { HIT_EXCERPT, HIT_PROCESSES, @@ -118,36 +108,42 @@ public enum HitAnnotation HIT_DATASOURCE, HIT_PATHWAY, } - + private final Model model; private int maxHitsPerPage; private final Analyzer analyzer; - private final File indexFile; + private final Path indexFile; private SearcherManager searcherManager; public final static int DEFAULT_MAX_HITS_PER_PAGE = 100; - + + /** - * Main Constructor. + * Constructor. * - * @param model BioPAX object model to be indexed or searched. - * @param indexLocation full path to the index directory + * @param model the BioPAX Model to index or search + * @param indexLocation index directory location */ public SearchEngine(Model model, String indexLocation) { this.model = model; - this.indexFile = new File(indexLocation); + this.indexFile = Paths.get(indexLocation); initSearcherManager(); this.maxHitsPerPage = DEFAULT_MAX_HITS_PER_PAGE; - this.analyzer = new StandardAnalyzer(); + Map analyzersPerField = new HashMap<>(); + analyzersPerField.put(FIELD_NAME, new KeywordAnalyzer()); + analyzersPerField.put(FIELD_XREFID, new KeywordAnalyzer()); + analyzersPerField.put(FIELD_URI, new KeywordAnalyzer()); + analyzersPerField.put(FIELD_PATHWAY, new KeywordAnalyzer()); + this.analyzer = new PerFieldAnalyzerWrapper(new StandardAnalyzer(), analyzersPerField); } private void initSearcherManager() { try { - if(indexFile.exists()) - this.searcherManager = + if(Files.exists(indexFile)) + this.searcherManager = new SearcherManager(MMapDirectory.open(indexFile), new SearcherFactory()); - else - LOG.info(indexFile.getPath() + " does not exist."); + else + LOG.info(indexFile + " does not exist."); } catch (IOException e) { LOG.warn("Could not create a searcher: " + e); } @@ -166,440 +162,445 @@ public void setMaxHitsPerPage(int maxHitsPerPage) { * Gets the maximum no. hits per search results page (pagination parameter). * @return int value */ - public int getMaxHitsPerPage() { + public int getMaxHitsPerPage() { return maxHitsPerPage; } public SearchResult search(String query, int page, - Class filterByType, String[] datasources, - String[] organisms) + Class filterByType, String[] datasources, + String[] organisms) { - SearchResult response = null; - - LOG.debug("search: " + query + ", page: " + page + SearchResult response; + + LOG.debug("search: " + query + ", page: " + page + ", filterBy: " + filterByType + "; extra filters: ds in (" + Arrays.toString(datasources) + "), org. in (" + Arrays.toString(organisms) + ")"); - + IndexSearcher searcher = null; - - try { + + try { QueryParser queryParser = new MultiFieldQueryParser(DEFAULT_FIELDS, analyzer); queryParser.setAllowLeadingWildcard(true);//TODO do we really want leading wildcards (e.g. *sulin)? - - searcher = searcherManager.acquire(); - + searcher = searcherManager.acquire(); + //find and transform top docs to search hits (beans), considering pagination... if(!query.trim().equals("*")) { //if not "*" query, which is not supported out-of-the-box, then //create the lucene query - Query luceneQuery = queryParser.parse(query); -//do NOT (Lucene 4.1), or scoring/highlighting won't work for wildcard queries... -//luceneQuery = searcher.rewrite(luceneQuery); - LOG.debug("parsed lucene query is " + luceneQuery.getClass().getSimpleName()); - + Query q = queryParser.parse(query); + LOG.debug("parsed lucene query is " + q.getClass().getSimpleName()); + //create filter: type AND (d OR d...) AND (o OR o...) - Filter filter = createFilter(filterByType, datasources, organisms); - + Query filter = createFilter(filterByType, datasources, organisms); + + //final query with filter + q = (filter != null) + ? new BooleanQuery.Builder().add(q,Occur.MUST).add(filter,Occur.FILTER).build() + : q; + //get the first page of top hits - TopDocs topDocs = searcher.search(luceneQuery, filter, maxHitsPerPage); + TopDocs topDocs = searcher.search(q, maxHitsPerPage); + //get the required hits page if page>0 if(page>0) { - TopScoreDocCollector collector = TopScoreDocCollector.create(maxHitsPerPage*(page+1), true); - searcher.search(luceneQuery, filter, collector); + TopScoreDocCollector collector = TopScoreDocCollector.create(maxHitsPerPage*(page+1)); + searcher.search(q, collector); topDocs = collector.topDocs(page * maxHitsPerPage, maxHitsPerPage); } - + //transform docs to hits, use a highlighter to get excerpts - response = transform(luceneQuery, searcher, true, topDocs); - - } else { //find ALL objects of a particular BioPAX class (+ filters by organism, datasource) - if(filterByType==null) + response = transform(q, searcher, true, topDocs); + + } else { + //find ALL objects of a particular BioPAX class (+ filters by organism, datasource) + if(filterByType==null) { filterByType = Level3Element.class; + } //replace q="*" with a search for the class or its sub-class name in the TYPE field - BooleanQuery luceneQuery = new BooleanQuery(); + BooleanQuery.Builder b = new BooleanQuery.Builder(); for(Class subType : SimpleEditorMap.L3.getKnownSubClassesOf(filterByType)) { - luceneQuery.add(new TermQuery(new Term(FIELD_TYPE, subType.getSimpleName().toLowerCase())), Occur.SHOULD); + b.add(new TermQuery(new Term(FIELD_TYPE, subType.getSimpleName().toLowerCase())), Occur.SHOULD); } - Filter filter = createFilter(null, datasources, organisms); - + + Query filter = createFilter(null, datasources, organisms); + + //combine star and filter queries into one special boolean + Query q = (filter != null) + ? new BooleanQuery.Builder().add(b.build(),Occur.MUST).add(filter,Occur.FILTER).build() + : b.build(); + //get the first page of top hits - TopDocs topDocs = searcher.search(luceneQuery, filter, maxHitsPerPage); + TopDocs topDocs = searcher.search(q, maxHitsPerPage); + //get the required hits page if page>0 if(page>0) { - TopScoreDocCollector collector = TopScoreDocCollector.create(maxHitsPerPage*(page+1), true); - searcher.search(luceneQuery, filter, collector); - topDocs = collector.topDocs(page * maxHitsPerPage, maxHitsPerPage); + TopScoreDocCollector collector = TopScoreDocCollector.create(maxHitsPerPage*(page+1)); + searcher.search(q, collector); + topDocs = collector.topDocs(page * maxHitsPerPage, maxHitsPerPage); } - + //convert - response = transform(luceneQuery, searcher, false, topDocs); - } - + response = transform(q, searcher, false, topDocs); + } } catch (ParseException e) { throw new RuntimeException("getTopDocs: failed to parse the query string.", e); } catch (IOException e) { throw new RuntimeException("getTopDocs: failed.", e); } finally { try { - if(searcher!=null) { + if(searcher != null) { searcherManager.release(searcher); - searcher = null; } - } catch (IOException e) {} + } catch (IOException e) {} } - + response.setPage(page); - return response; } - + /** * Returns a SearchResult * that contains a List, * some parameters, totals, etc. */ - private SearchResult transform(Query query, IndexSearcher searcher, boolean highlight, TopDocs topDocs) - throws CorruptIndexException, IOException - { + private SearchResult transform(Query query, IndexSearcher searcher, boolean highlight, TopDocs topDocs) + throws IOException + { final SearchResult response = new SearchResult(); - final List hits = new ArrayList(); - + final List hits = new ArrayList<>(); + response.setMaxHitsPerPage(maxHitsPerPage); response.setHits(hits); - - for(ScoreDoc scoreDoc : topDocs.scoreDocs) { + + for(ScoreDoc scoreDoc : topDocs.scoreDocs) { Document doc = searcher.doc(scoreDoc.doc); String uri = doc.get(FIELD_URI); - BioPAXElement bpe = model.getByID(uri); + BioPAXElement bpe = model.getByID(uri); + Map annotations = bpe.getAnnotations(); LOG.debug("transform: doc:" + scoreDoc.doc + ", uri:" + uri); - + // use the highlighter (get matching fragments) // for this to work, all keywords were stored in the index field - if (highlight && doc.get(FIELD_KEYWORD) != null) { + if (highlight && doc.get(FIELD_KEYWORD) != null) { // use a Highlighter (store.YES must be enabled for 'keyword' field) - QueryScorer scorer = new QueryScorer(query, FIELD_KEYWORD); + QueryScorer scorer = new QueryScorer(query, FIELD_KEYWORD); //this fixes scoring/highlighting for all-field wildcard queries like q=insulin* //but not for term/prefix queries, i.e, q=name:insulin*, q=pathway:brca2. TODO - scorer.setExpandMultiTermQuery(true); - + scorer.setExpandMultiTermQuery(true); + //TODO try PostingsHighlighter once it's stable... // (see http://lucene.apache.org/core/4_10_0/highlighter/org/apache/lucene/search/postingshighlight/PostingsHighlighter.html) SimpleHTMLFormatter formatter = new SimpleHTMLFormatter("", ""); Highlighter highlighter = new Highlighter(formatter, scorer); highlighter.setTextFragmenter(new SimpleSpanFragmenter(scorer, 80)); - + final String text = StringUtils.join(doc.getValues(FIELD_KEYWORD), " "); try { TokenStream tokenStream = analyzer.tokenStream("", new StringReader(text)); String res = highlighter.getBestFragments(tokenStream, text, 7, "..."); if(res != null && !res.isEmpty()) { - bpe.getAnnotations().put(HitAnnotation.HIT_EXCERPT.name(), res); + annotations.put(HitAnnotation.HIT_EXCERPT.name(), res); } } catch (Exception e) {throw new RuntimeException(e);} } else if(highlight) { - LOG.warn("Highlighter skipped, because KEYWORD field was null; hit: " - + uri + ", " + bpe.getModelInterface().getSimpleName()); + LOG.warn("Highlighter skipped, because KEYWORD field was null; hit: " + + uri + ", " + bpe.getModelInterface().getSimpleName()); } // extract organisms (URI only) if not done before - if(doc.get(FIELD_ORGANISM) != null && !bpe.getAnnotations().containsKey(HitAnnotation.HIT_ORGANISM.name())) { - Set uniqueVals = new TreeSet(); + if(doc.get(FIELD_ORGANISM) != null && !annotations.containsKey(HitAnnotation.HIT_ORGANISM.name())) { + Set uniqueVals = new TreeSet<>(); for(String o : doc.getValues(FIELD_ORGANISM)) { //note: only URIS are stored in the index uniqueVals.add(o); } - bpe.getAnnotations().put(HitAnnotation.HIT_ORGANISM.name(), uniqueVals); + annotations.put(HitAnnotation.HIT_ORGANISM.name(), uniqueVals); } - + // extract values form the index if not previously done - if(doc.get(FIELD_DATASOURCE) != null && !bpe.getAnnotations().containsKey(HitAnnotation.HIT_DATASOURCE.name())) { + if(doc.get(FIELD_DATASOURCE) != null && !annotations.containsKey(HitAnnotation.HIT_DATASOURCE.name())) { Set uniqueVals = new TreeSet(); for(String d : doc.getValues(FIELD_DATASOURCE)) { //note: only URIS are stored in the index uniqueVals.add(d); } - bpe.getAnnotations().put(HitAnnotation.HIT_DATASOURCE.name(), uniqueVals); - } - + annotations.put(HitAnnotation.HIT_DATASOURCE.name(), uniqueVals); + } + // extract only pathway URIs if not previously done //(because names and IDs used to be stored in the index field as well) - if(doc.get(FIELD_PATHWAY) != null && !bpe.getAnnotations().containsKey(HitAnnotation.HIT_PATHWAY.name())) { + if(doc.get(FIELD_PATHWAY) != null && !annotations.containsKey(HitAnnotation.HIT_PATHWAY.name())) { Set uniqueVals = new TreeSet(); for(String d : doc.getValues(FIELD_PATHWAY)) { //only URIs were stored (though all names/ids were indexed/analyzed) if(!d.equals(uri)) //exclude itself uniqueVals.add(d); } - bpe.getAnnotations().put(HitAnnotation.HIT_PATHWAY.name(), uniqueVals); + annotations.put(HitAnnotation.HIT_PATHWAY.name(), uniqueVals); } - + //store the no. processes in the sub-network if not previously done - if(doc.get(FIELD_N_PARTICIPANTS)!=null && !bpe.getAnnotations().containsKey(HitAnnotation.HIT_PARTICIPANTS.name())) - bpe.getAnnotations().put(HitAnnotation.HIT_PARTICIPANTS.name(), Integer.valueOf(doc.get(FIELD_N_PARTICIPANTS))); - if(doc.get(FIELD_N_PROCESSES)!=null && !bpe.getAnnotations().containsKey(HitAnnotation.HIT_PROCESSES.name())) - bpe.getAnnotations().put(HitAnnotation.HIT_PROCESSES.name(), Integer.valueOf(doc.get(FIELD_N_PROCESSES))); + if(doc.get(FIELD_N_PARTICIPANTS)!=null && !annotations.containsKey(HitAnnotation.HIT_PARTICIPANTS.name())) + annotations.put(HitAnnotation.HIT_PARTICIPANTS.name(), Integer.valueOf(doc.get(FIELD_N_PARTICIPANTS))); + if(doc.get(FIELD_N_PROCESSES)!=null && !annotations.containsKey(HitAnnotation.HIT_PROCESSES.name())) + annotations.put(HitAnnotation.HIT_PROCESSES.name(), Integer.valueOf(doc.get(FIELD_N_PROCESSES))); //store the Lucene's score and explanation. - String excerpt = (String) bpe.getAnnotations().get(HitAnnotation.HIT_EXCERPT.name()); + String excerpt = (String) annotations.get(HitAnnotation.HIT_EXCERPT.name()); if(excerpt == null) excerpt = ""; excerpt += " -SCORE- " + scoreDoc.score + " -EXPLANATION- " + searcher.explain(query, scoreDoc.doc); - bpe.getAnnotations().put(HitAnnotation.HIT_EXCERPT.name(), excerpt); + annotations.put(HitAnnotation.HIT_EXCERPT.name(), excerpt); hits.add(bpe); } - + //set total no. hits response.setTotalHits(topDocs.totalHits); - + return response; } public void index() { final int numObjects = model.getObjects().size(); - LOG.info("index(), there are " + numObjects + " BioPAX objects to be (re-)indexed."); - IndexWriter iw; + LOG.info("index(), there are " + numObjects + " BioPAX objects to be (re-)indexed."); + IndexWriter iw; try { //close the searcher manager if the old index exists if(searcherManager != null) { searcherManager.close(); searcherManager = null; } - IndexWriterConfig conf = new IndexWriterConfig(Version.LATEST, analyzer); + IndexWriterConfig conf = new IndexWriterConfig(analyzer); iw = new IndexWriter(FSDirectory.open(indexFile), conf); //cleanup iw.deleteAll(); iw.commit(); } catch (IOException e) { throw new RuntimeException("Failed to create a new IndexWriter.", e); - } + } final IndexWriter indexWriter = iw; ExecutorService exec = Executors.newFixedThreadPool(30); - + final AtomicInteger numLeft = new AtomicInteger(numObjects); - final org.biopax.paxtools.util.Filter dataPropertiesToConsider - = new org.biopax.paxtools.util.Filter() { - @Override - public boolean filter(DataPropertyEditor editor) { - final String prop = editor.getProperty(); - //to include in the index, as keywords, only the following properties - // (basically, to exclude float type properties, embedded xml, db names, etc.): - return (prop.equalsIgnoreCase("author") || prop.equalsIgnoreCase("availability") - || prop.equalsIgnoreCase("chemicalFormula") || prop.equalsIgnoreCase("comment") - || prop.equalsIgnoreCase("controlType") || prop.equalsIgnoreCase("conversionDirection") - || prop.equalsIgnoreCase("eCNumber") || prop.equalsIgnoreCase("id") - || prop.equalsIgnoreCase("name") || prop.equalsIgnoreCase("displayName") - || prop.equalsIgnoreCase("standardName") || prop.equalsIgnoreCase("sequence") - || prop.equalsIgnoreCase("source") || prop.equalsIgnoreCase("year") - || prop.equalsIgnoreCase("term") || prop.equalsIgnoreCase("stepDirection") - || prop.equalsIgnoreCase("structureData") || prop.equalsIgnoreCase("templateDirection") - || prop.equalsIgnoreCase("title") || prop.equalsIgnoreCase("url") - ); - } + final org.biopax.paxtools.util.Filter dataPropertiesToConsider = editor -> { + final String prop = editor.getProperty(); + //to include in the index, as keywords, only the following properties + // (basically, to exclude float type properties, embedded xml, db names, etc.): + return (prop.equalsIgnoreCase("author") || prop.equalsIgnoreCase("availability") + || prop.equalsIgnoreCase("chemicalFormula") || prop.equalsIgnoreCase("comment") + || prop.equalsIgnoreCase("controlType") || prop.equalsIgnoreCase("conversionDirection") + || prop.equalsIgnoreCase("eCNumber") || prop.equalsIgnoreCase("id") + || prop.equalsIgnoreCase("name") || prop.equalsIgnoreCase("displayName") + || prop.equalsIgnoreCase("standardName") || prop.equalsIgnoreCase("sequence") + || prop.equalsIgnoreCase("source") || prop.equalsIgnoreCase("year") + || prop.equalsIgnoreCase("term") || prop.equalsIgnoreCase("stepDirection") + || prop.equalsIgnoreCase("structureData") || prop.equalsIgnoreCase("templateDirection") + || prop.equalsIgnoreCase("title") || prop.equalsIgnoreCase("url") + ); }; final Fetcher fetcher = new Fetcher(SimpleEditorMap.L3, Fetcher.nextStepFilter); fetcher.setSkipSubPathways(true); - for(final BioPAXElement bpe : model.getObjects()) { + for(final BioPAXElement bpe : model.getObjects()) { // prepare & index each element in a separate thread - exec.execute(new Runnable() { - public void run() { - // get or infer some important values if possible from this, child or parent objects: - Set keywords = ModelUtils.getKeywords(bpe, 3, dataPropertiesToConsider); - // a hack to remove special (debugging) biopax comments - for(String s : new HashSet(keywords)) { - //exclude additional comments generated by normalizer, merger, etc. - if(s.startsWith("REPLACED ") || s.contains("ADDED")) - keywords.remove(s); - } - - bpe.getAnnotations().put(FIELD_KEYWORD, keywords); - bpe.getAnnotations().put(FIELD_DATASOURCE, ModelUtils.getDatasources(bpe)); - bpe.getAnnotations().put(FIELD_ORGANISM, ModelUtils.getOrganisms(bpe)); - bpe.getAnnotations().put(FIELD_PATHWAY, ModelUtils.getParentPathways(bpe)); - //- includes itself if bpe is a pathway - - //set (PEs/Genes), (interactions/pathways) index fields: - if(bpe instanceof org.biopax.paxtools.model.level3.Process) { - int numProc = fetcher.fetch(bpe, Process.class).size(); //except itself - int numPeAndG = fetcher.fetch(bpe, PhysicalEntity.class).size() - + fetcher.fetch(bpe, Gene.class).size(); - bpe.getAnnotations().put(FIELD_N_PARTICIPANTS, Integer.toString(numPeAndG)); - bpe.getAnnotations().put(FIELD_N_PROCESSES, Integer.toString(numProc)); - } else if(bpe instanceof Complex) { - int numPEs = fetcher.fetch(bpe, PhysicalEntity.class).size(); - bpe.getAnnotations().put(FIELD_N_PARTICIPANTS, Integer.toString(numPEs)); - } + exec.execute(() -> { + // get or infer some important values if possible from this, child or parent objects: + Set keywords = ModelUtils.getKeywords(bpe, 3, dataPropertiesToConsider); + // a hack to remove special (debugging) biopax comments + for(String s : new HashSet<>(keywords)) { + //exclude additional comments generated by normalizer, merger, etc. + if(s.startsWith("REPLACED ") || s.contains("ADDED")) + keywords.remove(s); + } - //add IDs of uni. and rel. xrefs of this element and its children - if(bpe instanceof Entity || bpe instanceof EntityReference) - { - final Set ids = new HashSet(); - - //fetch all children of (implicit) type XReferrable, which means - either - //BioSource or ControlledVocabulary or Evidence or Provenance or Entity or EntityReference - //(we actually want only the latter two types and their sub-types; will skip the rest later on): - Set children = fetcher.fetch(bpe, XReferrable.class); - //include itself (- for fetcher only gets child elements) - children.add((XReferrable) bpe); - for(XReferrable child : children) { - //skip IDs of Evidence,CV,Provenance (included into 'keyword' field anyway) - if(!(child instanceof Entity || child instanceof EntityReference)) - continue; - // collect standard bio IDs (skip publications); try/use id-mapping to associate more IDs: - for(Xref x : child.getXref()) { - if (!(x instanceof PublicationXref) && x.getId()!=null && x.getDb()!=null) { - ids.add(x.getId()); - } + Map annotations = bpe.getAnnotations(); + annotations.put(FIELD_KEYWORD, keywords); + annotations.put(FIELD_DATASOURCE, ModelUtils.getDatasources(bpe)); + annotations.put(FIELD_ORGANISM, ModelUtils.getOrganisms(bpe)); + annotations.put(FIELD_PATHWAY, ModelUtils.getParentPathways(bpe)); + //- includes itself if bpe is a pathway + + //set (PEs/Genes), (interactions/pathways) index fields: + if(bpe instanceof Process) { + int numProc = fetcher.fetch(bpe, Process.class).size(); //except itself + int numPeAndG = fetcher.fetch(bpe, PhysicalEntity.class).size() + + fetcher.fetch(bpe, Gene.class).size(); + annotations.put(FIELD_N_PARTICIPANTS, Integer.toString(numPeAndG)); + annotations.put(FIELD_N_PROCESSES, Integer.toString(numProc)); + } else if(bpe instanceof Complex) { + int numPEs = fetcher.fetch(bpe, PhysicalEntity.class).size(); + annotations.put(FIELD_N_PARTICIPANTS, Integer.toString(numPEs)); + } + + //add IDs of uni. and rel. xrefs of this element and its children + if(bpe instanceof Entity || bpe instanceof EntityReference) + { + final Set ids = new HashSet<>(); + + //fetch all children of (implicit) type XReferrable, which means - either + //BioSource or ControlledVocabulary or Evidence or Provenance or Entity or EntityReference + //(we actually want only the latter two types and their sub-types; will skip the rest later on): + Set children = fetcher.fetch(bpe, XReferrable.class); + //include itself (- for fetcher only gets child elements) + children.add((XReferrable) bpe); + for(XReferrable child : children) { + //skip IDs of Evidence,CV,Provenance (included into 'keyword' field anyway) + if(!(child instanceof Entity || child instanceof EntityReference)) + continue; + // collect standard bio IDs (skip publications); try/use id-mapping to associate more IDs: + for(Xref x : child.getXref()) { + if (!(x instanceof PublicationXref) && x.getId()!=null && x.getDb()!=null) { + ids.add(x.getId()); } } - if(!ids.isEmpty()) { - bpe.getAnnotations().put(SearchEngine.FIELD_XREFID, ids); - } } - - index(bpe, indexWriter); - - //count, log a progress message - int left = numLeft.decrementAndGet(); - if(left % 10000 == 0) - LOG.info("index(), biopax objects left to index: " + left); + if(!ids.isEmpty()) { + annotations.put(SearchEngine.FIELD_XREFID, ids); + } } + + index(bpe, indexWriter); + + //count, log a progress message + int left = numLeft.decrementAndGet(); + if(left % 10000 == 0) + LOG.info("index(), biopax objects left to index: " + left); }); } - + exec.shutdown(); //stop accepting new tasks try { //wait exec.awaitTermination(Long.MAX_VALUE, TimeUnit.SECONDS); } catch (InterruptedException e) { throw new RuntimeException("Interrupted!", e); } - + try { indexWriter.close(); //wait for pending op., auto-commit, close. } catch (IOException e) { throw new RuntimeException("Failed to close IndexWriter.", e); - } - + } + //finally, create a new searcher manager initSearcherManager(); } - - + + // internal methods - + /** * Creates a new Lucene Document that corresponds to a BioPAX object. * It does not check whether the document exists (should not be there, * because the {@link #index()} method cleans up the index) - * + * * Some fields also include biopax data type property values not only from * the biopax object but also from its child elements, up to some depth * (using key-value pairs in the pre-computed bpe.annotations map): - * + * * 'uri' - biopax object's absolute URI, analyze=no, store=yes; - * + * * 'name' - names, analyze=yes, store=yes; boosted; - * + * * 'keyword' - infer from this bpe and its child objects' data properties, * such as Score.value, structureData, structureFormat, chemicalFormula, * availability, term, comment, patoData, author, source, title, url, published, * up to given depth/level; and also all 'pathway' field values are included here; * analyze=yes, store=yes; - * + * * 'datasource', 'organism' and 'pathway' - infer from this bpe and its child objects * up to given depth/level, analyze=no, store=yes; - * + * * 'size' - number of child processes, an integer as string; analyze=no, store=yes - * + * * @param bpe BioPAX object * @param indexWriter index writer - */ - void index(BioPAXElement bpe, IndexWriter indexWriter) { + */ + void index(BioPAXElement bpe, IndexWriter indexWriter) { // create a new document final Document doc = new Document(); - + // save URI (not indexed field) Field field = new StoredField(FIELD_URI, bpe.getUri()); doc.add(field); - + // index and store but not analyze/tokenize the biopax class name: field = new StringField(FIELD_TYPE, bpe.getModelInterface().getSimpleName().toLowerCase(), Field.Store.YES); doc.add(field); - + // make index fields from the annotations map (of pre-calculated/inferred values) - if(!bpe.getAnnotations().isEmpty()) { - if(bpe.getAnnotations().containsKey(FIELD_PATHWAY)) { - addPathways((Set)bpe.getAnnotations().get(FIELD_PATHWAY), doc); + Map annotations = bpe.getAnnotations(); + if(!annotations.isEmpty()) { + if(annotations.containsKey(FIELD_PATHWAY)) { + addPathways((Set)annotations.get(FIELD_PATHWAY), doc); } - if(bpe.getAnnotations().containsKey(FIELD_ORGANISM)) { - addOrganisms((Set)bpe.getAnnotations().get(FIELD_ORGANISM), doc); + if(annotations.containsKey(FIELD_ORGANISM)) { + addOrganisms((Set)annotations.get(FIELD_ORGANISM), doc); } - if(bpe.getAnnotations().containsKey(FIELD_DATASOURCE)) { - addDatasources((Set)bpe.getAnnotations().get(FIELD_DATASOURCE), doc); + if(annotations.containsKey(FIELD_DATASOURCE)) { + addDatasources((Set)annotations.get(FIELD_DATASOURCE), doc); } - if(bpe.getAnnotations().containsKey(FIELD_KEYWORD)) { - addKeywords((Set)bpe.getAnnotations().get(FIELD_KEYWORD), doc); + if(annotations.containsKey(FIELD_KEYWORD)) { + addKeywords((Set)annotations.get(FIELD_KEYWORD), doc); } - if(bpe.getAnnotations().containsKey(FIELD_N_PARTICIPANTS)) { + if(annotations.containsKey(FIELD_N_PARTICIPANTS)) { field = new StoredField(FIELD_N_PARTICIPANTS, - Integer.parseInt((String)bpe.getAnnotations().get(FIELD_N_PARTICIPANTS))); + Integer.parseInt((String)annotations.get(FIELD_N_PARTICIPANTS))); doc.add(field); } - if(bpe.getAnnotations().containsKey(FIELD_N_PROCESSES)) { - field = new IntField(FIELD_N, - Integer.parseInt((String)bpe.getAnnotations().get(FIELD_N_PROCESSES)), Field.Store.NO); - doc.add(field); - field = new StoredField(FIELD_N_PROCESSES, - Integer.parseInt((String)bpe.getAnnotations().get(FIELD_N_PROCESSES))); - doc.add(field); + if(annotations.containsKey(FIELD_N_PROCESSES)) { + doc.add(new StoredField(FIELD_N_PROCESSES, + Integer.parseInt((String)annotations.get(FIELD_N_PROCESSES)))); } - if(bpe.getAnnotations().containsKey(FIELD_XREFID)) { + if(annotations.containsKey(FIELD_XREFID)) { //index biological IDs as keywords - addKeywords((Set)bpe.getAnnotations().get(FIELD_XREFID), doc); + addKeywords((Set)annotations.get(FIELD_XREFID), doc); //index all IDs using "xrefid" fields - for (String id : (Set)bpe.getAnnotations().get(FIELD_XREFID)) { + for (String id : (Set)annotations.get(FIELD_XREFID)) { Field f = new StringField(FIELD_XREFID, id.toLowerCase(), Field.Store.NO); doc.add(f); } } } - bpe.getAnnotations().remove(FIELD_KEYWORD); - bpe.getAnnotations().remove(FIELD_DATASOURCE); - bpe.getAnnotations().remove(FIELD_ORGANISM); - bpe.getAnnotations().remove(FIELD_PATHWAY); - bpe.getAnnotations().remove(FIELD_N_PARTICIPANTS); - bpe.getAnnotations().remove(FIELD_N_PROCESSES); - bpe.getAnnotations().remove(FIELD_XREFID); - - // name + + //cleanup the biopax object from temporary annotations (saves memory) + annotations.remove(FIELD_KEYWORD); + annotations.remove(FIELD_DATASOURCE); + annotations.remove(FIELD_ORGANISM); + annotations.remove(FIELD_PATHWAY); + annotations.remove(FIELD_N_PARTICIPANTS); + annotations.remove(FIELD_N_PROCESSES); + annotations.remove(FIELD_XREFID); + + // name (we store both original and lowercased names due to use of StringField and KeywordAnalyser) if(bpe instanceof Named) { Named named = (Named) bpe; if(named.getStandardName() != null) { - field = new TextField(FIELD_NAME, named.getStandardName(), Field.Store.NO); - field.setBoost(3.5f); - doc.add(field); + String stdName = named.getStandardName().trim(); + doc.add(new StringField(FIELD_NAME, stdName.toLowerCase(), Field.Store.NO)); + doc.add(new StringField(FIELD_NAME, stdName, Field.Store.NO)); } if(named.getDisplayName() != null && !named.getDisplayName().equalsIgnoreCase(named.getStandardName())) { - field = new TextField(FIELD_NAME, named.getDisplayName(), Field.Store.NO); - field.setBoost(3.0f); - doc.add(field); + String dspName = named.getDisplayName().trim(); + doc.add(new StringField(FIELD_NAME, dspName.toLowerCase(), Field.Store.NO)); + doc.add(new StringField(FIELD_NAME, dspName, Field.Store.NO)); } for(String name : named.getName()) { - if(name.equalsIgnoreCase(named.getDisplayName()) || name.equalsIgnoreCase(named.getStandardName())) - continue; - field = new TextField(FIELD_NAME, name.toLowerCase(), Field.Store.NO); - field.setBoost(2.5f); - doc.add(field); + if(!name.equalsIgnoreCase(named.getDisplayName()) && !name.equalsIgnoreCase(named.getStandardName())) { + name = name.trim(); + doc.add(new StringField(FIELD_NAME, name.toLowerCase(), Field.Store.NO)); + doc.add(new StringField(FIELD_NAME, name, Field.Store.NO)); + } + doc.add(new TextField(FIELD_KEYWORD, name.toLowerCase(), Field.Store.NO)); } } @@ -629,18 +630,17 @@ private void addDatasources(Set set, Document doc) { } } - private void addOrganisms(Set set, Document doc) { + private void addOrganisms(Set set, Document doc) { for(BioSource bs : set) { // store URI as is (not indexed, untokinized) doc.add(new StoredField(FIELD_ORGANISM, bs.getUri())); - + // add organism names for(String s : bs.getName()) { doc.add(new TextField(FIELD_ORGANISM, s.toLowerCase(), Field.Store.NO)); } // add taxonomy - for(UnificationXref x : - new ClassFilterSet(bs.getXref(), UnificationXref.class)) { + for(UnificationXref x : new ClassFilterSet<>(bs.getXref(), UnificationXref.class)) { if(x.getId() != null) doc.add(new TextField(FIELD_ORGANISM, x.getId().toLowerCase(), Field.Store.NO)); } @@ -662,16 +662,16 @@ private void addPathways(Set set, Document doc) { for(Pathway pw : set) { //add URI as is (do not lowercase; do not index; store=yes - required to report hits, e.g., as xml) doc.add(new StoredField(FIELD_PATHWAY, pw.getUri())); - + // add names to the 'pathway' (don't store) and 'keywords' (store, don't index) fields for (String s : pw.getName()) { doc.add(new TextField(FIELD_PATHWAY, s.toLowerCase(), Field.Store.NO)); doc.add(new StoredField(FIELD_KEYWORD, s.toLowerCase()));//for highlighting only, not indexed } - + // add unification xref IDs too for (UnificationXref x : new ClassFilterSet( - pw.getXref(), UnificationXref.class)) { + pw.getXref(), UnificationXref.class)) { if (x.getId() != null) { // index in both 'pathway' (don't store) and 'keywords' (store, don't index) doc.add(new TextField(FIELD_PATHWAY, x.getId().toLowerCase(), Field.Store.NO)); @@ -681,95 +681,86 @@ private void addPathways(Set set, Document doc) { } } - /** - * Creates a search filter like - * type AND (datasource OR datasource...) + /* + * Creates a search filter like + * type AND (datasource OR datasource...) * AND (organism OR organism OR...) - * - * Both names (partial or full) and URIs should work as filter values. - * - * @param type - * @param datasources - * @param organisms - */ - private Filter createFilter(Class type, - String[] datasources, String[] organisms) { - - BooleanQuery filterQuery = new BooleanQuery(); - - //AND datasources + * + * Both names (partial or full) and URIs should work as filter values. + */ + private Query createFilter(Class type, String[] datasources, String[] organisms) + { + BooleanQuery.Builder builder = new BooleanQuery.Builder(); + + //AND datasources if (datasources != null && datasources.length > 0) { - filterQuery.add(subQuery(datasources, FIELD_DATASOURCE), Occur.MUST); + builder.add(subQuery(datasources, FIELD_DATASOURCE), Occur.MUST); } //AND organisms if (organisms != null && organisms.length > 0) { - filterQuery.add(subQuery(organisms, FIELD_ORGANISM), Occur.MUST); - } - //AND type + builder.add(subQuery(organisms, FIELD_ORGANISM), Occur.MUST); + } + //AND type if(type != null) { //add biopax class filter - BooleanQuery query = new BooleanQuery(); - query.add(new TermQuery(new Term(FIELD_TYPE, type.getSimpleName().toLowerCase())), Occur.SHOULD);//OR + BooleanQuery.Builder query = new BooleanQuery.Builder(). + add(new TermQuery(new Term(FIELD_TYPE, type.getSimpleName().toLowerCase())), Occur.SHOULD);//OR //for each biopax subclass (interface), add the name to the filter query for(Class subType : SimpleEditorMap.L3.getKnownSubClassesOf(type)) { query.add(new TermQuery(new Term(FIELD_TYPE, subType.getSimpleName().toLowerCase())), Occur.SHOULD);//OR - } - filterQuery.add(query, Occur.MUST); + } + builder.add(query.build(), Occur.MUST); } - - if(!filterQuery.clauses().isEmpty()) { - LOG.debug("filterQuery: " + filterQuery.toString()); - return new CachingWrapperFilter( new QueryWrapperFilter(filterQuery) ); //TODO why CachingWrapperFilter, QueryWrapperFilter? - } else + + BooleanQuery filter = builder.build(); + //TODO: use LRUQueryCache with the filter somewhere, e.g.: + // Query q = queryCache.doCache(filter, defaultCachingPolicy); + + if(!filter.clauses().isEmpty()) { + return filter; + } else return null; } - /** - * Filter values here are joint with 'OR' operator, - * but if a value has internal whitespace symbols, this also makes a sub-query, - * in which terms are joint with 'AND'. This is to allow filtering - * by datasource/organism's full name, partial name, or uri - * and allowing multiple datasources/organisms. - * - * @param filterValues - * @param filterField - * @return + + /* + * Values are joint with OR, but if a value + * has whitespace symbols, it also makes a sub-query, + * in which terms are joint with AND. This is to filter + * by datasource/organism's full name, partial name, uri, + * using multiple datasources/organisms. */ - private Query subQuery(String[] filterValues, String filterField) { - BooleanQuery query = new BooleanQuery(); - final Pattern pattern = Pattern.compile("\\s"); + private Query subQuery(String[] filterValues, String filterField) + { + BooleanQuery.Builder query = new BooleanQuery.Builder(); + final Pattern pattern = Pattern.compile("\\s"); for(String v : filterValues) { //if v has whitespace chars (several words), make a "word1 AND word2 AND..." subquery if(pattern.matcher(v).find()) { - BooleanQuery bq = new BooleanQuery(); -//was bug: text with spaces and 'of', 'for', 'and', etc., did not match anything (we have to use the same analyzer as during indexing!) -// for(String w : v.split("\\s+")) { -// bq.add(new TermQuery(new Term(filterField, w.toLowerCase())), Occur.MUST); -// LOG.debug("subQuery, add part: " + w.toLowerCase()); -// } + BooleanQuery.Builder bq = new BooleanQuery.Builder(); try { //use the same analyser as when indexing TokenStream tokenStream = analyzer.tokenStream(filterField, new StringReader(v)); CharTermAttribute chattr = tokenStream.addAttribute(CharTermAttribute.class); tokenStream.reset(); while(tokenStream.incrementToken()) { - //'of', 'and', 'for',.. never occur as tokens (this is how the std. analyzer works) + //'of', 'and', 'for',.. never occur as tokens (this is how the analyzer works) String token = chattr.toString(); bq.add(new TermQuery(new Term(filterField, token)), Occur.MUST); } - tokenStream.end(); + tokenStream.end(); tokenStream.close(); } catch (IOException e) { //should never happen as we use StringReader throw new RuntimeException("Failed to open a token stream; " - + "field:" + filterField + ", value:" + v,e); + + "field:" + filterField + ", value:" + v,e); } - query.add(bq, Occur.SHOULD); + query.add(bq.build(), Occur.SHOULD); } else { query.add(new TermQuery(new Term(filterField, v.toLowerCase())), Occur.SHOULD); - } + } } - - return query; + + return query.build(); } } diff --git a/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java b/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java index a2313d8bb..5a17150a9 100644 --- a/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java +++ b/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java @@ -1,12 +1,10 @@ -/** - * - */ package org.biopax.paxtools.search; import static org.junit.Assert.*; import java.io.File; import java.io.IOException; +import java.util.Map; import java.util.zip.GZIPInputStream; import org.biopax.paxtools.io.SimpleIOHandler; @@ -28,7 +26,7 @@ public class SearchEngineTest { final static Logger log = LoggerFactory.getLogger(SearchEngineTest.class); @Test - public final void testSearch() throws IOException { + public final void testSearch() { SimpleIOHandler reader = new SimpleIOHandler(); Model model = reader.convertFromOWL(getClass().getResourceAsStream("/pathwaydata1.owl")); SearchEngine searchEngine = new SearchEngine(model, indexLocation + "index1"); @@ -130,15 +128,15 @@ public final void testHitsOrder() throws IOException { assertFalse(response.getHits().isEmpty()); int i=0; for(BioPAXElement bpe : response.getHits()) { + Map ann = bpe.getAnnotations(); log.debug(String.format("Hit %d: %s; participants: %s; processes: %s; excerpt: %s", - ++i, bpe.getUri(), bpe.getAnnotations().get(HitAnnotation.HIT_PARTICIPANTS.name()), - bpe.getAnnotations().get(HitAnnotation.HIT_PROCESSES.name()), - bpe.getAnnotations().get(HitAnnotation.HIT_EXCERPT.name()))); + ++i, bpe.getUri(), ann.get(HitAnnotation.HIT_PARTICIPANTS.name()), + ann.get(HitAnnotation.HIT_PROCESSES.name()), + ann.get(HitAnnotation.HIT_EXCERPT.name()))); } assertEquals(3, response.getHits().size()); assertEquals(3, response.getTotalHits()); - assertEquals("http://purl.org/pc2/7/Pathway_3f75176b9a6272a62f9257f0540dc63b", response.getHits().get(0).getUri()); - //the order of hits is alright, though we'd love to see REACT_12034.3 on top... + assertEquals("http://identifiers.org/reactome/REACT_12034.3", response.getHits().get(0).getUri()); // more accurate search in all the default fields using quotation marks around - response = searchEngine.search("\"signaling by bmp\"", 0, Pathway.class, null, null); @@ -153,8 +151,8 @@ public final void testHitsOrder() throws IOException { assertFalse(response.getHits().isEmpty()); // for(BioPAXElement bpe : response.getHits()) { // log.debug(String.format("Hit: %s; size: %s; excerpt: %s", bpe.getUri(), -// bpe.getAnnotations().get(HitAnnotation.HIT_SIZE.name()) -// , bpe.getAnnotations().get(HitAnnotation.HIT_EXCERPT.name()))); +// bpe.getAnnotation(HitAnnotation.HIT_SIZE.name()) +// , bpe.getAnnotation(HitAnnotation.HIT_EXCERPT.name()))); // } //there are three BMP pathways (one is an empty pathway), and a sub-pathway (should not match) - assertEquals(1, response.getHits().size()); @@ -168,8 +166,8 @@ public final void testHitsOrder() throws IOException { assertFalse(response.getHits().isEmpty()); // for(BioPAXElement bpe : response.getHits()) { // log.debug(String.format("Hit: %s; size: %s; excerpt: %s", bpe.getUri(), -// bpe.getAnnotations().get(HitAnnotation.HIT_SIZE.name()) -// , bpe.getAnnotations().get(HitAnnotation.HIT_EXCERPT.name()))); +// bpe.getAnnotation(HitAnnotation.HIT_SIZE.name()) +// , bpe.getAnnotation(HitAnnotation.HIT_EXCERPT.name()))); // } //there is one pathway, and no sub-pathways of it assertEquals(1, response.getHits().size()); @@ -181,8 +179,8 @@ public final void testHitsOrder() throws IOException { assertFalse(response.getHits().isEmpty()); // for(BioPAXElement bpe : response.getHits()) { // log.debug(String.format("Hit: %s; size: %s; excerpt: %s", bpe.getUri(), -// bpe.getAnnotations().get(HitAnnotation.HIT_SIZE.name()) -// , bpe.getAnnotations().get(HitAnnotation.HIT_EXCERPT.name()))); +// bpe.getAnnotation(HitAnnotation.HIT_SIZE.name()) +// , bpe.getAnnotation(HitAnnotation.HIT_EXCERPT.name()))); // } assertEquals(2, response.getTotalHits()); // - the second pathway is a trivial one, member of Pathway_3f75176b9a6272a62f9257f0540dc63b and of many other parent pathways. diff --git a/pom.xml b/pom.xml index 9a2a9c809..1c8c6ed98 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.biopax.paxtools paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT Paxtools @@ -43,6 +43,7 @@ UTF-8 1.7.25 -Dfile.encoding=UTF-8 + 17 @@ -215,7 +216,7 @@ maven-compiler-plugin 3.11.0 - 8 + 11 @@ -360,7 +361,7 @@ junit junit - 4.12 + 4.13.2 test diff --git a/psimi-converter/pom.xml b/psimi-converter/pom.xml index 3a0c9e24f..c4bf37475 100644 --- a/psimi-converter/pom.xml +++ b/psimi-converter/pom.xml @@ -3,7 +3,7 @@ org.biopax.paxtools paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT 4.0.0 diff --git a/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java b/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java index 0491d97d4..a10cd59aa 100644 --- a/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java +++ b/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java @@ -74,7 +74,7 @@ class EntryMapper { private static final ArrayList GENETIC_INTERACTIONS; static { - GENETIC_INTERACTIONS = new ArrayList(); + GENETIC_INTERACTIONS = new ArrayList<>(); GENETIC_INTERACTIONS.add("dosage growth defect"); GENETIC_INTERACTIONS.add("dosage lethality"); GENETIC_INTERACTIONS.add("dosage rescue"); @@ -128,7 +128,7 @@ public EntryMapper(Model model, boolean forceInteractionToComplex) { public void run(Entry entry) { // get availabilities - final Set avail = new HashSet(); + final Set avail = new HashSet<>(); if(entry.hasAvailabilities()) { for (Availability a : entry.getAvailabilities()) if (a.hasValue()) @@ -140,7 +140,7 @@ public void run(Entry entry) { //build a skip-set of "interactions" linked by participant.interactionRef element; //we'll then create Complex type participants from these in-participant interactions. - Set participantInteractions = new HashSet(); + Set participantInteractions = new HashSet<>(); for(Interaction interaction : entry.getInteractions()) { for(Participant participant : interaction.getParticipants()) { //checking for hasInteraction()==true only is sufficient; @@ -248,7 +248,7 @@ private Entity processInteraction(Interaction interaction, Set avail, shortName = (names.hasShortLabel()) ? names.getShortLabel() : ""; } - final Set interactionVocabularies = new HashSet(); + final Set interactionVocabularies = new HashSet<>(); if (interaction.hasInteractionTypes()) { for(CvType interactionType : interaction.getInteractionTypes()) { //generate InteractionVocabulary and set interactionType @@ -260,14 +260,14 @@ private Entity processInteraction(Interaction interaction, Set avail, // using experiment descriptions, create Evidence objects // (yet, no experimental forms/roles/entities are created here) - Set bpEvidences = new HashSet(); + Set bpEvidences = new HashSet<>(); if (interaction.hasExperiments()) { bpEvidences = createBiopaxEvidences(interaction); } //A hack for e.g. IntAct or BIND "gene-protein" interactions (ChIp and EMSA experiments) // where the interactor type should probably not be 'gene' (but 'dna' or 'rna') - Set participantTypes = new HashSet(); + Set participantTypes = new HashSet<>(); for(Participant p : interaction.getParticipants()) { if(p.hasInteractor()) { String type = getName(p.getInteractor().getInteractorType().getNames()); @@ -296,7 +296,7 @@ private Entity processInteraction(Interaction interaction, Set avail, } // interate through the psi-mi participants, create corresp. biopax entities - final Set bpParticipants = new HashSet(); + final Set bpParticipants = new HashSet<>(); for (Participant participant : interaction.getParticipants()) { // get paxtools physical entity participant and add to participant list // (this also adds experimental evidence and forms) @@ -308,7 +308,7 @@ private Entity processInteraction(Interaction interaction, Set avail, } // Process interaction attributes. - final Set comments = new HashSet(); + final Set comments = new HashSet<>(); // Set GeneticInteraction flag. // As of BioGRID v3.1.72 (at least), genetic interaction code can reside // as an attribute of the Interaction via "BioGRID Evidence Code" key @@ -366,7 +366,7 @@ private Entity processInteraction(Interaction interaction, Set avail, } // add xrefs - Set bpXrefs = new HashSet(); + Set bpXrefs = new HashSet<>(); if (interaction.hasXref()) { bpXrefs.addAll(getXrefs(interaction.getXref())); } @@ -380,7 +380,7 @@ private Entity processInteraction(Interaction interaction, Set avail, private Set createBiopaxEvidences(Interaction interaction) { - Set evidences = new HashSet(); + Set evidences = new HashSet<>(); for (ExperimentDescription experimentDescription : interaction.getExperiments()) { // build and add evidence @@ -502,8 +502,9 @@ private Entity createBiopaxEntity(Participant participant, Set avail, Pr //try to reuse existing experimental form entity expEntity = findEquivalentEntity(expEntity); - if(!bpModel.contains(expEntity)) + if(!bpModel.containsID(expEntity.getUri())) { bpModel.add(expEntity); + } //workaround a PSI-MI parser issue (no exp. or exp.refs means to apply to all interaction's experiments): if(experimentalInteractor.hasExperiments()) { @@ -537,8 +538,9 @@ private Entity createBiopaxEntity(Participant participant, Set avail, Pr } //finally, add, if new, entity to the model and return - if(!bpModel.contains(entity)) + if(!bpModel.containsID(entity.getUri())) { bpModel.add(entity); + } return entity; } @@ -615,7 +617,7 @@ private Entity createParticipant(Participant participant, Interactor interactor, // get names/synonyms from the psimi interactor (participant does not have them) String name = null; String shortName = null; - Set synonyms = new HashSet(); + Set synonyms = new HashSet<>(); Names psiNames = interactor.getNames(); if (psiNames != null) { name = (psiNames.hasFullName()) ? psiNames.getFullName() : null; @@ -874,7 +876,7 @@ private boolean sameNameOrUndefined(BioSource a, BioSource b) { * of SequenceInterval (sequence locations). */ private Set getSequenceLocation(Collection rangeList) { - Set toReturn = new HashSet(); + Set toReturn = new HashSet<>(); // if we have a locationType, lets process for (Range range : rangeList) { @@ -1029,13 +1031,13 @@ private T findOrCreateControlledVocabulary( private Set getXrefs(psidev.psi.mi.xml.model.Xref psiXREF) { // set to return - Set toReturn = new HashSet(); + Set toReturn = new HashSet<>(); // check args if (psiXREF == null) return toReturn; // create the list of all other psimi xrefs - List psiDBRefList = new ArrayList(); + List psiDBRefList = new ArrayList<>(); DbReference primaryRef = psiXREF.getPrimaryRef(); if(primaryRef != null) { //looks, it should never be null in a valid PSI-MI model @@ -1202,10 +1204,10 @@ private String encode(String id) { * controlled vocabulary objects which represent evidence code(s). */ private Set getEvidenceCodes(ExperimentDescription experimentDescription) { - Set toReturn = new HashSet(); + Set toReturn = new HashSet<>(); // get experiment methods - Set cvTypeSet = new HashSet(3); + Set cvTypeSet = new HashSet<>(3); //skip if "unspecified method" (MI:0686) is the interaction detection method if(experimentDescription.getInteractionDetectionMethod() != null && !"MI:0686".equalsIgnoreCase(experimentDescription.getInteractionDetectionMethod().getXref().getPrimaryRef().getId())) @@ -1243,13 +1245,13 @@ private Score getScoreOrConfidence(Confidence psiConfidence) { OpenCvType ocv = psiConfidence.getUnit(); // psiConfidence.unit.xref maps to confidence.xref - Set bpXrefs = new HashSet(); + Set bpXrefs = new HashSet<>(); if (ocv != null && ocv.getXref() != null) { bpXrefs.addAll(getXrefs(ocv.getXref())); } // used to store names and attributes - Set comments = new HashSet(); + Set comments = new HashSet<>(); // psiConfidence.unit.names maps to confidence comment if (ocv != null && ocv.getNames() != null) { @@ -1274,7 +1276,7 @@ private Score getScoreOrConfidence(Confidence psiConfidence) { private Set getAttributes(Collection attributes) { // set to return - Set toReturn = new HashSet(); + Set toReturn = new HashSet<>(); // iterate over the attributes for (Attribute attribute : attributes) { @@ -1305,7 +1307,7 @@ private Set getAttributes(Collection attributes) { private void createAddExperimentalForm(Participant participant, Evidence pEvidence, Entity expEntity, ExperimentDescription exp) { - Set efs = new HashSet(); + Set efs = new HashSet<>(); for(Feature f : participant.getFeatures()) { if(exp==null || f.getExperiments().contains(exp) || f.getExperiments().isEmpty()) { EntityFeature feature = getFeature(ModificationFeature.class, f); @@ -1315,7 +1317,7 @@ private void createAddExperimentalForm(Participant participant, } } - Set efvs = new HashSet(); + Set efvs = new HashSet<>(); if (participant.hasExperimentalRoles()) { for (ExperimentalRole role : participant.getExperimentalRoles()) { if(exp==null || role.getExperiments().contains(exp) || role.getExperiments().isEmpty()) { diff --git a/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java b/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java index 2b6471238..eb457ecea 100644 --- a/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java +++ b/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java @@ -257,7 +257,7 @@ public void testMappingIntAct() { } assertNotNull(bpModel); assertFalse(bpModel.getObjects().isEmpty()); - Set evs = bpModel.getObjects(Evidence.class); + Collection evs = bpModel.getObjects(Evidence.class); assertFalse(evs.isEmpty()); MolecularInteraction interaction = null; for(MolecularInteraction mi : bpModel.getObjects(MolecularInteraction.class)) { diff --git a/sbgn-converter/pom.xml b/sbgn-converter/pom.xml index 674952f0d..26618a8d3 100644 --- a/sbgn-converter/pom.xml +++ b/sbgn-converter/pom.xml @@ -2,7 +2,7 @@ paxtools org.biopax.paxtools - 5.3.1-SNAPSHOT + 6.0.0-SNAPSHOT 4.0.0 diff --git a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java index 347f7f081..db9670eba 100644 --- a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java +++ b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/L3ToSBGNPDConverter.java @@ -137,7 +137,7 @@ public class L3ToSBGNPDConverter { static { factory = new ObjectFactory(); - typeMatchMap = new HashMap, String>(); + typeMatchMap = new HashMap<>(); typeMatchMap.put(Protein.class, GlyphClazz.MACROMOLECULE.getClazz()); typeMatchMap.put(SmallMolecule.class, GlyphClazz.SIMPLE_CHEMICAL.getClazz()); typeMatchMap.put(Dna.class, GlyphClazz.NUCLEIC_ACID_FEATURE.getClazz()); @@ -146,8 +146,6 @@ public class L3ToSBGNPDConverter { typeMatchMap.put(RnaRegion.class, GlyphClazz.NUCLEIC_ACID_FEATURE.getClazz()); typeMatchMap.put(NucleicAcid.class, GlyphClazz.NUCLEIC_ACID_FEATURE.getClazz()); typeMatchMap.put(PhysicalEntity.class, GlyphClazz.UNSPECIFIED_ENTITY.getClazz()); - //TODO: remove SimplePhysicalEntity.class key (- abstract type)? - typeMatchMap.put(SimplePhysicalEntity.class, GlyphClazz.UNSPECIFIED_ENTITY.getClazz()); typeMatchMap.put(Complex.class, GlyphClazz.COMPLEX.getClazz()); typeMatchMap.put(Gene.class, GlyphClazz.NUCLEIC_ACID_FEATURE.getClazz()); @@ -181,7 +179,7 @@ public L3ToSBGNPDConverter(UbiqueDetector ubiqueDet, FeatureDecorator featStrGen this.featStrGen = (featStrGen != null) ? featStrGen : new CommonFeatureStringGenerator(); this.doLayout = doLayout; this.useTwoGlyphsForReversibleConversion = true; - this.sbgn2BPMap = new HashMap>(); + this.sbgn2BPMap = new HashMap<>(); this.flattenComplexContent = true; this.maxNodes = 1000; } @@ -222,15 +220,11 @@ public void setFlattenComplexContent(boolean flattenComplexContent) { * @param file file to write */ public void writeSBGN(Model model, String file) { - // Create the model - Sbgn sbgn = createSBGN(model); - - // Write in file try { + Sbgn sbgn = createSBGN(model); SbgnUtil.writeToFile(sbgn, new File(file)); - } - catch (JAXBException e) { - throw new RuntimeException("writeSBGN, SbgnUtil.writeToFile failed", e); + } catch (Exception e) { + throw new RuntimeException("writeSBGN failed", e); } } @@ -267,10 +261,10 @@ public void writeSBGN(Model model, OutputStream stream) { public Sbgn createSBGN(Model model) { assert model.getLevel().equals(BioPAXLevel.L3) : "This method only supports L3 graphs"; - glyphMap = new HashMap(); - compartmentMap = new HashMap(); - arcMap = new HashMap(); - ubiqueSet = new HashSet(); + glyphMap = new HashMap<>(); + compartmentMap = new HashMap<>(); + arcMap = new HashMap<>(); + ubiqueSet = new HashSet<>(); int n = 0; //approximate number of SBGN nodes @@ -314,10 +308,10 @@ public Sbgn createSBGN(Model model) { createGiProcess((GeneticInteraction) interaction); } else if(!(interaction instanceof Control)) { createBasicProcess(interaction); - } else { //a Control special case, because these are normally added inside the methods in cases above + } else { //a Control, special case Control control = (Control) interaction; - //Control without any controlled process but with controller and controlledOf - if(control.getControlled()==null || control.getControlled().isEmpty()) { + //a Control without controlled process but with controller and is controlledOf + if(control.getControlled().isEmpty()) { Glyph g = createControlStructure(control); processControllers(control.getControlledOf(), g); }//else - do nothing - as it's converted anyway when the controlled interactions are processed @@ -493,7 +487,7 @@ private Glyph createGlyphBasics(Entity e, boolean idIsFinal) // Record the mapping if (idIsFinal) { - Set uris = new HashSet(); + Set uris = new HashSet<>(); uris.add(e.getUri()); sbgn2BPMap.put(g.getId(), uris); } @@ -517,7 +511,7 @@ private Glyph getGlyphToLink(Entity e, String linkID) // Create a new glyph for each use of ubique Glyph g = createGlyphBasics(e, false); g.setId(convertID(e.getUri()) + "_" + ModelUtils.md5hex(linkID)); - Set uris = new HashSet(); + Set uris = new HashSet<>(); uris.add(e.getUri()); sbgn2BPMap.put(g.getId(), uris); if(e instanceof PhysicalEntity && ((PhysicalEntity)e).getCellularLocation() != null) { @@ -569,7 +563,7 @@ private void buildGeneric(PhysicalEntity generic, Glyph or, Glyph container) { String gid = g.getId() + "_" + ModelUtils.md5hex("memberof_" + or.getId()); g.setId(gid); glyphMap.put(gid, g); - Set uris = new HashSet(); + Set uris = new HashSet<>(); uris.add(m.getUri()); sbgn2BPMap.put(gid, uris); assignLocation(m, g); @@ -613,7 +607,7 @@ private void addComplexAsMember(Complex cx, Glyph container) { * @return members to display */ private Set getFlattenedMembers(Complex cx) { - Set set = new HashSet(); + Set set = new HashSet<>(); for (PhysicalEntity mem : cx.getComponent()) { if (mem instanceof Complex) { if (!hasNonComplexMember((Complex) mem)) { @@ -655,7 +649,7 @@ private Glyph createComplexMember(PhysicalEntity pe, Glyph container) { g.setId(g.getId() + "_" + ModelUtils.md5hex(container.getId())); glyphMap.put(g.getId(), g); - Set uris = new HashSet(); + Set uris = new HashSet<>(); uris.add(pe.getUri()); sbgn2BPMap.put(g.getId(), uris); @@ -805,7 +799,7 @@ private String extractGeneSymbol(Xref xref) * @return list of state variables */ private List getInformation(Entity e) { - List list = new ArrayList(); + List list = new ArrayList<>(); // Add the molecule type before states if this is a nucleic acid or gene if (e instanceof NucleicAcid || e instanceof Gene) { @@ -959,7 +953,7 @@ private void createProcessAndConnections(Conversion cnv, ConversionDirectionType processControllers(cnv.getControlledOf(), process); // Record mapping - Set uris = new HashSet(); + Set uris = new HashSet<>(); uris.add(cnv.getUri()); sbgn2BPMap.put(process.getId(), uris); } @@ -991,11 +985,16 @@ private void createProcessAndConnections(TemplateReaction tr) { glyphMap.put(process.getId(), process); final Set products = tr.getProduct(); - final Set participants = new HashSet( //new modifiable set - new ClassFilterSet(tr.getParticipant(), PhysicalEntity.class)); + + // parent property 'participant' is sometimes defined directly + // for a TemplateReaction object despite 'product', 'template' + // must be used instead (this is bad biopax data modeling practice; e.g. in Reactome); + // we can try to infer template/product and link what's left + // after first processing actual 'product' and 'template' prop values. + final Set participants = //a new modifiable set to + new HashSet<>(new ClassFilterSet<>(tr.getParticipant(), PhysicalEntity.class)); // link products, if any - // ('participant' property is there defined sometimes instead of or in addition to 'product' or 'template') for (PhysicalEntity pe : products) { Glyph g = getGlyphToLink(pe, process.getId()); createArc(process, g, ArcClazz.PRODUCTION.getClazz(), null); @@ -1017,7 +1016,7 @@ private void createProcessAndConnections(TemplateReaction tr) { createArc(sas, process, ArcClazz.CONSUMPTION.getClazz(), null); } - //infer input or output type arc for the rest of participants + //infer input or output type arc for the rest of participants that left there, if any for (PhysicalEntity pe : participants) { Glyph g = getGlyphToLink(pe, process.getId()); if(template==null) @@ -1028,7 +1027,7 @@ private void createProcessAndConnections(TemplateReaction tr) { // Associate controllers processControllers(tr.getControlledOf(), process); // Record mapping - sbgn2BPMap.put(process.getId(), new HashSet(Collections.singleton(tr.getUri()))); + sbgn2BPMap.put(process.getId(), new HashSet<>(Collections.singleton(tr.getUri()))); } private void createBasicProcess(Interaction interaction) { @@ -1038,12 +1037,12 @@ private void createBasicProcess(Interaction interaction) { process.setId(convertID(interaction.getUri())); glyphMap.put(process.getId(), process); // Associate participants - for (PhysicalEntity pe : new ClassFilterSet(interaction.getParticipant(), PhysicalEntity.class)) { + for (PhysicalEntity pe : new ClassFilterSet<>(interaction.getParticipant(), PhysicalEntity.class)) { Glyph g = getGlyphToLink(pe, process.getId()); createArc(g, process, ArcClazz.CONSUMPTION.getClazz(), null); } // Record mapping - sbgn2BPMap.put(process.getId(), new HashSet(Collections.singleton(interaction.getUri()))); + sbgn2BPMap.put(process.getId(), new HashSet<>(Collections.singleton(interaction.getUri()))); // Associate controllers processControllers(interaction.getControlledOf(), process); } @@ -1077,7 +1076,7 @@ private void createGiProcess(GeneticInteraction interaction) { createArc(g, process, ArcClazz.LOGIC_ARC.getClazz(), null); } // Record mapping - sbgn2BPMap.put(process.getId(), new HashSet(Collections.singleton(interaction.getUri()))); + sbgn2BPMap.put(process.getId(), new HashSet<>(Collections.singleton(interaction.getUri()))); // Associate controllers processControllers(interaction.getControlledOf(), process); } @@ -1099,7 +1098,7 @@ private Glyph createControlStructure(Control ctrl) { cg = getGlyphToLink(controllers.iterator().next(), convertID(ctrl.getUri())); } else { // This list will contain handles for each participant of the AND structure - List toConnect = new ArrayList(); + List toConnect = new ArrayList<>(); // Bundle controllers if necessary Glyph gg = handlePEGroup(controllers, convertID(ctrl.getUri())); @@ -1155,7 +1154,7 @@ private Glyph handlePEGroup(Set pes, String context) { * @return glyphs of entities */ private List getGlyphsOfPEs(Set pes, String context) { - List gs = new ArrayList(); + List gs = new ArrayList<>(); for (PhysicalEntity pe : pes) if (glyphMap.containsKey(convertID(pe.getUri()))) @@ -1259,7 +1258,7 @@ private int getControllerSize(Set ctrlSet) { * @return size of representable controllers */ private Set getControllers(Control ctrl) { - Set controllers = new HashSet(); + Set controllers = new HashSet<>(); for (Controller clr : ctrl.getController()) { if (clr instanceof PhysicalEntity && glyphMap.containsKey(convertID(clr.getUri()))) { controllers.add((PhysicalEntity) clr); @@ -1338,8 +1337,8 @@ private void createArc(Object source, Object target, String clazz, Stoichiometry * @return set of roots */ private Set getRootGlyphs(Collection glyphCol) { - Set root = new HashSet(glyphCol); - Set children = new HashSet(); + Set root = new HashSet<>(glyphCol); + Set children = new HashSet<>(); for (Glyph glyph : glyphCol) { addChildren(glyph, children); diff --git a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/SBGNLayoutManager.java b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/SBGNLayoutManager.java index 0152482b6..b89c9b86b 100644 --- a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/SBGNLayoutManager.java +++ b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/SBGNLayoutManager.java @@ -69,7 +69,7 @@ public void createLayout(final Sbgn sbgn, boolean doLayout) //Set compartmentRef to all children of a Complex node. Glyph compartment = (Glyph)g.getCompartmentRef(); if(compartment != null && glyphClazzOneOf(g, GlyphClazz.COMPLEX)) { - setCompartmentRefForComplexMembers(g, compartment, new HashSet()); + setCompartmentRefForComplexMembers(g, compartment, new HashSet<>()); } } @@ -77,7 +77,7 @@ public void createLayout(final Sbgn sbgn, boolean doLayout) // This list holds the glyphs that will be deleted after corresponding glyph // is added to child glyph of another glyph. if(!idToCompartmentGlyphs.isEmpty()) { - List deletedList = new ArrayList(); + List deletedList = new ArrayList<>(); for (Glyph g : sbgn.getMap().getGlyph()) { Glyph containerCompartment = (Glyph) g.getCompartmentRef(); if (containerCompartment != null) { @@ -218,7 +218,7 @@ private void assignProcessAndLogicOpNodesToCompartment(Sbgn sbgn) List arcList = sbgn.getMap().getArc(); // Keeps track of process and logical operator nodes that will be assigned to a compartment. - ArrayList targetNodes = new ArrayList(); + ArrayList targetNodes = new ArrayList<>(); //Iterate over glyphs of sbgn map for(Glyph glyph: glyphList) diff --git a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/VNode.java b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/VNode.java index f61e5d2aa..ffe324c85 100644 --- a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/VNode.java +++ b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/VNode.java @@ -98,7 +98,7 @@ public VNode(Glyph g) INFO_BOUND = new Bound(MAX_STATE_AND_INFO_WIDTH,MAX_STATE_AND_INFO_HEIGHT); STATE_BOUND = new Bound(MAX_STATE_AND_INFO_WIDTH,MAX_STATE_AND_INFO_HEIGHT); - stateGlyphs = new ArrayList(); + stateGlyphs = new ArrayList<>(); infoGlyphs = new ArrayList(); this.glyph = g; diff --git a/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java b/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java index 912e05e56..103cbe192 100644 --- a/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java +++ b/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java @@ -1,7 +1,5 @@ package org.biopax.paxtools.io.sbgn; -import static junit.framework.Assert.*; - import org.apache.commons.lang3.StringUtils; import org.biopax.paxtools.impl.MockFactory; import org.biopax.paxtools.io.BioPAXIOHandler; @@ -23,6 +21,9 @@ import javax.xml.bind.Unmarshaller; import java.io.*; import java.util.*; +import java.util.stream.Collectors; + +import static org.junit.Assert.*; public class SBGNConverterTest { @@ -34,7 +35,7 @@ public class SBGNConverterTest @BeforeClass public static void setUp() throws JAXBException { - blacklist = new ListUbiqueDetector(new HashSet(Arrays.asList( + blacklist = new ListUbiqueDetector(new HashSet<>(Arrays.asList( "http://pid.nci.nih.gov/biopaxpid_685", "http://pid.nci.nih.gov/biopaxpid_678", "http://pid.nci.nih.gov/biopaxpid_3119", @@ -42,7 +43,6 @@ public static void setUp() throws JAXBException { "http://pathwaycommons.org/pc2/SmallMolecule_3037a14ebec3a95b8dab68e6ea5c946f", "http://pathwaycommons.org/pc2/SmallMolecule_4ca9a2cfb6a8a6b14cee5d7ed5945364" ))); - JAXBContext context = JAXBContext.newInstance("org.sbgn.bindings"); unmarshaller = context.createUnmarshaller(); marshaller = context.createMarshaller(); @@ -230,7 +230,6 @@ public void testConvertBadWikiPathway() throws Exception { SbgnUtil.isValid(outFile); //ignore validation errors for now... Sbgn result = (Sbgn) unmarshaller.unmarshal(outFile); assertFalse(result.getMap().getGlyph().isEmpty()); - //TODO: add assertions } @@ -288,10 +287,11 @@ public void testConvertTRs() throws JAXBException { f.bindInPairs("product", tr0,p[0],tr0,p[1]); tr0.setTemplate(t[0]); - // no template (will infer) + // no template - will infer it from the other participant + // (this is a bad practice though - 'template' prop must be used instead) TemplateReaction tr1 = m.addNew(TemplateReaction.class,"tr_1"); f.bindInPairs("product", tr1,p[2]); - f.bindInPairs("participant", tr1,t[1]); + f.bindInPairs("participant", tr1,t[1]); //this call might be ignored or throw an ex. in the future // only product (will infer some unknown input process/entity) TemplateReaction tr2 = m.addNew(TemplateReaction.class,"tr_2"); @@ -376,21 +376,11 @@ public void testConvertControlsChain() throws Exception { assertFalse(filtered.isEmpty()); } -// private Collection filterGlyphsByClazz(Collection collection, String clazz) { -// Set filtered = new HashSet(); -// for(Glyph g : collection) -// if(g.getClazz().equals(clazz)) -// filtered.add(g); -// -// return filtered; -// } + private Collection filterGlyphsByClazz(Collection collection, String clazz) { + return collection.stream().filter(g -> g.getClazz().equals(clazz)).collect(Collectors.toUnmodifiableSet()); + } private Collection filterArcsByClazz(Collection collection, String clazz) { - Set filtered = new HashSet(); - for(Arc g : collection) - if(g.getClazz().equals(clazz)) - filtered.add(g); - - return filtered; + return collection.stream().filter(g -> g.getClazz().equals(clazz)).collect(Collectors.toUnmodifiableSet()); } } From dad2c267557d003c9c663a66fbd3e0e946d1e807 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 13 Nov 2022 20:33:10 -0500 Subject: [PATCH 02/20] Paxtools-6: MiriamLink needs refactoring to use new JSON registry or else. --- .../paxtools/normalizer/MiriamLink.java | 12 +- .../paxtools/normalizer/Normalizer.java | 25 +- normalizer/src/main/resources/Miriam.xml | 6 +- normalizer/src/main/resources/registry.json | 40048 ++++++++++++++++ .../paxtools/controller/ModelUtils.java | 51 +- pom.xml | 2 +- 6 files changed, 40091 insertions(+), 53 deletions(-) create mode 100644 normalizer/src/main/resources/registry.json diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java index 536041934..0362d17ab 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java @@ -1,7 +1,5 @@ package org.biopax.paxtools.normalizer; - -//import java.io.IOException; import java.io.InputStream; import java.io.UnsupportedEncodingException; import java.net.*; @@ -21,7 +19,10 @@ /** * Singleton local MIRIAM data resolver with all methods static. - * + * + * todo: refactor to load/use the JSON data instead of XML,XSD (see: identifiers.org, https://registry.api.identifiers.org/resolutionApi/getResolverDataset) + * todo: use Compressed URIs, e.g. uniprot:P12345 instead of URLs like http://identifiers.org/uniprot:P12345 + * * @author rodche */ public class MiriamLink @@ -29,9 +30,8 @@ public class MiriamLink private static final Logger log = LoggerFactory.getLogger(MiriamLink.class); private static final String[] ARRAY_OF_STRINGS = {}; // a template to convert a Collection to String[] - /** default web service URL to get the Miriam.xml db content; see also: http://www.ebi.ac.uk/miriam/main/export/. - * Sometimes (e.g., 2016/01/07) the connection becomes EXTREMELY slow (1MB takes dozens minutes to download or stuck). - * */ + //default web service URL to get the Miriam.xml db content (todo: obsolete) + //see also: http://www.ebi.ac.uk/miriam/main/export/ //XML: "https://www.ebi.ac.uk/miriam/main/export/xml/"; //Schema: "http://www.ebi.ac.uk/miriam/static/main/xml/MiriamXML.xsd"; /** package name for jaxb to use */ diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index cfdf937a4..1e3af3e74 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -98,10 +98,9 @@ public String normalize(String biopaxOwlData) { /** - * Normalizes all xrefs (not unification xrefs only) to help normalizing/merging other objects, - * and also because some of the original xref URIs ("normalized") - * are in fact to be used for other biopax types (e.g., CV or ProteinReference); therefore - * this method will replace URI also for "bad" xrefs, i.e., those with empty/illegal 'db' or 'id' values. + * Normalizes xrefs to ease normalizing or merging other BioPAX objects later on, + * and also because some original xref URIs should in fact be used for different BioPAX types + * (for CV or ProteinReference instead); so, this will also replace URIs of xrefs having bad 'db' or 'id'. * * @param model biopax model to update */ @@ -110,7 +109,7 @@ private void normalizeXrefs(Model model) { final NormalizerMap map = new NormalizerMap(model); final String xmlBase = getXmlBase(model); //current base, the default or model's one, if set. - // use a copy of the xrefs set (to avoid concurrent modif. exception) + // use a copy of the xrefs set (to avoid concurrent exceptions) Set xrefs = new HashSet<>(model.getObjects(Xref.class)); for(Xref ref : xrefs) { @@ -142,7 +141,7 @@ else if(ref instanceof UnificationXref) { ref.setDb(MiriamLink.getName(ref.getDb()).toLowerCase()); } catch (IllegalArgumentException e) { // - unknown/unmatched db name (normalize using defaults) - if(ref.getIdVersion()!=null) { + if(ref.getIdVersion() != null) { idPart += "_" + ref.getIdVersion(); } map.put(ref, Normalizer.uri(xmlBase, ref.getDb(), idPart, ref.getModelInterface())); @@ -187,7 +186,7 @@ else if(!isValidDbId(ref.getDb(), ref.getId())) { } /* - * @param db must be valid MIRIAM db name or sinonym + * @param db must be valid MIRIAM db name or synonym * @trows IllegalArgumentException when db is unknown name. */ private boolean isValidDbId(String db, String id) { @@ -198,9 +197,10 @@ private boolean isValidDbId(String db, String id) { * Consistently generates a new BioPAX element URI * using given URI namespace (xml:base), BioPAX class, * and two different identifiers (at least one is required). + * * Miriam registry is used to get the standard db name and - * identifiers.org URI, if possible, only for relationship type vocabulary, - * publication xref, and entity reference types. + * identifiers.org URI, if possible, for relationship type vocabulary, + * publication xref, entity reference, and biosource types. * * @param xmlBase xml:base (common URI prefix for a BioPAX model), case-sensitive * @param dbName a bio data collection name or synonym, case-insensitive @@ -218,7 +218,7 @@ public static String uri(final String xmlBase, if (idPart != null) idPart = idPart.trim(); if (dbName != null) dbName = dbName.trim(); - // try to find a standard URI, if exists, for a publication xref, or at least a standard name: + // for some types, try to find a standard URI or at least a standard name: if (dbName != null) { try { @@ -243,8 +243,7 @@ public static String uri(final String xmlBase, } // If not returned above this point - no standard URI (Identifiers.org) was found - - // then let's consistently build a new URI from args, anyway, the other way around: - + // then let's consistently build a new hash-based URI from args. StringBuilder sb = new StringBuilder(); if (dbName != null) //lowercase for consistency sb.append(dbName.toLowerCase()); @@ -264,7 +263,7 @@ public static String uri(final String xmlBase, } else { - //replace the local part with its md5 sum string (32-byte) + //replace the local part with its md5 hash string (32-byte) localPart = ModelUtils.md5hex(localPart); } diff --git a/normalizer/src/main/resources/Miriam.xml b/normalizer/src/main/resources/Miriam.xml index 468a62d77..e2d979e55 100644 --- a/normalizer/src/main/resources/Miriam.xml +++ b/normalizer/src/main/resources/Miriam.xml @@ -1,11 +1,11 @@ - + - - + + diff --git a/normalizer/src/main/resources/registry.json b/normalizer/src/main/resources/registry.json new file mode 100644 index 000000000..d8b3feaf2 --- /dev/null +++ b/normalizer/src/main/resources/registry.json @@ -0,0 +1,40048 @@ +{ + "apiVersion": null, + "errorMessage": null, + "payload": { + "namespaces": [ + { + "id": 1, + "prefix": "chebi", + "mirId": "MIR:00000002", + "name": "ChEBI", + "pattern": "^CHEBI:\\d+$", + "description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.", + "created": "2019-06-11T14:15:26.925+0000", + "modified": "2019-06-11T14:15:26.925+0000", + "resources": [ + { + "id": 3, + "mirId": "MIR:00100009", + "urlPattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{$id}", + "name": "ChEBI (Chemical Entities of Biological Interest)", + "description": "ChEBI (Chemical Entities of Biological Interest)", + "official": true, + "providerCode": "ebi", + "sampleId": "36927", + "resourceHomeUrl": "https://www.ebi.ac.uk/chebi/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 4, + "mirId": "MIR:00100158", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/chebi/terms?obo_id=CHEBI:{$id}", + "name": "ChEBI through OLS", + "description": "ChEBI through OLS", + "official": false, + "providerCode": "ols", + "sampleId": "36927", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/chebi", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 6, + "mirId": "MIR:00100565", + "urlPattern": "http://purl.bioontology.org/ontology/CHEBI/CHEBI:{$id}", + "name": "ChEBI through BioPortal", + "description": "ChEBI through BioPortal", + "official": false, + "providerCode": "bptl", + "sampleId": "36927", + "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/CHEBI", + "institution": { + "id": 5, + "name": "National Center for Biomedical Ontology, Stanford", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "36927", + "namespaceEmbeddedInLui": true, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 7, + "prefix": "ensembl", + "mirId": "MIR:00000003", + "name": "Ensembl", + "pattern": "^((ENS[FPTG]\\\\d{11}(\\\\.\\\\d+)?)|(FB\\\\w{2}\\\\d{7})|(Y[A-Z]{2}\\\\d{3}[a-zA-Z](\\\\-[A-Z])?)|([A-Z_a-z0-9]+(\\\\.)?(t)?(\\\\d+)?([a-z])?))$", + "description": "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.", + "created": "2019-06-11T14:15:27.869+0000", + "modified": "2019-06-11T14:15:27.869+0000", + "resources": [ + { + "id": 9, + "mirId": "MIR:00100011", + "urlPattern": "https://www.ensembl.org/id/{$id}", + "name": "Ensembl at Sanger/EMBL-EBI", + "description": "Ensembl at Sanger/EMBL-EBI", + "official": true, + "providerCode": "ebi", + "sampleId": "ENSG00000139618", + "resourceHomeUrl": "https://www.ensembl.org/", + "institution": { + "id": 8, + "name": "Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 10, + "mirId": "MIR:00100561", + "urlPattern": "http://uswest.ensembl.org/id/{$id}", + "name": "Ensembl US West mirror", + "description": "Ensembl US West mirror", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ENSG00000139618", + "resourceHomeUrl": "http://uswest.ensembl.org/", + "institution": { + "id": 8, + "name": "Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 11, + "mirId": "MIR:00100562", + "urlPattern": "http://useast.ensembl.org/id/{$id}", + "name": "Ensembl US East mirror", + "description": "Ensembl US East mirror", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ENSG00000139618", + "resourceHomeUrl": "http://useast.ensembl.org/", + "institution": { + "id": 8, + "name": "Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 12, + "mirId": "MIR:00100563", + "urlPattern": "http://asia.ensembl.org/id/{$id}", + "name": "Ensembl Asia mirror", + "description": "Ensembl Asia mirror", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ENSG00000139618", + "resourceHomeUrl": "http://asia.ensembl.org/", + "institution": { + "id": 8, + "name": "Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "SG", + "countryName": "Singapore" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "ENSG00000139618", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 13, + "prefix": "ec-code", + "mirId": "MIR:00000004", + "name": "Enzyme Nomenclature", + "pattern": "^\\d+\\.-\\.-\\.-|\\d+\\.\\d+\\.-\\.-|\\d+\\.\\d+\\.\\d+\\.-|\\d+\\.\\d+\\.\\d+\\.(n)?\\d+$", + "description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.", + "created": "2019-06-11T14:15:28.483+0000", + "modified": "2019-06-11T14:15:28.483+0000", + "resources": [ + { + "id": 14, + "mirId": "MIR:00100001", + "urlPattern": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec={$id}", + "name": "IntEnZ (Integrated relational Enzyme database)", + "description": "IntEnZ (Integrated relational Enzyme database)", + "official": false, + "providerCode": "intenz", + "sampleId": "1.1.1.1", + "resourceHomeUrl": "https://www.ebi.ac.uk/intenz/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 16, + "mirId": "MIR:00100002", + "urlPattern": 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It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.", + "created": "2019-06-11T14:16:18.690+0000", + "modified": "2019-06-11T14:16:18.690+0000", + "resources": [ + { + "id": 534, + "mirId": "MIR:00100219", + "urlPattern": "https://www-is.biotoul.fr/scripts/ficheIS.php?name={$id}", + "name": "IS Finder at CNRS", + "description": "IS Finder at CNRS", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ISA1083-2", + "resourceHomeUrl": "http://www-is.biotoul.fr/i", + "institution": { + "id": 533, + "name": "Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "FR", + "countryName": "France" + } + }, + "location": { + "countryCode": "FR", + "countryName": "France" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "ISA1083-2", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 535, + "prefix": "jcm", + "mirId": "MIR:00000174", + "name": "Japan Collection of Microorganisms", + "pattern": "^\\d+$", + "description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.", + "created": "2019-06-11T14:16:18.921+0000", + "modified": "2019-06-11T14:16:18.921+0000", + "resources": [ + { + "id": 537, + "mirId": "MIR:00100220", + "urlPattern": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM={$id}", + "name": "JCM at RIKEN BioResource Center", + "description": "JCM at RIKEN BioResource Center", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "17254", + "resourceHomeUrl": "http://www.jcm.riken.go.jp/", + "institution": { + "id": 536, + "name": "RIKEN BioResource Center, Ibaraki", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "17254", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 538, + "prefix": "img.taxon", + "mirId": "MIR:00000175", + "name": "Integrated Microbial Genomes Taxon", + "pattern": "^\\d+$", + "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.", + "created": "2019-06-11T14:16:19.173+0000", + "modified": "2019-06-11T14:16:19.173+0000", + "resources": [ + { + "id": 540, + "mirId": "MIR:00100221", + "urlPattern": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid={$id}", + "name": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory", + "description": "Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "648028003", + "resourceHomeUrl": "http://img.jgi.doe.gov/", + "institution": { + "id": 539, + "name": "Lawrence Berkeley National Laboratory, Berkeley", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "648028003", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 541, + "prefix": "img.gene", + "mirId": "MIR:00000176", + "name": "Integrated Microbial Genomes Gene", + "pattern": "^\\d+$", + "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. 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This collection references compounds.", + "created": "2019-06-11T14:16:58.347+0000", + "modified": "2019-06-11T14:16:58.347+0000", + "resources": [ + { + "id": 998, + "mirId": "MIR:00100443", + "urlPattern": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id={$id}", + "name": "BitterDB Compound at The Hebrew University of Jerusalem", + "description": "BitterDB Compound at The Hebrew University of Jerusalem", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "46", + "resourceHomeUrl": "http://bitterdb.agri.huji.ac.il/dbbitter.php", + "institution": { + "id": 995, + "name": "The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "IL", + "countryName": "Israel" + } + }, + "location": { + "countryCode": "IL", + "countryName": "Israel" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "46", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 999, + "prefix": "bioproject", + "mirId": "MIR:00000349", + "name": "BioProject", + "pattern": "^PRJ[DEN][A-Z]\\d+$", + "description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. 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It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.", + "created": "2019-06-11T14:16:59.017+0000", + "modified": "2019-06-11T14:16:59.017+0000", + "resources": [ + { + "id": 1005, + "mirId": "MIR:00100447", + "urlPattern": "https://www.ebi.ac.uk/biosamples/sample/{$id}", + "name": "BioSamples Database at EBI", + "description": "BioSamples Database at EBI", + "official": true, + "providerCode": "ebi", + "sampleId": "SAMEA2397676", + "resourceHomeUrl": "https://www.ebi.ac.uk/biosamples/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1006, + "mirId": "MIR:00100706", + "urlPattern": "http://www.ncbi.nlm.nih.gov/biosample?term={$id}", + "name": "BioSample at NCBI", + "description": "BioSample at NCBI", + "official": false, + "providerCode": "ncbi", + "sampleId": "SAMN00000002", + "resourceHomeUrl": "http://www.ncbi.nlm.nih.gov/biosample", + "institution": { + "id": 26, + "name": "National Center for Biotechnology Information", + "homeUrl": "https://www.ncbi.nlm.nih.gov/", + "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", + "rorId": "https://ror.org/02meqm098", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1008, + "mirId": "MIR:00100707", + "urlPattern": "http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc={$id}", + "name": "BioSample at DNA Data Bank of Japan", + "description": "BioSample at DNA Data Bank of Japan", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "SAMD00005257", + "resourceHomeUrl": "http://trace.ddbj.nig.ac.jp/biosample/", + "institution": { + "id": 1007, + "name": "Institution DNA Data Bank of Japan, Shizuoka", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "SAMEA2397676", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1009, + "prefix": "piroplasma", + "mirId": "MIR:00000351", + "name": "PiroplasmaDB", + "pattern": "^TA\\d+$", + "description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "created": "2019-06-11T14:16:59.494+0000", + "modified": "2019-06-11T14:16:59.494+0000", + "resources": [ + { + "id": 1011, + "mirId": "MIR:00100448", + "urlPattern": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id={$id}", + "name": "PiroplasmaBD at EuPathDB", + "description": "PiroplasmaBD at EuPathDB", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "TA14985", + "resourceHomeUrl": "http://piroplasmadb.org/", + "institution": { + "id": 1010, + "name": "Center for Tropical & Emerging Global Diseases, University of Georgia, Georgia", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "TA14985", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1012, + "prefix": "unite", + "mirId": "MIR:00000352", + "name": "Unite", + "pattern": "^UDB\\d{6}$", + "description": "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. 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The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", + "created": "2019-06-11T14:17:16.858+0000", + "modified": "2019-06-11T14:17:16.858+0000", + "resources": [ + { + "id": 1218, + "mirId": "MIR:00100545", + "urlPattern": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession={$id}", + "name": "PANTHER Pathway Component at USC (Los Angeles)", + "description": "PANTHER Pathway Component at USC (Los Angeles)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "P00266", + "resourceHomeUrl": "http://www.pantherdb.org/", + "institution": { + "id": 94, + "name": "Keck School of Medicine, University of Southern California", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "P00266", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1219, + "prefix": "gmd.profile", + "mirId": "MIR:00000423", + "name": "Golm Metabolome Database Profile", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.", + "created": "2019-06-11T14:17:17.038+0000", + "modified": "2019-06-11T14:17:17.038+0000", + "resources": [ + { + "id": 1220, + "mirId": "MIR:00100546", + "urlPattern": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId={$id}", + "name": "Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology", + "description": "Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "10b38aaf-b977-4950-85b8-f4775f66658d", + "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", + "institution": { + "id": 806, + "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "10b38aaf-b977-4950-85b8-f4775f66658d", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1221, + "prefix": "gmd.gcms", + "mirId": "MIR:00000424", + "name": "Golm Metabolome Database GC-MS spectra", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.", + "created": "2019-06-11T14:17:17.255+0000", + "modified": "2019-06-11T14:17:17.255+0000", + "resources": [ + { + "id": 1222, + "mirId": "MIR:00100547", + "urlPattern": "http://gmd.mpimp-golm.mpg.de/Spectrums/{$id}", + "name": "Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology", + "description": "Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "53d583d8-40c6-40e1-9296-23f821cd77a5", + "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", + "institution": { + "id": 806, + "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "53d583d8-40c6-40e1-9296-23f821cd77a5", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1223, + "prefix": "gmd.ref", + "mirId": "MIR:00000425", + "name": "Golm Metabolome Database Reference Substance", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.", + "created": "2019-06-11T14:17:17.475+0000", + "modified": "2019-06-11T14:17:17.475+0000", + "resources": [ + { + "id": 1224, + "mirId": "MIR:00100548", + "urlPattern": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/{$id}", + "name": "Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology", + "description": "Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "8cf84adb-b4db-4807-ac98-0004247c35df", + "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", + "institution": { + "id": 806, + "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "8cf84adb-b4db-4807-ac98-0004247c35df", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1225, + "prefix": "gmd.analyte", + "mirId": "MIR:00000426", + "name": "Golm Metabolome Database Analyte", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", + "created": "2019-06-11T14:17:17.661+0000", + "modified": "2019-06-11T14:17:17.661+0000", + "resources": [ + { + "id": 1226, + "mirId": "MIR:00100549", + "urlPattern": "http://gmd.mpimp-golm.mpg.de/Analytes/{$id}", + "name": "Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology", + "description": "Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", + "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", + "institution": { + "id": 806, + "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1227, + "prefix": "intact.molecule", + "mirId": "MIR:00000427", + "name": "IntAct Molecule", + "pattern": "^EBI\\-[0-9]+$", + "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", + "created": "2019-06-11T14:17:17.850+0000", + "modified": "2019-06-11T14:17:17.850+0000", + "resources": [ + { + "id": 1228, + "mirId": "MIR:00100550", + "urlPattern": "https://www.ebi.ac.uk/intact/molecule/{$id}", + "name": "IntAct Molecule at EBI", + "description": "IntAct Molecule at EBI", + "official": false, + "providerCode": "ebi", + "sampleId": "EBI-366083", + "resourceHomeUrl": "https://www.ebi.ac.uk/intact/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "EBI-366083", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1229, + "prefix": "depod", + "mirId": "MIR:00000428", + "name": "DEPOD", + "pattern": "^[A-Z0-9]+$", + "description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.", + "created": "2019-06-11T14:17:18.034+0000", + "modified": "2019-06-11T14:17:18.034+0000", + "resources": [ + { + "id": 1231, + "mirId": "MIR:00100551", + "urlPattern": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene={$id}", + "name": "DEPOD at EMBL", + "description": "DEPOD at EMBL", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "PTPN1", + "resourceHomeUrl": "http://www.depod.bioss.uni-freiburg.de", + "institution": { + "id": 1230, + "name": "European Molecular Biology Laboratory EMBL, Heidelberg", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "PTPN1", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1232, + "prefix": "cst", + "mirId": "MIR:00000429", + "name": "Cell Signaling Technology Pathways", + "pattern": "^[A-Za-z0-9_-]+$", + "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.", + "created": "2019-06-11T14:17:18.324+0000", + "modified": "2019-06-11T14:17:18.324+0000", + "resources": [ + { + "id": 1234, + "mirId": "MIR:00100552", + "urlPattern": "http://www.cellsignal.com/reference/pathway/{$id}.html", + "name": "CST Pathways at Cell Signaling Technology", + "description": "CST Pathways at Cell Signaling Technology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "Akt_PKB", + "resourceHomeUrl": "http://www.cellsignal.com/pathways/index.html", + "institution": { + "id": 1233, + "name": "Cell Signaling Technology, Inc., Danvers, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "Akt_PKB", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1241, + "prefix": "phytozome.locus", + "mirId": "MIR:00000432", + "name": "Phytozome Locus", + "pattern": "^[A-Za-z0-9]+$", + "description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.", + "created": "2019-06-11T14:17:19.049+0000", + "modified": "2019-06-11T14:17:19.049+0000", + "resources": [ + { + "id": 1243, + "mirId": "MIR:00100556", + "urlPattern": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:{$id}", + "name": "Phytozome Locus at Joint Genome Institute", + "description": "Phytozome Locus at Joint Genome Institute", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "Glyma0021s00410", + "resourceHomeUrl": "http://www.phytozome.net/", + "institution": { + "id": 1242, + "name": "Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "Glyma0021s00410", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1244, + "prefix": "subtilist", + "mirId": "MIR:00000433", + "name": "SubtiList", + "pattern": "^BG\\d+$", + "description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.", + "created": "2019-06-11T14:17:19.310+0000", + "modified": "2019-06-11T14:17:19.310+0000", + "resources": [ + { + "id": 1246, + "mirId": "MIR:00100557", + "urlPattern": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+{$id}", + "name": "SubtiList at Pasteur Institute", + "description": "SubtiList at Pasteur Institute", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "BG11523", + "resourceHomeUrl": "http://genolist.pasteur.fr/SubtiList/", + "institution": { + "id": 1245, + "name": "Pasteur Institute, Paris", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "FR", + "countryName": "France" + } + }, + "location": { + "countryCode": "FR", + "countryName": "France" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "BG11523", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1247, + "prefix": "dailymed", + "mirId": "MIR:00000434", + "name": "DailyMed", + "pattern": "^[A-Za-z0-9-]+", + "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", + "created": "2019-06-11T14:17:19.532+0000", + "modified": "2019-06-11T14:17:19.532+0000", + "resources": [ + { + "id": 1249, + "mirId": "MIR:00100558", + "urlPattern": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid={$id}", + "name": "DailyMed at NLM", + "description": "DailyMed at NLM", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54", + "resourceHomeUrl": "https://dailymed.nlm.nih.gov/dailymed/", + "institution": { + "id": 1248, + "name": "U.S. National Library of Medicine, Bethesda, Maryland", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1250, + "prefix": "sider.drug", + "mirId": "MIR:00000435", + "name": "SIDER Drug", + "pattern": "^\\d+$", + "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.", + "created": "2019-06-11T14:17:19.846+0000", + "modified": "2019-06-11T14:17:19.846+0000", + "resources": [ + { + "id": 1252, + "mirId": "MIR:00100559", + "urlPattern": "http://sideeffects.embl.de/drugs/{$id}/", + "name": "SIDER Drug v2 at EMBL (Heidelberg)", + "description": "SIDER Drug v2 at EMBL (Heidelberg)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "2244", + "resourceHomeUrl": "http://sideeffects.embl.de/", + "institution": { + "id": 1251, + "name": "Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "2244", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1253, + "prefix": "sider.effect", + "mirId": "MIR:00000436", + "name": "SIDER Side Effect", + "pattern": "^C\\d+$", + "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.", + "created": "2019-06-11T14:17:20.079+0000", + "modified": "2019-06-11T14:17:20.079+0000", + "resources": [ + { + "id": 1254, + "mirId": "MIR:00100560", + "urlPattern": "http://sideeffects.embl.de/se/{$id}/", + "name": "SIDER Side Effect v2 at EMBL (Heidelberg)", + "description": "SIDER Side Effect v2 at EMBL (Heidelberg)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "C0017565", + "resourceHomeUrl": "http://sideeffects.embl.de/", + "institution": { + "id": 1251, + "name": "Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "C0017565", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1255, + "prefix": "wikigenes", + "mirId": "MIR:00000437", + "name": "WikiGenes", + "pattern": "^\\d+$", + "description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.", + "created": "2019-06-11T14:17:20.303+0000", + "modified": "2019-06-11T14:17:20.303+0000", + "resources": [ + { + "id": 1257, + "mirId": "MIR:00100567", + "urlPattern": "http://www.wikigenes.org/e/gene/e/{$id}.html", + "name": "WikiGenes at Massachusetts Institute of Technology", + "description": "WikiGenes at Massachusetts Institute of Technology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "3771877", + "resourceHomeUrl": "http://www.wikigenes.org/", + "institution": { + "id": 1256, + "name": "Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "3771877", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1258, + "prefix": "broad", + "mirId": "MIR:00000438", + "name": "Broad Fungal Genome Initiative", + "pattern": "^S\\d+$", + "description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. 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It stands near to the Yuanmingyuan Garden and the Summer Palace.\nPeking University is proud of its outstanding faculty, including 48 members of the Chinese Academy of Sciences (CAS), 9 members of the Chinese Academy of Engineering (CAE), and 21 members of the Third World Academy of Sciences (TWAS).", + "rorId": null, + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "AT1G01030.1", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1310, + "prefix": "iuphar.ligand", + "mirId": "MIR:00000457", + "name": "IUPHAR ligand", + "pattern": "^\\d+$", + "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.", + "created": "2019-06-11T14:17:24.936+0000", + "modified": "2019-06-11T14:17:24.936+0000", + "resources": [ + { + "id": 1311, + "mirId": "MIR:00100592", + "urlPattern": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId={$id}", + "name": "IUPHAR ligand at University of Edinburgh", + "description": "IUPHAR ligand at University of Edinburgh", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "1755", + "resourceHomeUrl": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all", + "institution": { + "id": 827, + "name": "Centre for Cardiovascular Science, University of Edinburgh, Edinburgh", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "1755", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1312, + "prefix": "molbase", + "mirId": "MIR:00000458", + "name": "Molbase", + "pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$", + "description": "Molbase provides compound data information for researchers as well as listing suppliers and price information. 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An updated version of the database is available through [MIR:00000521].", + "created": "2019-06-11T14:17:25.610+0000", + "modified": "2019-06-11T14:17:25.610+0000", + "resources": [ + { + "id": 1320, + "mirId": "MIR:00100595", + "urlPattern": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName={$id}", + "name": "Yeast Intron Database version 3 at Baskin School of Engineering", + "description": "Yeast Intron Database version 3 at Baskin School of Engineering", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "SNR17A", + "resourceHomeUrl": "http://compbio.soe.ucsc.edu/yeast_introns.html", + "institution": { + "id": 1319, + "name": "University of California, Santa Cruz", + "homeUrl": "https://www.ucsc.edu", + "description": "UC Santa Cruz opened in 1965 with 650 students. 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This collection references Drosophila data.", + "created": "2019-06-11T14:17:25.854+0000", + "modified": "2019-06-11T14:17:25.854+0000", + "resources": [ + { + "id": 1323, + "mirId": "MIR:00100596", + "urlPattern": "http://func.mshri.on.ca/fly/genes/list_functional_scores/{$id}", + "name": "FuncBase Fly at Harvard Medical School", + "description": "FuncBase Fly at Harvard Medical School", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "10194", + "resourceHomeUrl": "http://func.mshri.on.ca/fly", + "institution": { + "id": 1322, + "name": "Harvard Medical School, Boston, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "10194", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1324, + "prefix": "funcbase.human", + "mirId": "MIR:00000462", + "name": "FuncBase Human", + "pattern": "^\\d+$", + "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. 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This collection references human data.", + "created": "2019-06-11T14:17:26.074+0000", + "modified": "2019-06-11T14:17:26.074+0000", + "resources": [ + { + "id": 1325, + "mirId": "MIR:00100597", + "urlPattern": "http://func.mshri.on.ca/human/genes/list_functional_scores/{$id}", + "name": "FuncBase Human at Harvard Medical School", + "description": "FuncBase Human at Harvard Medical School", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "119514", + "resourceHomeUrl": "http://func.mshri.on.ca/human/", + "institution": { + "id": 1322, + "name": "Harvard Medical School, Boston, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "119514", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1326, + "prefix": "funcbase.mouse", + "mirId": "MIR:00000463", + "name": "FuncBase Mouse", + "pattern": "^\\d+$", + "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. 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The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.", + "created": "2019-06-11T14:17:26.654+0000", + "modified": "2019-06-11T14:17:26.654+0000", + "resources": [ + { + "id": 1332, + "mirId": "MIR:00100600", + "urlPattern": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}", + "name": "YDPM at Stanford University School of Medicine", + "description": "YDPM at Stanford University School of Medicine", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "YAL001C", + "resourceHomeUrl": "http://www-deletion.stanford.edu/YDPM/", + "institution": { + "id": 1331, + "name": "Stanford University School of Medicine, Stanford, California", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "YAL001C", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1333, + "prefix": "wb.rnai", + "mirId": "MIR:00000466", + "name": "WormBase RNAi", + "pattern": "^WBRNAi\\d{8}$", + "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", + "created": "2019-06-11T14:17:26.886+0000", + "modified": "2019-06-11T14:17:26.886+0000", + "resources": [ + { + "id": 1334, + "mirId": "MIR:00100601", + "urlPattern": "https://www.wormbase.org/species/c_elegans/rnai/{$id}", + "name": "WormBase RNAi", + "description": "WormBase RNAi", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "WBRNAi00086878", + "resourceHomeUrl": "https://www.wormbase.org/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "WBRNAi00086878", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1335, + "prefix": "pass2", + "mirId": "MIR:00000468", + "name": "PASS2", + "pattern": "^\\d+$", + "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", + "created": "2019-06-11T14:17:27.086+0000", + "modified": "2019-06-11T14:17:27.086+0000", + "resources": [ + { + "id": 1337, + "mirId": "MIR:00100603", + "urlPattern": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id={$id}", + "name": "PASS2 at National centre for Biological Sciences (India)", + "description": "PASS2 at National centre for Biological Sciences (India)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "46977", + "resourceHomeUrl": "http://caps.ncbs.res.in/pass2/", + "institution": { + "id": 1336, + "name": "National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "IN", + "countryName": "India" + } + }, + "location": { + "countryCode": "IN", + "countryName": "India" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "46977", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1338, + "prefix": "iceberg.element", + "mirId": "MIR:00000469", + "name": "ICEberg element", + "pattern": "^\\d+$", + "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. 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This collection references ICE elements.", + "created": "2019-06-11T14:17:27.338+0000", + "modified": "2019-06-11T14:17:27.338+0000", + "resources": [ + { + "id": 1340, + "mirId": "MIR:00100604", + "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id}", + "name": "ICEberg element at Shanghai Jiaotong University", + "description": "ICEberg element at Shanghai Jiaotong University", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "100", + "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", + "institution": { + "id": 1339, + "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "100", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1341, + "prefix": "iceberg.family", + "mirId": "MIR:00000470", + "name": "ICEberg family", + "pattern": "^\\d+$", + "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", + "created": "2019-06-11T14:17:27.601+0000", + "modified": "2019-06-11T14:17:27.601+0000", + "resources": [ + { + "id": 1343, + "mirId": "MIR:00100605", + "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id={$id}", + "name": "ICEberg family at Shanghai Jiaotong University", + "description": "ICEberg family at Shanghai Jiaotong University", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "1", + "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", + "institution": { + "id": 1342, + "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp; Biotechnology, Shanghai Jiaotong University, Shanghai", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "1", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1344, + "prefix": "vfdb.genus", + "mirId": "MIR:00000471", + "name": "VFDB Genus", + "pattern": "^\\w+$", + "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.", + "created": "2019-06-11T14:17:27.811+0000", + "modified": "2019-06-11T14:17:27.811+0000", + "resources": [ + { + "id": 1346, + "mirId": "MIR:00100606", + "urlPattern": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus={$id}", + "name": "VFDB Genus at Institute of Pathogen Biology", + "description": "VFDB Genus at Institute of Pathogen Biology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "Chlamydia", + "resourceHomeUrl": "http://www.mgc.ac.cn/VFs/", + "institution": { + "id": 1345, + "name": "State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "Chlamydia", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1347, + "prefix": "vfdb.gene", + "mirId": "MIR:00000472", + "name": "VFDB Gene", + "pattern": "^\\w+$", + "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.", + "created": "2019-06-11T14:17:28.027+0000", + "modified": "2019-06-11T14:17:28.027+0000", + "resources": [ + { + "id": 1348, + "mirId": "MIR:00100607", + "urlPattern": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID={$id}", + "name": "VFDB Gene at Institute of Pathogen Biology", + "description": "VFDB Gene at Institute of Pathogen Biology", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "VFG2154", + "resourceHomeUrl": "http://www.mgc.ac.cn/VFs/", + "institution": { + "id": 1345, + "name": "State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "VFG2154", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1349, + "prefix": "mesh.2013", + "mirId": "MIR:00000473", + "name": "MeSH 2013", + "pattern": "^[A-Za-z0-9]+$", + "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.", + "created": "2019-06-11T14:17:28.224+0000", + "modified": "2019-06-11T14:17:28.224+0000", + "resources": [ + { + "id": 1350, + "mirId": "MIR:00100608", + "urlPattern": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index={$id}&view=expanded", + "name": "MeSH 2013 at National Library of Medicine", + "description": "MeSH 2013 at National Library of Medicine", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "17165", + "resourceHomeUrl": "http://www.nlm.nih.gov/mesh/", + "institution": { + "id": 792, + "name": "U.S. National Library of Medicine, National Institute of Health, Maryland", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "17165", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1351, + "prefix": "kegg.module", + "mirId": "MIR:00000474", + "name": "KEGG Module", + "pattern": "^([a-z]{3,5}_)?M\\d{5}$", + "description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.", + "created": "2019-06-11T14:17:28.414+0000", + "modified": "2019-06-11T14:17:28.414+0000", + "resources": [ + { + "id": 1352, + "mirId": "MIR:00100609", + "urlPattern": "http://www.kegg.jp/entry/{$id}", + "name": "KEGG Module at Kyoto University Bioinformatics Center", + "description": "KEGG Module at Kyoto University Bioinformatics Center", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "M00002", + "resourceHomeUrl": "http://www.kegg.jp/kegg/module.html", + "institution": { + "id": 367, + "name": "Department of Computational Biology, University of Tokyo, Tokyo", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "M00002", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1353, + "prefix": "kegg.disease", + "mirId": "MIR:00000475", + "name": "KEGG Disease", + "pattern": "^H\\d+$", + "description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.", + "created": "2019-06-11T14:17:28.601+0000", + "modified": "2019-06-11T14:17:28.601+0000", + "resources": [ + { + "id": 1354, + "mirId": "MIR:00100610", + "urlPattern": "http://www.kegg.jp/entry/{$id}", + "name": "KEGG Disease at Kyoto University Bioinformatics Center", + "description": "KEGG Disease at Kyoto University Bioinformatics Center", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "H00076", + "resourceHomeUrl": "http://www.genome.jp/kegg/disease/", + "institution": { + "id": 705, + "name": "Kyoto University Bioinformatics Center, Kyoto", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "H00076", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1355, + "prefix": "medlineplus", + "mirId": "MIR:00000476", + "name": "MedlinePlus", + "pattern": "^\\d+$", + "description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.", + "created": "2019-06-11T14:17:28.795+0000", + "modified": "2019-06-11T14:17:28.795+0000", + "resources": [ + { + "id": 1356, + "mirId": "MIR:00100611", + "urlPattern": "http://www.nlm.nih.gov/medlineplus/ency/article/{$id}.htm", + "name": "MedlinePlus at NCBI", + "description": "MedlinePlus at NCBI", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "002804", + "resourceHomeUrl": "http://www.nlm.nih.gov/medlineplus/", + "institution": { + "id": 26, + "name": "National Center for Biotechnology Information", + "homeUrl": "https://www.ncbi.nlm.nih.gov/", + "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", + "rorId": "https://ror.org/02meqm098", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "002804", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1360, + "prefix": "glycoepitope", + "mirId": "MIR:00000478", + "name": "GlycoEpitope", + "pattern": "^EP\\d{4}$", + "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", + "created": "2019-06-11T14:17:29.214+0000", + "modified": "2019-06-11T14:17:29.214+0000", + "resources": [ + { + "id": 1362, + "mirId": "MIR:00100613", + "urlPattern": "https://www.glycoepitope.jp/epitopes/{$id}", + "name": "GlycoEpitope at Ritsumeikan University", + "description": "GlycoEpitope at Ritsumeikan University", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "EP0311", + "resourceHomeUrl": "https://www.glycoepitope.jp/epitopes/", + "institution": { + "id": 1361, + "name": "Kawasaki laboratory, Research Center for Glycobiotechnology, Ritsumeikan University", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "EP0311", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1363, + "prefix": "jcggdb", + "mirId": "MIR:00000479", + "name": "JCGGDB", + "pattern": "^JCGG-STR\\d{6}$", + "description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.", + "created": "2019-06-11T14:17:29.437+0000", + "modified": "2019-06-11T14:17:29.437+0000", + "resources": [ + { + "id": 1365, + "mirId": "MIR:00100614", + "urlPattern": "http://jcggdb.jp/idb/jcggdb/{$id}", + "name": "JCGGDB at Advanced Science Institute (Japan)", + "description": "JCGGDB at Advanced Science Institute (Japan)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "JCGG-STR008690", + "resourceHomeUrl": "http://jcggdb.jp/index_en.html", + "institution": { + "id": 1364, + "name": "RIKEN Advanced Science Institute", + "homeUrl": "http://www.riken.jp/en/about/reports/evaluation/asi/", + "description": "Established by RIKEN in April 2008, based on the DRI (Discovery Research Institute) and the FRS (Frontier Research System). ASI is unique since it is structured as comprehensive system supporting the full range of scientific fields including high energy/nuclear/astro-physics, condensed matter physics, chemistry, electronic engineering, biology and medicine.", + "rorId": "https://ror.org/030vbmf58", + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "JCGG-STR008690", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1366, + "prefix": "noncodev4.gene", + "mirId": "MIR:00000480", + "name": "NONCODE v4 Gene", + "pattern": "^NONHSAG\\d{5}$", + "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.", + "created": "2019-06-11T14:17:29.649+0000", + "modified": "2019-06-11T14:17:29.649+0000", + "resources": [ + { + "id": 1367, + "mirId": "MIR:00100616", + "urlPattern": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id={$id}", + "name": "NONCODE v4 Gene at Chinese Academy of Sciences", + "description": "NONCODE v4 Gene at Chinese Academy of Sciences", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "NONHSAG00001", + "resourceHomeUrl": "http://www.bioinfo.org/NONCODEv4/", + "institution": { + "id": 737, + "name": "Chinese Academy of Sciences", + "homeUrl": "http://english.cas.cn/", + "description": "The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches.", + "rorId": "https://ror.org/034t30j35", + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "NONHSAG00001", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1884, + "prefix": "vfb", + "mirId": "MIR:00000680", + "name": "Virtual Fly Brain", + "pattern": "^[0-9a-zA-Z]{8}$", + "description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.", + "created": "2019-06-11T14:18:19.150+0000", + "modified": "2019-06-11T14:18:19.150+0000", + "resources": [ + { + "id": 1886, + "mirId": "MIR:00100911", + "urlPattern": "http://virtualflybrain.org/reports/{$id}", + "name": "Virtual Fly Brain", + "description": "Virtual Fly Brain", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "00000001", + "resourceHomeUrl": "https://VirtualFlyBrain.org", + "institution": { + "id": 1885, + "name": "The University of Cambridge", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "00000001", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1368, + "prefix": "noncodev4.rna", + "mirId": "MIR:00000481", + "name": "NONCODE v4 Transcript", + "pattern": "^NONHSAT\\d{6}$", + "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.", + "created": "2019-06-11T14:17:29.833+0000", + "modified": "2019-06-11T14:17:29.833+0000", + "resources": [ + { + "id": 1369, + "mirId": "MIR:00100617", + "urlPattern": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id={$id}", + "name": "NONCODE v4 Transcript at Chinese Academy of Sciences", + "description": "NONCODE v4 Transcript at Chinese Academy of Sciences", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "NONHSAT000001", + "resourceHomeUrl": "http://www.bioinfo.org/NONCODEv4/", + "institution": { + "id": 737, + "name": "Chinese Academy of Sciences", + "homeUrl": "http://english.cas.cn/", + "description": "The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches.", + "rorId": "https://ror.org/034t30j35", + "location": { + "countryCode": "CN", + "countryName": "China" + } + }, + "location": { + "countryCode": "CN", + "countryName": "China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "NONHSAT000001", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1370, + "prefix": "oryzabase.gene", + "mirId": "MIR:00000482", + "name": "Oryzabase Gene", + "pattern": "^\\d+$", + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", + "created": "2019-06-11T14:17:30.027+0000", + "modified": "2019-06-11T14:17:30.027+0000", + "resources": [ + { + "id": 1372, + "mirId": "MIR:00100618", + "urlPattern": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/{$id}", + "name": "Oryzabase v4 Gene at National Institute of Genetics (Japan)", + "description": "Oryzabase v4 Gene at National Institute of Genetics (Japan)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "117", + "resourceHomeUrl": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "institution": { + "id": 1371, + "name": "Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "117", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1373, + "prefix": "oryzabase.mutant", + "mirId": "MIR:00000483", + "name": "Oryzabase Mutant", + "pattern": "^\\d+$", + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.", + "created": "2019-06-11T14:17:30.248+0000", + "modified": "2019-06-11T14:17:30.248+0000", + "resources": [ + { + "id": 1374, + "mirId": "MIR:00100619", + "urlPattern": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/{$id}", + "name": "Oryzabase v4 Mutant at National Institute of Genetics (Japan)", + "description": "Oryzabase v4 Mutant at National Institute of Genetics (Japan)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "21393", + "resourceHomeUrl": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "institution": { + "id": 1371, + "name": "Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "JP", + "countryName": "Japan" + } + }, + "location": { + "countryCode": "JP", + "countryName": "Japan" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "21393", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1375, + "prefix": "oryzabase.strain", + "mirId": "MIR:00000484", + "name": "Oryzabase Strain", + "pattern": "^\\d+$", + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. 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This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", + "created": "2019-06-11T14:17:36.823+0000", + "modified": "2019-06-11T14:17:36.823+0000", + "resources": [ + { + "id": 1442, + "mirId": "MIR:00100657", + "urlPattern": "https://www.ebi.ac.uk/ega/studies/{$id}", + "name": "EGA Study at European Bioinformatics Institute", + "description": "EGA Study at European Bioinformatics Institute", + "official": true, + "providerCode": "ebi", + "sampleId": "EGAS00000000001", + "resourceHomeUrl": "https://www.ebi.ac.uk/ega/studies", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1443, + "mirId": "MIR:00100851", + "urlPattern": "https://www.omicsdi.org/dataset/ega/{$id}", + "name": "EGA Study through OmicsDI", + "description": "EGA Study through OmicsDI", + "official": false, + "providerCode": "omicsdi", + "sampleId": "EGAS00000000001", + "resourceHomeUrl": "https://www.omicsdi.org/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "EGAS00000000001", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1444, + "prefix": "ega.dataset", + "mirId": "MIR:00000512", + "name": "European Genome-phenome Archive Dataset", + "pattern": "^EGAD\\d{11}$", + "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. 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This collection references 'Datasets'.", + "created": "2019-06-11T14:17:37.233+0000", + "modified": "2019-06-11T14:17:37.233+0000", + "resources": [ + { + "id": 1445, + "mirId": "MIR:00100658", + "urlPattern": "https://www.ebi.ac.uk/ega/datasets/{$id}", + "name": "EGA Dataset at European Bioinformatics Institute", + "description": "EGA Dataset at European Bioinformatics Institute", + "official": true, + "providerCode": "ebi", + "sampleId": "EGAD00000000001", + "resourceHomeUrl": "https://www.ebi.ac.uk/ega/dataset", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1446, + "mirId": "MIR:00100852", + "urlPattern": "https://www.omicsdi.org/dataset/ega/{$id}", + "name": "EGA Dataset through OmicsDI", + "description": "EGA Dataset through OmicsDI", + "official": false, + "providerCode": "omicsdi", + "sampleId": "EGAD00000000001", + "resourceHomeUrl": "https://www.omicsdi.org/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "EGAD00000000001", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1453, + "prefix": "pride.project", + "mirId": "MIR:00000515", + "name": "PRIDE Project", + "pattern": "^P(X|R)D\\d{6}$", + "description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.", + "created": "2019-06-11T14:17:38.030+0000", + "modified": "2019-06-11T14:17:38.030+0000", + "resources": [ + { + "id": 1454, + "mirId": "MIR:00100662", + "urlPattern": "https://www.ebi.ac.uk/pride/archive/projects/{$id}", + "name": "PRIDE Project at EBI", + "description": "PRIDE Project at EBI", + "official": true, + "providerCode": "ebi", + "sampleId": "PXD000440", + "resourceHomeUrl": "https://www.ebi.ac.uk/pride/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1455, + "mirId": "MIR:00100858", + "urlPattern": "https://www.omicsdi.org/dataset/pride/{$id}", + "name": "PRIDE Project through OmicsDI", + "description": "PRIDE Project through OmicsDI", + "official": false, + "providerCode": "omicsdi", + "sampleId": "PXD000440", + "resourceHomeUrl": "https://www.omicsdi.org/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "PXD000440", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1456, + "prefix": "antibodyregistry", + "mirId": "MIR:00000516", + "name": "Antibody Registry", + "pattern": "^\\d{6}$", + "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", + "created": "2019-06-11T14:17:38.379+0000", + "modified": "2019-06-11T14:17:38.379+0000", + "resources": [ + { + "id": 1458, + "mirId": "MIR:00100664", + "urlPattern": "http://antibodyregistry.org/AB_{$id}", + "name": "Antibody Registry at University of California", + "description": "Antibody Registry at University of California", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "493771", + "resourceHomeUrl": "http://antibodyregistry.org/", + "institution": { + "id": 1457, + "name": "Neuroscience Information Framework, University of California, San Diego, California", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "493771", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1459, + "prefix": "mamo", + "mirId": "MIR:00000517", + "name": "Mathematical Modelling Ontology", + "pattern": "^MAMO_\\d{7}$", + "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", + "created": "2019-06-11T14:17:38.625+0000", + "modified": "2019-06-11T14:17:38.625+0000", + "resources": [ + { + "id": 1460, + "mirId": "MIR:00100665", + "urlPattern": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id}", + "name": "MAMO through BioPortal", + "description": "MAMO through BioPortal", + "official": false, + "providerCode": "bptl", + "sampleId": "MAMO_0000026", + "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/MAMO", + "institution": { + "id": 5, + "name": "National Center for Biomedical Ontology, Stanford", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1461, + "mirId": "MIR:00100758", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form={$id}", + "name": "MaMO through OLS", + "description": "MaMO through OLS", + "official": false, + "providerCode": "ols", + "sampleId": "MAMO_0000026", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/mamo", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "MAMO_0000026", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1462, + "prefix": "eo", + "mirId": "MIR:00000518", + "name": "Plant Environment Ontology", + "pattern": "^(P)?EO\\:\\d{7}$", + "description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", + "created": "2019-06-11T14:17:38.985+0000", + "modified": "2019-06-11T14:17:38.985+0000", + "resources": [ + { + "id": 1463, + "mirId": "MIR:00100667", + "urlPattern": "http://archive.gramene.org/db/ontology/search?query=EO:{$id}", + "name": "Plant Environment Ontology through Gramene", + "description": "Plant Environment Ontology through Gramene", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "0007404", + "resourceHomeUrl": "http://archive.gramene.org/db/ontology/search_term?id=EO:0007359", + "institution": { + "id": 556, + "name": "Cold Spring Harbor Laboratory, New York", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1464, + "mirId": "MIR:00100668", + "urlPattern": "http://purl.bioontology.org/ontology/PECO/EO:{$id}", + "name": "Plant Environment Ontology through BioPortal", + "description": "Plant Environment Ontology through BioPortal", + "official": false, + "providerCode": "bptl", + "sampleId": "0007404", + "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/PECO", + "institution": { + "id": 5, + "name": "National Center for Biomedical Ontology, Stanford", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1465, + "mirId": "MIR:00100669", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=EO:{$id}", + "name": "Plant Environment Ontology through OLS", + "description": "Plant Environment Ontology through OLS", + "official": false, + "providerCode": "ols", + "sampleId": "0007404", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/eo", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "0007404", + "namespaceEmbeddedInLui": true, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1466, + "prefix": "idot", + "mirId": "MIR:00000519", + "name": "Identifiers.org Terms", + "pattern": "^[A-Za-z]+$", + "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", + "created": "2019-06-11T14:17:39.487+0000", + "modified": "2019-06-11T14:17:39.487+0000", + "resources": [ + { + "id": 1467, + "mirId": "MIR:00100670", + "urlPattern": "https://biomodels.net/vocab/idot.rdf#{$id}", + "name": "IdoT via biomodels.net", + "description": "IdoT via biomodels.net", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "identifierPattern", + "resourceHomeUrl": "https://identifiers.org/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "identifierPattern", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1470, + "prefix": "yeastintron", + "mirId": "MIR:00000521", + "name": "Yeast Intron Database v4.3", + "pattern": "^[A-Z0-9]+$", + "description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].", + "created": "2019-06-11T14:17:39.906+0000", + "modified": "2019-06-11T14:17:39.906+0000", + "resources": [ + { + "id": 1471, + "mirId": "MIR:00100673", + "urlPattern": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id}", + "name": "Yeast Intron Database version 4.3 at Baskin School of Engineering", + "description": "Yeast Intron Database version 4.3 at Baskin School of Engineering", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "SNR17A", + "resourceHomeUrl": "http://intron.ucsc.edu/yeast4.3/", + "institution": { + "id": 1319, + "name": "University of California, Santa Cruz", + "homeUrl": "https://www.ucsc.edu", + "description": "UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n", + "rorId": "https://ror.org/03s65by71", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "SNR17A", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1472, + "prefix": "ardb", + "mirId": "MIR:00000522", + "name": "Antibiotic Resistance Genes Database", + "pattern": "^[A-Z_]{3}[0-9]{4,}$", + "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", + "created": "2019-06-11T14:17:40.104+0000", + "modified": "2019-06-11T14:17:40.104+0000", + "resources": [ + { + "id": 1474, + "mirId": "MIR:00100678", + "urlPattern": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term={$id}", + "name": "ARDB at University of Maryland", + "description": "ARDB at University of Maryland", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "CAE46076", + "resourceHomeUrl": "http://ardb.cbcb.umd.edu/", + "institution": { + "id": 1473, + "name": "Center for Bioinformatics and Computational Biology, University of Maryland, Maryland", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "CAE46076", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1475, + "prefix": "proteomicsdb.protein", + "mirId": "MIR:00000524", + "name": "ProteomicsDB Protein", + "pattern": "^\\d+$", + "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.", + "created": "2019-06-11T14:17:40.344+0000", + "modified": "2019-06-11T14:17:40.344+0000", + "resources": [ + { + "id": 1477, + "mirId": "MIR:00100680", + "urlPattern": "https://www.proteomicsdb.org/#human/proteinDetails/{$id}/summary", + "name": "Proteomics DB Protein at Center for Integrated Protein Science", + "description": "Proteomics DB Protein at Center for Integrated Protein Science", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "53504", + "resourceHomeUrl": "https://www.proteomicsdb.org/#human", + "institution": { + "id": 1476, + "name": "Center for Integrated Protein Science, Munich,", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "53504", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1478, + "prefix": "proteomicsdb.peptide", + "mirId": "MIR:00000525", + "name": "ProteomicsDB Peptide", + "pattern": "^\\d+$", + "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.", + "created": "2019-06-11T14:17:40.583+0000", + "modified": "2019-06-11T14:17:40.583+0000", + "resources": [ + { + "id": 1480, + "mirId": "MIR:00100681", + "urlPattern": "https://www.proteomicsdb.org/#human/proteinDetails/{$id}/peptides/", + "name": "Proteomics DB Peptide at Center for Integrated Protein Science", + "description": "Proteomics DB Peptide at Center for Integrated Protein Science", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "53504", + "resourceHomeUrl": "https://www.proteomicsdb.org/#peptideSearch", + "institution": { + "id": 1479, + "name": "Center for Integrated Protein Science, Munich", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "53504", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1481, + "prefix": "hpm.protein", + "mirId": "MIR:00000526", + "name": "Human Proteome Map Protein", + "pattern": "^\\d+$", + "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.", + "created": "2019-06-11T14:17:40.825+0000", + "modified": "2019-06-11T14:17:40.825+0000", + "resources": [ + { + "id": 1482, + "mirId": "MIR:00100682", + "urlPattern": "http://www.humanproteomemap.org/protein.php?hpm_id={$id}", + "name": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)", + "description": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "1968", + "resourceHomeUrl": "http://www.humanproteomemap.org/index.php", + "institution": { + "id": 1087, + "name": "Institute of Bioinformatics, International Tech Park, Bangalore", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "IN", + "countryName": "India" + } + }, + "location": { + "countryCode": "IN", + "countryName": "India" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "1968", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1483, + "prefix": "hpm.peptide", + "mirId": "MIR:00000527", + "name": "Human Proteome Map Peptide", + "pattern": "^\\d+$", + "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.", + "created": "2019-06-11T14:17:41.032+0000", + "modified": "2019-06-11T14:17:41.032+0000", + "resources": [ + { + "id": 1484, + "mirId": "MIR:00100683", + "urlPattern": "http://www.humanproteomemap.org/spectrum.php?pep_id={$id}", + "name": "Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)", + "description": "Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "9606117", + "resourceHomeUrl": "http://www.humanproteomemap.org/index.php", + "institution": { + "id": 1087, + "name": "Institute of Bioinformatics, International Tech Park, Bangalore", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "IN", + "countryName": "India" + } + }, + "location": { + "countryCode": "IN", + "countryName": "India" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "9606117", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1485, + "prefix": "drugbankv4.target", + "mirId": "MIR:00000528", + "name": "DrugBank Target v4", + "pattern": "^BE\\d{7}$", + "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.", + "created": "2019-06-11T14:17:41.273+0000", + "modified": "2019-06-11T14:17:41.273+0000", + "resources": [ + { + "id": 1487, + "mirId": "MIR:00100687", + "urlPattern": "http://www.drugbank.ca/biodb/bio_entities/{$id}", + "name": "DrugBank Target information version 4", + "description": "DrugBank Target information version 4", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "BE0000048", + "resourceHomeUrl": "http://www.drugbank.ca/targets", + "institution": { + "id": 1486, + "name": "Departments of Computing Science, Biological Sciences, University of Alberta", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CA", + "countryName": "Canada" + } + }, + "location": { + "countryCode": "CA", + "countryName": "Canada" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "BE0000048", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1488, + "prefix": "zinc", + "mirId": "MIR:00000529", + "name": "ZINC", + "pattern": "^(ZINC)?\\d+$", + "description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.", + "created": "2019-06-11T14:17:41.559+0000", + "modified": "2019-06-11T14:17:41.559+0000", + "resources": [ + { + "id": 1490, + "mirId": "MIR:00100688", + "urlPattern": "http://zinc15.docking.org/substances/{$id}", + "name": "ZINC at University of California (San Francisco)", + "description": "ZINC at University of California (San Francisco)", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ZINC1084", + "resourceHomeUrl": "http://zinc15.docking.org/", + "institution": { + "id": 1489, + "name": "Shoichet Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "ZINC1084", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1491, + "prefix": "foodb.compound", + "mirId": "MIR:00000530", + "name": "FooDB Compound", + "pattern": "^FDB\\d+$", + "description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.", + "created": "2019-06-11T14:17:41.796+0000", + "modified": "2019-06-11T14:17:41.796+0000", + "resources": [ + { + "id": 1492, + "mirId": "MIR:00100689", + "urlPattern": "http://foodb.ca/compounds/{$id}", + "name": "FooDB database of food additives at University of Alberta", + "description": "FooDB database of food additives at University of Alberta", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "FDB002100", + "resourceHomeUrl": "http://foodb.ca/foods", + "institution": { + "id": 334, + "name": "University of Alberta", + "homeUrl": "https://www.ualberta.ca", + "description": "The University of Alberta in Edmonton is one of Canada's top teaching and research universities, with an international reputation for excellence across the humanities, sciences, creative arts, business, engineering and health sciences.", + "rorId": "https://ror.org/0160cpw27", + "location": { + "countryCode": "CA", + "countryName": "Canada" + } + }, + "location": { + "countryCode": "CA", + "countryName": "Canada" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "FDB002100", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1493, + "prefix": "unii", + "mirId": "MIR:00000531", + "name": "UNII", + "pattern": "^[A-Z0-9]+$", + "description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.", + "created": "2019-06-11T14:17:41.988+0000", + "modified": "2019-06-11T14:17:41.988+0000", + "resources": [ + { + "id": 1494, + "mirId": "MIR:00100690", + "urlPattern": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno={$id}", + "name": "UNII at U.S. Food and Drug Administration", + "description": "UNII at U.S. Food and Drug Administration", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "3G6A5W338E", + "resourceHomeUrl": "http://fdasis.nlm.nih.gov/srs/", + "institution": { + "id": 1238, + "name": "U.S. Food and Drug Administration, Maryland", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "3G6A5W338E", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1495, + "prefix": "orphanet.ordo", + "mirId": "MIR:00000532", + "name": "Orphanet Rare Disease Ontology", + "pattern": "^Orphanet(_|:)C?\\d+$", + "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", + "created": "2019-06-11T14:17:42.194+0000", + "modified": "2019-06-11T14:17:42.194+0000", + "resources": [ + { + "id": 1496, + "mirId": "MIR:00100705", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form={$id}", + "name": "ORDO via OLS", + "description": "ORDO via OLS", + "official": true, + "providerCode": "ols", + "sampleId": "Orphanet_C023", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/ordo", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "Orphanet_C023", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1497, + "prefix": "psipar", + "mirId": "MIR:00000533", + "name": "Protein Affinity Reagents", + "pattern": "^PAR:\\d+$", + "description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.", + "created": "2019-06-11T14:17:42.461+0000", + "modified": "2019-06-11T14:17:42.461+0000", + "resources": [ + { + "id": 1498, + "mirId": "MIR:00100709", + "urlPattern": "https://www.ebi.ac.uk/ontology-lookup/?termId={$id}", + "name": "Protein Affinity Reagents through OLS", + "description": "Protein Affinity Reagents through OLS", + "official": false, + "providerCode": "ols", + "sampleId": "PAR:0116", + "resourceHomeUrl": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "PAR:0116", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1499, + "prefix": "clinvar.record", + "mirId": "MIR:00000534", + "name": "ClinVar Record", + "pattern": "^RCV\\d+(\\.\\d+)?$", + "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", + "created": "2019-06-11T14:17:42.685+0000", + "modified": "2019-06-11T14:17:42.685+0000", + "resources": [ + { + "id": 1501, + "mirId": "MIR:00100710", + "urlPattern": "http://www.ncbi.nlm.nih.gov/clinvar/{$id}/", + "name": "ClinVar Record at NCBI", + "description": "ClinVar Record at NCBI", + "official": false, + "providerCode": "ncbi", + "sampleId": "RCV000033555.3", + "resourceHomeUrl": "http://www.ncbi.nlm.nih.gov/clinvar/", + "institution": { + "id": 26, + "name": "National Center for Biotechnology Information", + "homeUrl": "https://www.ncbi.nlm.nih.gov/", + "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", + "rorId": "https://ror.org/02meqm098", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "RCV000033555.3", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1502, + "prefix": "mgnify.proj", + "mirId": "MIR:00000535", + "name": "MGnify Project", + "pattern": "^[A-Z]+[0-9]+$", + "description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", + "created": "2019-06-11T14:17:42.938+0000", + "modified": "2019-06-11T14:17:42.938+0000", + "resources": [ + { + "id": 1503, + "mirId": "MIR:00100711", + "urlPattern": "https://www.ebi.ac.uk/metagenomics/projects/{$id}", + "name": "MGnify Project", + "description": "MGnify Project", + "official": false, + "providerCode": "ebi", + "sampleId": "ERP004492", + "resourceHomeUrl": "https://www.ebi.ac.uk/metagenomics", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "ERP004492", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1504, + "prefix": "euclinicaltrials", + "mirId": "MIR:00000536", + "name": "EU Clinical Trials", + "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", + "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", + "created": "2019-06-11T14:17:43.129+0000", + "modified": "2019-06-11T14:17:43.129+0000", + "resources": [ + { + "id": 1506, + "mirId": "MIR:00100712", + "urlPattern": "https://www.clinicaltrialsregister.eu/ctr-search/search?query={$id}", + "name": "EU Clinical Trials at European Medicines Agency", + "description": "EU Clinical Trials at European Medicines Agency", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "2008-005144-16", + "resourceHomeUrl": "https://www.clinicaltrialsregister.eu/", + "institution": { + "id": 1505, + "name": "European Medicines Agency, London", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "2008-005144-16", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1507, + "prefix": "google.patent", + "mirId": "MIR:00000537", + "name": "Google Patents", + "pattern": "^[A-Z]{2}\\d+([A-Z])?$", + "description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.", + "created": "2019-06-11T14:17:43.371+0000", + "modified": "2019-06-11T14:17:43.371+0000", + "resources": [ + { + "id": 1509, + "mirId": "MIR:00100714", + "urlPattern": "https://www.google.com/patents/{$id}", + "name": "Google Patents at Google", + "description": "Google Patents at Google", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "US4145692", + "resourceHomeUrl": "https://www.google.com/patents/", + "institution": { + "id": 1508, + "name": "Google Incorporated", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "US4145692", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1510, + "prefix": "uspto", + "mirId": "MIR:00000538", + "name": "USPTO", + "pattern": "^(D|PP|R|T|H|X|AI)?\\d+$", + "description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.", + "created": "2019-06-11T14:17:43.583+0000", + "modified": "2019-06-11T14:17:43.583+0000", + "resources": [ + { + "id": 1512, + "mirId": "MIR:00100715", + "urlPattern": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/{$id}", + "name": "USPTO patents at USPTO", + "description": "USPTO patents at USPTO", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "4145692", + "resourceHomeUrl": "http://patft.uspto.gov/netahtml/PTO/index.html", + "institution": { + "id": 1511, + "name": "United States Patent and Trademark Office", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "4145692", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1513, + "prefix": "cpc", + "mirId": "MIR:00000539", + "name": "Cooperative Patent Classification", + "pattern": "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$", + "description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.", + "created": "2019-06-11T14:17:43.853+0000", + "modified": "2019-06-11T14:17:43.853+0000", + "resources": [ + { + "id": 1515, + "mirId": "MIR:00100716", + "urlPattern": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC={$id}", + "name": "Cooperative Patent Classification at Espace", + "description": "Cooperative Patent Classification at Espace", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "A01M1/026", + "resourceHomeUrl": "https://worldwide.espacenet.com/classification", + "institution": { + "id": 1514, + "name": "Espace, European Patent Office", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "A01M1/026", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1516, + "prefix": "gwascentral.study", + "mirId": "MIR:00000540", + "name": "GWAS Central Study", + "pattern": "^HGVST\\d+$", + "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.", + "created": "2019-06-11T14:17:44.062+0000", + "modified": "2019-06-11T14:17:44.062+0000", + "resources": [ + { + "id": 1517, + "mirId": "MIR:00100717", + "urlPattern": "https://www.gwascentral.org/study/{$id}", + "name": "GWAS Central Study at University of Leicester", + "description": "GWAS Central Study at University of Leicester", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "HGVST1828", + "resourceHomeUrl": "https://www.gwascentral.org/studies", + "institution": { + "id": 1079, + "name": "Department of Genetics, University of Leicester, Leicester", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "HGVST1828", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1518, + "prefix": "exac.variant", + "mirId": "MIR:00000541", + "name": "ExAC Variant", + "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", + "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.", + "created": "2019-06-11T14:17:44.275+0000", + "modified": "2019-06-11T14:17:44.275+0000", + "resources": [ + { + "id": 1520, + "mirId": "MIR:00100718", + "urlPattern": "http://exac.broadinstitute.org/variant/{$id}", + "name": "ExAC Variant at Exome Aggregation Consortium", + "description": "ExAC Variant at Exome Aggregation Consortium", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "22-46615880-T-C", + "resourceHomeUrl": "http://exac.broadinstitute.org/", + "institution": { + "id": 1519, + "name": "Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "22-46615880-T-C", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1521, + "prefix": "gwascentral.marker", + "mirId": "MIR:00000542", + "name": "GWAS Central Marker", + "pattern": "^HGVM\\d+$", + "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.", + "created": "2019-06-11T14:17:44.511+0000", + "modified": "2019-06-11T14:17:44.511+0000", + "resources": [ + { + "id": 1522, + "mirId": "MIR:00100719", + "urlPattern": "https://www.gwascentral.org/marker/{$id}", + "name": "GWAS Central Marker at University of Leicester", + "description": "GWAS Central Marker at University of Leicester", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "HGVM15354", + "resourceHomeUrl": "https://www.gwascentral.org/markers/", + "institution": { + "id": 1079, + "name": "Department of Genetics, University of Leicester, Leicester", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "HGVM15354", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1555, + "prefix": "bigg.metabolite", + "mirId": "MIR:00000556", + "name": "BiGG Metabolite", + "pattern": "^[a-z_A-Z0-9]+$", + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references individual metabolotes.", + "created": "2019-06-11T14:17:47.850+0000", + "modified": "2019-06-11T14:17:47.850+0000", + "resources": [ + { + "id": 1556, + "mirId": "MIR:00100733", + "urlPattern": "http://bigg.ucsd.edu/models/universal/metabolites/{$id}", + "name": "BiGG Metabolite at University of Cakifornia", + "description": "BiGG Metabolite at University of Cakifornia", + "official": false, + "providerCode": "ucsd", + "sampleId": "12dgr161", + "resourceHomeUrl": "http://bigg.ucsd.edu/universal/metabolites", + "institution": { + "id": 190, + "name": "University of California, San Diego", + "homeUrl": "https://ucsd.edu/", + "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", + "rorId": "https://ror.org/0168r3w48", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "12dgr161", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1525, + "prefix": "lincs.cell", + "mirId": "MIR:00000544", + "name": "LINCS Cell", + "pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)", + "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. 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The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", + "created": "2019-06-11T14:17:44.903+0000", + "modified": "2019-06-11T14:17:44.903+0000", + "resources": [ + { + "id": 1527, + "mirId": "MIR:00100721", + "urlPattern": "http://lincsportal.ccs.miami.edu/cells/#/view/{$id}", + "name": "LINCS Portal", + "description": "LINCS Portal", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "LCL-2085", + "resourceHomeUrl": "http://lincsportal.ccs.miami.edu/cells/", + "institution": { + "id": 1526, + "name": "University of Miami, BD2K-LINCS DCIC", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "LCL-2085", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1528, + "prefix": "lincs.protein", + "mirId": "MIR:00000545", + "name": "LINCS Protein", + "pattern": "^\\d+$", + "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). 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The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", + "created": "2019-06-11T14:17:45.396+0000", + "modified": "2019-06-11T14:17:45.396+0000", + "resources": [ + { + "id": 1532, + "mirId": "MIR:00100723", + "urlPattern": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/{$id}", + "name": "LINCS Portal", + "description": "LINCS Portal", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "LSM-6306", + "resourceHomeUrl": "http://lincsportal.ccs.miami.edu/SmallMolecules/", + "institution": { + "id": 1531, + "name": "University of Miami, BD2K-LINCS DCIC, USA", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "LSM-6306", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1533, + "prefix": "exac.transcript", + "mirId": "MIR:00000547", + "name": "ExAC Transcript", + "pattern": "^ENST\\d{11}$", + "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. 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This collection references transcript information.", + "created": "2019-06-11T14:17:45.691+0000", + "modified": "2019-06-11T14:17:45.691+0000", + "resources": [ + { + "id": 1534, + "mirId": "MIR:00100724", + "urlPattern": "http://exac.broadinstitute.org/transcript/{$id}", + "name": "ExAC Transcript at Exome Aggregation Consortium", + "description": "ExAC Transcript at Exome Aggregation Consortium", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ENST00000407236", + "resourceHomeUrl": "http://exac.broadinstitute.org/", + "institution": { + "id": 1519, + "name": "Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "ENST00000407236", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1535, + "prefix": "exac.gene", + "mirId": "MIR:00000548", + "name": "ExAC Gene", + "pattern": "^ENSG\\d{11}$", + "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.", + "created": "2019-06-11T14:17:45.890+0000", + "modified": "2019-06-11T14:17:45.890+0000", + "resources": [ + { + "id": 1536, + "mirId": "MIR:00100725", + "urlPattern": "http://exac.broadinstitute.org/gene/{$id}", + "name": "ExAC Gene at Exome Aggregation Consortium", + "description": "ExAC Gene at Exome Aggregation Consortium", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "ENSG00000169174", + "resourceHomeUrl": "http://exac.broadinstitute.org/", + "institution": { + "id": 1519, + "name": "Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "ENSG00000169174", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1542, + "prefix": "unipathway.compound", + "mirId": "MIR:00000551", + "name": "UniPathway Compound", + "pattern": "^UPC\\d{5}$", + "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.", + "created": "2019-06-11T14:17:46.612+0000", + "modified": "2019-06-11T14:17:46.612+0000", + "resources": [ + { + "id": 1544, + "mirId": "MIR:00100728", + "urlPattern": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid={$id}", + "name": "UniPathway Compound at Swiss Institute of Bioinformatics (SIB)", + "description": "UniPathway Compound at Swiss Institute of Bioinformatics (SIB)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "UPC04349", + "resourceHomeUrl": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", + "institution": { + "id": 1730, + "name": "SIB Swiss Institute of Bioinformatics", + "homeUrl": "https://www.sib.swiss", + "description": "SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide.", + "rorId": "https://ror.org/002n09z45", + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + } + }, + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + }, + "deprecated": true, + "deprecationDate": "2019-10-01T12:10:54.792+0000" + } + ], + "sampleId": "UPC04349", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1545, + "prefix": "seed", + "mirId": "MIR:00000552", + "name": "SEED Subsystem", + "pattern": "^\\w+$", + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "created": "2019-06-11T14:17:46.875+0000", + "modified": "2019-06-11T14:17:46.875+0000", + "resources": [ + { + "id": 1547, + "mirId": "MIR:00100729", + "urlPattern": "https://registry.identifiers.org/deprecation/resources/MIR:00100729/{$id}", + "name": "SEED Subsystem at Argonne National Laboratory", + "description": "SEED Subsystem at Argonne National Laboratory", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "Biotin_biosynthesis", + "resourceHomeUrl": "http://seed-viewer.theseed.org/seedviewer.cgi", + "institution": { + "id": 1546, + "name": "Argonne National Laboratory", + "homeUrl": "https://www.anl.gov", + "description": "Argonne is a multidisciplinary science and engineering research center, where talented scientists and engineers work together to answer the biggest questions facing humanity, from how to obtain affordable clean energy to protecting ourselves and our environment.", + "rorId": "https://ror.org/05gvnxz63", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": true, + "deprecationDate": "2019-10-08T08:49:23.021+0000" + } + ], + "sampleId": "Biotin_biosynthesis", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1548, + "prefix": "seed.compound", + "mirId": "MIR:00000553", + "name": "SEED Compound", + "pattern": "^cpd\\d+$", + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "created": "2019-06-11T14:17:47.133+0000", + "modified": "2019-06-11T14:17:47.133+0000", + "resources": [ + { + "id": 1549, + "mirId": "MIR:00100730", + "urlPattern": "http://modelseed.org/biochem/compounds/{$id}", + "name": "SEED Compound at Argonne National Laboratory", + "description": "SEED Compound at Argonne National Laboratory", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "cpd15380", + "resourceHomeUrl": "http://modelseed.org/", + "institution": { + "id": 1546, + "name": "Argonne National Laboratory", + "homeUrl": "https://www.anl.gov", + "description": "Argonne is a multidisciplinary science and engineering research center, where talented scientists and engineers work together to answer the biggest questions facing humanity, from how to obtain affordable clean energy to protecting ourselves and our environment.", + "rorId": "https://ror.org/05gvnxz63", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "cpd15380", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1550, + "prefix": "bigg.model", + "mirId": "MIR:00000554", + "name": "BiGG Model", + "pattern": "^[a-z_A-Z0-9]+$", + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references individual models.", + "created": "2019-06-11T14:17:47.362+0000", + "modified": "2019-06-11T14:17:47.362+0000", + "resources": [ + { + "id": 1552, + "mirId": "MIR:00100731", + "urlPattern": "http://bigg.ucsd.edu/models/{$id}", + "name": "BiGG Model at University of California", + "description": "BiGG Model at University of California", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "iECABU_c1320", + "resourceHomeUrl": "http://bigg.ucsd.edu/models", + "institution": { + "id": 190, + "name": "University of California, San Diego", + "homeUrl": "https://ucsd.edu/", + "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", + "rorId": "https://ror.org/0168r3w48", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "iECABU_c1320", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1553, + "prefix": "bigg.compartment", + "mirId": "MIR:00000555", + "name": "BiGG Compartment", + "pattern": "^[a-z_A-Z]+$", + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references model compartments.", + "created": "2019-06-11T14:17:47.621+0000", + "modified": "2019-06-11T14:17:47.621+0000", + "resources": [ + { + "id": 1554, + "mirId": "MIR:00100732", + "urlPattern": "http://bigg.ucsd.edu/compartments/{$id}", + "name": "BiGG Compartment at University of California", + "description": "BiGG Compartment at University of California", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "c", + "resourceHomeUrl": "http://bigg.ucsd.edu/compartments/", + "institution": { + "id": 190, + "name": "University of California, San Diego", + "homeUrl": "https://ucsd.edu/", + "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", + "rorId": "https://ror.org/0168r3w48", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "c", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1537, + "prefix": "wikidata", + "mirId": "MIR:00000549", + "name": "Wikidata", + "pattern": "^(Q|P)\\d+$", + "description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.", + "created": "2019-06-11T14:17:46.087+0000", + "modified": "2020-11-30T14:15:44.647+0000", + "resources": [ + { + "id": 1538, + "mirId": "MIR:00100726", + "urlPattern": "http://www.wikidata.org/entity/{$id}", + "name": "Wikidata at Wikimedia Foundation", + "description": "Wikidata at Wikimedia Foundation", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "Q2207226", + "resourceHomeUrl": "https://www.wikidata.org/", + "institution": { + "id": 1111, + "name": "Wikimedia Foundation, San Francisco, California", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "Q2207226", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1557, + "prefix": "bigg.reaction", + "mirId": "MIR:00000557", + "name": "BiGG Reaction", + "pattern": "^[a-z_A-Z0-9]+$", + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references reactions.", + "created": "2019-06-11T14:17:48.059+0000", + "modified": "2019-06-11T14:17:48.059+0000", + "resources": [ + { + "id": 1558, + "mirId": "MIR:00100734", + "urlPattern": "http://bigg.ucsd.edu/models/universal/reactions/{$id}", + "name": "BiGG Reaction at University of California", + "description": "BiGG Reaction at University of California", + "official": false, + "providerCode": "ucsd", + "sampleId": "13GS", + "resourceHomeUrl": "http://bigg.ucsd.edu/universal/reactions", + "institution": { + "id": 190, + "name": "University of California, San Diego", + "homeUrl": "https://ucsd.edu/", + "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", + "rorId": "https://ror.org/0168r3w48", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "13GS", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1561, + "prefix": "umls", + "mirId": "MIR:00000559", + "name": "UMLS", + "pattern": "^C\\d+$", + "description": "The Unified Medical Language System is a repository of biomedical vocabularies. 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UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.", + "created": "2019-06-11T14:17:48.502+0000", + "modified": "2019-06-11T14:17:48.502+0000", + "resources": [ + { + "id": 1562, + "mirId": "MIR:00100736", + "urlPattern": "http://linkedlifedata.com/resource/umls/id/{$id}", + "name": "Unified Medical Language System at LinkedLifeData", + "description": "Unified Medical Language System at LinkedLifeData", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "C0021390", + "resourceHomeUrl": "http://linkedlifedata.com/", + "institution": { + "id": 63, + "name": "Linkedlifedata, Ontotext, Sofia", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "BG", + "countryName": "Bulgaria" + } + }, + "location": { + "countryCode": "BG", + "countryName": "Bulgaria" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "C0021390", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1565, + "prefix": "emdb", + "mirId": "MIR:00000561", + "name": "Electron Microscopy Data Bank", + "pattern": "^EMD-\\d{4}$", + "description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.", + "created": "2019-06-11T14:17:48.947+0000", + "modified": "2019-06-11T14:17:48.947+0000", + "resources": [ + { + "id": 1566, + "mirId": "MIR:00100738", + "urlPattern": "https://www.ebi.ac.uk/pdbe/entry/emdb/{$id}", + "name": "EMDB at Protein Data Bank in Europe", + "description": "EMDB at Protein Data Bank in Europe", + "official": false, + "providerCode": "ebi", + "sampleId": "EMD-1001", + "resourceHomeUrl": "https://www.ebi.ac.uk/pdbe/emdb/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "EMD-1001", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1567, + "prefix": "mirtarbase", + "mirId": "MIR:00000562", + "name": "miRTarBase", + "pattern": "^MIRT\\d{6}$", + "description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.", + "created": "2019-06-11T14:17:49.171+0000", + "modified": "2019-06-11T14:17:49.171+0000", + "resources": [ + { + "id": 1569, + "mirId": "MIR:00100739", + "urlPattern": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid={$id}", + "name": "miRTarBase at National Chiao Tung University", + "description": "miRTarBase at National Chiao Tung University", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "MIRT000002", + "resourceHomeUrl": "http://mirtarbase.mbc.nctu.edu.tw/", + "institution": { + "id": 1568, + "name": "Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "TW", + "countryName": "Taiwan, Province of China" + } + }, + "location": { + "countryCode": "TW", + "countryName": "Taiwan, Province of China" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "MIRT000002", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1570, + "prefix": "meddra", + "mirId": "MIR:00000563", + "name": "MedDRA", + "pattern": "^\\d+$", + "description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).", + "created": "2019-06-11T14:17:49.428+0000", + "modified": "2019-06-11T14:17:49.428+0000", + "resources": [ + { + "id": 1571, + "mirId": "MIR:00100740", + "urlPattern": "http://purl.bioontology.org/ontology/MEDDRA/{$id}", + "name": "MedDRA through BioPortal", + "description": "MedDRA through BioPortal", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "10015919", + "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/MEDDRA", + "institution": { + "id": 5, + "name": "National Center for Biomedical Ontology, Stanford", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "10015919", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1572, + "prefix": "dashr", + "mirId": "MIR:00000564", + "name": "DASHR", + "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", + "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.", + "created": "2019-06-11T14:17:49.634+0000", + "modified": "2019-06-11T14:17:49.634+0000", + "resources": [ + { + "id": 1574, + "mirId": "MIR:00100741", + "urlPattern": "http://lisanwanglab.org/DASHR/entry/{$id}", + "name": "DASHR at University of Pennsylvania", + "description": "DASHR at University of Pennsylvania", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "hsa-mir-200a", + "resourceHomeUrl": "http://lisanwanglab.org/DASHR/", + "institution": { + "id": 1573, + "name": "Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "hsa-mir-200a", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1575, + "prefix": "dashr.expression", + "mirId": "MIR:00000565", + "name": "DASHR expression", + "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", + "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.", + "created": "2019-06-11T14:17:49.866+0000", + "modified": "2019-06-11T14:17:49.866+0000", + "resources": [ + { + "id": 1576, + "mirId": "MIR:00100742", + "urlPattern": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#{$id}#exprPerTissueTable", + "name": "DASHR expression at University of Pennsylvania", + "description": "DASHR expression at University of Pennsylvania", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "hsa-mir-200a", + "resourceHomeUrl": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0", + "institution": { + "id": 1573, + "name": "Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "hsa-mir-200a", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1577, + "prefix": "splash", + "mirId": "MIR:00000566", + "name": "SPLASH", + "pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$", + "description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.", + "created": "2019-06-11T14:17:50.083+0000", + "modified": "2019-06-11T14:17:50.083+0000", + "resources": [ + { + "id": 1579, + "mirId": "MIR:00100746", + "urlPattern": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/{$id}", + "name": "Mass Bank of North America (MoNA)", + "description": "Mass Bank of North America (MoNA)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "splash10-0zq2000000-77302b0326a418630a84", + "resourceHomeUrl": "http://mona.fiehnlab.ucdavis.edu/", + "institution": { + "id": 1578, + "name": "University of Californai, Davis, California", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "splash10-0zq2000000-77302b0326a418630a84", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1563, + "prefix": "mesh", + "mirId": "MIR:00000560", + "name": "MeSH", + "pattern": "^(C|D)\\d{6,9}$", + "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.", + "created": "2019-06-11T14:17:48.752+0000", + "modified": "2020-04-21T17:40:51.334+0000", + "resources": [ + { + "id": 1564, + "mirId": "MIR:00100737", + "urlPattern": "http://id.nlm.nih.gov/mesh/{$id}", + "name": "MeSH Linked Data at National Library of Medicine", + "description": "MeSH Linked Data at National Library of Medicine", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "C000100", + "resourceHomeUrl": "http://id.nlm.nih.gov/mesh/", + "institution": { + "id": 792, + "name": "U.S. National Library of Medicine, National Institute of Health, Maryland", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "C000100", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1580, + "prefix": "metanetx.chemical", + "mirId": "MIR:00000567", + "name": "MetaNetX chemical", + "pattern": "^(MNXM\\d+|BIOMASS|WATER)$", + "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.", + "created": "2019-06-11T14:17:50.332+0000", + "modified": "2021-02-26T09:36:59.253+0000", + "resources": [ + { + "id": 1582, + "mirId": "MIR:00100748", + "urlPattern": "https://www.metanetx.org/chem_info/{$id}", + "name": "MetaNetX chemical at SIB Swiss Institute of Bioinformatics", + "description": "MetaNetX chemical at SIB Swiss Institute of Bioinformatics", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "MNXM1723", + "resourceHomeUrl": "https://www.metanetx.org/", + "institution": { + "id": 1581, + "name": "Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + } + }, + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "MNXM1723", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1583, + "prefix": "metanetx.reaction", + "mirId": "MIR:00000568", + "name": "MetaNetX reaction", + "pattern": "^(MNXR\\d+|EMPTY)$", + "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.", + "created": "2019-06-11T14:17:50.605+0000", + "modified": "2021-02-26T09:43:13.847+0000", + "resources": [ + { + "id": 1584, + "mirId": "MIR:00100749", + "urlPattern": "https://www.metanetx.org/equa_info/{$id}", + "name": "MetaNetX reaction at SIB Swiss Institute of Bioinformatics", + "description": "MetaNetX reaction at SIB Swiss Institute of Bioinformatics", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "MNXR101574", + "resourceHomeUrl": "https://www.metanetx.org/", + "institution": { + "id": 1581, + "name": "Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + } + }, + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "MNXR101574", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1587, + "prefix": "unipathway.reaction", + "mirId": "MIR:00000570", + "name": "UniPathway Reaction", + "pattern": "^UCR\\d{5}$", + "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.", + "created": "2019-06-11T14:17:51.017+0000", + "modified": "2019-06-11T14:17:51.017+0000", + "resources": [ + { + "id": 1588, + "mirId": "MIR:00100752", + "urlPattern": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid={$id}", + "name": "UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)", + "description": "UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)", + "official": false, + "providerCode": "CURATOR_REVIEW", + "sampleId": "UCR00226", + "resourceHomeUrl": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", + "institution": { + "id": 1730, + "name": "SIB Swiss Institute of Bioinformatics", + "homeUrl": "https://www.sib.swiss", + "description": "SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide.", + "rorId": "https://ror.org/002n09z45", + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + } + }, + "location": { + "countryCode": "CH", + "countryName": "Switzerland" + }, + "deprecated": true, + "deprecationDate": "2019-10-01T12:11:20.049+0000" + } + ], + "sampleId": "UCR00226", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1589, + "prefix": "hp", + "mirId": "MIR:00000571", + "name": "Human Phenotype Ontology", + "pattern": "^HP:\\d{7}$", + "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", + "created": "2019-06-11T14:17:51.237+0000", + "modified": "2019-06-11T14:17:51.237+0000", + "resources": [ + { + "id": 1592, + "mirId": "MIR:00100754", + "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/hp/terms?obo_id=HP:{$id}", + "name": "Human Phenotype Ontology through OLS", + "description": "Human Phenotype Ontology through OLS", + "official": false, + "providerCode": "ols", + "sampleId": "0000118", + "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/hp", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1591, + "mirId": "MIR:00100753", + "urlPattern": "https://hpo.jax.org/app/browse/term/HP:{$id}", + "name": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics", + "description": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics", + "official": true, + "providerCode": "CURATOR_REVIEW", + "sampleId": "0000118", + "resourceHomeUrl": "http://human-phenotype-ontology.github.io/", + "institution": { + "id": 1590, + "name": "Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin", + "homeUrl": "CURATOR_REVIEW", + "description": "CURATOR_REVIEW", + "rorId": null, + "location": { + "countryCode": "DE", + "countryName": "Germany" + } + }, + "location": { + "countryCode": "DE", + "countryName": "Germany" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "0000118", + "namespaceEmbeddedInLui": true, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 1593, + "prefix": "sasbdb", + "mirId": "MIR:00000572", + "name": "SASBDB", + "pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$", + "description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. 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This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. 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The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a \"peer\"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. ", + "created": "2022-03-15T08:27:12.699+0000", + "modified": "2022-03-15T08:27:12.699+0000", + "resources": [ + { + "id": 3204, + "mirId": "MIR:00000950", + "urlPattern": "https://discover.pennsieve.io/package/{$id}", + "name": "Pennsieve Discover", + "description": "Pennsieve Discover is a public repository for scientific datasets and specializes in FAIR distribution of public datasets that combine large files and graph based metadata records. 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The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.", + "created": "2021-05-10T19:40:34.200+0000", + "modified": "2022-03-31T16:55:06.915+0000", + "resources": [ + { + "id": 2639, + "mirId": "MIR:00000811", + "urlPattern": "https://caninecommons.cancer.gov/#/study/{$id}", + "name": "Integrated Canine Data Commons", + "description": "Integrated Canine Data Commons at National Cancer Institute (USA)", + "official": true, + "providerCode": "icdc", + "sampleId": "000009", + "resourceHomeUrl": "https://caninecommons.cancer.gov/#/", + "institution": { + "id": 2637, + "name": "National Cancer Institute", + "homeUrl": "https://www.cancer.gov/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/040gcmg81' with Wikidata IDs [Q664846], and ISNI IDs [0000 0004 1936 8075]", + "rorId": "https://ror.org/040gcmg81", + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "000009", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 361, + "prefix": "pdb-ccd", + "mirId": "MIR:00000113", + "name": "Chemical Component Dictionary", + "pattern": "^\\w{1,3}$", + "description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.", + "created": "2019-06-11T14:16:03.054+0000", + "modified": "2022-05-18T15:48:21.884+0000", + "resources": [ + { + "id": 362, + "mirId": "MIR:00100146", + "urlPattern": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/{$id}", + "name": "Protein Data Bank Chemical Component Dictionary at EBI", + "description": "Protein Data Bank Chemical Component Dictionary at EBI", + "official": false, + "providerCode": "ebi", + "sampleId": "AB0", + "resourceHomeUrl": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/", + "institution": { + "id": 2, + "name": "European Bioinformatics Institute", + "homeUrl": "https://www.ebi.ac.uk", + "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", + "rorId": "https://ror.org/02catss52", + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + } + }, + "location": { + "countryCode": "GB", + "countryName": "United Kingdom" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "AB0", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3252, + "prefix": "civic.sid", + "mirId": "MIR:00000953", + "name": "CIViC Source", + "pattern": "^[0-9]+$", + "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", + "created": "2022-08-08T18:32:17.171+0000", + "modified": "2022-08-08T18:32:17.171+0000", + "resources": [ + { + "id": 3253, + "mirId": "MIR:00000952", + "urlPattern": "https://civicdb.org/links/sources/{$id}", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "official": true, + "providerCode": "civicdb", + "sampleId": "62", + "resourceHomeUrl": "https://civicdb.org/", + "institution": { + "id": 2750, + "name": "Washington University in St. Louis", + "homeUrl": "https://wustl.edu/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "62", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3255, + "prefix": "civic.tid", + "mirId": "MIR:00000955", + "name": "CIViC Therapy", + "pattern": "^[0-9]+$", + "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", + "created": "2022-08-08T18:33:25.710+0000", + "modified": "2022-08-08T18:33:25.710+0000", + "resources": [ + { + "id": 3256, + "mirId": "MIR:00000954", + "urlPattern": "https://civicdb.org/links/drugs/{$id}", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", + "official": true, + "providerCode": "civicdb", + "sampleId": "14", + "resourceHomeUrl": "https://civicdb.org/", + "institution": { + "id": 2750, + "name": "Washington University in St. Louis", + "homeUrl": "https://wustl.edu/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "14", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3258, + "prefix": "civic.did", + "mirId": "MIR:00000957", + "name": "CIViC Disease", + "pattern": "^[0-9]+$", + "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", + "created": "2022-08-08T18:34:15.882+0000", + "modified": "2022-08-08T18:34:15.882+0000", + "resources": [ + { + "id": 3259, + "mirId": "MIR:00000956", + "urlPattern": "https://civicdb.org/links/diseases/{$id}", + "name": "Clinical Interpretation of Variants in Cancer (CIViC)", + "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.https://civicdb.org/\n", + "official": true, + "providerCode": "civicdb", + "sampleId": "46", + "resourceHomeUrl": "https://civicdb.org/", + "institution": { + "id": 2750, + "name": "Washington University in St. Louis", + "homeUrl": "https://wustl.edu/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "46", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3263, + "prefix": "metatlas", + "mirId": "MIR:00000959", + "name": "Metabolic Atlas", + "pattern": "^MA[MR]\\d{5}[a-z]?$", + "description": "Metabolic Atlas facilitates metabolic modelling by presenting open source genome-scale metabolic models for easy browsing and analysis.", + "created": "2022-08-08T18:36:40.981+0000", + "modified": "2022-08-08T18:36:40.981+0000", + "resources": [ + { + "id": 3264, + "mirId": "MIR:00000958", + "urlPattern": "https://metabolicatlas.org/identifier/MetabolicAtlas/{$id}", + "name": "Metabolic Atlas", + "description": "Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. The goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications.", + "official": true, + "providerCode": "metatlas", + "sampleId": "MAR01234", + "resourceHomeUrl": "https://metabolicatlas.org", + "institution": { + "id": 3262, + "name": "National Bioinformatics Infrastructure Sweden", + "homeUrl": "https://nbis.se", + "description": "NBIS (National Bioinformatics Infrastructure Sweden) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities and the Knut and Alice Wallenberg Foundation, providing state-of-the-art bioinformatics to the Swedish life science researchers community. NBIS is also the Swedish contact point to the European infrastructure for biological information ELIXIR.\n\nPresent NBIS staff has expertise in protein bioinformatics, mass spectrometry (MS), next generation sequencing (NGS), large-scale data handling and integration, metagenomics, systems biology, biostatistics and RNAseq.\n\nNBIS is predominantly offering bioinformatics support in various projects, depending on the user needs. In the projects, the NBIS persons are working close to the research group, and they spend part of their time to teach the users in order to propagate the bioinformatics knowledge. Furthermore, NBIS provides infrastructure and tools for bioinformatics analyses in order to facilitate these analyses for the users.\n\nNBIS forms the bioinformatics platform at the Science for Life Laboratory.", + "rorId": null, + "location": { + "countryCode": "SE", + "countryName": "Sweden" + } + }, + "location": { + "countryCode": "SE", + "countryName": "Sweden" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "MAR01234", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3271, + "prefix": "ror", + "mirId": "MIR:00000961", + "name": "ROR", + "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", + "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", + "created": "2022-08-15T19:28:35.707+0000", + "modified": "2022-08-18T13:14:34.725+0000", + "resources": [ + { + "id": 3272, + "mirId": "MIR:00001056", + "urlPattern": "https://ror.org/{$id}", + "name": "ROR", + "description": "ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ", + "official": true, + "providerCode": "ror", + "sampleId": "03yrm5c26", + "resourceHomeUrl": "https://ror.org", + "institution": { + "id": 3270, + "name": "California Digital Library", + "homeUrl": "https://www.cdlib.org/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03yrm5c26' with Wikidata IDs [Q5020447], and ISNI IDs [0000 0001 1957 5136]", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "03yrm5c26", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3292, + "prefix": "clb", + "mirId": "MIR:00000964", + "name": "ChecklistBank", + "pattern": "^[0-9]+(LR)?$", + "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", + "created": "2022-11-03T14:17:05.019+0000", + "modified": "2022-11-03T14:17:05.019+0000", + "resources": [ + { + "id": 3293, + "mirId": "MIR:00000963", + "urlPattern": "https://www.checklistbank.org/dataset/{$id}", + "name": "ChecklistBank", + "description": "ChecklistBank at GBIF. Codeveloped with the Catalogue of Life", + "official": true, + "providerCode": "clb", + "sampleId": "1010", + "resourceHomeUrl": "https://www.checklistbank.org", + "institution": { + "id": 3291, + "name": "Global Biodiversity Information Facility", + "homeUrl": "https://www.gbif.org/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", + "rorId": null, + "location": { + "countryCode": "DK", + "countryName": "Denmark" + } + }, + "location": { + "countryCode": "DK", + "countryName": "Denmark" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "1010", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3298, + "prefix": "drugcentral", + "mirId": "MIR:00000966", + "name": "DrugCentral", + "pattern": "^[0-9]+$", + "description": "DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.", + "created": "2022-11-04T09:54:32.976+0000", + "modified": "2022-11-04T09:54:32.976+0000", + "resources": [ + { + "id": 3299, + "mirId": "MIR:00000965", + "urlPattern": "https://drugcentral.org/drugcard/{$id}", + "name": "University of New Mexico", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", + "official": true, + "providerCode": "drugcentral", + "sampleId": "257", + "resourceHomeUrl": "http://www.unm.edu/", + "institution": { + "id": 3297, + "name": "University of New Mexico", + "homeUrl": "http://www.unm.edu/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", + "rorId": null, + "location": { + "countryCode": "US", + "countryName": "United States" + } + }, + "location": { + "countryCode": "US", + "countryName": "United States" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "257", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3307, + "prefix": "skm", + "mirId": "MIR:00000968", + "name": "Stress Knowledge Map", + "pattern": "^rx[0-9]{5}$", + "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", + "created": "2022-11-04T12:17:30.200+0000", + "modified": "2022-11-04T12:17:30.200+0000", + "resources": [ + { + "id": 3308, + "mirId": "MIR:00000967", + "urlPattern": "https://skm.nib.si/api/pss/reactions?reaction_id={$id}&return_field=summary", + "name": "National Institute of Biology", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03s5t0r17' with no Wikidata information, and ISNI IDs [0000 0004 0637 0790]", + "official": true, + "providerCode": "skm", + "sampleId": "rx00408", + "resourceHomeUrl": "http://www.nib.si/eng/", + "institution": { + "id": 3306, + "name": "National Institute of Biology", + "homeUrl": "http://www.nib.si/eng/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03s5t0r17' with no Wikidata information, and ISNI IDs [0000 0004 0637 0790]", + "rorId": null, + "location": { + "countryCode": "SI", + "countryName": "Slovenia" + } + }, + "location": { + "countryCode": "SI", + "countryName": "Slovenia" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "rx00408", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3311, + "prefix": "col", + "mirId": "MIR:00000969", + "name": "Catalogue of Life", + "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", + "description": "Identifier of a taxon or synonym in the Catalogue of Life", + "created": "2022-11-04T13:50:22.141+0000", + "modified": "2022-11-04T13:50:22.141+0000", + "resources": [ + { + "id": 3312, + "mirId": "MIR:00000970", + "urlPattern": "https://www.checklistbank.org/dataset/3LR/taxon/{$id}", + "name": "ChecklistBank", + "description": "ChecklistBank, an index and repository for taxonomic data, hosted at GBIF\n", + "official": true, + "providerCode": "clb", + "sampleId": "4QHKG", + "resourceHomeUrl": "https://www.checklistbank.org", + "institution": { + "id": 3291, + "name": "Global Biodiversity Information Facility", + "homeUrl": "https://www.gbif.org/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", + "rorId": null, + "location": { + "countryCode": "DK", + "countryName": "Denmark" + } + }, + "location": { + "countryCode": "DK", + "countryName": "Denmark" + }, + "deprecated": false, + "deprecationDate": null + }, + { + "id": 3328, + "mirId": "MIR:00000971", + "urlPattern": "https://www.catalogueoflife.org/data/taxon/{$id}", + "name": "Catalogue of Life (COL)", + "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", + "official": false, + "providerCode": "col", + "sampleId": "4QHKG", + "resourceHomeUrl": "https://www.catalogueoflife.org", + "institution": { + "id": 3291, + "name": "Global Biodiversity Information Facility", + "homeUrl": "https://www.gbif.org/", + "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", + "rorId": null, + "location": { + "countryCode": "DK", + "countryName": "Denmark" + } + }, + "location": { + "countryCode": "DK", + "countryName": "Denmark" + }, + "deprecated": false, + "deprecationDate": null + } + ], + "sampleId": "4QHKG", + "namespaceEmbeddedInLui": false, + "deprecated": false, + "deprecationDate": null + } + ] + } +} \ No newline at end of file diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java index 30c8300e5..9c649e8ec 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java @@ -124,7 +124,7 @@ public static void replace(Model model, final Map traverser.traverse(bpe, null));//model is not used by traveser + model.getObjects().parallelStream().forEach(bpe -> traverser.traverse(bpe, null));//model is not used } @@ -160,21 +160,21 @@ public static Set getRootElements(final Model model /** - * Iteratively removes "dangling" elements of given type and its sub-types, + * Iteratively removes "dangling" elements of given type and its subtypes, * e.g. Xref.class objects, from the BioPAX model. * * If the "model" does not contain any root Entity class objects, * and the second parameter is basic UtilityClass.class (i.e., not its sub-class), * then it simply logs a warning and quits shortly (otherwise, it would * remove everything from the model). Do not use basic Entity.class either - * (but a sub-class is OK) for the same reason (it would delete everything). + * (but a subclass is OK) for the same reason (it would delete everything). * * This, however, does not change relationships * among objects, particularly, some inverse properties, * such as entityReferenceOf or xrefOf, may still * refer to a removed object. * @param model to modify - * @param clazz filter-class (filter by this type and sub-classes) + * @param clazz filter-class (filter by this type and subclasses) * @param biopax type * @return removed objects */ @@ -515,7 +515,7 @@ private static boolean scanAndAddToFeatureSet(EntityReference er, boolean fix, b if (fix) { er.addEntityFeature(ef); - //TODO resolve inverse functional prop. constraint violation (e.g., copy/replace the e.f. before adding if it has entityFeatureOf not null)? + //TODO: fix inverse functional constraint violation: copy the "ef" if entityFeatureOf is not null! } } return check; @@ -582,7 +582,7 @@ private static boolean checkCommonEntityReferenceForTwoPEs(PhysicalEntity first, return true; } else { - LOG.warn("These two physicalEntities do not share an EntityReference. They can not be compared! " + + LOG.warn("These two PhysicalEntities do not share an EntityReference. They can not be compared! " + "Skipping"); return false; } @@ -590,9 +590,10 @@ private static boolean checkCommonEntityReferenceForTwoPEs(PhysicalEntity first, } /** - * In Paxtools v6, controlled property won't accept multiple values - * (due to the OWL functional property restriction, which we so far forgot of); - * so, let's make sure every Control has at most one controlled process. + * Property "controlled" (OWL Functional prop!) should not accept multiple values, but it unfortunately does. + * + * Let's fix/copy Controls to make sure every one has at most one controlled process, not many. + * * @param model biopax model * @param control to be cloned to set one controlled per control */ @@ -600,17 +601,6 @@ public static void fixControlled(Model model, Control control) { //TODO: implement } - /** - * In all interactions and complexes, replace generic physical entities (have members) - * with their corresponding members; clone the parent object, if needed, for each member. - * - * @param model biopax model - * @param generic physical entity (PE) that has member PEs - */ - public static void normalizeGeneric(Model model, PhysicalEntity generic) { - //TODO: implement?.. - } - /** * Converts each generic simple (except a Complex) physical entity having memberPhysicalEntity property set * into equivalent physical entity with a generic entity reference (have memberEntityReference values). @@ -627,11 +617,14 @@ public static void normalizeGenerics(Model model) { final Set simplePEsToDo = new HashSet<>(); - for (SimplePhysicalEntity spe : model.getObjects(SimplePhysicalEntity.class)) - if (spe.getEntityReference() == null && !spe.getMemberPhysicalEntity().isEmpty()) + for (SimplePhysicalEntity spe : model.getObjects(SimplePhysicalEntity.class)) { + if (spe.getEntityReference() == null && !spe.getMemberPhysicalEntity().isEmpty()) { simplePEsToDo.add(spe); + } + } final Map,EntityReference> memberMap = new HashMap<>(); + for (SimplePhysicalEntity pe : simplePEsToDo) { try { @@ -669,7 +662,7 @@ private static void createGenericEntityRef(Model model, SimplePhysicalEntity spe { //generate a new URI in the same namespace (xml:base) and create and add a new EntityReference String syntheticId = model.getXmlBase() + - firstEntityReference.getModelInterface().getSimpleName() + "_"+ md5hex(spe.getUri()); + firstEntityReference.getModelInterface().getSimpleName() + "_" + md5hex(spe.getUri()); er = (EntityReference) model.addNew(firstEntityReference.getModelInterface(), syntheticId); er.addComment("auto-generated generic entity reference"); @@ -712,7 +705,7 @@ public static void addMissingEntityReference(Model model, SimplePhysicalEntity p return; //nothing to do. //continue for a simple PE - // use a specific EntityReference sub-class depending on the PE class: + // use a specific EntityReference subclass depending on the PE class: Class type = null; if(pe instanceof Protein) type = ProteinReference.class; @@ -726,7 +719,7 @@ else if (pe instanceof Rna) type = RnaReference.class; else if (pe instanceof RnaRegion) type = RnaRegionReference.class; - else {} //impossible SimplePhysicalEntity subtype} + else {} //impossible SimplePhysicalEntity subtype //generate a new URI in the same namespace (xml:base) String syntheticId = model.getXmlBase() + type.getSimpleName() + "_"+ md5hex(pe.getUri()); @@ -740,8 +733,6 @@ else if (pe instanceof RnaRegion) for(UnificationXref ux : new HashSet<>(new ClassFilterSet<>(pe.getXref(),UnificationXref.class))) pe.removeXref(ux); - er.addComment("auto-generated by Paxtools"); - pe.setEntityReference(er); } @@ -790,7 +781,7 @@ private static void copySimplePointers(Model model, Named source, Named target) target.addXref(xref); } - //copy evidence and dataSource if (Named) source and target are same sub-type - either Entity or ER only: + //copy evidence and dataSource if (Named) source and target are same subtype - either Entity or ER only: if(source instanceof Entity && target instanceof Entity) { Entity src = (Entity) source; for (Evidence ev : src.getEvidence()) { @@ -823,8 +814,8 @@ private static void copySimplePointers(Model model, Named source, Named target) public static void replaceEquivalentFeatures(Model model) { - EquivalenceGrouper equivalents = new EquivalenceGrouper(); - HashMap mapped = new HashMap(); + EquivalenceGrouper equivalents = new EquivalenceGrouper<>(); + HashMap mapped = new HashMap<>(); HashSet scheduled = new HashSet<>(); for (EntityFeature ef : model.getObjects(EntityFeature.class)) diff --git a/pom.xml b/pom.xml index 1c8c6ed98..0cb36e5d8 100644 --- a/pom.xml +++ b/pom.xml @@ -216,7 +216,7 @@ maven-compiler-plugin 3.11.0 - 11 + 17 From e38711d22591305b509651b92534dc25e7c892af Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 19 Nov 2022 02:22:18 -0500 Subject: [PATCH 03/20] Paxtools-6: serialize/deserialize Model - - can finally serialize/deserialize Model using java.io; - fixed some concurrent and equivalence bugs; - got rid of the 'public' modifiers and removed todo in the console commands impl. class; - added new 'toSer' console command (serialize a Model to a binary file); --- .../{PaxtoolsMain.java => Commands.java} | 132 +++++------------- .../main/java/org/biopax/paxtools/Main.java | 12 +- .../paxtools/controller/ModelUtils.java | 57 +++++++- .../level3/BiochemicalPathwayStepImpl.java | 3 +- .../paxtools/impl/level3/CatalysisImpl.java | 17 +++ .../paxtools/impl/level3/ConversionImpl.java | 27 ++-- .../paxtools/impl/level3/EntityImpl.java | 6 +- .../paxtools/impl/level3/EvidenceImpl.java | 4 +- .../paxtools/impl/level3/InteractionImpl.java | 5 +- .../paxtools/impl/level3/PathwayImpl.java | 31 ++-- .../paxtools/impl/level3/PathwayStepImpl.java | 14 ++ .../impl/level3/SimplePhysicalEntityImpl.java | 4 +- .../impl/level3/TemplateReactionImpl.java | 5 +- .../paxtools/io/BioPAXIOHandlerAdapter.java | 9 +- .../paxtools/model/level3/Modulation.java | 2 +- .../biopax/paxtools/util/BiopaxSafeSet.java | 3 +- .../paxtools/util/EquivalenceGrouper.java | 7 +- .../paxtools/util/SetEquivalenceChecker.java | 29 ++-- .../paxtools/controller/ModelUtilsTest.java | 22 ++- .../paxtools/model/BioPAXFactoryTest.java | 5 +- .../L3/biopax3-short-metabolic-pathway.owl | 11 +- 21 files changed, 210 insertions(+), 195 deletions(-) rename paxtools-console/src/main/java/org/biopax/paxtools/{PaxtoolsMain.java => Commands.java} (91%) diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java similarity index 91% rename from paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java rename to paxtools-console/src/main/java/org/biopax/paxtools/Commands.java index c0e49ac20..2cc99d957 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/PaxtoolsMain.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java @@ -34,15 +34,16 @@ import java.util.*; import java.util.zip.GZIPInputStream; -/** - * Various console utility functions +/* + * BioPAX data tools. + * This is only called from Main class. */ -public final class PaxtoolsMain { - final static Logger log = LoggerFactory.getLogger(PaxtoolsMain.class); +final class Commands { + final static Logger log = LoggerFactory.getLogger(Commands.class); private static SimpleIOHandler io; - private PaxtoolsMain() { + private Commands() { throw new UnsupportedOperationException("Non-instantiable utility class."); } @@ -52,10 +53,10 @@ private PaxtoolsMain() { } /* - * using arguments: + * arguments: * [-crossSpecies] [-subPathways] [-notPathway] [organisms=9606,mouse,10090,rat,human,..] */ - public static void toGSEA(String[] argv) throws IOException { + static void toGSEA(String[] argv) throws IOException { //argv[0] is the command name ('toGsea') boolean crossSpecies = false; //cross-check is enabled (i.e., no mixing different species IDs in one row) boolean subPathways = false; //no sub-pathways (i.e., going into sub-pathways is not enabled) @@ -91,14 +92,7 @@ else if(argv[i].startsWith("organisms=")) { gseaConverter.writeToGSEA(io.convertFromOWL(getInputStream(argv[1])), new FileOutputStream(argv[2])); } - /* - * - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - * - * @param argv - * @throws IOException - */ - public static void getNeighbors(String[] argv) throws IOException + static void getNeighbors(String[] argv) throws IOException { // set strings vars String in = argv[1]; @@ -138,16 +132,11 @@ public static void getNeighbors(String[] argv) throws IOException } } - /* - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - * @param argv - * @throws IOException - */ - public static void fetch(String[] argv) throws IOException { + static void fetch(String[] argv) throws IOException { // set strings vars String in = argv[1]; String out = argv[2]; - String[] uris = new String[0]; //empty means - all + String[] uris = new String[]{}; //empty boolean absoluteUris = false; if(argv.length > 3) { for(int i=3; i 0) - biopaxWriter.convertToOWL(model, new FileOutputStream(out), uris); - else - biopaxWriter.convertToOWL(model, new FileOutputStream(out)); - + biopaxWriter.convertToOWL(model, new FileOutputStream(out), uris); log.info("Done."); } - - /* - * Detects and converts a BioPAX Level 1, 2, - * or PSI-MI/MITAB model to BioPAX Level3.. - * - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void toLevel3(String[] argv) throws IOException { + static void toLevel3(String[] argv) throws IOException { final String input = argv[1]; final String output = argv[2]; @@ -264,12 +242,7 @@ else if (buf.contains("BioPAX Validator Webservice - * - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void validate(String[] argv) throws IOException + static void validate(String[] argv) throws IOException { String input = argv[1]; String output = argv[2]; @@ -399,14 +364,7 @@ public boolean accept(File dir, String name) { } } - /* - * Exports a biopax model to SIF or/and customizable ExtendedSIF format - * (default classic SIF has only 3 data columns; ExtendedSIF and customized - * can have more colums plus nodes description at the bottom, after a blank line). - * - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void toSifnx(String[] argv) throws IOException { + static void toSifnx(String[] argv) throws IOException { boolean extended = false; //if it stays 'false', then andSif==true will be in effect automatically boolean andSif = false; //if extended==false, SIF will be generated as it would be andSif==true boolean mergeInteractions = true; @@ -509,10 +467,7 @@ public static void toSifnx(String[] argv) throws IOException { log.info("toSIF: done."); } - /* - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void sifnxToSif(String inputFile, String outputFile) throws IOException { + static void sifnxToSif(String inputFile, String outputFile) throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(getInputStream(inputFile))); OutputStreamWriter writer = new OutputStreamWriter(new FileOutputStream(outputFile)); //skip the first line (headers) @@ -529,11 +484,7 @@ public static void sifnxToSif(String inputFile, String outputFile) throws IOExce writer.close(); } - /* - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void integrate(String[] argv) throws IOException { - + static void integrate(String[] argv) throws IOException { Model model1 = getModel(io, argv[1]); Model model2 = getModel(io, argv[2]); @@ -544,11 +495,7 @@ public static void integrate(String[] argv) throws IOException { io.convertToOWL(model1, new FileOutputStream(argv[3])); } - /* - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void merge(String[] argv) throws IOException { - + static void merge(String[] argv) throws IOException { Model model1 = getModel(io, argv[1]); Model model2 = getModel(io, argv[2]); @@ -559,25 +506,14 @@ public static void merge(String[] argv) throws IOException { io.convertToOWL(model1, new FileOutputStream(argv[3])); } - /* - * Generates a blacklist file - * (to optionally use it to exclude ubiquitous small molecules, - * like ATP, when performing graph queries and exporting to - * SIF formats). - * - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void blacklist(String[] argv) throws IOException { + static void blacklist(String[] argv) throws IOException { Model model = getModel(io, argv[1]); BlacklistGenerator3 gen = new BlacklistGenerator3(); Blacklist blacklist = gen.generateBlacklist(model); blacklist.write(new FileOutputStream(argv[2])); } - /* - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void pattern(String[] argv) { + static void pattern(String[] argv) { Dialog.main(argv); } @@ -585,11 +521,7 @@ private static Model getModel(BioPAXIOHandler io, String fName) throws IOExcepti return io.convertFromOWL(getInputStream(fName)); } - - /* - * TODO: should not be public API, but is already used from ext. apps, such as PaxtoolsR... - */ - public static void summarize(String[] argv) throws IOException { + static void summarize(String[] argv) throws IOException { log.debug("Importing the input model from " + argv[1] + "..."); final Model model = getModel(io, argv[1]); final PrintStream out = new PrintStream(argv[2]); @@ -942,15 +874,7 @@ private static void summarizeChebiIds(Model model, PrintStream out) { out.println(String.format("Total\t\t%d\t(%3.1f%%)", numSmrsNoChebi, ((float)numSmrsNoChebi)/totalSmrs*100)); } - /** - * A summary of BioPAX class and property values in the model - * (experimental, messy; for data troubleshooting). - * - * @param model input Model - * @param out output file - * @throws IOException when an I/O exception occurs - */ - public static void summarize(Model model, PrintStream out) throws IOException { + static void summarize(Model model, PrintStream out) throws IOException { HashMap hm = new HashMap(); final SimpleEditorMap em = SimpleEditorMap.get(model.getLevel()); @@ -1150,6 +1074,16 @@ else if(bpe instanceof SequenceEntityReference && ((SequenceEntityReference)bpe) ); } + static void toSer(String[] argv) throws IOException { + String in = argv[1]; + String out = argv[2]; + log.info("Loading BioPAX data from " + in); + Model model = io.convertFromOWL(getInputStream(in)); + log.info("Writing Paxtools Model to (binary file) " + out); + ModelUtils.serialize(model, new FileOutputStream(out)); + log.info("Done."); + } + private static List> sortToName( Set> classes) { diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java index 3dfc180c3..830716985 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java @@ -4,11 +4,10 @@ import java.io.*; -import static org.biopax.paxtools.PaxtoolsMain.*; +import static org.biopax.paxtools.Commands.*; /** - * PaxtoolsMain console application - * (very useful BioPAX utilities). + * Paxtools console application (useful BioPAX tools). */ public final class Main { final static Logger log = LoggerFactory.getLogger(Main.class); @@ -112,6 +111,9 @@ enum Command { {public void run(String[] argv) throws IOException{blacklist(argv);} }, pattern("\n\t- BioPAX pattern search tool (opens a new dialog window)") {public void run(String[] argv){pattern(argv);} }, + toSer(" \n" + + "\t- converts BioPAX data to serialized Model.java (bytes)") + {public void run(String[] argv) throws IOException { toSer(argv); } }, help("\n\t- prints this screen and exits\n") {public void run(String[] argv){ help();} }; @@ -125,10 +127,10 @@ enum Command { } private static void help() { - System.out.println("(PaxtoolsMain Console) Available Operations:\n"); + System.out.println("Available commands:"); for (Command cmd : Command.values()) { System.out.println(cmd.name() + " " + cmd.description); } - System.out.println("Commands can also use compressed input files (only '.gz').\n"); + System.out.println("Commands can also use compressed input files (only '.gz')."); } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java index 9c649e8ec..0746322b9 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java @@ -13,8 +13,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; +import java.io.*; import java.lang.reflect.Method; import java.security.MessageDigest; import java.security.NoSuchAlgorithmException; @@ -124,7 +123,7 @@ public static void replace(Model model, final Map traverser.traverse(bpe, null));//model is not used + model.getObjects().stream().forEach(bpe -> traverser.traverse(bpe, null));//model is not used } @@ -153,7 +152,7 @@ public static Set getRootElements(final Model model pe -> (pe instanceof ObjectPropertyEditor) // filter ); - model.getObjects().parallelStream().forEach(e -> traverser.traverse(e, null)); + model.getObjects().stream().forEach(e -> traverser.traverse(e, null)); return result; } @@ -1326,5 +1325,53 @@ public static boolean isGeneric(BioPAXElement e) { ); //false when e==null } -} + /** + * Serialize a not too large object (mainly for testing). + * @param o + * @return + * @throws IOException + */ + public static byte[] serialize(Object o) throws IOException { + ByteArrayOutputStream baos = new ByteArrayOutputStream(); + serialize(o, baos); + return baos.toByteArray(); + } + + /** + * Deserialize a not too large object (mainly for testing). + * @param bytes + * @return object + * @throws IOException + * @throws ClassNotFoundException + */ + public static Object deserialize(byte[] bytes) throws IOException, ClassNotFoundException { + return deserialize(new ByteArrayInputStream(bytes)); + } + + /** + * Serialize. + * @param o + * @param os + * @throws IOException + */ + public static void serialize(Object o, OutputStream os) throws IOException { + ObjectOutputStream oos = new ObjectOutputStream(os); + oos.writeObject(o); + oos.close(); + } + + /** + * Deserialize. + * @param is + * @return object + * @throws IOException + * @throws ClassNotFoundException + */ + public static Object deserialize(InputStream is) throws IOException, ClassNotFoundException { + ObjectInputStream ois = new ObjectInputStream(is); + Object o = ois.readObject(); + ois.close(); + return o; + } +} diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalPathwayStepImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalPathwayStepImpl.java index 31798940c..bd8014641 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalPathwayStepImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/BiochemicalPathwayStepImpl.java @@ -6,6 +6,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.Serializable; import java.util.AbstractSet; import java.util.Iterator; import java.util.NoSuchElementException; @@ -111,7 +112,7 @@ public Set getStepProcess() } - private class StepProcessSet extends AbstractSet + private class StepProcessSet extends AbstractSet implements Serializable { @Override public Iterator iterator() { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/CatalysisImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/CatalysisImpl.java index 22970c7f0..f271242df 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/CatalysisImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/CatalysisImpl.java @@ -1,10 +1,12 @@ package org.biopax.paxtools.impl.level3; +import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.model.level3.Process; import org.biopax.paxtools.util.BPCollections; import org.biopax.paxtools.util.IllegalBioPAXArgumentException; +import org.biopax.paxtools.util.SetEquivalenceChecker; import java.util.Set; @@ -82,4 +84,19 @@ protected boolean checkControlled(Process controlled) { return controlled instanceof Conversion; } + + @Override + protected boolean semanticallyEquivalent(BioPAXElement element) { + boolean equivalence = false; + if (element instanceof Catalysis && super.semanticallyEquivalent(element)) { + Catalysis other = (Catalysis) element; + equivalence = (this.getControlType() == other.getControlType()) + && (this.getCatalysisDirection() == other.getCatalysisDirection()) + && SetEquivalenceChecker.isEquivalent(this.getCofactor(), other.getCofactor()) + && SetEquivalenceChecker.isEquivalent(this.getController(), other.getController()) + && SetEquivalenceChecker.isEquivalent(this.getControlled(), other.getControlled()); + } + return equivalence; + } + } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java index e45692939..d093d851e 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ConversionImpl.java @@ -60,9 +60,8 @@ public void addRight(PhysicalEntity right) public void removeRight(PhysicalEntity right) { if(right != null) { - if(this.right.remove(right)) { - super.removeParticipant(right); - } + this.right.remove(right); + super.removeParticipant(right); } } @@ -83,9 +82,8 @@ public void addLeft(PhysicalEntity left) public void removeLeft(PhysicalEntity left) { if(left != null) { - if(this.left.remove(left)) { - super.removeParticipant(left); - } + this.left.remove(left); + super.removeParticipant(left); } } @@ -130,20 +128,17 @@ public void setConversionDirection(ConversionDirectionType spontanousType) @Override protected boolean semanticallyEquivalent(BioPAXElement element) { - if(element.getModelInterface()== this.getModelInterface()) + if(element.getModelInterface() == this.getModelInterface()) { Conversion that = (Conversion) element; if(that.getSpontaneous()==this.getSpontaneous() && - that.getConversionDirection() == this.getConversionDirection()) + that.getConversionDirection() == this.getConversionDirection())//TODO: what if one is REVERSIBLE or opposite? { - if(SetEquivalenceChecker.isEquivalent(this.getLeft(), that.getLeft())) - { - return SetEquivalenceChecker.isEquivalent(this.getRight(), that.getRight()); - } - else if(SetEquivalenceChecker.isEquivalent(this.getLeft(), that.getRight())) - { - return(SetEquivalenceChecker.isEquivalent(this.getRight(), that.getLeft())); - } + return SetEquivalenceChecker.isEquivalent(this.getLeft(), that.getLeft()) + && SetEquivalenceChecker.isEquivalent(this.getRight(), that.getRight()) + || SetEquivalenceChecker.isEquivalent(this.getLeft(), that.getRight()) + && SetEquivalenceChecker.isEquivalent(this.getRight(), that.getLeft()); + //TODO: Why don't we call super.semanticallyEquivalent here (to check xrefs, evidence)? } } return false; diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EntityImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EntityImpl.java index b68f8dffd..934896973 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EntityImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EntityImpl.java @@ -124,14 +124,14 @@ public void removeEvidence(Evidence oldEvidence) protected boolean semanticallyEquivalent(BioPAXElement element) { boolean equivalence = false; - if (element instanceof Entity) + if (element instanceof Entity && element.getModelInterface() == this.getModelInterface()) { Entity otherEntity = (Entity) element; equivalence = hasEquivalentIntersection(dataSource, otherEntity.getDataSource()) && hasEquivalentIntersection( - new ClassFilterSet(getXref(), UnificationXref.class), - new ClassFilterSet(otherEntity.getXref(), UnificationXref.class)) + new ClassFilterSet<>(getXref(), UnificationXref.class), + new ClassFilterSet<>(otherEntity.getXref(), UnificationXref.class)) && hasEquivalentIntersection(evidence, otherEntity.getEvidence()); } return equivalence; diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EvidenceImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EvidenceImpl.java index 266ebc2d9..6713765b6 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EvidenceImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/EvidenceImpl.java @@ -185,8 +185,8 @@ protected boolean semanticallyEquivalent(BioPAXElement element) { //consider publication xrefs! boolean hasCommonPublicationXref = hasEquivalentIntersection( - new ClassFilterSet(getXref(), PublicationXref.class), - new ClassFilterSet(that.getXref(), PublicationXref.class)); + new ClassFilterSet<>(getXref(), PublicationXref.class), + new ClassFilterSet<>(that.getXref(), PublicationXref.class)); return super.semanticallyEquivalent(element) && hasAllEquivEvidenceCodes && hasCommonPublicationXref; } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java index 52863e4bd..0636e1149 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/InteractionImpl.java @@ -78,9 +78,8 @@ public void addParticipant(Entity aParticipant) public void removeParticipant(Entity aParticipant) { if (aParticipant != null) { - if(this.participant.remove(aParticipant)) { - aParticipant.getParticipantOf().remove(this); - } + participant.remove(aParticipant); + aParticipant.getParticipantOf().remove(this); } } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayImpl.java index 400dec2c2..4c2b8a300 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayImpl.java @@ -1,22 +1,20 @@ package org.biopax.paxtools.impl.level3; +import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.model.level3.Process; import org.biopax.paxtools.util.BPCollections; +import org.biopax.paxtools.util.SetEquivalenceChecker; import java.util.Set; public class PathwayImpl extends ProcessImpl implements Pathway { -// ------------------------------ FIELDS ------------------------------ - private Set pathwayComponent; private Set pathwayOrder; private BioSource organism; private Set controllerOf; -// --------------------------- CONSTRUCTORS --------------------------- - public PathwayImpl() { this.pathwayComponent = BPCollections.I.createSafeSet(); @@ -24,20 +22,11 @@ public PathwayImpl() this.controllerOf = BPCollections.I.createSafeSet(); } -// ------------------------ INTERFACE METHODS ------------------------ - - -// --------------------- Interface BioPAXElement --------------------- - public Class getModelInterface() { return Pathway.class; } -// --------------------- Interface Pathway --------------------- - -// --------------------- ACCESORS and MUTATORS--------------------- - public Set getPathwayComponent() { return this.pathwayComponent; @@ -95,4 +84,20 @@ public Set getControllerOf() return controllerOf; } + @Override + protected boolean semanticallyEquivalent(BioPAXElement element) { + boolean equivalence = false; + if (element instanceof Pathway) { //super method is not called intentionally (similar to ConversionImpl) + Pathway other = (Pathway) element; + equivalence = + ( + (organism == null && other.getOrganism() == null) + || (organism != null && organism.isEquivalent(other.getOrganism())) + ) + && SetEquivalenceChecker.isEquivalent(this.getPathwayComponent(), other.getPathwayComponent()) + && SetEquivalenceChecker.isEquivalent(this.getPathwayOrder(), other.getPathwayOrder()); + } + return equivalence; + } + } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayStepImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayStepImpl.java index 48af54dd7..2e362ad5a 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayStepImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/PathwayStepImpl.java @@ -1,8 +1,10 @@ package org.biopax.paxtools.impl.level3; +import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.model.level3.Process; import org.biopax.paxtools.util.BPCollections; +import org.biopax.paxtools.util.SetEquivalenceChecker; import java.util.Set; @@ -105,4 +107,16 @@ protected void setPathwayOrderOf(Pathway pathwayOrderOf) { this.pathwayOrderOf = pathwayOrderOf; } + + @Override + protected boolean semanticallyEquivalent(BioPAXElement element) { + boolean equivalence = false; + if (element instanceof PathwayStep) { + PathwayStep other = (PathwayStep) element; + equivalence = SetEquivalenceChecker.hasEquivalentIntersection(evidence, other.getEvidence()) + && SetEquivalenceChecker.isEquivalent(this.getStepProcess(), other.getStepProcess()) + && SetEquivalenceChecker.isEquivalent(this.getNextStep(), other.getNextStep()); + } + return equivalence; + } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java index c98c3a4d7..665c06173 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java @@ -69,9 +69,9 @@ public int equivalenceCode() @Override protected boolean semanticallyEquivalent(BioPAXElement element) { - if(!(element instanceof SimplePhysicalEntity)) + if(!(element instanceof SimplePhysicalEntity)) { return false; - + } SimplePhysicalEntity that = (SimplePhysicalEntity) element; return ( (that.getEntityReference()!=null) ? that.getEntityReference().isEquivalent(getEntityReference()) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java index 2881cd448..01173804f 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TemplateReactionImpl.java @@ -46,9 +46,8 @@ public void addProduct(PhysicalEntity product) public void removeProduct(PhysicalEntity product) { if(product != null) { - if (this.product.remove(product)) { - super.removeParticipant(product); - } + this.product.remove(product); + super.removeParticipant(product); } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java b/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java index 4b7652191..9fb84def1 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java @@ -371,16 +371,12 @@ protected StringPropertyEditor getRDFCommentEditor(BioPAXElement bpe) */ public void convertToOWL(Model model, OutputStream outputStream, String... ids) { - if (ids.length == 0) - { + if (ids.length == 0) { convertToOWL(model, outputStream); - } else - { + } else { Model m = model.getLevel().getDefaultFactory().createModel(); m.setXmlBase(model.getXmlBase()); - Fetcher fetcher = new Fetcher(SimpleEditorMap.get(model.getLevel())); //no Filters anymore - for (String uri : ids) { BioPAXElement bpe = model.getByID(uri); @@ -389,7 +385,6 @@ public void convertToOWL(Model model, OutputStream outputStream, String... ids) fetcher.fetch(bpe, m); } } - convertToOWL(m, outputStream); } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/Modulation.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/Modulation.java index 2fcd91924..011b97524 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/Modulation.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/Modulation.java @@ -21,7 +21,7 @@ * one Control instance can control another Control instance. The semantics of the use of these properties are as * follows: * - * Multiple separate controls controlling a conversion means that they control in parallel (e.g. different enzymes + * Multiple separate Controls for a Conversion means they control it in parallel (e.g. different enzymes * catalyzing the same reaction). Generally, their effect on the rate of the reaction is cumulative. * * A control with multiple controllers indicates a dependency between these controllers, diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java index 7f185c39c..5da993dc8 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java @@ -2,6 +2,7 @@ import org.biopax.paxtools.model.BioPAXElement; +import java.io.Serializable; import java.util.*; @@ -13,7 +14,7 @@ * * @author rodche */ -public class BiopaxSafeSet extends AbstractSet +public class BiopaxSafeSet extends AbstractSet implements Serializable { //initial map is to be reset to a modifiable instance on first write private final static Map empty = Collections.emptyMap(); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java index 5af590db8..32d5edd93 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java @@ -17,7 +17,7 @@ * are equivalent. This logic is implemented in isEquivalent() and equivalenceCode() * methods. * - * For most Java collections that uses hashCode and equals there is no easy way to plug-in a + * For most Java collections that uses hashCode and equals there is no easy way to plug in a * comparator to switch to different comparison behavior. This is a simple Set implementation that uses * equivalence codes when possible. It uses HashMap as the underlying implementation and will use a special bucket in * the case of clashes. @@ -58,12 +58,12 @@ public EquivalanceBucket access(final T element) } } return value; - } private EquivalanceBucket access(final T element, final boolean parity) { final Object[] trap = new Object[]{null}; + //noinspection SuspiciousMethodCalls if (this.buckets.contains(new Object() { public int hashCode() @@ -95,11 +95,10 @@ public EquivalenceGrouper() public void add(T bpe) { - // If this is the case then we will simply return false when // we have something that matches the evcode // AND if that something is a bucket contains something that is equivalent to bpe - // AND if that something is not a bucket and it is equivalent to bpe + // AND if that something is not a bucket, and it is equivalent to bpe EquivalanceBucket bucket = access(bpe); if (bucket == null) { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java index 664fb785d..b5aab71e8 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java @@ -4,6 +4,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.util.Collection; import java.util.HashSet; import java.util.List; import java.util.Set; @@ -21,14 +22,14 @@ public class SetEquivalenceChecker { * @param Both sets should be of type that extends from T. * @return true iff both sets are of equal size and all objects in set1 has an equivalent object in set2. */ - public static boolean isEquivalent(Set set1, Set set2) + public static boolean isEquivalent(Collection set1, Collection set2) { if (set1 != null && !set1.isEmpty() && set2 != null && !set2.isEmpty()) { int size = set1.size(); if (size == set2.size()) { - EquivalenceGrouper grouper = new EquivalenceGrouper(); + EquivalenceGrouper grouper = new EquivalenceGrouper<>(); grouper.addAll(set1); if (grouper.getBuckets().size() == size) { @@ -54,7 +55,7 @@ public static boolean isEquivalent(Set se * @param query BPE to look for equivalents in set * @return true iff there is an element of set that is equivalent to query. */ - public static boolean containsEquivalent(Set set, BioPAXElement query) + public static boolean containsEquivalent(Collection set, BioPAXElement query) { if (set != null && query != null) { @@ -75,8 +76,8 @@ public static boolean containsEquivalent(Set set, BioPA * @param Both sets should be of type that extends from T. * @return elements of set1 that has an equivalent element in set2 */ - public static Set findEquivalentIntersection(Set set1, - Set set2) + public static Set findEquivalentIntersection(Collection set1, + Collection set2) { Set value = new HashSet<>(); @@ -111,31 +112,31 @@ public static Set findEquivalentIntersection(Set Both sets should be of type that extends from T. - * @return true iff there are at least one equivalent element between set1 and set2, or both sets are empty.. + * @return true iff there are at least one equivalent element between set1 and set2, or both sets are empty. */ - public static boolean hasEquivalentIntersection(Set set1, - Set set2) + public static boolean hasEquivalentIntersection(Collection set1, + Collection set2) { - if (!set1.isEmpty() && !set2.isEmpty()) - { - EquivalenceGrouper grouper1 = new EquivalenceGrouper(set1); + if (!set1.isEmpty() && !set2.isEmpty()) { + EquivalenceGrouper grouper1 = new EquivalenceGrouper<>(set1); int size1 = grouper1.getBuckets().size(); if(set1.size() > size1) LOG.warn("hasEquivalentIntersection: the first set already contains equivalent objects"); - EquivalenceGrouper grouper2 = new EquivalenceGrouper(set2); + EquivalenceGrouper grouper2 = new EquivalenceGrouper<>(set2); int size2 = grouper2.getBuckets().size(); if(set2.size() > size2) LOG.warn("hasEquivalentIntersection: the second set already contains equivalent objects"); //now add both sets into one grouper - - EquivalenceGrouper grouper = new EquivalenceGrouper(); + EquivalenceGrouper grouper = new EquivalenceGrouper<>(); grouper.addAll(set1); grouper.addAll(set2); return (grouper.getBuckets().size() < size1 + size2); } else if(set1.isEmpty() ^ set2.isEmpty()) { //only one of sets is empty return false; - } else //both empty + } else { //both empty return true; + } } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java index d0300b53a..383ba8272 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java @@ -9,6 +9,7 @@ import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.util.IllegalBioPAXArgumentException; +import org.biopax.paxtools.util.SetEquivalenceChecker; import org.junit.Assert; import org.junit.Test; @@ -138,17 +139,15 @@ private void printModel(Model model) { System.out.println(bytes.toString()); } - - public final void testMetrics() + public final void printMetrics() { Model model = SimpleIOHandlerTest.getL3Model(new SimpleIOHandler()); Map,Integer> metrics = ModelUtils.generateClassMetrics(model); System.out.println("metrics = " + metrics); - } - + @Test public final void testRemoveObjectsIfDangling() { Model model = (new SimpleIOHandler()).convertFromOWL( @@ -311,4 +310,19 @@ public void testBase62() { String shortUri = ModelUtils.shortenUri("http://www.ctdbase.org/", longUri); Assert.assertEquals("http://www.ctdbase.org/k9viXaDIiOW", shortUri); } + + @Test + public final void testSerializeDeserializeModel() throws Exception { + SimpleIOHandler io = new SimpleIOHandler(); + Model m1 = io.convertFromOWL(SimpleIOHandlerTest.class.getClassLoader() + .getResourceAsStream("L3" + File.separator + "biopax3-short-metabolic-pathway.owl")); + byte[] s1 = ModelUtils.serialize(m1); + Model m2 = (Model) ModelUtils.deserialize(s1); + + assertEquals(m1.size(), m2.size()); + assertTrue(SetEquivalenceChecker.isEquivalent(m1.getObjects(), m2.getObjects())); + + //REM: if we'd write/read m1,m2 to/from string/bytes and then compare, + //it would not match as the elements processing order is not guaranteed ;) + } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java index b9107221d..bd4d4e76b 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java @@ -1,9 +1,7 @@ package org.biopax.paxtools.model; -import org.biopax.paxtools.model.level3.EntityReference; +import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.model.level3.Process; -import org.biopax.paxtools.model.level3.SequenceSite; -import org.biopax.paxtools.model.level3.SimplePhysicalEntity; import org.junit.Test; import static org.junit.Assert.*; @@ -26,5 +24,6 @@ public void canInstantiate() throws Exception { assertFalse(factory.canInstantiate(Process.class)); assertFalse(factory.canInstantiate(EntityReference.class)); assertFalse(factory.canInstantiate(SimplePhysicalEntity.class)); + assertTrue(factory.canInstantiate(Interaction.class)); } } \ No newline at end of file diff --git a/paxtools-core/src/test/resources/L3/biopax3-short-metabolic-pathway.owl b/paxtools-core/src/test/resources/L3/biopax3-short-metabolic-pathway.owl index c5ffaeac8..725ffaac2 100755 --- a/paxtools-core/src/test/resources/L3/biopax3-short-metabolic-pathway.owl +++ b/paxtools-core/src/test/resources/L3/biopax3-short-metabolic-pathway.owl @@ -261,15 +261,8 @@ >0.4 - beta-D-Glucose 6-phosphate ketol-isomerase - - - - 1.0 - - + beta-D-Glucose 6-phosphate ketol-isomerase + From 74052cf9dd967322bb2e178a042c47f3bdea4783 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Wed, 23 Nov 2022 21:28:25 -0500 Subject: [PATCH 04/20] Paxtools-6: comments, some polishing in the console app classes. --- logback.xml | 25 --- .../java/org/biopax/paxtools/Commands.java | 167 ++++++++---------- .../main/java/org/biopax/paxtools/Main.java | 2 +- .../src/main/resources/logback.xml | 7 +- 4 files changed, 75 insertions(+), 126 deletions(-) delete mode 100644 logback.xml diff --git a/logback.xml b/logback.xml deleted file mode 100644 index 7fbb824d9..000000000 --- a/logback.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - true - - - - - - - - - %d %-5level [%thread] %logger{25} - %msg%n - true - - - - - - - - - - \ No newline at end of file diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java index 2cc99d957..ba10aacb2 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java @@ -32,6 +32,7 @@ import java.io.*; import java.lang.reflect.Method; import java.util.*; +import java.util.concurrent.TimeUnit; import java.util.zip.GZIPInputStream; /* @@ -312,12 +313,7 @@ static void validate(String[] argv) throws IOException // collect files if (fileOrDir.isDirectory()) { // validate all the OWL files in the folder - FilenameFilter filter = new FilenameFilter() { - public boolean accept(File dir, String name) { - return (name.endsWith(".owl")); - } - }; - for (String s : fileOrDir.list(filter)) { + for (String s : fileOrDir.list((dir, name) -> (name.endsWith(".owl")))) { files.add(new File(fileOrDir.getCanonicalPath() + File.separator + s)); } @@ -336,7 +332,7 @@ public boolean accept(File dir, String name) { } catch (Exception ex) { // fall-back: not using the remote validator; trying to read files String msg = "Unable to check with the biopax-validator web service: \n " + - ex.toString() + + ex + "\n Fall-back: trying to parse the file(s) with paxtools " + "(up to the first syntax error in each file)...\n"; log.error(msg, ex); @@ -475,10 +471,12 @@ static void sifnxToSif(String inputFile, String outputFile) throws IOException { while(reader.ready()) { String line = reader.readLine(); //stop at the first blank line (because next come nodes with attributes) - if(line==null || line.isEmpty()) + if(line==null || line.isEmpty()) { break; - //keep only the first three columns (otherwise, it's not gonna be SIF format) - writer.write(StringUtils.join(Arrays.copyOfRange(line.split("\t", 4), 0, 3), '\t') + '\n'); + } + //keep only the first three columns (otherwise, it's not SIF format) + writer.write(StringUtils.join(Arrays.copyOfRange(line.split("\t", 4), + 0, 3), '\t') + '\n'); } reader.close(); writer.close(); @@ -554,7 +552,7 @@ static void summarize(String[] argv) throws IOException { * output uri, type, names, standard identifiers (in JSON format). */ private static void mapUriToIds(Model model, PrintStream out) { - Set elements = new TreeSet(); + Set elements = new TreeSet<>(); //write one by one to insert EOLs and make potentially a very large file human-readable - for(PhysicalEntity pe : model.getObjects(PhysicalEntity.class)) @@ -635,7 +633,7 @@ private static Set identifiers(final PhysicalEntity entity, final String } - private static void summarizePathways(Model model, PrintStream out) throws IOException { + private static void summarizePathways(Model model, PrintStream out) { final PathAccessor directChildPathwaysAccessor = new PathAccessor("Pathway/pathwayComponent:Pathway"); final PathAccessor pathwayComponentAccessor = new PathAccessor("Pathway/pathwayComponent"); final PathAccessor pathwayOrderStepProcessAccessor = new PathAccessor("Pathway/pathwayOrder/stepProcess"); @@ -658,7 +656,7 @@ private static void summarizePathways(Model model, PrintStream out) throws IOExc for(Pathway p : fetcher.fetch(pathway, Pathway.class)) { sb.append(p.getUri()).append(";"); } - out.println(sb.toString()); + out.println(sb); } // print pathway names, etc. after a blank line and title line out.println("\nPATHWAY_URI\tDATASOURCE\tDISPLAY_NAME\tALL_NAMES" + @@ -673,24 +671,23 @@ private static void summarizePathways(Model model, PrintStream out) throws IOExc .append(datasource).append('\t') .append(pathway.getDisplayName()).append('\t'); //all names - for(String name : pathway.getName()) + for(String name : pathway.getName()) { sb.append('"').append(name).append('"').append(";"); + } //"size" sb.append('\t').append(size); - out.println(sb.toString()); + out.println(sb); } } private static void summarizeHgncIds(Model model, PrintStream out) { - boolean verbose = true; //TODO use another parameter here - //Analyse SERs (Protein-, Dna* and Rna* references) - HGNC usage, coverage,.. //Calc. the no. non-generic ERs having >1 different HGNC symbols and IDs, or none, etc. Set haveMultipleHgnc = new HashSet<>(); Map numErs = new HashMap<>(); Map numProblematicErs = new HashMap<>(); PathAccessor pa = new PathAccessor("EntityReference/entityReferenceOf/dataSource", model.getLevel()); - Set problemErs = new TreeSet(); + Set problemErs = new TreeSet<>(); for(EntityReference ser : model.getObjects(EntityReference.class)) { //skip if it's a SMR or generic if(ser instanceof SmallMoleculeReference || !ser.getMemberEntityReference().isEmpty()) @@ -701,16 +698,17 @@ private static void summarizeHgncIds(Model model, PrintStream out) { if(ser.getUri().startsWith("http://identifiers.org/hgnc")) { String s = ser.getUri().substring(ser.getUri().lastIndexOf("/")+1); - if(s.startsWith("HGNC:")) + if(s.startsWith("HGNC:")) { hgncIds.add(s); - else + } else { hgncSymbols.add(s); + } } for(Xref x : ser.getXref()) { - if(x instanceof PublicationXref || x.getDb()==null || x.getId()==null) + if(x instanceof PublicationXref || x.getDb()==null || x.getId()==null) { continue; //skip - + } if(x.getDb().toLowerCase().startsWith("hgnc") && !x.getId().toLowerCase().startsWith("hgnc:")) { hgncSymbols.add(x.getId().toLowerCase()); } @@ -719,35 +717,35 @@ else if(x.getDb().toLowerCase().startsWith("hgnc") && x.getId().toLowerCase().st } } - if(hgncIds.size()>1 || hgncSymbols.size()>1) + if(hgncIds.size()>1 || hgncSymbols.size()>1) { haveMultipleHgnc.add((SequenceEntityReference) ser); + } //increment "no hgnc" and "total" counts by data source for(Object provenance : pa.getValueFromBean(ser)) { if (hgncSymbols.isEmpty() && hgncIds.isEmpty()) { - if (verbose) { - problemErs.add(String.format("%s\t%s\t%s", - ((Provenance) provenance).getDisplayName(), ser.getDisplayName(), ser.getUri())); - } - + problemErs.add(String.format("%s\t%s\t%s", + ((Provenance)provenance).getDisplayName(), ser.getDisplayName(), ser.getUri())); MutableInt n = numProblematicErs.get(provenance); - if (n == null) + if (n == null) { numProblematicErs.put((Provenance) provenance, new MutableInt(1)); - else + } else { n.increment(); + } } - MutableInt tot = numErs.get(provenance); - if (tot == null) + if (tot == null) { numErs.put((Provenance) provenance, new MutableInt(1)); - else + } else { tot.increment(); + } } } + //print results - if(verbose) { - out.println("SequenceEntityReferences (not generics) without any HGNC Symbol:"); - for(String line : problemErs) out.println(line); + out.println("SequenceEntityReferences (not generics) without any HGNC Symbol:"); + for(String line : problemErs) { + out.println(line); } out.println("The number of SERs (not generic) having more than one HGNC Symbols: " + haveMultipleHgnc.size()); out.println("\nNumber of SequenceEntityReferences (not generics) without any HGNC ID, by data source:"); @@ -764,8 +762,6 @@ else if(x.getDb().toLowerCase().startsWith("hgnc") && x.getId().toLowerCase().st } private static void summarizeUniprotIds(Model model, PrintStream out) { - boolean verbose = true; //TODO use another parameter here - //Analyse PRs - UniProt ID coverage,.. Map numErs = new HashMap<>(); Map numProblematicErs = new HashMap<>(); @@ -773,23 +769,21 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { Set problemErs = new TreeSet(); for(ProteinReference pr : model.getObjects(ProteinReference.class)) { //skip a generic one - if(!pr.getMemberEntityReference().isEmpty()) + if(!pr.getMemberEntityReference().isEmpty()) { continue; + } for(Object provenance : pa.getValueFromBean(pr)) { if(!pr.getUri().startsWith("http://identifiers.org/uniprot") && !pr.getXref().toString().toLowerCase().contains("uniprot")) { - - if (verbose) { - problemErs.add(String.format("%s\t%s\t%s", - ((Provenance) provenance).getDisplayName(), pr.getDisplayName(), pr.getUri())); - } - + problemErs.add(String.format("%s\t%s\t%s", + ((Provenance) provenance).getDisplayName(), pr.getDisplayName(), pr.getUri())); MutableInt n = numProblematicErs.get(provenance); - if (n == null) + if (n == null) { numProblematicErs.put((Provenance) provenance, new MutableInt(1)); - else + } else { n.increment(); + } } //increment total PRs per datasource @@ -802,9 +796,9 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { } //print results - if(verbose) { - out.println("\nProteinReferences (not generics) without any UniProt AC:"); - for(String line : problemErs) out.println(line); + out.println("\nProteinReferences (not generics) without any UniProt AC:"); + for(String line : problemErs) { + out.println(line); } out.println("\nNumber of ProteinReferences (not generics) without any UniProt AC, by data source:"); int totalErs = 0; @@ -820,7 +814,6 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { } private static void summarizeChebiIds(Model model, PrintStream out) { - boolean verbose = true; //TODO use another parameter here //Analyse SMRs - ChEBI usage, coverage,.. Map numErs = new HashMap<>(); Map numProblematicErs = new HashMap<>(); @@ -828,39 +821,34 @@ private static void summarizeChebiIds(Model model, PrintStream out) { Set problemErs = new TreeSet(); for(SmallMoleculeReference smr : model.getObjects(SmallMoleculeReference.class)) { //skip a generic SMR - if(!smr.getMemberEntityReference().isEmpty()) + if(!smr.getMemberEntityReference().isEmpty()) { continue; - + } for(Object provenance : pa.getValueFromBean(smr)) { if(!smr.getUri().startsWith("http://identifiers.org/chebi/CHEBI:") && !smr.getXref().toString().contains("CHEBI:")) { - - if (verbose) { - problemErs.add(String.format("%s\t%s\t%s", - ((Provenance) provenance).getDisplayName(), smr.getDisplayName(), smr.getUri())); - } - + problemErs.add(String.format("%s\t%s\t%s", + ((Provenance) provenance).getDisplayName(), smr.getDisplayName(), smr.getUri())); MutableInt n = numProblematicErs.get(provenance); - if (n == null) + if (n == null) { numProblematicErs.put((Provenance) provenance, new MutableInt(1)); - else + } else { n.increment(); + } } - //increment total SMRs per datasource MutableInt tot = numErs.get(provenance); - if(tot == null) - numErs.put((Provenance)provenance, new MutableInt(1)); - else + if(tot == null) { + numErs.put((Provenance) provenance, new MutableInt(1)); + } else { tot.increment(); + } } } //print results - if(verbose) { - out.println("\nSmallMoleculeReferences (not generics) without any ChEBI ID:"); - for(String line : problemErs) out.println(line); - } + out.println("\nSmallMoleculeReferences (not generics) without any ChEBI ID:"); + for(String line : problemErs) out.println(line); out.println("\nNumber of SmallMoleculeReferences (not generics) without any ChEBI ID, by data source:"); int totalSmrs = 0; int numSmrsNoChebi = 0; @@ -876,7 +864,6 @@ private static void summarizeChebiIds(Model model, PrintStream out) { static void summarize(Model model, PrintStream out) throws IOException { HashMap hm = new HashMap(); - final SimpleEditorMap em = SimpleEditorMap.get(model.getLevel()); for (Class clazz : sortToName(em.getKnownSubClassesOf(BioPAXElement.class))) @@ -929,7 +916,6 @@ else if (returnType.equals(Set.class) && } } } - if (!cnt.isEmpty()) { String name = "-" @@ -1028,7 +1014,7 @@ else if(spe instanceof NucleicAcid) out.println("\n\t-" + genericSpeLackingEr + " of which have member physical entities (are generic).\n"); out.println("\n\t- by data source:\n"); for(String key : numSpeLackErByProvider.keySet()) { - out.println(String.format("\n\t\t-- %s -> %d\n", key, numSpeLackErByProvider.get(key))); + out.println(String.format("%n\t\t-- %s -> %d%n", key, numSpeLackErByProvider.get(key))); } out.println("\n\t- " + speLackingErAndId + " neither have 'entityReference' nor xref/id (except publications):\n"); if(speLackingErAndId > 0) { @@ -1040,7 +1026,7 @@ else if(spe instanceof NucleicAcid) int erLackingId = 0; for(EntityReference er : model.getObjects(EntityReference.class)) { if(er.getMemberEntityReference().isEmpty() && - (er.getXref().isEmpty() || new ClassFilterSet(er.getXref(), PublicationXref.class) + (er.getXref().isEmpty() || new ClassFilterSet<>(er.getXref(), PublicationXref.class) .size() == er.getXref().size())) { erLackingId++; @@ -1066,8 +1052,8 @@ else if(bpe instanceof SequenceEntityReference && ((SequenceEntityReference)bpe) } out.println( String.format( - "\n%d Genes, %d Pathways, %d SequenceEntityReferences " + - "(%d in NucleicAcidRef. and %d in PRs) have NULL 'organism'.\n", + "%n%d Genes, %d Pathways, %d SequenceEntityReferences " + + "(%d in NucleicAcidRef. and %d in PRs) have NULL 'organism'.%n", genesLackingOrganism, pwLackingOrganism, serLackingOrganism, narLackingOrganism, serLackingOrganism-narLackingOrganism ) @@ -1078,24 +1064,19 @@ static void toSer(String[] argv) throws IOException { String in = argv[1]; String out = argv[2]; log.info("Loading BioPAX data from " + in); + long start = System.currentTimeMillis(); Model model = io.convertFromOWL(getInputStream(in)); log.info("Writing Paxtools Model to (binary file) " + out); ModelUtils.serialize(model, new FileOutputStream(out)); - log.info("Done."); + long stop = System.currentTimeMillis(); + log.info(String.format("Done (in %d sec)", TimeUnit.MILLISECONDS.toSeconds(stop-start))); } private static List> sortToName( - Set> classes) - { - List> list = new ArrayList>(classes); - Collections.sort(list, new Comparator>() { - public int compare(Class clazz1, Class clazz2) - { - return clazz1.getName().substring(clazz1.getName().lastIndexOf(".")+1).compareTo( - clazz2.getName().substring(clazz2.getName().lastIndexOf(".")+1)); - } - }); - + Set> classes) { + List> list = new ArrayList<>(classes); + Collections.sort(list, Comparator.comparing( + clazz -> clazz.getName().substring(clazz.getName().lastIndexOf(".") + 1))); return list; } @@ -1109,7 +1090,6 @@ private static List getOrdering(final Map map) { else return cnt2 - cnt1; }); - return list; } @@ -1119,14 +1099,12 @@ private static Collection filterToExactClass(Collection cnt, Object key) { - if (!cnt.containsKey(key)) + if (!cnt.containsKey(key)) { cnt.put(key, 0); + } cnt.put(key, cnt.get(key) + 1); } diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java index 830716985..e52b26a3c 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java @@ -112,7 +112,7 @@ enum Command { pattern("\n\t- BioPAX pattern search tool (opens a new dialog window)") {public void run(String[] argv){pattern(argv);} }, toSer(" \n" + - "\t- converts BioPAX data to serialized Model.java (bytes)") + "\t- converts BioPAX data to serialized Model (bytes); for very large models requires more stack size, JVM option: -Xss256g or more") {public void run(String[] argv) throws IOException { toSer(argv); } }, help("\n\t- prints this screen and exits\n") {public void run(String[] argv){ help();} }; diff --git a/paxtools-console/src/main/resources/logback.xml b/paxtools-console/src/main/resources/logback.xml index fc1a90553..b95abf829 100644 --- a/paxtools-console/src/main/resources/logback.xml +++ b/paxtools-console/src/main/resources/logback.xml @@ -16,12 +16,7 @@ - - - - - - + From fb3b304c76c0557d40a34f2310d2c49dc2744bb2 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Wed, 23 Nov 2022 21:59:56 -0500 Subject: [PATCH 05/20] Paxtools-6: added timing to the "fetch" command. --- .../src/main/java/org/biopax/paxtools/Commands.java | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java index ba10aacb2..95a7c9aa2 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java @@ -135,6 +135,7 @@ static void getNeighbors(String[] argv) throws IOException static void fetch(String[] argv) throws IOException { // set strings vars + long start = System.currentTimeMillis(); String in = argv[1]; String out = argv[2]; String[] uris = new String[]{}; //empty @@ -160,7 +161,8 @@ else if(param.startsWith("-absolute")) { SimpleIOHandler biopaxWriter = new SimpleIOHandler(model.getLevel()); biopaxWriter.absoluteUris(absoluteUris); biopaxWriter.convertToOWL(model, new FileOutputStream(out), uris); - log.info("Done."); + long stop = System.currentTimeMillis(); + log.info(String.format("Done (in %d sec)", TimeUnit.MILLISECONDS.toSeconds(stop-start))); } static void toLevel3(String[] argv) throws IOException { @@ -863,7 +865,7 @@ private static void summarizeChebiIds(Model model, PrintStream out) { } static void summarize(Model model, PrintStream out) throws IOException { - HashMap hm = new HashMap(); + HashMap hm = new HashMap<>(); final SimpleEditorMap em = SimpleEditorMap.get(model.getLevel()); for (Class clazz : sortToName(em.getKnownSubClassesOf(BioPAXElement.class))) @@ -983,7 +985,7 @@ else if (returnType.equals(Set.class) && int molLackingErAndId = 0; int naLackingErAndId = 0; //rem: na - nucleic acid //a map that contains the no. SPEs that have null entityReference by data source - Map numSpeLackErByProvider = new TreeMap(); + Map numSpeLackErByProvider = new TreeMap<>(); for(SimplePhysicalEntity spe : model.getObjects(SimplePhysicalEntity.class)) { if(spe.getEntityReference()==null) { speLackingEr++; @@ -996,7 +998,7 @@ else if (returnType.equals(Set.class) && numSpeLackErByProvider.put(providers, n); if(spe.getXref().isEmpty() || - new ClassFilterSet(spe.getXref(), PublicationXref.class) + new ClassFilterSet<>(spe.getXref(), PublicationXref.class) .size() == spe.getXref().size()) { speLackingErAndId++; From 9c234b58aaecfefdcb64acb18de160a915eddaba Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 4 Feb 2023 19:26:54 -0500 Subject: [PATCH 06/20] Paxtools-6: polishing --- .../biopax/paxtools/io/gsea/GMTConverter.java | 22 +++----- .../paxtools/io/gsea/GSEAConverter.java | 3 +- .../paxtools/io/gsea/GSEAConverterTest.java | 18 ++----- .../client/BiopaxValidatorClient.java | 4 +- .../paxtools/examples/SimpleIOExample.java | 5 -- .../paxtools/controller/ConversionScore.java | 2 - .../biopax/paxtools/controller/Visitor.java | 2 +- .../paxtools/impl/level3/ProvenanceImpl.java | 33 ++++-------- .../biopax/paxtools/io/SimpleIOHandler.java | 53 ++++--------------- .../biopax/paxtools/util/package-info.java | 2 - .../controller/EditorMapImplTest.java | 11 ++-- .../controller/SimpleEditorMapTest.java | 20 +++---- .../query/wrapperL3/package-info.java | 2 +- .../wrapperL3undirected/package-info.java | 2 +- 14 files changed, 44 insertions(+), 135 deletions(-) diff --git a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java index da5baa1f5..0254d7efe 100644 --- a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java +++ b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GMTConverter.java @@ -17,29 +17,23 @@ import java.util.*; /** - * An advanced BioPAX to GMT format converter, which can output IDs of - * both (or either) genetic elements and chemicals - * (the output file may be run with the GSEA software if gene/protein IDs are there used). + * An advanced BioPAX to GMT format converter, which can output IDs of genetic elements or chemicals + * (the output file can be loaded with the GSEA software if gene/protein IDs are used). * - * Each output entry (row) consists of three columns (tab separated): + * Each output entry (row) consists of three columns (tab separated): * name (URI), description, and the list of identifiers (of the same type). * For all ERs not associated with any pathway, "other" is used for name and uri. * - * The "idtype" is what specified by Constructor parameter 'idType'. - * - * The list may have one or more IDs of the same type per PR, + * The list may have one or more IDs of the same type per Protein Reference (PR), * e.g., UniProt IDs or HGNC Symbols; PRs not having an xref of * given db/id type are ignored. If there are less than three protein - * references per entry, it will not be printed. + * references per entry in total, it will not be printed. * * Note, this code assumes that the model has successfully been validated * and perhaps normalized (using the BioPAX Validator, Paxtools Normalizer). * A BioPAX L1 or L2 model is first converted to the L3. - * - * TODO: work in progress; add ER sub-class parameter/filter; consider using PE's xrefs as well... make public. */ -final class GMTConverter -{ +final class GMTConverter { private final static Logger LOG = LoggerFactory.getLogger(GMTConverter.class); private final IdFetcher idFetcher; @@ -187,11 +181,11 @@ protected void visit(Object range, BioPAXElement domain, Model model, PropertyEd if(!entries.isEmpty()) toReturn.addAll(entries); entityReferences.removeAll(ers);//keep not processed PRs (a PR can be processed multiple times) - LOG.debug("- collected " + entries.size() + "entries."); + LOG.debug("- collected " + entries.size() + " entries."); } } - //when there're no pathways, only empty pathays, pathways w/o PRs, then use all/rest of PRs - + //when there are no pathways, only empty, or pathways without any PRs, then use the rest of PRs - //organize PRs by species (GSEA s/w can handle only same species identifiers in a data row) if(!entityReferences.isEmpty() && !skipOutsidePathways) { LOG.info("Creating entries for the rest of PRs (outside any pathway)..."); diff --git a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java index 6423d0b99..d0ff9eb0f 100644 --- a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java +++ b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java @@ -221,7 +221,6 @@ public Collection convert(final Model model) LOG.debug("Begin converting " + currentPathwayName + " pathway, uri=" + currentPathway.getUri()); // collect sequence entity references from current pathway - //TODO: add Fetcher.evidenceFilter? Fetcher fetcher = new Fetcher(SimpleEditorMap.L3, Fetcher.nextStepFilter); fetcher.setSkipSubPathways(ignoreSubPathways); Set pathwaySers = fetcher.fetch(currentPathway, SequenceEntityReference.class); @@ -237,7 +236,7 @@ public Collection convert(final Model model) if(!entries.isEmpty()) toReturn.addAll(entries); sequenceEntityReferences.removeAll(pathwaySers);//keep not processed PRs (can be processed multiple times) - LOG.debug("- collected " + entries.size() + "entries."); + LOG.debug("- collected " + entries.size() + " entries."); } } diff --git a/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java b/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java index 6d921e4cd..e67e4b722 100644 --- a/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java +++ b/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java @@ -3,7 +3,6 @@ import org.biopax.paxtools.io.BioPAXIOHandler; import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.Model; -import org.junit.BeforeClass; import org.junit.Test; import java.io.*; @@ -17,18 +16,10 @@ public class GSEAConverterTest { static BioPAXIOHandler handler = new SimpleIOHandler(); - static PrintStream out; - - @BeforeClass - public static void setUp() throws IOException { - out = new PrintStream(new FileOutputStream( - GSEAConverterTest.class.getResource("/").getFile() + File.separator + "GSEAConverterTest.out.txt", false)); - } @Test public void testWriteL2GSEA() throws Exception { // write the output - out.println("testWriteL2GSEA:"); InputStream in = getClass().getResourceAsStream("/L2/biopax_id_557861_mTor_signaling.owl"); Model level2 = handler.convertFromOWL(in); GSEAConverter gseaConverter = new GSEAConverter("GENE_SYMBOL", true); @@ -45,7 +36,7 @@ public void testWriteL2GSEA() throws Exception { assertEquals("GENE_SYMBOL", entry.idType()); assertEquals(27, entry.identifiers().size()); // dump the output - (new GSEAConverter("GENE_SYMBOL", true)).writeToGSEA(level2, out); + (new GSEAConverter("GENE_SYMBOL", true)).writeToGSEA(level2, System.out); // NO more hacks that enabled using xref.id prefixes, like 'NP', 'GO', instead of true 'DB' names... gseaConverter = new GSEAConverter("NP", true); @@ -67,18 +58,15 @@ public void testWriteL2GSEA() throws Exception { assertEquals("9606", entry.taxID()); assertEquals("ref_seq", entry.idType()); assertEquals(33, entry.identifiers().size()); - (new GSEAConverter("NP", true)).writeToGSEA(level2, out); + (new GSEAConverter("NP", true)).writeToGSEA(level2, System.out); } @Test public void testWriteL3GSEA() throws Exception { - // write the output - out.println("testWriteL3GSEA:"); InputStream in = getClass().getResourceAsStream("/L3/biopax3-short-metabolic-pathway.owl"); Model level3 = handler.convertFromOWL(in); GSEAConverter gseaConverter = new GSEAConverter("uniprot", true); Collection entries = gseaConverter.convert(level3); - //TODO check anything? - (new GSEAConverter("uniprot", true)).writeToGSEA(level3, out); + (new GSEAConverter("uniprot", true)).writeToGSEA(level3, System.out); } } \ No newline at end of file diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java b/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java index 438f11634..530fc8989 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java @@ -149,7 +149,7 @@ public void validate(boolean autofix, String profile, RetFormat retFormat, Behav if(autofix) meb.addTextBody("autofix", "true"); -//TODO add extra options (normalizer.fixDisplayName, normalizer.inferPropertyOrganism, normalizer.inferPropertyDataSource, normalizer.xmlBase)? +//TODO: add options (normalizer.fixDisplayName, normalizer.inferPropertyOrganism, normalizer.inferPropertyDataSource, normalizer.xmlBase) if(profile != null && !profile.isEmpty()) meb.addTextBody("profile", profile); if(retFormat != null) @@ -170,7 +170,6 @@ else if(biopaxUrl != null) { //execute the query and get results as string HttpEntity httpEntity = meb.build(); -// httpEntity.writeTo(System.err); String content = Executor.newInstance()//Executor.newInstance(httpClient) .execute(Request.Post(url).body(httpEntity)) .returnContent().asString(); @@ -223,7 +222,6 @@ private String location(final String url) throws IOException { public String handleResponse(HttpResponse httpResponse) throws ClientProtocolException, IOException { Header header = httpResponse.getLastHeader("Location"); -// System.out.println("header=" + header); return (header != null) ? header.getValue().trim() : null; } }); diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/SimpleIOExample.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/SimpleIOExample.java index 8d2e1b3b7..03b98ebe7 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/SimpleIOExample.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/SimpleIOExample.java @@ -30,11 +30,6 @@ public static void main(String[] args) throws IOException { Model model = biopaxIO.convertFromOWL(new FileInputStream(args[0])); // write (as BioPAX OWL) output(model); - // TODO play with model... - /* - * if(model == null || model.getLevel() != BioPAXLevel.L3) { throw new - * IllegalArgumentException(" is not supported!"); } - */ // Well, let's do something with a (new) BioPAX model diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ConversionScore.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ConversionScore.java index 598f87233..23294c316 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ConversionScore.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ConversionScore.java @@ -8,8 +8,6 @@ /** * Encapsulation of scores of conversions, and related information - * - * @author rodche //TODO Annotate */ public class ConversionScore implements Comparable { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Visitor.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Visitor.java index 36669ed97..a94711d79 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Visitor.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Visitor.java @@ -23,5 +23,5 @@ public interface Visitor * @param model model on which the visiting operation will be done * @param editor editor */ - public void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor); //TODO looks, using of makes editor "read-only"... + void visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ProvenanceImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ProvenanceImpl.java index 47b408bfc..e232b21b1 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ProvenanceImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ProvenanceImpl.java @@ -21,42 +21,27 @@ public Class getModelInterface() return Provenance.class; } - /* - * (non-Javadoc) - * @see org.biopax.paxtools.impl.BioPAXElementImpl#toString() - * - * TODO this probably makes inconsistent strings (on different systems); fix, if it matters.... - * - */ - @Override public String toString() - { + @Override public String toString() { try { StringBuilder s = new StringBuilder(); - for (String name : new TreeSet(this.getName())) + for (String name : new TreeSet<>(this.getName())) { s.append(name).append(";"); + } - if (!getXref().isEmpty()) - { - TreeSet xrefs = new TreeSet(new Comparator() { - @Override - public int compare(Xref o1, Xref o2) { - return o1.toString().compareTo(o2.toString()); - } - }); - xrefs.addAll(getXref()); //this also removes duplicate equivalent xrefs (having same id/db) - + if (!getXref().isEmpty()) { + TreeSet xrefs = new TreeSet<>(Comparator.comparing(Xref::toString)); + xrefs.addAll(getXref()); //removes duplicate equivalent xrefs (same id and db) s.append(" ("); - for (Xref anXref : xrefs) + for (Xref anXref : xrefs) { s.append(anXref).append(";"); + } s.append(")"); } return s.toString(); - } catch (Exception e) { - // possible issues - when in a persistent context (e.g., lazy - // collections init...) + // possible in a persistent context (e.g., lazy collections init) log.warn("toString: ", e); return getUri(); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java b/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java index c7a9ee75d..da8f89a30 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java @@ -150,28 +150,21 @@ public String getXmlStreamInfo() @Override protected void init(InputStream in) { - try - { + try { XMLInputFactory xmlf = XMLInputFactory.newInstance(); //this is to return string with encoded chars as one event (not splitting) xmlf.setProperty("javax.xml.stream.isCoalescing", true); r = xmlf.createXMLStreamReader(in); - - triples = new LinkedList(); - - } - catch (XMLStreamException e) - { + triples = new LinkedList<>(); + } catch (XMLStreamException e) { //e.printStackTrace(); throw new BioPaxIOException(e.getClass().getSimpleName() + " " + e.getMessage() + "; " + e.getLocation()); } - } @Override protected void reset(InputStream in) { - - this.triples=null; + this.triples = null; try { r.close(); @@ -180,13 +173,13 @@ public String getXmlStreamInfo() { throw new RuntimeException("Can't close the stream"); } - r=null; + r = null; super.reset(in); } @Override protected Map readNameSpaces() { - Map ns = new HashMap(); + Map ns = new HashMap<>(); try { if (r.getEventType() == START_DOCUMENT) @@ -308,8 +301,10 @@ public String getXmlStreamInfo() throw new BioPaxIOException(e.getClass().getSimpleName() + " " + e.getMessage() + "; " + e.getLocation()); } - for (Triple triple : triples) + Iterator it = triples.iterator(); + while (it.hasNext()) { + Triple triple = it.next(); try { bindValue(triple, model); @@ -318,8 +313,8 @@ public String getXmlStreamInfo() { log.warn("Binding " + e); } + it.remove(); //save some RAM; O(1) } - } /** @@ -860,33 +855,5 @@ public boolean isMergeDuplicates() return this.mergeDuplicates; } - - /** - * Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string. - * - * @param model a BioPAX object model to convert to the RDF/XML format - * @return the BioPAX data in the RDF/XML format - * @throws IllegalArgumentException if model is null - * @throws OutOfMemoryError when it cannot be stored in a byte array (max 2Gb). - */ - public static String convertToOwl(Model model) - { - if (model == null) throw new IllegalArgumentException(); - - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - - (new SimpleIOHandler(model.getLevel())).convertToOWL(model, outputStream); - - try - { - return outputStream.toString("UTF-8"); - } - catch (UnsupportedEncodingException e) - { - log.error("convertToOwl, outputStream.toString failed", e); - return outputStream.toString(); - } - } - } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/package-info.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/package-info.java index 02cb3c5fb..44a24ea4d 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/package-info.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/package-info.java @@ -1,6 +1,4 @@ /** * This package contains various collections and utilities that is used by the other packages and modules of paxtools. -* -* TODO describe which classes are public API and which not (or are SPI, legacy, etc. made public for some good reason) */ package org.biopax.paxtools.util; diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java index f217ba91b..ccfebe25f 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java @@ -11,29 +11,24 @@ import static org.junit.Assert.assertNull; import static org.junit.Assert.assertTrue; -/** - */ public class EditorMapImplTest { @Test public void testGetKnownSubClassesOf() throws Exception { - Set> organism = SimpleEditorMap.L3.getSubclassEditorsForProperty( - "organism", BioPAXElement.class); + Set> organism = SimpleEditorMap.L3 + .getSubclassEditorsForProperty("organism", BioPAXElement.class); assertTrue(organism.size() == 3); } @Test - public void testSomePropertyRange() throws Exception - { + public void testSomePropertyRange() { PropertyEditor entityReferencePropEditor = SimpleEditorMap.L3.getEditorForProperty("entityReference", Protein.class); assertEquals(EntityReference.class, entityReferencePropEditor.getRange()); //TODO: entityReferencePropEditor.getRange() should probably be specific sub-class, ProteinReference here, taking OWL restrictions into account... - entityReferencePropEditor = SimpleEditorMap.L3.getEditorForProperty("entityReference", Gene.class); assertNull(entityReferencePropEditor); } - } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java index ca8761785..b2fcf30fc 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java @@ -38,7 +38,6 @@ public void testSimpleEditorMap() throws Exception * Currently (before 10-Apr-2011), it seems impossible * to clear a single-cardinality property by * using the corresponding property editor - * TODO Is this what we really want? (i.e., cannot set to 'unknown'/null) */ @Test public void testClearSingularProperty() { @@ -49,21 +48,15 @@ public void testClearSingularProperty() { ProteinReference pr = fac.create(ProteinReference.class, "PR"); BioSource bs = fac.create(BioSource.class, "BS"); PropertyEditor editor = em.getEditorForProperty("organism", ProteinReference.class); + pr.setOrganism(bs); - - pr.setOrganism(null); - assertNull(pr.getOrganism()); - - pr.setOrganism(bs); - editor.removeValueFromBean(bs, pr); assertNull(pr.getOrganism()); - + + pr.setOrganism(bs); editor.setValueToBean(null, pr); - /* - assertNotNull(pr.getOrganism()); // no effect! Is this the behavior we want? - */ - // after re-factoring (AbstractPropertyEditor) + + // ok, after fixing/re-factoring (AbstractPropertyEditor) assertNull(pr.getOrganism()); assertTrue(editor.isUnknown(pr.getOrganism())); @@ -78,8 +71,7 @@ public void testClearSingularProperty() { assertFalse(editor.isUnknown(dg.getPh())); editor.setValueToBean(null, dg); - //assertFalse(editor.isUnknown(dg.getPh())); // no effect: cannot go back to 'unknown' by using null! - assertTrue(editor.isUnknown(dg.getPh())); // after re-factoring + assertTrue(editor.isUnknown(dg.getPh())); // fixed after re-factoring editor.setValueToBean(BioPAXElement.UNKNOWN_FLOAT, dg); assertTrue(editor.isUnknown(dg.getPh())); diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/package-info.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/package-info.java index 1e43ff501..e490bc9f1 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/package-info.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/package-info.java @@ -1,4 +1,4 @@ /** -* This package contains TODO annotate! +* */ package org.biopax.paxtools.query.wrapperL3; \ No newline at end of file diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/package-info.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/package-info.java index 1970d82d3..8fa171b35 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/package-info.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/package-info.java @@ -1,4 +1,4 @@ /** -* This package contains TODO annotate! +* */ package org.biopax.paxtools.query.wrapperL3undirected; \ No newline at end of file From 349b6dd13454d12c19f40de25e0b1d5a215e3223 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 11 Jun 2023 21:43:29 -0400 Subject: [PATCH 07/20] Paxtools-6: lots of changes - - migrated from Miriam to Bioregistry.io ID resolver; - updated Normalizer, tests accordignly; - removed the paxtools-search module (not universal, hard to maintain); - refactored core BiopaxSafeSet, BiopaxElements; - some bug fixes, reverts (from rev 4ead66ddc557b42f673b43cb8dab6355555f7ee4) such as - - backed to use Set instead Collection interface in Model; - fixed/reverted memory waste bug in ModelImpl - returned UnmodifiableImplicitSet, exposedObjectSet; - removed toSer CLI command, ModelUtils serialize/deserialize methods (it's slower than r/w RDF/XML; also requires huge stack); - Normalizer now makes bioregistry.io URI or CURIE or shorter than before URIs when unable to match id type; --- .../paxtools/io/gsea/GSEAConverter.java | 19 +- json-converter/pom.xml | 2 - .../io/jsonld/JsonldBiopaxConverterTest.java | 2 - normalizer/pom.xml | 43 +- .../paxtools/normalizer/MiriamLink.java | 591 - .../biopax/paxtools/normalizer/Namespace.java | 68 + .../paxtools/normalizer/Normalizer.java | 541 +- .../paxtools/normalizer/NormalizerMap.java | 93 + .../biopax/paxtools/normalizer/Resolver.java | 236 + normalizer/src/main/resources/Miriam.xml | 24209 ------- normalizer/src/main/resources/Miriam.xsd | 268 - .../org/biopax/paxtools/normalizer/readme.md | 14 + .../biopax/paxtools/normalizer/registry.json | 53017 ++++++++++++++++ .../biopax/paxtools/normalizer/spellmap.json | 63 + .../biopax/paxtools/normalizer/synonymap.json | 43 + normalizer/src/main/resources/registry.json | 40048 ------------ .../paxtools/normalizer/MiriamLinkTest.java | 186 - .../paxtools/normalizer/NormalizerTest.java | 380 +- .../paxtools/normalizer/ResolverTest.java | 50 + .../pattern/miner/CommonIDFetcher.java | 9 +- .../pattern/miner/ConfigurableIDFetcher.java | 16 +- .../pattern/miner/ExtendedSIFWriter.java | 2 +- .../paxtools/pattern/miner/SIFToText.java | 2 +- .../biopax/paxtools/pattern/TempTests.java | 2 +- .../pattern/miner/SIFSearcherTest.java | 2 +- .../java/org/biopax/paxtools/Commands.java | 53 +- .../main/java/org/biopax/paxtools/Main.java | 174 +- .../biopax/paxtools/controller/IdFetcher.java | 16 +- .../paxtools/controller/ModelUtils.java | 59 +- .../paxtools/impl/BioPAXElementImpl.java | 10 +- .../org/biopax/paxtools/impl/MockFactory.java | 3 +- .../org/biopax/paxtools/impl/ModelImpl.java | 71 +- .../paxtools/impl/level3/ScoreImpl.java | 81 +- .../impl/level3/SimplePhysicalEntityImpl.java | 5 +- .../paxtools/impl/level3/TransportImpl.java | 2 +- .../biopax/paxtools/impl/level3/XrefImpl.java | 197 +- .../biopax/paxtools/io/SimpleIOHandler.java | 31 +- .../biopax/paxtools/model/BioPAXFactory.java | 6 - .../java/org/biopax/paxtools/model/Model.java | 24 +- .../paxtools/model/level3/BioSource.java | 2 +- .../paxtools/util/AbstractFilterSet.java | 1 - .../biopax/paxtools/util/BPCollections.java | 116 +- .../biopax/paxtools/util/BiopaxElements.java | 98 + .../paxtools/util/BiopaxSafeCollection.java | 74 - .../biopax/paxtools/util/BiopaxSafeSet.java | 92 +- .../paxtools/util/EquivalenceGrouper.java | 9 +- .../paxtools/util/SetEquivalenceChecker.java | 19 +- .../paxtools/controller/ModelUtilsTest.java | 27 +- .../paxtools/controller/SimpleMergerTest.java | 634 +- .../paxtools/impl/level3/EqualsEtcTest.java | 54 +- .../impl/level3/EquivalenceImplTest.java | 6 +- .../impl/level3/ModelCoverageTest.java | 8 +- .../paxtools/io/SimpleIOHandlerTest.java | 185 +- .../paxtools/model/BioPAXFactoryTest.java | 8 +- paxtools-search/pom.xml | 74 - .../org/biopax/paxtools/search/Indexer.java | 5 - .../biopax/paxtools/search/SearchEngine.java | 766 - .../biopax/paxtools/search/SearchResult.java | 58 - .../org/biopax/paxtools/search/Searcher.java | 20 - .../biopax/paxtools/search/package-info.java | 8 - .../paxtools/search/SearchEngineTest.java | 191 - .../src/test/resources/logback-test.xml | 25 - .../src/test/resources/pathwaydata1.owl | 504 - .../test/resources/three-bmp-pathways.owl.gz | Bin 386188 -> 0 bytes pom.xml | 21 +- .../paxtools/converter/psi/EntryMapper.java | 122 +- .../paxtools/converter/psi/TestMapping.java | 194 +- .../io/sbgn/idmapping/EntrezGene.java | 4 +- 68 files changed, 55185 insertions(+), 68778 deletions(-) delete mode 100644 normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java create mode 100644 normalizer/src/main/java/org/biopax/paxtools/normalizer/Namespace.java create mode 100644 normalizer/src/main/java/org/biopax/paxtools/normalizer/NormalizerMap.java create mode 100644 normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java delete mode 100644 normalizer/src/main/resources/Miriam.xml delete mode 100644 normalizer/src/main/resources/Miriam.xsd create mode 100644 normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md create mode 100644 normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json create mode 100644 normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json create mode 100644 normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json delete mode 100644 normalizer/src/main/resources/registry.json delete mode 100644 normalizer/src/test/java/org/biopax/paxtools/normalizer/MiriamLinkTest.java create mode 100644 normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java create mode 100644 paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxElements.java delete mode 100644 paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java delete mode 100644 paxtools-search/src/main/java/org/biopax/paxtools/search/Indexer.java delete mode 100644 paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java delete mode 100644 paxtools-search/src/main/java/org/biopax/paxtools/search/SearchResult.java delete mode 100644 paxtools-search/src/main/java/org/biopax/paxtools/search/Searcher.java delete mode 100644 paxtools-search/src/main/java/org/biopax/paxtools/search/package-info.java delete mode 100644 paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java delete mode 100644 paxtools-search/src/test/resources/logback-test.xml delete mode 100644 paxtools-search/src/test/resources/pathwaydata1.owl delete mode 100644 paxtools-search/src/test/resources/three-bmp-pathways.owl.gz diff --git a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java index d0ff9eb0f..b9acef19f 100644 --- a/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java +++ b/gsea-converter/src/main/java/org/biopax/paxtools/io/gsea/GSEAConverter.java @@ -66,11 +66,10 @@ public GSEAConverter() * Constructor. * * See class declaration for more information. - * @param idType - identifier type, name of the resource, either the string value + * @param idType - identifier type, name, prefix of the resource, either the string value * of the most of EntityReference's xref.db properties in the BioPAX data, - * e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase", - * or the <namespace> part in normalized EntityReference URIs - * http://identifiers.org/<namespace>/<ID> + * e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt", + * or the namespace prefix part in normalized EntityReference URIs, such as in identifiers.org/chebi:ID * (it depends on the actual data; so double-check before using in this constructor). * @param crossSpeciesCheckEnabled - if true, enforces no cross species participants in output */ @@ -85,9 +84,8 @@ public GSEAConverter(String idType, boolean crossSpeciesCheckEnabled) * See class declaration for more information. * @param idType - identifier type, name of the resource, either the string value * of the most of EntityReference's xref.db properties in the BioPAX data, - * e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase", - * or the <namespace> part in normalized EntityReference URIs - * http://identifiers.org/<namespace>/<ID> + * e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt", + * or the namespace/prefix part in normalized EntityReference URIs * (it depends on the actual data; so double-check before using in this constructor). * @param crossSpeciesCheckEnabled - if true, enforces no cross species participants in output * @param skipSubPathways - if true, do not traverse into any sub-pathways to collect entity references @@ -107,9 +105,8 @@ public GSEAConverter(String idType, boolean crossSpeciesCheckEnabled, boolean sk * See class declaration for more information. * @param idType - identifier type, name of the resource, either the string value * of the most of EntityReference's xref.db properties in the BioPAX data, - * e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt" or "UniProt knowledgebase", - * or the <namespace> part in normalized EntityReference URIs - * http://identifiers.org/<namespace>/<ID>, such as 'hgnc.symbol', 'uniprot' + * e.g., "HGNC Symbol", "NCBI Gene", "RefSeq", "UniProt", + * or the namespace/prefix part in normalized EntityReference URIs, e.g., 'hgnc.symbol', 'uniprot' * (it depends on the actual data; so double-check before using in this constructor). * @param crossSpeciesCheckEnabled - if true, enforces no cross species participants in output * @param skipSubPathwaysOf - do not look inside sub-pathways of pathways of given data sources to collect entity references @@ -333,7 +330,7 @@ void processEntityReferences(Collection sers, GMTEntry // a shortcut if we are converting validated normalized BioPAX model: // get the primary ID from the URI of the ProteinReference final String uri = ser.getUri(); - if (uri.startsWith("http://identifiers.org/") && uri.contains(db)) + if (uri.contains("identifiers.org/") && uri.contains(db)) { String accession = ser.getUri(); accession = accession.substring(accession.lastIndexOf("/") + 1); diff --git a/json-converter/pom.xml b/json-converter/pom.xml index e329100ef..882767328 100644 --- a/json-converter/pom.xml +++ b/json-converter/pom.xml @@ -42,8 +42,6 @@ org.apache.jena apache-jena-libs pom - - 3.2.0 diff --git a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java index 55ed9ac17..8b118211d 100644 --- a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java +++ b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java @@ -1,7 +1,5 @@ package org.biopax.paxtools.io.jsonld; -import static org.junit.Assert.*; - import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; diff --git a/normalizer/pom.xml b/normalizer/pom.xml index 523e85b7f..d674bcdf5 100644 --- a/normalizer/pom.xml +++ b/normalizer/pom.xml @@ -3,8 +3,8 @@ 4.0.0 normalizer - BioPAX Normalizer and MiriamLink - A BioPAX Normalizer and modified off-line MiriamLink (MIRIAM, EBI, OLS) + BioPAX Normalizer and Resolver + A BioPAX Normalizer and Bio ID Resolver 2009-2015 paxtools @@ -14,43 +14,20 @@ https://biopax.github.io/Paxtools - - - - org.codehaus.mojo - jaxb2-maven-plugin - 1.6 - - - generate-sources - - xjc - - - - - false - net.biomodels.miriam - true - ${basedir}/src/main/resources - - - - com.sun.activation - javax.activation - 1.2.0 - - - - - - ${project.groupId} paxtools-core ${project.version} + + com.fasterxml.jackson.core + jackson-databind + + + org.projectlombok + lombok + diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java deleted file mode 100644 index 0362d17ab..000000000 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/MiriamLink.java +++ /dev/null @@ -1,591 +0,0 @@ -package org.biopax.paxtools.normalizer; - -import java.io.InputStream; -import java.io.UnsupportedEncodingException; -import java.net.*; -import java.util.*; -import java.util.regex.Pattern; - - -import javax.xml.bind.JAXBContext; -import javax.xml.bind.JAXBException; -import javax.xml.bind.Unmarshaller; - -import net.biomodels.miriam.*; -import net.biomodels.miriam.Miriam.Datatype; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - - -/** - * Singleton local MIRIAM data resolver with all methods static. - * - * todo: refactor to load/use the JSON data instead of XML,XSD (see: identifiers.org, https://registry.api.identifiers.org/resolutionApi/getResolverDataset) - * todo: use Compressed URIs, e.g. uniprot:P12345 instead of URLs like http://identifiers.org/uniprot:P12345 - * - * @author rodche - */ -public class MiriamLink -{ - private static final Logger log = LoggerFactory.getLogger(MiriamLink.class); - private static final String[] ARRAY_OF_STRINGS = {}; // a template to convert a Collection to String[] - - //default web service URL to get the Miriam.xml db content (todo: obsolete) - //see also: http://www.ebi.ac.uk/miriam/main/export/ - //XML: "https://www.ebi.ac.uk/miriam/main/export/xml/"; - //Schema: "http://www.ebi.ac.uk/miriam/static/main/xml/MiriamXML.xsd"; - /** package name for jaxb to use */ - public static final String BINDING = "net.biomodels.miriam"; - - /** object of the generated from the Miriam schema type */ - private static final Miriam miriam; - - - private static final Map datatypesHash = new HashMap(); - - public static boolean useObsoleteDatatypes = true; - public static boolean useObsoleteResources = true; - - /** - * Default constructor: initialization of some parameters - * */ - protected MiriamLink() { - } - - /** - * Initialization - */ - static - { - try - { - JAXBContext jc = JAXBContext.newInstance(BINDING); - Unmarshaller unmarshaller = jc.createUnmarshaller(); - Miriam mir = null; - InputStream is = MiriamLink.class.getResourceAsStream("/Miriam.xml"); - if(is != null) { - mir = (Miriam) unmarshaller.unmarshal(is); - } else { - throw new RuntimeException("Miriam.xml db is missing or broken. " + - "Please download the XML and schema from http://www.ebi.ac.uk/miriam/main/export/ " + - "and put at the classpath's root"); - } - miriam = mir; - log.info("MIRIAM XML imported, version: " + miriam.getDataVersion() + ", datatypes: " - + miriam.getDatatype().size()); - } - catch (JAXBException e) { - throw new RuntimeException(e); - } - - // build the name-datatype static hash (once!) - for(Datatype dt : miriam.getDatatype()) { - // index by name - datatypesHash.put(dt.getName().toUpperCase(), dt); - - // by identifier - datatypesHash.put(dt.getId().toUpperCase(), dt); - - // index by each synonym - // (Miriam must guarantee: different datatypes cannot have the same synonym!) - Synonyms synonyms = dt.getSynonyms(); - if (synonyms != null) { - for (String syn : synonyms.getSynonym()) { - datatypesHash.put(syn.toUpperCase(), dt); - } - } - - // index by each URI - for(Uris uris : dt.getUris()) { - for(Uri uri : uris.getUri()) { - datatypesHash.put(uri.getValue(), dt); - } - } - } - } - - - /** - * Retrieves the current version of MIRIAM Web Services. - * - * @return Current version of the Web Services - */ - public static String getServicesVersion() - { - return miriam.getDate().toString() - + "; " + miriam.getDataVersion().toString(); - } - - - /** - * Retrieves the unique (official) URI of a data type (example: "urn:miriam:uniprot"). - * - * @param datatypeKey - ID, name, synonym, or (incl. deprecated) URI (URN or URL) of a data type (examples: "UniProt") - * @return unique URI of the data type - * - * @throws IllegalArgumentException when datatype not found - */ - public static String getDataTypeURI(String datatypeKey) - { - Datatype datatype = getDatatype(datatypeKey); - return getOfficialDataTypeURI(datatype); - } - - - /** - * Retrieves all the URIs of a data type, including all the deprecated ones - * (examples: "urn:miriam:uniprot", "http://www.uniprot.org/", "urn:lsid:uniprot.org:uniprot", ...). - * - * @param datatypeKey name (or synonym), ID, or URI (URN or URL) of the data type (examples: "ChEBI", "UniProt") - * @return all the URIs of a data type (including the deprecated ones) - * - * @throws IllegalArgumentException when datatype not found - */ - public static String[] getDataTypeURIs(String datatypeKey) - { - Set alluris = new HashSet<>(); - Datatype datatype = getDatatype(datatypeKey); - for(Uris uris : datatype.getUris()) { - for(Uri uri : uris.getUri()) { - alluris.add(uri.getValue()); - } - } - return alluris.toArray(ARRAY_OF_STRINGS); - } - - - /** - * Retrieves the location (or country) of a resource (example: "United Kingdom"). - * - * @param resourceId identifier of a resource (example: "MIR:00100009") - * @return the location (the country) where the resource is managed - */ - public static String getResourceLocation(String resourceId) - { - Resource resource = getResource(resourceId); - return resource.getDataLocation(); - } - - - /** - * Retrieves the institution which manages a resource (example: "European Bioinformatics Institute"). - * - * @param resourceId identifier of a resource (example: "MIR:00100009") - * @return the institution managing the resource - */ - public static String getResourceInstitution(String resourceId) - { - Resource resource = getResource(resourceId); - return resource.getDataInstitution(); - } - - - /** - * Retrieves the unique MIRIAM URI of a specific entity (example: "urn:miriam:obo.go:GO%3A0045202"). - * - * @param name - name, URI/URL, or ID of a data type (examples: "ChEBI", "MIR:00000005") - * @param id identifier of an entity within the data type (examples: "GO:0045202", "P62158") - * @return unique standard MIRIAM URI of a given entity - * - * @throws IllegalArgumentException when datatype not found - */ - public static String getURI(String name, String id) - { - Datatype datatype = getDatatype(name); - String db = datatype.getName(); - if(checkRegExp(id, db)) { - try { - return getOfficialDataTypeURI(datatype) + ":" + URLEncoder.encode(id, "UTF-8"); - } catch (UnsupportedEncodingException e) { - throw new RuntimeException("UTF-8 encoding error of id=" + id, e); - } - } else - throw new IllegalArgumentException( - "ID pattern mismatch. db=" + db + ", id=" + id - + ", regexp: " + datatype.getPattern()); - } - - - /** - * Retrieves the definition of a data type. - * - * @param datatypeKey - ID, name or URI (URN or URL) of a data type - * @return definition of the data type - * - * @throws IllegalArgumentException when datatype not found - */ - public static String getDataTypeDef(String datatypeKey) - { - Datatype datatype = getDatatype(datatypeKey); - return datatype.getDefinition(); - } - - - /** - * Retrieves the physical locationS (URLs) of web pageS providing knowledge about an entity. - * - * @param datatypeKey name (can be a synonym), ID, or URI of a data type (examples: "Gene Ontology", "UniProt") - * @param entityId identifier of an entity within the given data type (examples: "GO:0045202", "P62158") - * @return physical locationS (URL templates) of web pageS providing knowledge about the given entity - * - * @throws IllegalArgumentException when datatype not found - */ - public static String[] getLocations(String datatypeKey, String entityId) - { - Set locations = new HashSet<>(); - Datatype datatype = getDatatype(datatypeKey); - for (Resource resource : getResources(datatype)) { - String link = resource.getDataEntry(); - try { - link = link.replaceFirst("\\$id", URLEncoder.encode(entityId, "UTF-8")); - } catch (UnsupportedEncodingException e) { - throw new RuntimeException(e); - } - locations.add(link); - } - return locations.toArray(ARRAY_OF_STRINGS); - } - - - /** - * Retrieves home page URLs of a datatype. - * - * @param datatypeKey - name (can be a synonym), ID, or URI (URL or URN) of a data type - * @return array of strings containing all the address of the main page of the resources of the data type - * - * @throws IllegalArgumentException when datatype not found - */ - public static String[] getDataResources(String datatypeKey) - { - Set locations = new HashSet<>(); - Datatype datatype = getDatatype(datatypeKey); - for (Resource resource : getResources(datatype)) { - String link = resource.getDataResource(); - locations.add(link); - } - return locations.toArray(ARRAY_OF_STRINGS); - } - - - /** - * To know if a URI of a data type is deprecated. - * - * @param uri (URN or URL) of a data type - * @return answer ("true" or "false") to the question: is this URI deprecated? - */ - public static boolean isDeprecated(String uri) - { - Datatype datatype = datatypesHash.get(uri); - String urn = getOfficialDataTypeURI(datatype); - return !uri.equalsIgnoreCase(urn); - } - - - /** - * Retrieves the pattern (regular expression) used by the identifiers within a data type. - * - * @param datatypeKey data type ID, name (or synonym), or URI (URL or URN) - * @return pattern of the data type - * - * @throws IllegalArgumentException when datatype not found - */ - public static String getDataTypePattern(String datatypeKey) - { - Datatype datatype = getDatatype(datatypeKey); - return datatype.getPattern(); - } - - - /** - * Retrieves the preferred name of a data type. - * - * @param datatypeKey URI (URL or URN), ID, or nickname of a data type - * @return the common name of the data type - * - * @throws IllegalArgumentException when not found - */ - public static String getName(String datatypeKey) - { - Datatype datatype = getDatatype(datatypeKey); - return datatype.getName(); - } - - - /** - * Retrieves all the synonyms (incl. the preferred name) of a data type. - * - * @param datatypeKey ID, any name, or URI (URL or URN) of a data type - * @return all the data type's synonyms (incl. preferred name) - */ - public static String[] getNames(String datatypeKey) - { - Set names = new HashSet<>(); - Datatype datatype = getDatatype(datatypeKey); - names.add(datatype.getName()); - Synonyms synonyms = datatype.getSynonyms(); - if(synonyms != null) - for(String name : synonyms.getSynonym()) { - names.add(name); - } - return names.toArray(ARRAY_OF_STRINGS); - } - - - /** - * Retrieves the list of preferred names of all the data types available. - * - * @return list of names of all the data types - */ - public static String[] getDataTypesName() - { - Set dataTypeNames = new HashSet<>(); - for(Datatype datatype : miriam.getDatatype()) { - dataTypeNames.add(datatype.getName()); - } - return dataTypeNames.toArray(ARRAY_OF_STRINGS); - } - - - /** - * Retrieves the internal identifier (stable and perennial) of - * all the data types (for example: "MIR:00000005"). - * - * @return list of the identifier of all the data types - */ - public static String[] getDataTypesId() - { - Set dataTypeIds = new HashSet<>(); - for(Datatype datatype : miriam.getDatatype()) { - dataTypeIds.add(datatype.getId()); - } - return dataTypeIds.toArray(new String[] {}); - } - - - /** - * Retrieves the official URI (it will always be URN) of - * a data type corresponding to the deprecated one. - * - * @param uri deprecated URI (URN or URL) of a data type - * @return the official URI of a data type corresponding to the deprecated one - * @deprecated use getDataTypeURI instead - */ - public static String getOfficialDataTypeURI(String uri) - { - return getDataTypeURI(uri); - } - - - /** - * Checks if the identifier given follows the regular expression - * of its data type (also provided). - * - * @param identifier internal identifier used by the data type - * @param datatype name, synonym or URI of a data type - * @return "true" if the identifier follows the regular expression, "false" otherwise - * - * @throws IllegalArgumentException when datatype not found - */ - public static boolean checkRegExp(String identifier, String datatype) - { - Datatype dt = getDatatype(datatype); - return Pattern.compile(dt.getPattern()).matcher(identifier).find(); - } - - - /** - * Retrieves the unique (official) URI of a data type - * (example: "http://identifiers.org/uniprot"). - * - * @param datatype net.biomodels.miriam.Miriam.Datatype - * @return URI - */ - public static String getOfficialDataTypeURI(Datatype datatype) { - for(Uris uris : datatype.getUris()) { - for(Uri uri : uris.getUri()) { - if(!isDeprecated(uri) && uri.getType() == UriType.URN) { - return uri.getValue(); - } - } - } - - return null; - } - - - private static boolean isDeprecated(Uri uri) { - if(uri.isDeprecated()!=null && uri.isDeprecated()) { - return true; - } else { - return false; - } - } - - - /** - * Gets Miriam Datatype by its ID, Name, Synonym, or URI (URN/URL) - * - * @param datatypeKey - a datatype ID, name, synonym, or URI - * @return MIRIAM Datatype bean - * - * @throws IllegalArgumentException when not found - */ - public static Datatype getDatatype(String datatypeKey) - { - Datatype dt = null; - if(containsIdOrName(datatypeKey)) - dt = datatypesHash.get(datatypeKey.toUpperCase()); - else if(containsUri(datatypeKey)) - dt = datatypesHash.get(datatypeKey); - else - throw new IllegalArgumentException("Datatype not found : " + datatypeKey); - - if(!useObsoleteDatatypes - && dt.isObsolete() != null - && dt.isObsolete().booleanValue() == true) - throw new IllegalArgumentException("Datatype " + - datatypeKey + "(" + dt.getName() + ") is obsolete" + - " (and useObsoleteDatatypes=false)"); - - // return - return dt; - } - - - /** - * Retrieves the internal identifier (stable and perennial) of - * all the resources (for example: "MIR:00100008" (bind) ). - * - * @return list of the identifiers of all data types - */ - public static String[] getResourcesId() - { - Set ids = new HashSet<>(); - for(Datatype datatype : miriam.getDatatype()) { - for (Resource resource : getResources(datatype)) { - ids.add(resource.getId()); - } - } - return ids.toArray(new String[] {}); - } - - - /** - * Retrieves the resource by id (for example: "MIR:00100008" (bind) ). - * - * @param resourceId - resource identifier (similar to, but not a data type identifier!) - * @return MIRIAM Resource bean - */ - public static Resource getResource(String resourceId) - { - for(Datatype datatype : miriam.getDatatype()) { - for (Resource resource : getResources(datatype)) { - if (resource.getId().equalsIgnoreCase(resourceId)) - return resource; - } - } - - throw new IllegalArgumentException("Resource not found : " + resourceId); - } - - - /** - * Check whether Miriam contains a data type record with this - * name (any synonym) or identifier (case insensitive) - * - * @param searchKey - ID, name, or synonym (case insensitive) - * @return true/false - */ - public static boolean containsIdOrName(String searchKey) { - return datatypesHash.keySet().contains(searchKey.toUpperCase()); - } - - - /** - * Check whether Miriam contains a data type record with this URI - * (case sensitive) - * - * @param searchUri - URI (case sensitive) - * @return true/false - */ - public static boolean containsUri(String searchUri) { - return datatypesHash.keySet().contains(searchUri); - } - - - /** - * Gets the list of Miriam {@link Resource} from - * the datatype, also taking the 'obsolete' flag/state - * into account. - * - * @param datatype a MIRIAM Datatype - * @return the list of MIRIAM Resources in that datatype - */ - private static List getResources(Datatype datatype) { - List toReturn = new ArrayList<>(); - - Resources resources = datatype.getResources(); - if (resources != null) { - for (Resource resource : resources.getResource()) { - if(useObsoleteResources // ok to collect (- do not care about obsolete) - || resource.isObsolete() == null // undefined - here means non-obsolete (ok) - || !resource.isObsolete().booleanValue()) { - toReturn.add(resource); - } - } - } - - return toReturn; - } - - - /** - * Converts a MIRIAM URN into its equivalent Identifiers.org URL. - * - * @see #getURI(String, String) - use this to get the URN - * @see #getIdentifiersOrgURI(String, String) - prefered URI - * - * @param urn - an existing Miriam URN, e.g., "urn:miriam:obo.go:GO%3A0045202" - * @return the Identifiers.org URL corresponding to the data URN, e.g., "http://identifiers.org/obo.go/GO:0045202" - * - * @deprecated this method applies {@link URLDecoder#decode(String)} to the last part of the URN, which may not always work as expected (test yours!) - */ - public static String convertUrn(String urn) { - String[] tokens = urn.split(":"); - return "http://identifiers.org/" + tokens[tokens.length-2] - + "/" + URLDecoder.decode(tokens[tokens.length-1]); - } - - - /** - * Gets the Identifiers.org URI/URL of the entity (example: "http://identifiers.org/obo.go/GO:0045202"). - * - * @param name - name, URI/URL, or ID of a data type (examples: "ChEBI", "MIR:00000005") - * @param id identifier of an entity within the data type (examples: "GO:0045202", "P62158") - * @return Identifiers.org URL for the id - * - * @throws IllegalArgumentException when datatype not found - */ - public static String getIdentifiersOrgURI(String name, String id) - { - String url = null; - Datatype datatype = getDatatype(name); - String db = datatype.getName(); - if(checkRegExp(id, db)) { - uris: - for(Uris uris : datatype.getUris()) { - for(Uri uri : uris.getUri()) { - if(uri.getValue().startsWith("http://identifiers.org/")) { - url = uri.getValue() + id; - break uris; - } - } - } - } else - throw new IllegalArgumentException( - "ID pattern mismatch. db=" + db + ", id=" + id - + ", regexp: " + datatype.getPattern()); - - return url; - } -} diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Namespace.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Namespace.java new file mode 100644 index 000000000..8017d9166 --- /dev/null +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Namespace.java @@ -0,0 +1,68 @@ +package org.biopax.paxtools.normalizer; + +import lombok.Data; +import lombok.NoArgsConstructor; +import org.apache.commons.lang3.StringUtils; + +import java.util.Collections; +import java.util.HashSet; +import java.util.Set; + +@Data +@NoArgsConstructor +public class Namespace { + String prefix; // The prefix for this resource + + /* + A generalization of the concept of the "namespace embedded in local unique identifier". + Many OBO foundry ontologies use the redundant uppercase name of the ontology in the local identifier, + such as the GO, which makes the prefixes have a redundant usage as in ``GO:GO:1234567``. + The `banana` tag explicitly annotates the part in the local identifier that should be stripped, if found. + */ + String banana; + + String banana_peel; // Delimiter used in banana, e.g. "_" or ":" + +// String preferred_prefix; //preferred spelling/capitalization of the prefix + + String name; // The name of the resource, preferred name + + Set synonyms = Collections.emptySet(); //all the names, prefixes and "synonyms" from this entry and each node listed in the "mappings" + + String pattern; // ID regex (excl. banana+peel...) + + String description; + + boolean deprecated; + + /** + * A flag denoting if the namespace is embedded in the LUI (if this is true, and it is not accompanied by a banana, + * assume that the banana is the prefix in all caps plus a colon, as is standard in OBO). + * Here is an example, remark from bioregistry.io/registry/chebi: MIRIAM Namespace Embedded in LUI + * The legacy MIRIAM standard for generating CURIEs with this resource annotates the namespaceEmbeddedInLUI as true. + * This means that you may see local unique identifiers that include a redundant prefix and delimiter + * (also known as a banana) and therefore look like a CURIE. For Chemical Entities of Biological Interest, + * the banana looks like CHEBI:. Therefore, you may see local unique identifiers (LUI) for this resource that look + * like CHEBI:24867 (instead of the canonical form 24867) and CURIEs for this resource that look + * like chebi:CHEBI:24867 (instead of the canonical form chebi:24867). + */ + boolean namespace_in_lui; + + /** + * @return + * @see #namespace_in_lui + */ + public String getBanana() { + return (namespace_in_lui && StringUtils.isEmpty(banana)) ? StringUtils.upperCase(prefix) : banana; + } + + public String getBanana_peel() { + if (StringUtils.isNotEmpty(getBanana())) { + // assume ":" when banana_peel is empty/null + return StringUtils.isNotEmpty(banana_peel) ? banana_peel : ":"; + } else { + return ""; //empty banana - empty peel + } + } + +} diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index 1e3af3e74..71dc29c0c 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -2,14 +2,12 @@ import org.apache.commons.lang3.StringUtils; import org.biopax.paxtools.controller.ModelUtils; -import org.biopax.paxtools.controller.ShallowCopy; import org.biopax.paxtools.converter.LevelUpgrader; import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.biopax.paxtools.util.BPCollections; import org.biopax.paxtools.util.ClassFilterSet; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -17,7 +15,6 @@ import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.InputStream; -import java.io.UnsupportedEncodingException; import java.util.*; /** @@ -35,10 +32,77 @@ public final class Normalizer { private String xmlBase; // Normalizer will generate URIs using a strategy specified by the system property - // (the default is biopax.normalizer.uri.strategy=md5, to generate 32-byte digest hex string for xrefs's uris) + // (the default is biopax.normalizer.uri.strategy=md5 to generate 32-byte digest hex string) public static final String PROPERTY_NORMALIZER_URI_STRATEGY = "biopax.normalizer.uri.strategy"; public static final String VALUE_NORMALIZER_URI_STRATEGY_SIMPLE = "simple"; public static final String VALUE_NORMALIZER_URI_STRATEGY_MD5 = "md5"; //default strategy + + //short "codes" to use e.g. in a generated URI for some of instantiable BioPAX types: + public static final Map typeCodes = Map.ofEntries( + //Entity class (lower-case values): + Map.entry("BiochemicalReaction","br"), + Map.entry("TransportWithBiochemicalReaction","tbr"), + Map.entry("TemplateReaction","tr"), + Map.entry("TemplateReactionRegulation","trr"), + Map.entry("DnaRegion","dg"), + Map.entry("RnaRegion","rg"), + Map.entry("Pathway","pw"), + Map.entry("PhysicalEntity","pe"), + Map.entry("SmallMolecule","sm"), + Map.entry("Protein","p"), + Map.entry("Gene","g"), + Map.entry("Complex","c"), + Map.entry("Catalysis","cat"), + Map.entry("ChemicalStructure","cs"), + Map.entry("ComplexAssembly","ca"), + Map.entry("Control","ct"), + Map.entry("Conversion","r"), + Map.entry("Transport","t"), + Map.entry("GeneticInteraction","gi"), + Map.entry("Interaction","i"), + Map.entry("Modulation","m"), + Map.entry("MolecularInteraction","mi"), + Map.entry("Degradation","deg"), + //UtilityClass (upper-case values): + Map.entry("BioSource","BIO"), + Map.entry("Provenance","PRO"), + Map.entry("RelationshipXref","RX"), + Map.entry("PublicationXref","PX"), + Map.entry("UnificationXref","UX"), + Map.entry("CellularLocationVocabulary","LV"), + Map.entry("ControlledVocabulary","V"), + Map.entry("CellVocabulary","CV"), + Map.entry("TissueVocabulary","TV"), + Map.entry("PhenotypeVocabulary","PV"), + Map.entry("EvidenceCodeVocabulary","EV"), + Map.entry("EntityReferenceTypeVocabulary","ERV"), + Map.entry("ExperimentalFormVocabulary","XFV"), + Map.entry("InteractionVocabulary","IV"), + Map.entry("RelationshipTypeVocabulary","RTV"), + Map.entry("SequenceModificationVocabulary","SMV"), + Map.entry("SequenceRegionVocabulary","SRV"), + Map.entry("SmallMoleculeReference","SMR"), + Map.entry("BiochemicalPathwayStep","BPS"), + Map.entry("PathwayStep","PS"), + Map.entry("DeltaG","DG"), + Map.entry("KPrime","KP"), + Map.entry("DnaReference","DR"), + Map.entry("DnaRegionReference","DGR"), + Map.entry("RnaReference","RR"), + Map.entry("RnaRegionReference","RGR"), + Map.entry("EntityFeature","EF"), + Map.entry("BindingFeature","BF"), + Map.entry("CovalentBindingFeature","CF"), + Map.entry("FragmentFeature","FF"), + Map.entry("ModificationFeature","MF"), + Map.entry("ExperimentalForm","XF"), + Map.entry("Evidence","E"), + Map.entry("ProteinReference","PR"), + Map.entry("SequenceInterval","SI"), + Map.entry("SequenceLocation","SL"), + Map.entry("SequenceSite","SS"), + Map.entry("Stoichiometry","S") + ); /** * Constructor @@ -49,53 +113,7 @@ public Normalizer() { fixDisplayName = true; xmlBase = ""; } - - - /** - * Normalizes BioPAX OWL data and returns - * the result as BioPAX OWL (string). - * - * This public method is actually intended to use - * outside the BioPAX Validator framework, with not too large models. - * - * @param biopaxOwlData RDF/XML BioPAX content string - * @return normalized BioPAX RDF/XML - * @deprecated this method will fail if the data exceeds ~1Gb (max UTF8 java String length) - */ - public String normalize(String biopaxOwlData) { - - if(biopaxOwlData == null || biopaxOwlData.length() == 0) - throw new IllegalArgumentException("no data. " + description); - - // quick-fix for older BioPAX L3 version (v0.9x) property 'taxonXref' (range: BioSource) - biopaxOwlData = biopaxOwlData.replaceAll("taxonXref","xref"); - - // build the model - Model model = null; - try { - model = biopaxReader.convertFromOWL( - new ByteArrayInputStream(biopaxOwlData.getBytes("UTF-8"))); - } catch (UnsupportedEncodingException e) { - throw new IllegalArgumentException("Failed! " + description, e); - } - - if(model == null) { - throw new IllegalArgumentException("Failed to create Model! " - + description); - } - - // auto-convert to Level3 model - if (model.getLevel() != BioPAXLevel.L3) { - log.info("Converting model to BioPAX Level3..."); - model = (new LevelUpgrader()).filter(model); - } - - normalize(model); // L3 only! - - // return as BioPAX OWL - return convertToOWL(model); - } - + /** * Normalizes xrefs to ease normalizing or merging other BioPAX objects later on, @@ -105,80 +123,75 @@ public String normalize(String biopaxOwlData) { * @param model biopax model to update */ private void normalizeXrefs(Model model) { - final NormalizerMap map = new NormalizerMap(model); final String xmlBase = getXmlBase(model); //current base, the default or model's one, if set. // use a copy of the xrefs set (to avoid concurrent exceptions) Set xrefs = new HashSet<>(model.getObjects(Xref.class)); - for(Xref ref : xrefs) - { - //skip not well-defined ones (incl. PublicationXrefs w/o db/id - won't normalize) - if(ref.getDb() == null || ref.getId() == null) + for(Xref ref : xrefs) { + //won't normalize xrefs missing db or id property value (e.g., some of PublicationXrefs) + if(ref.getDb() == null || ref.getId() == null) { continue; + } + + String quickFixDb = StringUtils + .replaceIgnoreCase(ref.getDb(),"uniprotkb", "uniprot") + .toLowerCase(); + ref.setDb(quickFixDb); - ref.setDb(ref.getDb().toLowerCase()); //set lowercase String idPart = ref.getId(); if(ref instanceof RelationshipXref) { - // only normalize (replace URI of) RXs that could potentially clash with other RX, CVs, ERs; - // skip, won't bother, for all other RXs... - if(!ref.getUri().startsWith("http://identifiers.org/")) - continue; - //RXs might have the same db, id but different rel. type. RelationshipTypeVocabulary cv = ((RelationshipXref) ref).getRelationshipType(); - if(ref.getIdVersion()!=null) { + if(ref.getIdVersion() != null) { idPart += "_" + ref.getIdVersion(); } if(cv != null && !cv.getTerm().isEmpty()) { idPart += "_" + StringUtils.join(cv.getTerm(), '_').toLowerCase(); } - } - else if(ref instanceof UnificationXref) { - // first, try to normalize the db name (using MIRIAM EBI registry) - try { - ref.setDb(MiriamLink.getName(ref.getDb()).toLowerCase()); - } catch (IllegalArgumentException e) { - // - unknown/unmatched db name (normalize using defaults) - if(ref.getIdVersion() != null) { - idPart += "_" + ref.getIdVersion(); - } - map.put(ref, Normalizer.uri(xmlBase, ref.getDb(), idPart, ref.getModelInterface())); - continue; //shortcut (non-standard db name) - } - - // a hack for uniprot/isoform xrefs + } else if(ref instanceof UnificationXref) { + // fix 'uniprot' instead 'uniprot isoform' and vice versa mistakes if (ref.getDb().startsWith("uniprot")) { //auto-fix (guess) for possibly incorrect db/id (can be 'uniprot isoform' with/no idVersion, etc..) if (isValidDbId("uniprot isoform", ref.getId()) && ref.getId().contains("-")) //the second condition is important { //then it's certainly an isoform id; so - fix the db name ref.setDb("uniprot isoform"); //fix the db - } - else { + } else { //id does not end with "-\\d+", i.e., not a isoform id //(idVersion is a different thing, but id db was "uniprot isoform" they probably misused idVersion) - if(ref.getDb().equals("uniprot isoform")) - { - if(ref.getIdVersion() != null && ref.getIdVersion().matches("^\\d+$")) - idPart = ref.getId()+"-"+ref.getIdVersion(); //guess, by idVersion, they actually meant isoform + if(ref.getDb().equals("uniprot isoform")) { + if(ref.getIdVersion() != null && ref.getIdVersion().matches("^\\d+$")) { + idPart = ref.getId() + "-" + ref.getIdVersion(); //guess idVersion is isoform number + } if(isValidDbId(ref.getDb(), idPart)) { ref.setId(idPart); //moved the isoform # to the ID ref.setIdVersion(null); } else if(!isValidDbId(ref.getDb(), ref.getId())) { - //certainly not isoform (might not even uniprot, but try...) - ref.setDb("uniprot knowledgebase"); //guess, fix + //certainly not isoform + ref.setDb("uniprot"); //guess, fix } idPart = ref.getId(); } } + } else { //not an uniprot kind UX + //try to tell if it's a standard id type name + Namespace ns = Resolver.getNamespace(ref.getDb()); + if(ns != null) { + ref.setDb(ns.getName().toLowerCase()); //update to the standard name + } else { + if(ref.getIdVersion() != null) { + idPart += "_" + ref.getIdVersion(); + } + } } } - // shelve it for URI replace - map.put(ref, Normalizer.uri(xmlBase, ref.getDb(), idPart, ref.getModelInterface())); + // make a new URI and save in the URI replacement map + String newUri = Normalizer.uri(xmlBase, ref.getDb(), idPart, ref.getModelInterface()); + map.put(ref, newUri); } // execute replace xrefs @@ -190,17 +203,17 @@ else if(!isValidDbId(ref.getDb(), ref.getId())) { * @trows IllegalArgumentException when db is unknown name. */ private boolean isValidDbId(String db, String id) { - return MiriamLink.checkRegExp(id, db); + return Resolver.checkRegExp(id, db); } /** - * Consistently generates a new BioPAX element URI + * Generates a new BioPAX element URI * using given URI namespace (xml:base), BioPAX class, * and two different identifiers (at least one is required). * - * Miriam registry is used to get the standard db name and - * identifiers.org URI, if possible, for relationship type vocabulary, - * publication xref, entity reference, and biosource types. + * ID registry data is used to get the standard db name and + * URI, if possible, for relationship type vocabulary, + * publication xref, entity reference, and bio source types. * * @param xmlBase xml:base (common URI prefix for a BioPAX model), case-sensitive * @param dbName a bio data collection name or synonym, case-insensitive @@ -209,66 +222,94 @@ private boolean isValidDbId(String db, String id) { * @return URI * @throws IllegalArgumentException if either type is null or both 'dbName' and 'idPart' are all nulls. */ - public static String uri(final String xmlBase, - String dbName, String idPart, Class type) - { - if(type == null || (dbName == null && idPart == null)) - throw new IllegalArgumentException("'Either type' is null, or both dbName and idPart are nulls."); + public static String uri(final String xmlBase, String dbName, String idPart, Class type) { + return uri(xmlBase, dbName, idPart, type, true); + } + + /** + * Generates a new BioPAX element URI + * using given URI namespace (xml:base), BioPAX class, + * and two different identifiers (at least one is required). + * + * Registry is optionally used to get the standard db name and URI, if possible. + * + * @param xmlBase xml:base (common URI prefix for a BioPAX model), case-sensitive + * @param dbName a bio data collection name or synonym, case-insensitive + * @param idPart optional (can be null), e.g., xref.id, case-sensitive + * @param type BioPAX class + * @param useRegistry use or not the ID types registry data + * @return URI + * @throws IllegalArgumentException if either type is null or both 'dbName' and 'idPart' are all nulls. + */ + public static String uri(final String xmlBase, String dbName, String idPart, + Class type, boolean useRegistry) { + + if(type == null || (dbName == null && idPart == null)) { + throw new IllegalArgumentException("Type is null or both dbName and idPart are null"); + } - if (idPart != null) idPart = idPart.trim(); - if (dbName != null) dbName = dbName.trim(); + String uri = null; + if (idPart != null) { + idPart = idPart.trim(); + } + if (dbName != null) { + dbName = dbName.trim().toLowerCase(); + } // for some types, try to find a standard URI or at least a standard name: - if (dbName != null) - { - try { - // try to get the preferred/standard name - // for any type, for consistency - dbName = MiriamLink.getName(dbName); - // a shortcut: a standard and resolvable URI exists for some BioPAX types - if ((type.equals(PublicationXref.class) && "pubmed".equalsIgnoreCase(dbName)) - || type.equals(RelationshipTypeVocabulary.class) - || ProteinReference.class.isAssignableFrom(type) - || SmallMoleculeReference.class.isAssignableFrom(type) - || (type.equals(BioSource.class) && "taxonomy".equalsIgnoreCase(dbName) - && idPart!=null && idPart.matches("^\\d+$")) - ) - { //get the standard URI and quit (success), or fail and continue making a new URI below... - return MiriamLink.getIdentifiersOrgURI(dbName, idPart); + if (dbName != null && useRegistry) { + Namespace ns = Resolver.getNamespace(dbName); //a synonym or (mis)spelling can match as well + if (ns != null) { + String prefix = ns.getPrefix(); + // make a bioregistry.io URI or CURIE for some of the BioPAX types + if (type.equals(RelationshipTypeVocabulary.class) + || ProteinReference.class.isAssignableFrom(type) + || SmallMoleculeReference.class.isAssignableFrom(type) + || (type.equals(BioSource.class) && "ncbitaxon".equalsIgnoreCase(prefix) + && idPart != null && idPart.matches("^\\d+$"))) { + // makes URL + uri = Resolver.getURI(prefix, idPart); //can be null when there's id-pattern mismatch + } else if (type.equals(UnificationXref.class) && !"pubmed".equalsIgnoreCase(prefix) || + (type.equals(PublicationXref.class) && "pubmed".equalsIgnoreCase(prefix))) { + //use CURIE for these xref types + uri = Resolver.getCURIE(prefix, idPart); } - } catch (IllegalArgumentException e) { - log.info(String.format("uri(for a %s): db:%s, id:%s are not standard; %s)", - type.getSimpleName(), dbName, idPart, e.getMessage())); } } - // If not returned above this point - no standard URI (Identifiers.org) was found - - // then let's consistently build a new hash-based URI from args. - StringBuilder sb = new StringBuilder(); - if (dbName != null) //lowercase for consistency - sb.append(dbName.toLowerCase()); - + if(StringUtils.isNotEmpty(uri)) { + return uri; //done + } + + // No standard URI was found; let's consistently build a hash-based URI: + StringBuilder sb = new StringBuilder(); + if (dbName != null) { + sb.append(dbName); + } if (idPart != null) { - if (dbName != null) sb.append("_"); + if (dbName != null) { + sb.append("_"); + } sb.append(idPart); } - String localPart = sb.toString(); String strategy = System.getProperty(PROPERTY_NORMALIZER_URI_STRATEGY, VALUE_NORMALIZER_URI_STRATEGY_MD5); - if(VALUE_NORMALIZER_URI_STRATEGY_SIMPLE.equals(strategy) || Xref.class.isAssignableFrom(type)) - //i.e., for xrefs, always use the simple URI strategy (makes them human-readable) - { - //simply replace "unsafe" symbols with underscore (some uri clashes might be possible but rare...) + if(VALUE_NORMALIZER_URI_STRATEGY_SIMPLE.equals(strategy) || Xref.class.isAssignableFrom(type)) { + //for xrefs, always use the simple URI strategy (human-readable) + //replace unsafe symbols with underscore localPart = localPart.replaceAll("[^-\\w]", "_"); - } - else - { + } else { //replace the local part with its md5 hash string (32-byte) localPart = ModelUtils.md5hex(localPart); } - + // create URI using the xml:base and digest of other values: - return ((xmlBase != null) ? xmlBase : "") + type.getSimpleName() + "_" + localPart; + String prefix = typeCodes.get(type.getSimpleName()); + if(prefix == null) { + prefix = type.getSimpleName(); + } + uri = ((xmlBase != null) ? xmlBase : "") + prefix + "_" + localPart; + return uri; } @@ -332,23 +373,18 @@ private String convertToOWL(Model model) { private Collection getUnificationXrefsSorted(XReferrable r) { - List urefs = new ArrayList<>(); - for(UnificationXref ux : new ClassFilterSet(r.getXref(), UnificationXref.class)) + for(UnificationXref ux : new ClassFilterSet<>(r.getXref(), UnificationXref.class)) { if(ux.getDb() != null && ux.getId() != null) { urefs.add(ux); } } - - Collections.sort(urefs, new Comparator() { - public int compare(UnificationXref o1, UnificationXref o2) { - String s1 = o1.getDb() + o1.getId(); - String s2 = o2.getDb() + o2.getId(); - return s1.compareTo(s2); - } + Collections.sort(urefs, (o1, o2) -> { + String s1 = o1.getDb() + o1.getId(); + String s2 = o2.getDb() + o2.getId(); + return s1.compareTo(s2); }); - return urefs; } @@ -356,7 +392,7 @@ public int compare(UnificationXref o1, UnificationXref o2) { /** * Finds one preferred unification xref, if possible. * Preferred db values are: - * "ncbi gene" - for NucleicAcidReference and the sub-classes; + * "entrez gene" - for NucleicAcidReference and the subclasses; * "uniprot" or "refseq" for ProteinReference; * "chebi" - for SmallMoleculeReference; * @@ -366,7 +402,6 @@ public int compare(UnificationXref o1, UnificationXref o2) { private UnificationXref findPreferredUnificationXref(XReferrable bpe) { UnificationXref toReturn = null; - Collection orderedUrefs = getUnificationXrefsSorted(bpe); //use preferred db prefix for different type of ER @@ -383,9 +418,9 @@ private UnificationXref findPreferredUnificationXref(XReferrable bpe) toReturn = findSingleUnificationXref(orderedUrefs, "pubchem"); } else if(bpe instanceof NucleicAcidReference) { //that includes NucleicAcidRegionReference, etc. sub-classes; - toReturn = findSingleUnificationXref(orderedUrefs, "ncbi gene"); + toReturn = findSingleUnificationXref(orderedUrefs, "entrez"); if(toReturn==null) - toReturn = findSingleUnificationXref(orderedUrefs, "entrez"); + toReturn = findSingleUnificationXref(orderedUrefs, "ncbi gene"); //todo: impossible when xrefs already normalized?.. } else { //for other XReferrable types (BioSource or ControlledVocabulary) //use if there's only one xref (return null if many) @@ -440,7 +475,7 @@ public void normalize(Model model) { model.setXmlBase(xmlBase); // Normalize/merge xrefs, first, and then CVs - // (also because some of original xrefs might have "normalized" URIs + // (also because original xrefs might have "normalized" URIs // that, in fact, must be used for other biopax types, such as CV or ProteinReference) log.info("Normalizing xrefs..." + description); normalizeXrefs(model); @@ -454,7 +489,7 @@ public void normalize(Model model) { log.info("Normalizing CVs..." + description); normalizeCVs(model); - //normalize BioSource objects (better, as it is here, go after Xrefs and CVs) + //normalize BioSource objects (after Xrefs and CVs!) log.info("Normalizing organisms..." + description); normalizeBioSources(model); @@ -482,7 +517,7 @@ private void normalizeCVs(Model model) { // process ControlledVocabulary objects (all sub-classes) for(ControlledVocabulary cv : model.getObjects(ControlledVocabulary.class)) { - //it does not check/fix the CV terms though (but a validation rule can do if run before the normalizer)... + //it does not check/fix the CV terms (but Validator can do if run before the Normalizer) UnificationXref uref = findPreferredUnificationXref(cv); //usually, there's only one such xref if (uref != null) { // so let's generate a consistent URI @@ -500,16 +535,13 @@ private void normalizeCVs(Model model) { private void normalizeBioSources(Model model) { - NormalizerMap map = new NormalizerMap(model); - - for(BioSource bs : model.getObjects(BioSource.class)) - { + for(BioSource bs : model.getObjects(BioSource.class)) { UnificationXref uref = findPreferredUnificationXref(bs); //normally, the xref db is 'Taxonomy' (or a valid synonym) if (uref != null - && (uref.getDb().toLowerCase().contains("taxonomy") || uref.getDb().equalsIgnoreCase("newt"))) - { + && (uref.getDb().toLowerCase().contains("taxonomy") + || uref.getDb().equalsIgnoreCase("newt"))) { String idPart = uref.getId(); //tissue/cellType terms can be added below: @@ -520,17 +552,14 @@ private void normalizeBioSources(Model model) { String uri = (idPart.equals(uref.getId()) //- no tissue or celltype were attached && idPart.matches("^\\d+$")) //- is positive integer id - ? uri(xmlBase, uref.getDb(), idPart, BioSource.class) - : "http://identifiers.org/taxonomy/" + idPart; - // the latter is intentionally invalid identifiers.org/taxonomy URI - good (and important) for merging + ? uri(xmlBase, uref.getDb(), idPart, BioSource.class) : "bioregistry.io/ncbitaxon:" + idPart; map.put(bs, uri); - - } else - log.debug("Won't normalize BioSource" - + " : no taxonomy unification xref found in " + bs.getUri() - + ". " + description); - } - + } else { + log.debug("Won't normalize BioSource" + + " : no taxonomy unification xref found in " + bs.getUri() + + ". " + description); + } + } map.doSubs(); } @@ -542,10 +571,10 @@ private void normalizeERs(Model model) { for (EntityReference bpe : model.getObjects(EntityReference.class)) { //skip those with already normalized URIs - if(bpe.getUri().startsWith("http://identifiers.org/")) { + if(bpe.getUri().contains("identifiers.org/")) { log.info("Skip already normalized: " + bpe.getUri()); continue; - } + } UnificationXref uref = findPreferredUnificationXref(bpe); if (uref != null) { @@ -555,9 +584,9 @@ private void normalizeERs(Model model) { final String db = uref.getDb(); final String id = uref.getId(); // get the standard ID - String uri = null; + String uri; try { // make a new ID for the element - uri = MiriamLink.getIdentifiersOrgURI(db, id); + uri = Resolver.getURI(db, id); } catch (Exception e) { log.error("Cannot get a Miriam standard ID for " + bpe + " (" + bpe.getModelInterface().getSimpleName() @@ -582,62 +611,47 @@ private void normalizeERs(Model model) { /** * Auto-generates standard and other names for the datasource - * from either its ID (if URN) or one of its existing names (preferably - standard name) + * from either its URI or one of the names (preferably - standard name) * * @param pro data source (BioPAX Provenance) */ public static void autoName(Provenance pro) { - if(!(pro.getUri().startsWith("urn:miriam:") || pro.getUri().startsWith("http://identifiers.org/")) - && pro.getName().isEmpty()) { - log.info("Skipping: cannot normalize Provenance: " + pro.getUri()); + String uri = pro.getUri(); + String key; + if(StringUtils.startsWithIgnoreCase(uri, "urn:miriam:") + || StringUtils.containsIgnoreCase(uri,"identifiers.org/") + || StringUtils.containsIgnoreCase(uri, "bioregistry.io/")) { + key = StringUtils.removeEnd(uri,"/"); //removes ending '/' if present + } else if (pro.getStandardName() != null) { + key = pro.getStandardName(); + } else { + key = pro.getDisplayName(); } - else { // i.e., 'name' is not empty or ID is the URN - final SortedSet names = new TreeSet(); - - String key = null; - if(pro.getUri().startsWith("urn:miriam:") || pro.getUri().startsWith("http://identifiers.org/")) { - key = pro.getUri(); - } else if (pro.getStandardName() != null) { - key = pro.getStandardName(); - } else { - key = pro.getDisplayName(); // can be null + + if (key != null) { + Namespace ns = Resolver.getNamespace(key); + if(ns != null) { + pro.setStandardName(ns.getName()); + pro.addName(ns.getPrefix()); } - - if (key != null) { - try { - names.addAll(Arrays.asList(MiriamLink.getNames(key))); - pro.setStandardName(MiriamLink.getName(key)); - // get the datasource description - String description = MiriamLink.getDataTypeDef(pro.getStandardName()); - pro.addComment(description); - } catch (IllegalArgumentException e) { - // ignore (then, names is still empty...) + } + + if(StringUtils.isBlank(pro.getStandardName())) { + // find a standard name in names + for (String name : pro.getName()) { + Namespace ns = Resolver.getNamespace(name); + if(ns != null) { + String stdName = ns.getName(); + pro.setStandardName(stdName); + pro.addName(ns.getPrefix()); + break; } - } - - // when the above failed (no match in Miriam), or key was null - - if(names.isEmpty()) { - // finally, trying to find all valid names for each existing one - for (String name : pro.getName()) { - try { - names.addAll(Arrays.asList(MiriamLink.getNames(name))); - } catch (IllegalArgumentException e) { - // ignore - } - } - // pick up the first name, get the standard name - if(!names.isEmpty()) - pro.setStandardName(MiriamLink - .getName(names.iterator().next())); } - - // and add all the synonyms if any - for(String name : names) - pro.addName(name); - - //set display name if not set (standard name is set already) - if(pro.getDisplayName() == null) - pro.setDisplayName(pro.getStandardName()); + } + + //set display name if not set (standard name is set already) + if(pro.getDisplayName() == null) { + pro.setDisplayName(pro.getStandardName()); } } @@ -709,89 +723,4 @@ public void setXmlBase(String xmlBase) { this.xmlBase = xmlBase; } - - /** - * Helper class, to associate original - * and new (either copy or existing) objects - * within some biopax model and then execute - * batch replace. - * - * @author rodche - */ - private static class NormalizerMap { - - //a model to modify by replacing biopax objects - final Model model; - - // this is the biopax elements substitution map (old->new) - final Map subs; - - //the next map is to make sure the subs.values() all have different URIs - final Map uriToSub; - - final ShallowCopy copier; - - NormalizerMap(Model model) { - subs = BPCollections.I.createMap(100); - uriToSub = BPCollections.I.createMap(100); - this.model = model; - copier = new ShallowCopy(); - } - - - /** - * Creates (by URI) and saves the replacement object, - * but does not replace yet (call doSubs to replace). - * - * @param bpe - * @param newUri - */ - void put(BioPAXElement bpe, String newUri) - { - if(model.containsID(newUri)) { - // will use existing original (model) object that has the new Uri - map(bpe, model.getByID(newUri)); - } else if(uriToSub.containsKey(newUri)) { - // re-use the new object that's already added to replace another original - map(bpe, uriToSub.get(newUri)); - } else { - // will use the object's shallow copy that gets new Uri - BioPAXElement copy = copier.copy(bpe, newUri); - map(bpe, copy); - } - } - - /** - * Executes the batch replace - migrating - * to the normalized equivalent objects. - */ - void doSubs() { - for(BioPAXElement e : subs.keySet()) { - model.remove(e); - } - - try { - ModelUtils.replace(model, subs); - } catch (Exception e) { - log.error("Failed to replace BioPAX elements", e); - return; - } - - for(BioPAXElement e : subs.values()) { - if(!model.containsID(e.getUri())) { - model.add(e); - } - } - - for(BioPAXElement e : model.getObjects()) { - ModelUtils.fixDanglingInverseProperties(e, model); - } - } - - private void map(BioPAXElement bpe, BioPAXElement newBpe) { - subs.put(bpe, newBpe); - uriToSub.put(newBpe.getUri(), newBpe); - } - } - } diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/NormalizerMap.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/NormalizerMap.java new file mode 100644 index 000000000..b54806bed --- /dev/null +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/NormalizerMap.java @@ -0,0 +1,93 @@ +package org.biopax.paxtools.normalizer; + +import org.biopax.paxtools.controller.ModelUtils; +import org.biopax.paxtools.controller.ShallowCopy; +import org.biopax.paxtools.model.BioPAXElement; +import org.biopax.paxtools.model.Model; +import org.biopax.paxtools.util.BPCollections; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Map; + +/** + * A non-public helper class to map "old" (original) to "new" (replacement) objects + * in a BioPAX model and then to substitute/replace them all (update object properties, model). + * + * @author rodche + */ +class NormalizerMap { + static final Logger log = LoggerFactory.getLogger(NormalizerMap.class); + + //a model to modify by replacing some objects + final Model model; + + // biopax elements substitution map (old->new) + final Map subs; + + //a map that helps to make sure subs.values() all have different URIs + final Map uriToSub; + + final ShallowCopy copier; + + NormalizerMap(Model model) { + subs = BPCollections.I.createMap(); + uriToSub = BPCollections.I.createMap(); + this.model = model; + copier = new ShallowCopy(); //BioPAX L3 + } + + + /** + * Creates (by URI) and saves the replacement object, + * but does not replace yet (call doSubs to replace). + * + * @param bpe + * @param newUri + */ + void put(BioPAXElement bpe, String newUri) { + if (model.containsID(newUri)) { + // will use existing original (model) object that has the new Uri + map(bpe, model.getByID(newUri)); + } else if (uriToSub.containsKey(newUri)) { + // re-use the new object that's already added to replace another original + map(bpe, uriToSub.get(newUri)); + } else { + // will use the object's shallow copy that gets new Uri + BioPAXElement copy = copier.copy(bpe, newUri); + map(bpe, copy); + } + } + + /** + * Executes the batch replace - migrating + * to the normalized equivalent objects. + */ + void doSubs() { + for (BioPAXElement e : subs.keySet()) { + model.remove(e); + } + + try { + ModelUtils.replace(model, subs); + } catch (Exception e) { + log.error("Failed to replace BioPAX elements", e); + return; + } + + for (BioPAXElement e : subs.values()) { + if (!model.containsID(e.getUri())) { + model.add(e); + } + } + + for (BioPAXElement e : model.getObjects()) { + ModelUtils.fixDanglingInverseProperties(e, model); + } + } + + private void map(BioPAXElement bpe, BioPAXElement newBpe) { + subs.put(bpe, newBpe); + uriToSub.put(newBpe.getUri(), newBpe); + } +} diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java new file mode 100644 index 000000000..e44b4d6a1 --- /dev/null +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java @@ -0,0 +1,236 @@ +package org.biopax.paxtools.normalizer; + +import java.io.IOException; +import java.io.InputStream; +import java.util.*; +import java.util.concurrent.ConcurrentSkipListMap; +import java.util.regex.Pattern; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + + +/** + * Singleton bio identifier resolver utility. + */ +public class Resolver { + private static final Logger LOG = LoggerFactory.getLogger(Resolver.class); + private static final Map namespaces; + private static Map spellmap; // compressed name -> prefix (combines custom spellmap.json and registry) + private static Map synonymap;// synonym -> prefix (build from custom synonymap.json and registry) + + public static final String BIOREGISTRY_IO = "bioregistry.io/"; + + protected Resolver() { + } + + static { + InputStream is = null; + try { + ObjectMapper om = new ObjectMapper(); + om.disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES); //to quietly ignore the data we don't need +// om.setVisibility(VisibilityChecker.Std.defaultInstance().withFieldVisibility(JsonAutoDetect.Visibility.ANY)); + // load a map of "compressed" (non letter/digit chars were removed) spelling variants to combine with namespaces map + is = Resolver.class.getResourceAsStream("spellmap.json"); + spellmap = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>(){})); + // load a custom map of synonyms + is = Resolver.class.getResourceAsStream("synonymap.json"); + synonymap = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>(){})); + // load registry.json + is = Resolver.class.getResourceAsStream("registry.json"); + namespaces = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>(){})); + LOG.info("read registry.json to the namespaces map; size: " + namespaces.size()); + + //Post-process registry entries to add synonyms and spellings + namespaces.forEach((prefix, ns) -> { + ns.setPrefix(prefix); + //todo: skip for deprecated? + String uname = ns.getName().toUpperCase(); + String upref = prefix.toUpperCase(); + //add name, prefix, synonyms to the synonymap (uppercase) + //also - to spellmap (removing non-alphanumeric chars) + synonymap.put(uname, prefix); + synonymap.put(upref, prefix); + spellmap.put(uname.replaceAll("[^A-Z0-9]",""), prefix); + spellmap.put(upref.replaceAll("[^A-Z0-9]",""), prefix); + //add name, prefix, synonyms to synonymap + ns.getSynonyms().forEach(syn -> { + String s = syn.toUpperCase(); + synonymap.putIfAbsent(s, prefix); + spellmap.putIfAbsent(s.replaceAll("[^A-Z0-9]",""), prefix); + }); + }); + LOG.info("initialized"); + } catch (Exception e) { + throw new RuntimeException(e); + } finally { + if(is != null) { + try { + is.close(); + } catch (IOException e) { + } + } + } + } + + + /** + * Checks if the identifier given follows the regular expression + * of its data type (also provided). + * + * @param identifier internal identifier used by the data type + * @param datatype name, synonym or URI of a data type + * @return "true" if the identifier follows the regular expression, "false" otherwise + * @throws IllegalArgumentException when datatype not found + */ + public static boolean checkRegExp(String identifier, String datatype) { + Namespace dt = getNamespace(datatype); + if(dt == null) { + return false; + } + + //remove "banana" and "peel" prefix from the identifier if any defined and present + String banana = dt.getBanana(); + if(StringUtils.isNotBlank(banana)) { + identifier = identifier.replaceFirst(banana+dt.getBanana_peel(), ""); + } + + return Pattern.compile(dt.getPattern()).matcher(identifier).find(); + } + + + /** + * Gets Namespace by its Name, Prefix, URI (URN/URL), known synonym or misspelling. + * + * @param key a datatype name, prefix or URN/URL (case insensitive) + * @return Namespace bean or null + */ + public static Namespace getNamespace(String key) { + return getNamespace(key, true); + } + + + /** + * Gets Namespace by its Name, Prefix, URN/URL, or (optionally) spelling variant or synonym + * + * @param key a name (case insensitive) + * @param allowVariants to allow or not searching with some known synonyms/misspellings + * @return Namespace bean or null + */ + public static Namespace getNamespace(String key, boolean allowVariants) { + if(StringUtils.isBlank(key)) { + return null; + } + + //uppercase! + key = key.toUpperCase(); + //quick-fix some obsolete prefixes + key = StringUtils.removeEnd(key, "/"); + key = key.replaceFirst("OBO\\.", ""); + key = key.replaceFirst("PSI-", ""); + key = key.replaceFirst("URN:MIRIAM:", ""); + key = key.replaceFirst(".*IDENTIFIERS\\.ORG/(.*/)?", ""); //e.g. match both ".ORG/CHEBI/CHEBI:1234" and ".ORG/CHEBI:1234" variants + key = key.replaceFirst(".*BIOREGISTRY\\.IO/", ""); + + String prefix = key.toLowerCase(); + Namespace ns = namespaces.get(prefix); + //also try synonyms + if(ns == null) { + prefix = synonymap.get(key); //uppercase search + if(prefix != null) + ns = namespaces.get(prefix.toLowerCase()); + } + + if(ns == null && allowVariants) { + //keep only alphanumeric chars in the key (it's uppercase) and search the spellmap + prefix = spellmap.get(key.replaceAll("[^A-Z0-9]","")); + if(prefix != null) { + ns = namespaces.get(prefix.toLowerCase()); + } + } + + return ns; + } + + /** + * Builds a URI of the bioentity (e.g., "bioregistry.io/go:0045202") + * from the collection name/synonym and bio id. + * + * @param name - name, URI, or ID of a data collection (examples: "ChEBI", "go") + * @param id identifier of an entity within the data type (examples: "GO:0045202" or "0045202", "P62158") + * @return URI (without the protocol prefix) + */ + public static String getURI(String name, String id) { + String cid = getCURIE(name, id); + return cid != null ? BIOREGISTRY_IO + cid : null; + } + + /** + * Builds a normalized CURIE (Compact URI/ID) of the biochemical entity + * from the collection name/synonym and bio id. + * @param name bio namespace/db/collection name + * @param id bio identifier + * @return + */ + public static String getCURIE(String name, String id) { + Namespace ns = getNamespace(name, true); + if (ns != null) { + if (checkRegExp(id, name)) { + String prefix = ns.getPrefix(); + //remove "banana" and "peel" prefix from the identifier if any defined and present + String banana = ns.getBanana(); + if(StringUtils.isNotBlank(banana)) { + id = id.replaceFirst(banana + ns.getBanana_peel(), ""); + } + return prefix + ":" + id; + } + } + return null; + } + + /** + * Gets the unmodifiable map of the bio identifier types registry records. + * @return + */ + public static Map getNamespaces() { + return Collections.unmodifiableMap(namespaces); + } + + /** + * Gets the unmodifiable map - mapping an identifier type name/variant/synonym + * (non-alphanumeric chars are removed) to the corresponding record/namespace "prefix". + * All the key/values are upper case. + * @return + */ + public static Map getSpellmap() { + return Collections.unmodifiableMap(spellmap); + } + + /** + * Customize the mapping from a bio identifier type name/variant/synonym + * (non-alphanumeric chars should be removed) to the corresponding record/namespace "prefix". + * All the key/values should be stored in upper case. + * @return + */ + public static void setSpellmap(Map map) { + spellmap = map; + } + + /** + * + * @param name + * @return + */ + public static boolean isKnownNameOrVariant(String name) { + return name != null && ( + namespaces.containsKey(name.toLowerCase()) + || synonymap.containsKey(name.toUpperCase()) + || spellmap.containsKey(name.toUpperCase().replaceAll("[^a-zA-Z0-9]","")) + ); + } + +} diff --git a/normalizer/src/main/resources/Miriam.xml b/normalizer/src/main/resources/Miriam.xml deleted file mode 100644 index e2d979e55..000000000 --- a/normalizer/src/main/resources/Miriam.xml +++ /dev/null @@ -1,24209 +0,0 @@ - - - - - - - - - - - - BIND doesn't exist any more and its successor (BOND) is not open-access. Bulk downloads of BIND data (http://bond.unleashedinformatics.com/downloads/data/BIND/data/datasets/taxon/xml/) and a PSI-MI 2.5 translation (http://download.baderlab.org/BINDTranslation/) are available. - BIND - - Biomolecular Interaction Network Database - - BIND is a database of protein-protein interactions. This data-resource is not open-access. - - urn:miriam:bind - http://identifiers.org/bind/ - http://www.bind.ca/ - - bind - - - http://www.bind.ca/ - http://www.bind.ca/Action?identifier=bindid&idsearch=$id - BIND (Biomolecular Interaction Network Database) - Unleashed Informatics - Canada - - - - - May not be exploited for any commercial purpose without express written consent (BOND). - http://thomsonreuters.com/terms_of_use/ - - - This data is a subset of that found in BOND {MIR:00900214}. - http://bond.unleashedinformatics.com/Action?pg=23299 - - - - - - species - rule - reaction - event - parameter - - - - - - - ChEBI - Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. - - urn:miriam:chebi - http://identifiers.org/chebi/ - http://purl.obolibrary.org/obo/CHEBI - http://identifiers.org/obo.chebi/ - http://www.ebi.ac.uk/chebi/ - urn:miriam:obo.chebi - - chebi - - urn:miriam:pubmed:19854951 - urn:miriam:pubmed:19496059 - urn:miriam:pubmed:17932057 - urn:miriam:pubmed:22065232 - urn:miriam:pubmed:23180789 - - - - http://www.ebi.ac.uk/chebi/ - CHEBI:36927 - http://www.ebi.ac.uk/chebi/searchId.do?chebiId=$id - ChEBI (Chemical Entities of Biological Interest) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.ebi.ac.uk/ols/ontologies/chebi - CHEBI:36927 - https://www.ebi.ac.uk/ols/ontologies/chebi/terms?obo_id=$id - ChEBI through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/CHEBI - CHEBI:36927 - http://purl.bioontology.org/ontology/CHEBI/$id - ChEBI through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - chemical - metabolite - ontology - - - - - species - parameter - - - - - - - Ensembl - Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms. - - urn:miriam:ensembl - http://identifiers.org/ensembl/ - http://www.ensembl.org/ - - ensembl - - urn:miriam:pubmed:16381931 - - - - http://www.ensembl.org/ - ENSG00000139618 - http://www.ensembl.org/id/$id - Ensembl at Sanger/EMBL-EBI - Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://uswest.ensembl.org/ - ENSG00000139618 - http://uswest.ensembl.org/id/$id - Ensembl US West mirror - - USA - - - http://useast.ensembl.org/ - ENSG00000139618 - http://useast.ensembl.org/id/$id - Ensembl US East mirror - - USA - - - http://asia.ensembl.org/ - ENSG00000139618 - http://asia.ensembl.org/id/$id - Ensembl Asia mirror - - Singapore - - - - - While Ensembl data is nominally restricted to vertebrate species, it also includes out groups (Dorsophila, Saccharomyces and C. elegans) used in comparative analysis. These species can also be referenced through Ensembl Genomes datasets. - http://www.ensemblgenomes.org/info/data_access - - - This data collection uses some 'outlier' organisms, to normalise its dataset, which are not intended to be referenced directly in this collection. In addition, those outlier organisms may be referenced using non-standard identifiers. We recommend that human data be accessed using identifiers beginning with 'ENS', and outlier organisms be referenced through the appropriate collection: WormBase (http://identifiers.org/wormbase/), SGD (http://identifiers.org/sgd/) or FlyBase (http://identifiers.org/flybase/). - - - - eukaryotic - genome - nucleotide - schema.org - sequence - - - - - species - parameter - - - - - - - Enzyme Nomenclature - - Enzyme Classification - EC code - EC - - The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. - - urn:miriam:ec-code - http://identifiers.org/ec-code/ - urn:lsid:ec-code.org - http://www.ec-code.org/ - http://www.ebi.ac.uk/IntEnz/ - - ec-code - - urn:miriam:pubmed:10812475 - http://www.chem.qmul.ac.uk/iubmb/enzyme/ - - - - http://www.ebi.ac.uk/intenz/ - 1.1.1.1 - http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$id - IntEnZ (Integrated relational Enzyme database) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.genome.jp/dbget-bin/www_bfind?enzyme - 1.1.1.1 - http://www.genome.jp/dbget-bin/www_bget?ec:$id - KEGG Ligand Database for Enzyme Nomenclature - Kyoto University Bioinformatics Center - Japan - - - http://enzyme.expasy.org/ - 1.1.1.1 - http://enzyme.expasy.org/EC/$id - Enzyme nomenclature database, ExPASy (Expert Protein Analysis System) - Swiss Institute of Bioinformatics - Switzerland - - - http://www.enzyme-database.org/ - 1.1.1.1 - http://www.enzyme-database.org/query.php?ec=$id - ExploreEnz at Trinity College - Trinity College, Dublin - Ireland - - - https://www.ebi.ac.uk/enzymeportal - 1.1.1.1 - https://www.ebi.ac.uk/enzymeportal/search/ec/$id - Enzyme Portal through EMBL-EBI - Enzyme Portal at European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - classification - enzyme - protein - taxonomy - - - - - reaction - event - rule - species - - - - - component - reaction - - - - - catalysis - - - - - - - UniProt Knowledgebase - - UniProtKB - UniProt - Protein Knowledgebase - UniProt-TrEMBL - UniProt/TrEMBL - UniProtKB/Swiss-Prot - - The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information. - - urn:miriam:uniprot - http://identifiers.org/uniprot/ - urn:lsid:uniprot.org:uniprot - http://www.uniprot.org/ - urn:lsid:uniprot.org - - uniprot - - urn:miriam:pubmed:16381842 - urn:miriam:pubmed:23161681 - - - - http://www.uniprot.org/ - P0DP23 - http://purl.uniprot.org/uniprot/$id - Universal Protein Resource using Persistent URL system - UniProt Consortium - - - - http://www.ncbi.nlm.nih.gov/protein/ - P0DP23 - http://www.ncbi.nlm.nih.gov/protein/$id - UniProt through NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://www.ebi.uniprot.org/ - P62158 - http://www.ebi.uniprot.org/entry/$id - Universal Protein Resource - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.pir.uniprot.org/ - P62158 - http://www.pir.uniprot.org/cgi-bin/upEntry?id=$id - Universal Protein Resource - Georgetown University - USA - - - http://www.expasy.uniprot.org/ - P62158 - http://us.expasy.org/uniprot/$id - Universal Protein Resource, ExPASy (Expert Protein Analysis System) - Swiss Institute of Bioinformatics - Switzerland - - - http://www.uniprot.org/ - P0DP23 - http://www.uniprot.org/uniprot/$id - Universal Protein Resource - UniProt Consortium - USA, UK and Switzerland - - - - protein - sequence - - - - - species - speciesType - parameter - - - - - physicalEntity - - - - - - - Taxonomy - - NEWT - NCBI taxonomy - - The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. - - urn:miriam:taxonomy - http://identifiers.org/taxonomy/ - http://bio2rdf.org/taxonomy - http://purl.obolibrary.org/obo/NCBITaxon - http://www.uniprot.org/taxonomy/ - http://www.taxonomy.org/ - http://www.ncbi.nlm.nih.gov/Taxonomy/ - - taxonomy - - http://www.ncbi.nlm.nih.gov/books/NBK53758/ - - - - http://www.ncbi.nlm.nih.gov/Taxonomy/ - 9606 - http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$id - NCBI Taxonomy - National Center for Biotechnology Information (NCBI) - USA - - - http://www.uniprot.org/taxonomy/ - 9606 - http://purl.uniprot.org/taxonomy/$id - Taxonomy through UniProt PURL - UniProt Consortium - USA, UK and Switzerland - - - http://www.ebi.ac.uk/ena/ - 9606 - http://www.ebi.ac.uk/ena/data/view/Taxon:$id - European Nucleotide Archive (ENA) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/NCBITAXON - 9606 - http://purl.bioontology.org/ontology/NCBITAXON/$id - BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - http://taxonomy.bio2rdf.org/fct/ - 9606 - http://taxonomy.bio2rdf.org/describe/?url=http://bio2rdf.org/taxonomy:$id - Bio2RDF - Bio2RDF.org - - - - https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/ - 9606 - https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?short_form=NCBITaxon_$id - NCBI Taxonomy through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - taxonomy - - - - - model - species - parameter - - - - - - - BioModels Database - - BioModels - - BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. - - urn:miriam:biomodels.db - http://identifiers.org/biomodels.db/ - http://bio2rdf.org/biomodels - http://www.ebi.ac.uk/biomodels/ - - biomodels.db - - urn:miriam:pubmed:16381960 - urn:miriam:pubmed:20587024 - urn:miriam:pubmed:25414348 - urn:miriam:pubmed:25182954 - urn:miriam:doi:10.1002%2Fpsp4.3 - - - - http://www.ebi.ac.uk/biomodels/ - BIOMD0000000048 - http://www.ebi.ac.uk/biomodels-main/$id - BioModels Database - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://biomodels.caltech.edu/ - BIOMD0000000048 - http://biomodels.caltech.edu/$id - Caltech mirror - California Institute of Technology - USA - - - http://cu.biomodels.bio2rdf.org/fct/ - BIOMD0000000048 - http://cu.biomodels.bio2rdf.org/describe/?url=http://bio2rdf.org/biomodels:$id - Bio2RDF - Bio2RDF.org - - - - https://www.omicsdi.org/ - BIOMD0000000048 - https://www.omicsdi.org/dataset/biomodels/$id - BioModels through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - model - - - - - model - - - - - - - MIRIAM Registry collection - - MIRIAM Resources - MIRIAM - - MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. - - urn:miriam:miriam.collection - http://identifiers.org/miriam.collection/ - http://www.biomodels.net/MIRIAM/ - urn:miriam:miriam - http://biomodels.net/MIRIAM/ - urn:miriam:miriam.datatype - - miriam.collection - - urn:miriam:pubmed:18078503 - urn:miriam:pubmed:16333295 - - - - http://www.ebi.ac.uk/miriam/ - MIR:00000008 - http://www.ebi.ac.uk/miriam/main/$id - MIRIAM Resources (data collection) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - registry - schema.org - - - - - ICD - The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. - - urn:miriam:icd - http://identifiers.org/icd/ - http://www.who.int/classifications/icd/ - - icd - - http://www.who.int/classifications/icd/en/ - - - - http://www.who.int/classifications/icd/en/ - C34 - http://apps.who.int/classifications/icd10/browse/2010/en#/$id - International Statistical Classification of Diseases and Related Health Problems - German Institute of Medical Documentation and Information - Germany - - - - disease - schema.org - taxonomy - - - - - model - - - - - - - IntAct - IntAct provides a freely available, open source database system and analysis tools for protein interaction data. - - urn:miriam:intact - http://identifiers.org/intact/ - http://www.ebi.ac.uk/intact/ - - intact - - urn:miriam:pubmed:14681455 - urn:miriam:pubmed:17145710 - - - - http://www.ebi.ac.uk/intact/ - EBI-2307691 - http://www.ebi.ac.uk/intact/interaction/$id - IntAct at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - interaction - protein - - - - - reaction - event - rule - - - - - - - InterPro - InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. - - urn:miriam:interpro - http://identifiers.org/interpro/ - http://bio2rdf.org/interpro - http://purl.uniprot.org/interpro/ - http://www.ebi.ac.uk/interpro/ - - interpro - - urn:miriam:pubmed:15608177 - - - - http://www.ebi.ac.uk/interpro/ - IPR000100 - http://www.ebi.ac.uk/interpro/entry/$id - InterPro - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://interpro.bio2rdf.org/fct/ - IPR000100 - http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$id - Bio2RDF - Bio2RDF.org - - - - - domain - protein - - - - - species - parameter - - - - - - - KEGG Pathway - - - - KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. - - urn:miriam:kegg.pathway - http://identifiers.org/kegg.pathway/ - http://www.genome.jp/kegg/pathway/ - - kegg.pathway - - urn:miriam:pubmed:22700311 - - - - http://www.genome.jp/kegg/pathway.html - hsa00620 - http://www.kegg.jp/entry/$id - KEGG PATHWAY Database - Kyoto University Bioinformatics Center - Japan - - - - pathway - - - - - model - rule - reaction - event - - - - - - - KEGG Compound - - - - KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life. - - urn:miriam:kegg.compound - http://identifiers.org/kegg.compound/ - http://www.genome.jp/kegg/compound/ - - kegg.compound - - urn:miriam:pubmed:22700311 - - - - http://www.genome.jp/kegg/ligand.html - C12345 - http://www.kegg.jp/entry/$id - KEGG LIGAND Database - Kyoto University Bioinformatics Center - Japan - - - - chemical - metabolite - structure - - - - - species - parameter - - - - - - - KEGG Reaction - - - - KEGG reaction contains our knowledge on the universe of reactions that are relevant to life. - - urn:miriam:kegg.reaction - http://identifiers.org/kegg.reaction/ - http://www.genome.jp/kegg/reaction/ - - kegg.reaction - - urn:miriam:pubmed:22700311 - - - - http://www.genome.jp/kegg/reaction/ - R00100 - http://www.kegg.jp/entry/$id - KEGG Reaction Database - Kyoto University Bioinformatics Center - Japan - - - - reaction - - - - - reaction - event - rule - - - - - - - PubMed - PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. - - urn:miriam:pubmed - http://identifiers.org/pubmed/ - http://bio2rdf.org/pubmed - http://linkedlifedata.com/resource/pubmed/id/ - http://www.ncbi.nlm.nih.gov/PubMed/ - http://www.pubmed.gov/ - - pubmed - - urn:miriam:pubmed:16381840 - - - - http://www.ncbi.nlm.nih.gov/PubMed/ - 16333295 - http://www.ncbi.nlm.nih.gov/pubmed/$id - NCBI PubMed - National Center for Biotechnology Information (NCBI) - USA - - - http://www.hubmed.org/ - 16333295 - http://www.hubmed.org/display.cgi?uids=$id - HubMed - Alfred D. Eaton - United Kingdom - - - http://europepmc.org/ - 16333295 - http://europepmc.org/abstract/MED/$id - Europe PMC - Europe PubMed Central partners - UK - - - http://pubmed.bio2rdf.org/fct - 23735196 - http://pubmed.bio2rdf.org/describe/?url=http://bio2rdf.org/pubmed:$id - Bio2RDF - Bio2RDF.org - - - - http://linkedlifedata.com/ - 23735196 - http://linkedlifedata.com/resource/pubmed/id/$id - PubMed through Linkedlife data - Linkedlifedata, Ontotext, Sofia - Bulgaria - - - http://www.ebi.ac.uk/Databases/MEDLINE/medline.html - 16333295 - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-view+MedlineFull+[medline-PMID:$id] - PubMed through SRS@EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.ebi.ac.uk/citexplore/ - 16333295 - http://www.ebi.ac.uk/citexplore/citationDetails.do?dataSource=MED&externalId=$id - CiteXplore - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://ukpmc.ac.uk/ - 16333295 - http://ukpmc.ac.uk/abstract/MED/$id - PubMed through UK PubMed Central - UKPMC Funders Group - UK - - - - bibliography - schema.org - - - - - model - species - reaction - parameter - - - - - - - OMIM - - Online Mendelian Inheritance in Man - Mendelian Inheritance in Man - MIM - - Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. - - urn:miriam:omim - http://identifiers.org/omim/ - http://bio2rdf.org/omim - http://www.ncbi.nlm.nih.gov/OMIM/ - - omim - - urn:miriam:pubmed:15608251 - - - - http://omim.org/ - 603903 - http://omim.org/entry/$id - OMIM at John Hopkins - Johns Hopkins University, Baltimore, Maryland - USA - - - http://omim.bio2rdf.org/fct - 603903 - http://omim.bio2rdf.org/describe/?url=http://bio2rdf.org/omim:$id - Bio2RDF - Bio2RDF.org - - - - http://mirror.omim.org/ - 603903 - http://mirror.omim.org/entry/$id - OMIM mirror at John Hopkins - Johns Hopkins University, Baltimore, Maryland - USA - - - http://us-east.omim.org/ - 603903 - http://us-east.omim.org/entry/$id - OMIM (East Coast mirror) - OMIM, Virgina - USA - - - http://europe.omim.org/ - 603903 - http://europe.omim.org/entry/$id - OMIM (EBI mirror) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - disorder - human - phenotype - - - - - model - species - parameter - - - - - - - PIRSF - - Protein Information Resource - - The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. - - urn:miriam:pirsf - http://identifiers.org/pirsf/ - http://pir.georgetown.edu/pirsf/ - - pirsf - - urn:miriam:pubmed:14681371 - - - - http://pir.georgetown.edu/ - PIRSF000100 - http://pir.georgetown.edu/cgi-bin/ipcSF?id=$id - PIRSF - Georgetown University Medical Center - USA - - - - clustering - protein - - - - - species - parameter - - - - - - - Reactome - - Reactome Stable ID - - The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology. - - urn:miriam:reactome - http://identifiers.org/reactome/ - http://www.reactome.org/ - - reactome - - urn:miriam:pubmed:24243840 - - - - http://www.reactome.org/ - R-HSA-201451 - http://reactome.org/content/detail/$id - Reactome, a curated knowledgebase of biological pathways - Ontario Institute for Cancer Research, NYU Medical School, Cold Spring Harbor Laboratory and European Bioinformatics Institute - Canada / USA / UK - - - - human - pathway - reaction - schema.org - - - - - model - rule - reaction - event - species - - - - - - - DOI - - Digital Object Identifier - - The Digital Object Identifier System is for identifying content objects in the digital environment. - - urn:miriam:doi - http://identifiers.org/doi/ - http://www.doi.org/ - - doi - - - http://www.doi.org/ - 10.1038/nbt1156 - http://doi.org/$id - Digital Object Identifier - International DOI Foundation - United Kingdom - - - http://www.handle.net/index.html - 10.1038/nbt1156 - http://hdl.handle.net/$id - CNRI DOI Resolver - Corporation for National Research Initiatives - USA - - - http://doai.io/ - 10.1038/nbt1156 - http://doai.io/$id - DOAI (Digital Open Access Identifier) at CAPSH - CAPSH (Committee for the Accessibility of Publications in Sciences and Humanities), Paris - France - - - - bibliography - - - - - model - species - reaction - parameter - - - - - - - Protein Data Bank - - PDB - - The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. - - urn:miriam:pdb - http://identifiers.org/pdb/ - http://www.pdb.org/ - - pdb - - urn:miriam:pubmed:17142228 - urn:miriam:pubmed:10592235 - - - - http://www.pdb.org/ - 2gc4 - http://www.rcsb.org/pdb/explore/explore.do?structureId=$id - RCSB PDB - Rutgers, The State University of New Jersey - USA - - - http://www.pdbe.org/ - 2gc4 - http://www.pdbe.org/$id - Protein Databank in Europe (PDBe) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.proteopedia.org/ - 2gc4 - http://proteopedia.org/wiki/index.php/$id - Proteopedia - Weizmann Institute of Science - Israel - - - http://www.pdbj.org/ - 2gc4 - http://pdbj.org/mine/summary/$id - Protein Data Bank Japan (PDBj) - Institute for Protein Research, Osaka University - Japan - - - http://www.ebi.ac.uk/pdbsum/ - 2gc4 - http://www.ebi.ac.uk/pdbsum/$id - Protein Databank through PDBsum - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - structure - - - - - species - - - - - - - The EBI stopped providing this service. - CluSTr - The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons (Smith-Waterman) between protein sequences. - - urn:miriam:clustr - http://identifiers.org/clustr/ - http://www.ebi.ac.uk/clustr/ - - clustr - - urn:miriam:pubmed:15961444 - http://www.ebi.ac.uk/clustr/documentation.html - - - - http://www.ebi.ac.uk/clustr/ - HUMAN:55140:308.6 - http://www.ebi.ac.uk/clustr-srv/CCluster?interpro=yes&cluster_varid=$id - CluSTr Database - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - clustering - protein - - - - - species - - - - - - - Gene Ontology - - GO - - The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. - - urn:miriam:go - http://identifiers.org/go/ - http://bio2rdf.org/go - http://purl.obolibrary.org/obo/GO - http://www.geneontology.org/ - http://identifiers.org/obo.go/ - urn:miriam:obo.go - - go - - urn:miriam:pubmed:14681407 - urn:miriam:pubmed:10802651 - - - - http://www.ebi.ac.uk/QuickGO/ - GO:0006915 - http://www.ebi.ac.uk/QuickGO/GTerm?id=$id - QuickGO (Gene Ontology browser) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://amigo.geneontology.org/ - GO:0006915 - http://amigo.geneontology.org/amigo/term/$id - AmiGO 2 - The Gene Ontology Consortium - USA - - - http://www.informatics.jax.org/searches/GO_form.shtml - GO:0006915 - http://www.informatics.jax.org/searches/GO.cgi?id=$id - GO Browser - The Jackson Laboratory - USA - - - http://bioportal.bioontology.org/ontologies/GO - GO:0006915 - http://purl.bioontology.org/ontology/GO/$id - GO through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - http://www.pantherdb.org/ - GO:0000003 - http://www.pantherdb.org/panther/category.do?categoryAcc=$id - GO through PANTHER - Keck School of Medicine, University of Southern California - USA - - - https://www.ebi.ac.uk/ols/ontologies/go - GO:0006915 - https://www.ebi.ac.uk/ols/ontologies/go/terms?obo_id=$id - GO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://ep.ebi.ac.uk/EP/GO/ - GO:0006915 - http://www.bioinf.ebc.ee/EP/EP/GO/?Q=$id - EP:GO, Browser and analysis for Gene Ontology - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/ - GO:0006915 - http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/term/$id - GO through Amigo2 (prototype) - Berkeley Bioinformatics Open-source Projects, Lawrence Berkeley National Lab, Berkeley, California - USA - - - - ontology - - - - - model - compartment - species - rule - reaction - event - parameter - - - - - - - SGD - - Saccharomyces Genome Database - - The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. - - urn:miriam:sgd - http://identifiers.org/sgd/ - http://bio2rdf.org/sgd - http://www.yeastgenome.org/ - - sgd - - urn:miriam:pubmed:14681421 - - - - http://www.yeastgenome.org/ - S000003909 - http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=$id - SGD - Stanford University - USA - - - http://sgd.bio2rdf.org/fct - S000003909 - http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$id - Bio2RDF - Bio2RDF.org - - - - - - This data collection can be referenced through two different identifier patterns. We recommend the use of identifiers of the form 'S\d+'. - http://www.yeastgenome.org/help/community/nomenclature-conventions - - - - eukaryotic - genome - nucleotide - - - - - species - parameter - - - - - - - Systems Biology Ontology - - SBO - - The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. - - urn:miriam:sbo - http://identifiers.org/sbo/ - urn:miriam:biomodels.sbo - urn:miriam:obo.sbo - http://www.biomodels.net/SBO/ - http://biomodels.net/SBO/ - - sbo - - urn:miriam:pubmed:17118155 - - - - http://www.ebi.ac.uk/sbo/ - SBO:0000262 - http://www.ebi.ac.uk/sbo/main/$id - SBO - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.ebi.ac.uk/ols/ontologies/sbo - SBO:0000262 - https://www.ebi.ac.uk/ols/ontologies/sbo/terms?obo_id=$id - SBO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/SBO - SBO:0000262 - http://purl.bioontology.org/ontology/SBO/$id - SBO through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - compartment - event - model - parameter - reaction - rule - species - speciesType - - - - - - - KEGG Drug - - - - KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules. - - urn:miriam:kegg.drug - http://identifiers.org/kegg.drug/ - http://www.genome.jp/kegg/drug/ - - kegg.drug - - urn:miriam:pubmed:16381885 - - - - http://www.genome.jp/kegg/drug/ - D00123 - http://www.kegg.jp/entry/$id - KEGG DRUG Database - Kyoto University Bioinformatics Center - Japan - - - - drug - structure - - - - - species - - - - - - - KEGG Glycan - - - - KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. - - urn:miriam:kegg.glycan - http://identifiers.org/kegg.glycan/ - http://www.genome.jp/kegg/glycan/ - - kegg.glycan - - urn:miriam:pubmed:16014746 - - - - http://www.genome.jp/kegg/glycan/ - G00123 - http://www.kegg.jp/entry/$id - KEGG GLYCAN Database - Kyoto University Bioinformatics Center - Japan - - - - polysaccharide - structure - - - - - species - - - - - - - WormBase - WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references genes. - - urn:miriam:wormbase - http://identifiers.org/wormbase/ - http://bio2rdf.org/wormbase - http://www.wormbase.org/ - - wormbase - - urn:miriam:pubmed:11125056 - urn:miriam:pubmed:17099234 - urn:miriam:pubmed:17099225 - urn:miriam:pubmed:16988424 - urn:miriam:pubmed:16381915 - urn:miriam:pubmed:16232125 - urn:miriam:pubmed:15608221 - urn:miriam:pubmed:15489338 - urn:miriam:pubmed:14681445 - urn:miriam:pubmed:12519966 - - - - http://www.wormbase.org/ - WBGene00000001 - http://www.wormbase.org/db/gene/gene?name=$id;class=Gene - WormBase (Master) - Cold Spring Harbor Laboratory - USA - - - http://wormbase.bio2rdf.org/fct - WBGene00000001 - http://wormbase.bio2rdf.org/describe/?url=http://bio2rdf.org/wormbase:$id - Bio2RDF - Bio2RDF.org - - - - http://wormbase.sanger.ac.uk/ - WBGene00000001 - http://wormbase.sanger.ac.uk/db/gene/gene?name=$id;class=Gene - Sanger WormBase Mirror - Wellcome Trust Sanger Institute - United Kingdom - - - http://imbb.wormbase.org/ - WBGene00000001 - http://imbb.wormbase.org/db/gene/gene?name=$id;class=Gene - WormBase Mirror in Crete - Institute of Molecular Biology and Biotechnology - Greece - - - http://caltech.wormbase.org/ - WBGene00000001 - http://caltech.wormbase.org/db/gene/gene?name=$id;class=Gene - Caltech WormBase Mirror - California Institute of Technology - USA - - - http://crfb-3.univ-mrs.fr/ - WBGene00000001 - http://crfb-3.univ-mrs.fr/db/gene/gene?name=$id;class=Gene - WormBase Mirror at Marseille-Nice Genopole - Marseille-Nice Genopole - France - - - - - This data collection's records can be referenced through two different identifier patterns. We recommend the use of identifiers of the form 'WBGene\d{8}'. - http://www.wormbase.org/about/userguide/nomenclature - - - - expression - genome - nucleotide - protein - - - - - species - - - - - - - Pfam - - Protein Family Database - - The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. - - urn:miriam:pfam - http://identifiers.org/pfam/ - http://pfam.org/ - - pfam - - urn:miriam:pubmed:9847196 - urn:miriam:pubmed:14681378 - urn:miriam:pubmed:11752314 - urn:miriam:pubmed:10592242 - urn:miriam:pubmed:9399864 - urn:miriam:pubmed:9223186 - - - - http://pfam.xfam.org/ - PF01234 - http://pfam.xfam.org/family/$id - Pfam at EMBL-EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://pfam.sanger.ac.uk/ - PF01234 - http://pfam.sanger.ac.uk/family/$id/ - Sanger Pfam Mirror - Wellcome Trust Sanger Institute - United Kingdom - - - http://pfam.sbc.su.se/ - PF01234 - http://pfam.sbc.su.se/family/$id - Sweden Pfam Mirror - Karolinska Institutet - Sweden - - - http://pfam.janelia.org/ - PF01234 - http://pfam.janelia.org/family/$id - Janelia Farm Research Campus Pfam Mirror - Howard Hughes Medical Institute - USA - - - http://pfam.jouy.inra.fr/ - PF01234 - http://pfam.jouy.inra.fr/cgi-bin/getdesc?acc=$id - INRA Pfam Mirror - Institut National de la Recherche Agronomique - France - - - http://pfam.ccbb.re.kr/index.shtml - PF01234 - http://pfam.ccbb.re.kr/cgi-bin/getdesc?acc=$id - CCBB Pfam Mirror - Center for Computational Biology and Bioinformatics - Korea - - - - domain - protein - - - - - species - - - - - - - Nucleotide Sequence Database - - International Nucleotide Sequence Database Collaboration - INSDC - NCBI nucleotide - GenBank - - The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. - - urn:miriam:insdc - http://identifiers.org/insdc/ - http://www.insdc.org/ - - insdc - - urn:miriam:pubmed:17148479 - urn:miriam:pubmed:17202161 - urn:miriam:pubmed:2326192 - urn:miriam:pubmed:12436968 - http://www.ebi.ac.uk/embl/Contact/collaboration.html - http://insdc.org/ - http://www.ddbj.nig.ac.jp/sub/acc_def-e.html - - - - http://www.ncbi.nlm.nih.gov/Genbank/ - X58356 - http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$id - INSDC through GenBank - National Center for Biotechnology Information (NCBI) - USA - - - http://www.ddbj.nig.ac.jp/ - X58356 - http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$id - INSDC through DDBJ - DNA Data Bank of Japan, Mishima, Shizuoka - Japan - - - http://www.ebi.ac.uk/ena/ - X58356 - http://www.ebi.ac.uk/ena/data/view/$id - INSDC through European Nucleotide Archive (ENA) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.ncbi.nlm.nih.gov/nuccore/ - X58356 - http://www.ncbi.nlm.nih.gov/nuccore/$id - INSDC through Nucleotide database at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+EMBL - X58356 - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[EMBL:$id]+-view+EmblEntry - INSDC through SRS at EMBL-EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - nucleotide - sequence - - - - - species - - - - - - - FlyBase - FlyBase is the database of the Drosophila Genome Projects and of associated literature. - - urn:miriam:flybase - http://identifiers.org/flybase/ - http://www.flybase.org/ - - flybase - - http://www.flybase.org/static_pages/docs/flybase-publications.html - - - - http://flybase.org/ - FBgn0011293 - http://flybase.org/reports/$id.html - The FlyBase Database - The FlyBase Consortium - USA / United Kingdom - - - - eukaryotic - genome - nucleotide - - - - - species - - - - - - - Wormpep - Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. - - urn:miriam:wormpep - http://identifiers.org/wormpep/ - http://www.wormpep.org/ - - wormpep - - http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep_format.shtml - - - - http://www.wormbase.org/db/seq/protein - CE28239 - http://www.wormbase.org/db/seq/protein?name=WP:$id - Wormpep (Master) - Cold Spring Harbor Laboratory - USA - - - http://wormbase.sanger.ac.uk/ - CE28239 - http://wormbase.sanger.ac.uk/db/seq/protein?name=WP:$id - Sanger Wormpep Mirror - Wellcome Trust Sanger Institute - United Kingdom - - - http://imbb.wormbase.org/db/seq/protein - CE28239 - http://imbb.wormbase.org/db/seq/protein?name=$id - Wormpep Mirror in Crete - Institute of Molecular Biology and Biotechnology - Greece - - - http://caltech.wormbase.org/db/seq/protein - CE28239 - http://caltech.wormbase.org/db/seq/protein?name=$id - Caltech Wormpep Mirror - California Institute of Technology - USA - - - http://crfb-3.univ-mrs.fr/db/seq/protein - CE28239 - http://crfb-3.univ-mrs.fr/db/seq/protein?name=$id - Wormpep Mirror at Marseille-Nice Genopole - Marseille-Nice Genopole - France - - - - genome - protein - - - - - species - - - - - - - PROSITE - PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. - - urn:miriam:prosite - http://identifiers.org/prosite/ - http://www.prosite.org/ - - prosite - - urn:miriam:pubmed:16381852 - - - - http://www.expasy.org/prosite/ - PS00001 - http://prosite.expasy.org/$id - ExPASy PROSITE - Swiss Institute of Bioinformatics (SIB) - Switzerland - - - http://www.expasy.org/prosite/ - PS00001 - http://www.expasy.org/cgi-bin/get-prosite-entry?$id - Original PROSITE - Swiss Institute of Bioinformatics (SIB) - Switzerland - - - - domain - protein - - - - - species - - - - - - - PubChem-substance - - PubChem Substance - PubChem SID - - PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records. - - urn:miriam:pubchem.substance - http://identifiers.org/pubchem.substance/ - http://www.pubchem.gov/substance/ - - pubchem.substance - - urn:miriam:pubmed:17170002 - - - - http://pubchem.ncbi.nlm.nih.gov/ - 100101 - http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=$id - NCBI PubChem Substance - National Center for Biotechnology Information (NCBI) - USA - - - - chemical - - - - - species - parameter - - - - - - - PubChem-compound - - PubChem Compound - PubChem CID - - PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records. - - urn:miriam:pubchem.compound - http://identifiers.org/pubchem.compound/ - http://www.pubchem.gov/compound/ - - pubchem.compound - - urn:miriam:pubmed:17170002 - - - - http://pubchem.ncbi.nlm.nih.gov/ - 100101 - http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=$id - NCBI PubChem Compound - National Center for Biotechnology Information (NCBI) - USA - - - - chemical - metabolite - structure - - - - - species - parameter - - - - - - - arXiv - arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology. - - urn:miriam:arxiv - http://identifiers.org/arxiv/ - urn:oai:arXiv.org - http://arxiv.org/ - - arxiv - - - http://arxiv.org/ - 0807.4956v1 - http://arxiv.org/abs/$id - Cornell University arXiv - Cornell University - USA - - - - bibliography - - - - - model - - - - - - - ArrayExpress - ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. - - urn:miriam:arrayexpress - http://identifiers.org/arrayexpress/ - http://arrayexpress.org/ - - arrayexpress - - urn:miriam:pubmed:12519949 - - - - http://www.ebi.ac.uk/arrayexpress/ - E-MEXP-1712 - http://www.ebi.ac.uk/arrayexpress/experiments/$id - ArrayExpress - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.omicsdi.org/ - E-MEXP-1712 - https://www.omicsdi.org/dataset/arrayexpress-repository/$id - ArrayExpress through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - expression - microarray - nucleotide - - - - - Mouse Genome Database - - MGD - MGI - Mouse Genome Informatics - - The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. - - urn:miriam:mgi - http://identifiers.org/mgi/ - http://bio2rdf.org/mgi: - http://identifiers.org/mgd/ - http://mousegenome.org/ - urn:miriam:mgd - - mgi - - urn:miriam:pubmed:15608240 - http://www.informatics.jax.org/mgihome/projects/overview.shtml#aboutMGD - - - - http://www.informatics.jax.org/ - MGI:2442292 - http://www.informatics.jax.org/accession/$id - Mouse Genome Informatics Database - The Jackson Laboratory - USA - - - http://mgi.bio2rdf.org/fct - 2442292 - http://mgi.bio2rdf.org/describe/?url=http://bio2rdf.org/mgi:$id - Bio2RDF - Bio2RDF.org - - - - - expression - phenotype - sequence - - - - - species - - - - - - - SABIO-RK Reaction - SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. - - urn:miriam:sabiork.reaction - http://identifiers.org/sabiork.reaction/ - http://sabio.villa-bosch.de/reaction/ - - sabiork.reaction - - urn:miriam:doi:10.1186%2F1752-0509-1-S1-P4 - urn:miriam:doi:10.1186%2F1752-0509-1-S1-S6 - http://www.bioinfo.de/isb/2007/07/S1/05/ - http://www.springerlink.com/content/kw1kv13614272400/?p=9b9a98e3b7c04ec189cd2927fcc83808&pi=8 - - - - http://sabiork.h-its.org/ - 75 - http://sabiork.h-its.org/newSearch?q=sabioreactionid:$id - SABIO-RK reaction - Heidelberg Institute for Theoretical Studies (HITS gGmbH) - Germany - - - - kinetics - pathway - reaction - - - - - reaction - - - - - - - RefSeq - The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. - - urn:miriam:refseq - http://identifiers.org/refseq/ - - refseq - - urn:miriam:pubmed:17130148 - - - - http://www.ncbi.nlm.nih.gov/projects/RefSeq/ - NP_012345 - http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$id - The NCBI Reference Sequence database - NCBI, NIH, Bethesda, Maryland - USA - - - - annotation - mammalian - protein - sequence - - - - - species - - - - - - - Transport Classification Database - - TCDB - - The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. - - urn:miriam:tcdb - http://identifiers.org/tcdb/ - - tcdb - - urn:miriam:pubmed:16381841 - - - - http://www.tcdb.org/ - 5.A.1.1.1 - http://www.tcdb.org/search/result.php?tc=$id - TCDB - Division of Biological Sciences, UCSD - USA - - - - classification - interaction - protein - - - - - species - - - - - - - UniParc - The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases. - - urn:miriam:uniparc - http://identifiers.org/uniparc/ - - uniparc - - urn:miriam:pubmed:14681372 - - - - http://www.ebi.ac.uk/uniparc/ - UPI000000000A - http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$id - UniProt Archive (UniParc) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.uniprot.org/uniparc/ - UPI000000000A - http://www.uniprot.org/uniparc/$id - UniParc through UniProt - UniProt Consortium - USA, UK and Switzerland - - - - protein - - - - - species - - - - - - - MINT - The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals. - - urn:miriam:mint - http://identifiers.org/mint/ - - mint - - urn:miriam:pubmed:17135203 - - - - http://mint.bio.uniroma2.it/mint/ - MINT-10000 - http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$id - The Molecular INTeraction database (MINT) - University of Rome Tor Vergata, Rome - Italy - - - http://www.ebi.ac.uk/intact/ - MINT-7905142 - http://www.ebi.ac.uk/intact/query/interaction_id:$id - MINT subset through IntAct - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - interaction - protein - - - - - As of April 2013, this collection is no longer maintained. An ftp archive is available at ftp://ftp.ebi.ac.uk/pub/databases/IPI. - IPI - - International Protein Index - - The International Protein Index (IPI) provides complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases - - urn:miriam:ipi - http://identifiers.org/ipi/ - - ipi - - urn:miriam:pubmed:15221759 - - - - http://www.ebi.ac.uk/IPI - IPI00000001 - http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ipi&id=$id&format=default&style=html - IPI (International Protein Index) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - eukaryotic - protein - - - - - species - - - - - - - Database of Interacting Proteins - - DIP - - The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions - - urn:miriam:dip - http://identifiers.org/dip/ - - dip - - urn:miriam:pubmed:14681454 - - - - http://dip.doe-mbi.ucla.edu/ - DIP-743N - http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$id - Database of interacting proteins - UCLA - USA - - - - interaction - protein - - - - - species - - - - - - - Signaling Gateway - - SGMP - Signaling Gateway Molecule Pages - AfCS - UCSD Signaling Gateway Molecule Pages - UCSD - Molecule Pages - - The Signaling Gateway provides information on mammalian proteins involved in cellular signaling. - - urn:miriam:signaling-gateway - http://identifiers.org/signaling-gateway/ - - signaling-gateway - - urn:miriam:pubmed:17965093 - urn:miriam:pubmed:12478304 - urn:miriam:pubmed:21505029 - - - - http://www.signaling-gateway.org/molecule - A001094 - http://www.signaling-gateway.org/molecule/query?afcsid=$id - Signaling Gateway Molecule Pages - UC San Diego - USA - - - - mammalian - protein - - - - - RESID - The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. - - urn:miriam:resid - http://identifiers.org/resid/ - - resid - - urn:miriam:pubmed:15174124 - urn:miriam:doi:10.1093%2Fnar%2Fgkg038 - - - - http://pir0.georgetown.edu/resid/ - AA0001 - http://pir0.georgetown.edu/cgi-bin/resid?id=$id - RESID at Georgetown University - Georgetown University Medical Center, Washington - USA - - - http://www.ebi.ac.uk/RESID/ - AA0001 - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+6JSUg1NA6u4+-e+[RESID:'$id'] - RESID - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - structure - - - - - species - - - - - - - Rat Genome Database - - RGD - - Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. - - urn:miriam:rgd - http://identifiers.org/rgd/ - - rgd - - urn:miriam:pubmed:17151068 - - - - http://rgd.mcw.edu/ - 2018 - http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$id - Rat Genome Database - Medical College of Wisconsin - USA - - - - annotation - disease - eukaryotic - gene - genome - mammalian - nucleotide - pathway - phenotype - sequence - - - - - species - - - - - - - TAIR Protein - The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept - - urn:miriam:tair.protein - http://identifiers.org/tair.protein/ - - tair.protein - - urn:miriam:pubmed:12444417 - - - - http://arabidopsis.org/index.jsp - AASequence:1009107926 - http://arabidopsis.org/servlets/TairObject?accession=$id - The Arabidopsis Information Resource (TAIR) Protein - Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR) - USA - - - - eukaryotic - genome - plant - protein - - - - - species - - - - - - - TAIR Gene - The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. - - urn:miriam:tair.gene - http://identifiers.org/tair.gene/ - - tair.gene - - urn:miriam:pubmed:12444417 - - - - http://arabidopsis.org/index.jsp - Gene:2200934 - http://arabidopsis.org/servlets/TairObject?accession=$id - The Arabidopsis Information Resource (TAIR) Gene - Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR) - USA - - - - eukaryotic - gene - genome - nucleotide - plant - - - - - species - - - - - - - TAIR Locus - The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. - - urn:miriam:tair.locus - http://identifiers.org/tair.locus/ - - tair.locus - - urn:miriam:pubmed:12444417 - - - - http://arabidopsis.org/index.jsp - Locus:2200950 - http://www.arabidopsis.org/servlets/TairObject?accession=$id - The Arabidopsis Information Resource (TAIR) Locus - Carnegie Institution of Washington Department of Plant Biology and National Center for Genome Resources (NCGR) - USA - - - - eukaryotic - genome - plant - - - - - species - - - - - - - HMDB - - Human Metabolome Database - - The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. - - urn:miriam:hmdb - http://identifiers.org/hmdb/ - http://www.hmdb.ca/ - - hmdb - - urn:miriam:pubmed:17202168 - - - - http://www.hmdb.ca/ - HMDB00001 - http://www.hmdb.ca/metabolites/$id - The Human Metabolome Database - University of Alberta, Edmonton, AB - Canada - - - - chemical - human - metabolite - - - - - species - parameter - - - - - - - LIPID MAPS - - LMSD - - The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. - - urn:miriam:lipidmaps - http://identifiers.org/lipidmaps/ - - lipidmaps - - urn:miriam:pubmed:17098933 - urn:miriam:pubmed:15722563 - - - - http://www.lipidmaps.org - LMPR0102010012 - http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$id - Department of Bioengineering and the San Diego Supercomputer Center - University of California, San Diego - USA - - - - lipid - structure - taxonomy - - - - - species - - - - - - - PeptideAtlas - The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. - - urn:miriam:peptideatlas - http://identifiers.org/peptideatlas/ - - peptideatlas - - urn:miriam:pubmed:18451766 - - - - http://www.peptideatlas.org/ - PAp00000009 - https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$id - PeptideAtlas at ISB - Institute for Systems Biology, Seattle - USA - - - - mass spectrometry - - - - - species - parameter - - - - - - - GEO - - Gene Expression Omnibus - - The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. - - urn:miriam:geo - http://identifiers.org/geo/ - - geo - - urn:miriam:pubmed:11752295 - - - - http://www.ncbi.nlm.nih.gov/geo/ - GDS1234 - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$id - Gene Expression Omnibus at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - expression - microarray - nucleotide - - - - - Evidence Code Ontology - - ECO - - Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. - - urn:miriam:eco - http://identifiers.org/eco/ - urn:miriam:obo.eco - http://identifiers.org/obo.eco/ - - eco - - http://www.geneontology.org/GO.evidence.shtml - - - - https://www.ebi.ac.uk/ols/ontologies/eco - ECO:0000006 - https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=$id - Evidence Codes via the Ontology Lookup Service (OLS) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/ECO - ECO:0000006 - http://purl.bioontology.org/ontology/ECO/$id - Evidence Code Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - classification - - - - - Protein Modification Ontology - - PSI-MOD - MOD - - The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. - - urn:miriam:mod - http://identifiers.org/mod/ - http://identifiers.org/obo.psi-mod/ - urn:miriam:obo.psi-mod - urn:miriam:psimod - - mod - - http://psidev.sourceforge.net/mod/data/PSI-MOD.obo - - - - https://www.ebi.ac.uk/ols/ontologies/mod - MOD:00001 - https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=$id - Protein modifications ontology via the Ontology Lookup Service (OLS) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/PSIMOD - MOD:00001 - http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=$id - Protein modifications ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - protein - - - - - species - reaction - - - - - - - Saccharomyces genome database pathways - Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). - - urn:miriam:sgd.pathways - http://identifiers.org/sgd.pathways/ - - sgd.pathways - - urn:miriam:pubmed:14681421 - - - - http://pathway.yeastgenome.org/ - PWY3O-214 - http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$id - Saccharomyces cerevisiae pathways at SGD. - SGD, Stanford University - USA - - - - genome - pathway - sequence - - - - - model - reaction - - - - - - - BioGRID - BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe. - - urn:miriam:biogrid - http://identifiers.org/biogrid/ - - biogrid - - urn:miriam:pubmed:16381927 - - - - http://thebiogrid.org/ - 31623 - http://thebiogrid.org/$id - BioGRID database of physical and genetic interactions - Ontario Cancer Institute - Canada - - - - gene - interaction - protein - - - - - species - - - - - - - MEROPS - The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. - - urn:miriam:merops - http://identifiers.org/merops/ - - merops - - urn:miriam:pubmed:17991683 - - - - http://merops.sanger.ac.uk/index.htm - S01.001 - http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=$id - MEROPS database at Sanger Institute - Wellcome Trust Sanger Institute - United Kingdom - - - - enzyme - protein - - - - - species - - - - - - - PANTHER Family - The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families. - - urn:miriam:panther.family - http://identifiers.org/panther.family/ - urn:miriam:panther - - panther.family - - urn:miriam:pubmed:12952881 - - - - http://www.pantherdb.org/ - PTHR12345 - http://www.pantherdb.org/panther/family.do?clsAccession=$id - PANTHER Family at USC (Los Angeles) - Keck School of Medicine, University of Southern California - USA - - - - gene - - - - - species - - - - - - - PRINTS - - SPRINT - - PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. - - urn:miriam:prints - http://identifiers.org/prints/ - urn:miriam:sprint - - prints - - urn:miriam:pubmed:10592232 - - - - http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ - PR00001 - http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$id&display_opts=Prints&category=None&queryform=false&regexpr=off - PRINTS through SPRINT - University of Manchester - United Kingdom - - - - domain - protein - - - - - species - - - - - - - Ligand Expo - - Ligand Depot - - Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids. - - urn:miriam:ligandexpo - http://identifiers.org/ligandexpo/ - - ligandexpo - - urn:miriam:pubmed:15059838 - - - - http://ligand-depot.rutgers.edu/index.html - ABC - http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid - Ligand Expo at RutgersRCSB PDB - Rutgers, The State University of New Jersey - USA - - - http://ligand-expo.rcsb.org/ - ABC - http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$id&operation=ccid - Ligand Expo at Rutgers - Rutgers, The State University of New Jersey - USA - - - - interaction - structure - - - - - species - - - - - - - Aclame - ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. - - urn:miriam:aclame - http://identifiers.org/aclame/ - - aclame - - urn:miriam:pubmed:14681355 - - - - http://aclame.ulb.ac.be/ - mge:2 - http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=$id - Aclame database of mobile genetic elements - Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles - Belgium - - - - gene - - - - - species - - - - - - - ISBN - The International Standard Book Number (ISBN) is for identifying printed books. - - urn:miriam:isbn - http://identifiers.org/isbn/ - - isbn - - http://www.worldcat.org/whatis/default.jsp - - - - http://isbndb.com/ - 9781584885658 - http://isbndb.com/search-all.html?kw=$id - ISBNDB - ISBN Database - ISNBdb project, San Gabriel, California - USA - - - http://www.worldcat.org/ - 9781584885658 - http://www.worldcat.org/isbn/$id - ISBN database at WorldCat - OCLC Online Computer Library Center, Inc. Ohio - USA - - - - bibliography - - - - - model - species - parameter - reaction - - - - - - - PRIDE - The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. - - urn:miriam:pride - http://identifiers.org/pride/ - - pride - - urn:miriam:pubmed:16381953 - urn:miriam:pubmed:16041671 - urn:miriam:pubmed:18033805 - urn:miriam:pubmed:18428683 - - - - http://www.ebi.ac.uk/pride/ - 1 - http://www.ebi.ac.uk/pride/archive/assays/$id - PRIDE at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - - - - - model - - - - - - - 3DMET - 3DMET is a database collecting three-dimensional structures of natural metabolites. - - urn:miriam:3dmet - http://identifiers.org/3dmet/ - - 3dmet - - http://www.jsbi.org/journal/GIW04/GIW04P058.pdf - http://pubs.acs.org/doi/ipdf/10.1021/ci300309k - - - - http://www.3dmet.dna.affrc.go.jp/ - B00162 - http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$id - 3DMET database - Bioinformatics Research Unit, National Institute of Agrobiological Sciences - Japan - - - - chemical - metabolite - structure - - - - - species - parameter - - - - - - - FMA - - Foundational Model of Anatomy Ontology - - The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. - - urn:miriam:fma - http://identifiers.org/fma/ - http://identifiers.org/obo.fma/ - urn:miriam:obo.fma - - fma - - urn:miriam:pubmed:17271570 - - - - https://www.ebi.ac.uk/ols/ontologies/fma/ - FMA:67112 - https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=$id - Foundational Model of Anatomy via Ontology Lookup Service (OLS) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/FMA - FMA:67112 - http://purl.bioontology.org/ontology/FMA_subset/$id - Foundational Model of Anatomy through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - compartment - model - species - - - - - - - MatrixDB - MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. - - urn:miriam:matrixdb.association - http://identifiers.org/matrixdb.association/ - - matrixdb.association - - urn:miriam:pubmed:19147664 - - - - http://matrixdb.univ-lyon1.fr/ - P00747__P07355 - http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$id&class=Association - MatrixDB Association - Institut de Biologie et Chimie des Protéines, Lyon University - France - - - - interaction - lipid - polysaccharide - protein - - - - - species - - - - - - - NCBI Gene - - Entrez Gene - - Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. - - urn:miriam:ncbigene - http://identifiers.org/ncbigene/ - http://bio2rdf.org/ncbigene - urn:miriam:ncbi.gene - urn:miriam:entrez.gene - - ncbigene - - urn:miriam:pubmed:15608257 - - - - http://www.ncbi.nlm.nih.gov/gene - 100010 - http://www.ncbi.nlm.nih.gov/gene/$id - Entrez Gene (NCBI) - National Center for Biotechnology Information (NCBI) - USA - - - http://ncbigene.bio2rdf.org/fct - 100010 - http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$id - Bio2RDF - Bio2RDF.org - - - - - gene - genome - sequence - - - - - species - - - - - - - KEGG Genes - - - - KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources. - - urn:miriam:kegg.genes - http://identifiers.org/kegg.genes/ - http://www.genome.jp/kegg/genes/ - - kegg.genes - - urn:miriam:pubmed:16381885 - - - - http://www.genome.jp/kegg/genes.html - syn:ssr3451 - http://www.kegg.jp/entry/$id - KEGG GENES Database - Kyoto University Bioinformatics Center - Japan - - - - gene - - - - - species - - - - - - - BRENDA - BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. - - urn:miriam:brenda - http://identifiers.org/brenda/ - - brenda - - urn:miriam:pubmed:18984617 - - - - http://www.brenda-enzymes.org/ - 1.1.1.1 - http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$id - Brenda enzyme database - Technical University Braunschweig, Institute for Bioinformatics and Biochemistry - Germany - - - - enzyme - - - - - reaction - parameter - - - - - - - PubChem-bioassay - PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. - - urn:miriam:pubchem.bioassay - http://identifiers.org/pubchem.bioassay/ - - pubchem.bioassay - - urn:miriam:pubmed:17170002 - - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay - 1018 - http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=$id - PubChem Bioassay at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - chemical - - - - - species - parameter - - - - - - - Pathway Commons - Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. - - urn:miriam:pathwaycommons - http://identifiers.org/pathwaycommons/ - - pathwaycommons - - http://www.pathwaycommons.org/pc/ - - - - http://www.pathwaycommons.org/pc/ - 485991 - http://www.pathwaycommons.org/pc/record2.do?id=$id - Pathway Commons - Memorial Sloan-Kettering Cancer Center - USA - - - - - Interaction and pathway identifiers are not stable, and can vary between releases. - http://www.pathwaycommons.org/pc/faq.do#general - - - - pathway - - - - - reaction - - - - - - - HOVERGEN - HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. - - urn:miriam:hovergen - http://identifiers.org/hovergen/ - - hovergen - - urn:miriam:pubmed:15713731 - - - - http://pbil.univ-lyon1.fr/databases/hovergen.php - HBG004341 - http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$id&db=HOVERGEN - Hovergen - Laboratoire de Biométrie, Génétique et Biologie des Populations - France - - - - gene - - - - - species - - - - - - - Melanoma Molecular Map Project Biomaps - - MMMP Biomaps - - A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. - - urn:miriam:mmmp:biomaps - http://identifiers.org/biomaps/ - - biomaps - - http://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp - - - - http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp - 37 - http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$id - main webpage - Melanoma Molecular Map Project - - - - - pathway - - - - - reaction - species - - - - - - - WikiPathways - WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style. -All content is under the Creative Commons Attribution 3.0 Unported license. - - urn:miriam:wikipathways - http://identifiers.org/wikipathways/ - - wikipathways - - urn:miriam:pubmed:18651794 - - - - http://www.wikipathways.org/ - WP100 - http://www.wikipathways.org/instance/$id - Wikipathways - BiGCaT Bioinformatics (University of Maastricht) and Conklin Lab (UCSF). - Holland and USA - - - - pathway - - - - - model - reaction - - - - - - - MACiE - MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. - - urn:miriam:macie - http://identifiers.org/macie/ - - macie - - urn:miriam:pubmed:17082206 - - - - http://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html - M0001 - http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$id - MACiE database of mechanisms, annotation and classification in enzymes - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - classification - enzyme - - - - - reaction - species - - - - - - - miRBase Sequence - The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). - - urn:miriam:mirbase - http://identifiers.org/mirbase/ - - mirbase - - urn:miriam:pubmed:14681370 - urn:miriam:doi:10.1093%2Fnar%2Fgkj112 - - - - http://www.mirbase.org/ - MI0000001 - http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$id - miRBase Sequence Database - Faculty of Life Sciences, University of Manchester - UK - - - http://microrna.sanger.ac.uk/ - MI0000001 - http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=$id - miRBase Sequence Database - University of Manchester and Wellcome Trust Sanger institute - UK - - - - nucleotide - sequence - - - - - species - - - - - - - ZFIN Gene - ZFIN serves as the zebrafish model organism database. This collection references gene information. - - urn:miriam:zfin - http://identifiers.org/zfin/ - - zfin - - urn:miriam:pubmed:17991680 - - - - http://zfin.org - ZDB-GENE-041118-11 - http://zfin.org/$id - ZFIN Expression at University of Oregon - Zebrafish Information Network, University of Oregon - USA - - - - gene - - - - - species - - - - - - - HGNC - - HUGO Gene Nomenclature Committee - - The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database. - - urn:miriam:hgnc - http://identifiers.org/hgnc/ - http://bio2rdf.org/hgnc - - hgnc - - urn:miriam:pubmed:17984084 - urn:miriam:pubmed:20929869 - urn:miriam:pubmed:23161694 - - - - http://www.genenames.org - 2674 - http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$id - HUGO Genome Nomenclature Committee - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://hgnc.bio2rdf.org/fct - hgnc:2674 - http://hgnc.bio2rdf.org/describe/?url=http://bio2rdf.org/$id - Bio2RDF - Bio2RDF.org - - - - - gene - human - schema.org - - - - - species - - - - - - - Sequence Ontology - - SO - Sequence Types and Features - - The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. - - urn:miriam:so - http://identifiers.org/so/ - urn:miriam:obo.so - http://identifiers.org/obo.so/ - - so - - urn:miriam:pubmed:15892872 - - - - http://www.sequenceontology.org/ - SO:0000704 - http://www.sequenceontology.org/miso/current_release/term/$id - Sequence Ontology - Department of Molecular and Cellular Biology, University of California, Berkeley - USA - - - http://bioportal.bioontology.org/ontologies/SO - SO:0000704 - http://purl.bioontology.org/ontology/SO/$id - Sequence Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/so - SO:0000704 - https://www.ebi.ac.uk/ols/ontologies/so/terms?obo_id=$id - Sequence Ontology through Ontology Lookup Service (OLS) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - DNA - ontology - - - - - species - - - - - - - Rhea - Rhea is a manually annotated reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest), providing detailed information about structure, formulae and charge. It is populated with the reactions found in the EC list, IntEnz and ENZYME databases), as well as other biochemical reactions, including those that are often termed "spontaneous". - - urn:miriam:rhea - http://identifiers.org/rhea/ - - rhea - - urn:miriam:pubmed:25332395 - http://www.rhea-db.org/documentation - - - - http://www.rhea-db.org/ - 12345 - http://www.rhea-db.org/reaction?id=$id - Rhea - European Bioinformatics Institute and Swiss Institute of Bioinformatics - UK - - - - reaction - - - - - reaction - - - - - - - Unipathway - UniPathway is a manually curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway. - - urn:miriam:unipathway - http://identifiers.org/unipathway/ - - unipathway - - http://precedings.nature.com/documents/3214/version/1 - - - - http://www.grenoble.prabi.fr/obiwarehouse/unipathway - UPA00206 - http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$id - UniPathway - Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control - Switzerland - - - - pathway - - - - - model - reaction - - - - - - - ChEMBL compound - ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. - - urn:miriam:chembl.compound - http://identifiers.org/chembl.compound/ - http://bio2rdf.org/chembl - - chembl.compound - - urn:miriam:pubmed:19194660 - https://github.com/egonw/chembl.rdf - - - - https://www.ebi.ac.uk/chembldb/ - CHEMBL308052 - https://www.ebi.ac.uk/chembl/compound/inspect/$id - ChEMBL compound database at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://github.com/egonw/chembl.rdf - CHEMBL308052 - http://linkedchemistry.info/chembl/chemblid/$id - ChEMBL compound RDF - Maastricht University - The Netherlands - - - https://www.ebi.ac.uk/rdf/services/chembl/ - CHEMBL308052 - http://rdf.ebi.ac.uk/resource/chembl/molecule/$id - ChEMBL compound RDF through EBI RDF Platform - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - chemical - metabolite - - - - - species - parameter - - - - - - - ChEMBL target - ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. - - urn:miriam:chembl.target - http://identifiers.org/chembl.target/ - - chembl.target - - urn:miriam:pubmed:19194660 - https://github.com/egonw/chembl.rdf - - - - https://www.ebi.ac.uk/chembldb/ - CHEMBL3467 - https://www.ebi.ac.uk/chembl/target/inspect/$id - ChEMBL targets database at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://github.com/egonw/chembl.rdf - CHEMBL3467 - http://linkedchemistry.info/chembl/chemblid/$id - ChEMBL target RDF - Maastricht University - The Netherlands - - - http://rdf.ebi.ac.uk/resource/chembl/ - CHEMBL3467 - http://rdf.ebi.ac.uk/resource/chembl/target/$id - ChEMBL target RDF through EBI RDF Platform - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - - - - - parameter - species - - - - - - - SABIO-RK Kinetic Record - SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information. - - urn:miriam:sabiork.kineticrecord - http://identifiers.org/sabiork.kineticrecord/ - - sabiork.kineticrecord - - urn:miriam:pubmed:17822389 - urn:miriam:doi:10.1007%2F11799511_9 - urn:miriam:doi:10.2390%2Fbiecoll-jib-2007-49 - urn:miriam:doi:10.1186%2F1752-0509-1-S1-S6 - urn:miriam:doi:10.1186%2F1752-0509-1-S1-P4 - - - - http://sabiork.h-its.org/ - 5046 - http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$id - SABIO-RK Reaction Kinetics Database - Kinetic Dataset - Heidelberg Institute for Theoretical Studies (HITS gGmbH) - Germany - - - - kinetics - reaction - - - - - parameter - reaction - kineticLaw - - - - - - - Ligand-Gated Ion Channel database - - LGICdb - - The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. - - urn:miriam:lgic - http://identifiers.org/lgic/ - - lgic - - urn:miriam:pubmed:9847222 - - - - http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php - 5HT3Arano - http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$id.php - Ligand-Gated Ion Channel database at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - gene - protein - sequence - - - - - species - - - - - - - Anatomical Therapeutic Chemical - - ATC - - The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels. - - urn:miriam:atc - http://identifiers.org/atc/ - - atc - - http://www.whocc.no/atc_ddd_publications/guidelines/ - - - - http://www.whocc.no/atc_ddd_index/ - A10BA02 - http://www.whocc.no/atc_ddd_index/?code=$id - Anatomical Therapeutic Chemical Index at WHO - World Health Organisation - Switzerland - - - - classification - drug - - - - - species - - - - - - - PharmGKB Pathways - The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. -PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies. - - urn:miriam:pharmgkb.pathways - http://identifiers.org/pharmgkb.pathways/ - - pharmgkb.pathways - - urn:miriam:pubmed:11908751 - urn:miriam:pubmed:22103613 - - - - http://www.pharmgkb.org/ - PA146123006 - http://www.pharmgkb.org/pathway/$id - PharmGKB at Stanford - Department of Genetics, School of Medicine, Stanford University, Stanford, California - USA - - - - - The data may be used for research purposes only. - http://www.pharmgkb.org/home/policies/web-data.jsp - - - - pathway - pharmacogenomics - - - - - PharmGKB Disease - The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. - - urn:miriam:pharmgkb.disease - http://identifiers.org/pharmgkb.disease/ - - pharmgkb.disease - - urn:miriam:pubmed:11908751 - urn:miriam:pubmed:22103613 - - - - http://www.pharmgkb.org/ - PA447218 - http://www.pharmgkb.org/disease/$id - PharmGKB Disease at Stanford - Department of Genetics, School of Medicine, Stanford University, Stanford, California - USA - - - - - The data may be used for research purposes only. - http://www.pharmgkb.org/home/policies/web-data.jsp - - - - pharmacogenomics - - - - - model - - - - - - - PharmGKB Drug - The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. - - urn:miriam:pharmgkb.drug - http://identifiers.org/pharmgkb.drug/ - - pharmgkb.drug - - urn:miriam:pubmed:11908751 - urn:miriam:pubmed:22103613 - - - - http://www.pharmgkb.org/ - PA448710 - http://www.pharmgkb.org/drug/$id - PharmGKB Drug at Stanford - Department of Genetics, School of Medicine, Stanford University, Stanford, California - USA - - - - - The data may be used for research purposes only. - http://www.pharmgkb.org/home/policies/web-data.jsp - - - - drug - pharmacogenomics - - - - - TTD Drug - - Therapeutic Target Database - - The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. - - urn:miriam:ttd.drug - http://identifiers.org/ttd.drug/ - - ttd.drug - - urn:miriam:pubmed:11752352 - urn:miriam:pubmed:24265219 - - - - http://bidd.nus.edu.sg/group/ttd/ttd.asp - DAP000773 - http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$id - Therapeutic Target Database Drug - Computational Science Department, National University of Singapore - Singapore - - - - drug - structure - - - - - species - - - - - - - TTD Target - The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. - - urn:miriam:ttd.target - http://identifiers.org/ttd.target/ - - ttd.target - - urn:miriam:pubmed:11752352 - urn:miriam:pubmed:24265219 - - - - http://bidd.nus.edu.sg/group/ttd/ttd.asp - TTDS00056 - http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$id - Therapeutic Target Database Target - Computational Science Department, National University of Singapore - Singapore - - - - drug - pathway - - - - - species - - - - - - - NeuronDB - NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments. - - urn:miriam:neurondb - http://identifiers.org/neurondb/ - - neurondb - - http://senselab.med.yale.edu/NeuronDB/default.asp - - - - http://senselab.med.yale.edu/NeuronDB/ - 265 - http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$id - NeuronDB at SenseLab - Yale University School of Medicine - USA - - - - neuroscience - - - - - compartment - species - model - - - - - - - NeuroMorpho - NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. - - urn:miriam:neuromorpho - http://identifiers.org/neuromorpho/ - - neuromorpho - - urn:miriam:pubmed:16552417 - - - - http://neuromorpho.org/index.jsp - Rosa2 - http://neuromorpho.org/neuron_info.jsp?neuron_name=$id - NeuroMorpho - Krasnow Institute, Virginia - USA - - - - neuroscience - - - - - compartment - species - - - - - - - ChemIDplus - ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. - - urn:miriam:chemidplus - http://identifiers.org/chemidplus/ - - chemidplus - - http://www.nlm.nih.gov/pubs/factsheets/chemidplusfs.html - - - - http://chem.sis.nlm.nih.gov/chemidplus/chemidheavy.jsp - 000057272 - http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?regno=$id - ChemIDplus at National Library of Medicine - National Library of Medicine, Maryland - USA - - - - chemical - structure - - - - - parameter - species - - - - - - - BioSystems - The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. - - urn:miriam:biosystems - http://identifiers.org/biosystems/ - - biosystems - - urn:miriam:pubmed:19854944 - - - - http://www.ncbi.nlm.nih.gov/biosystems/ - 001 - http://www.ncbi.nlm.nih.gov/biosystems/$id - BioSystems database at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - gene - pathway - protein - - - - - model - reaction - species - - - - - - - CTD Chemical - The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. - - urn:miriam:ctd.chemical - http://identifiers.org/ctd.chemical/ - - ctd.chemical - - urn:miriam:pubmed:16675512 - - - - http://ctdbase.org/ - D001151 - http://ctdbase.org/detail.go?type=chem&acc=$id - Comparative Toxicogenomics Database (Chemical) - The Mount Desert Island Biological Laboratory - USA - - - - chemical - pharmacogenomics - - - - - CTD Disease - The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. - - urn:miriam:ctd.disease - http://identifiers.org/ctd.disease/ - - ctd.disease - - urn:miriam:pubmed:16675512 - - - - http://ctdbase.org/ - D053716 - http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$id - Comparative Toxicogenomics Database (Disease) - The Mount Desert Island Biological Laboratory - USA - - - - disease - pharmacogenomics - - - - - model - - - - - - - CTD Gene - The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. - - urn:miriam:ctd.gene - http://identifiers.org/ctd.gene/ - - ctd.gene - - urn:miriam:pubmed:16675512 - - - - http://ctdbase.org/ - 101 - http://ctdbase.org/detail.go?type=gene&acc=$id - Comparative Toxicogenomics Database (Gene) - The Mount Desert Island Biological Laboratory - USA - - - - gene - pharmacogenomics - - - - - species - - - - - - - BioNumbers - BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. - - - urn:miriam:bionumbers - http://identifiers.org/bionumbers/ - - bionumbers - - http://www.bionumbers.hms.harvard.edu/aboutus.aspx - - - - http://www.bionumbers.hms.harvard.edu/search.aspx - 104674 - http://www.bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=$id&ver=1 - BioNumbers database - Weizmann Institute - Israel - - - - registry - - - - - parameter - - - - - - - DrugBank - The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. - - urn:miriam:drugbank - http://identifiers.org/drugbank/ - http://bio2rdf.org/drugbank - - drugbank - - urn:miriam:pubmed:16381955 - - - - http://www.drugbank.ca/ - DB00001 - http://www.drugbank.ca/drugs/$id - DrugBank drug information - Departments of Computing Science & Biological Sciences, University of Alberta - Canada - - - http://drugbank.bio2rdf.org/fct/ - DB00001 - http://drugbank.bio2rdf.org/describe/?url=http://bio2rdf.org/drugbank:$id - Bio2RDF - Bio2RDF.org - - - - - drug - protein - - - - - species - parameter - - - - - - - T3DB - - Toxin and Toxin Target Database - - Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. - - urn:miriam:t3db - http://identifiers.org/t3db/ - - t3db - - http://www.t3db.org/about#cite - - - - http://www.t3db.org/ - T3D0001 - http://www.t3db.org/toxins/$id - Toxin and Toxin Target Database - University of Alberta - Canada - - - - drug - protein - - - - - species - parameter - - - - - - - Small Molecule Pathway Database - - SMPDB - - The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. - - urn:miriam:smpdb - http://identifiers.org/smpdb/ - - smpdb - - http://www.smpdb.ca/ - - - - http://www.smpdb.ca/pathways - SMP00001 - http://smpdb.ca/view/$id - Small Molecule Pathway Database - University of Alberta, Edmonton, AB - Canada - - - - chemical - human - metabolite - pathway - - - - - reaction - model - - - - - - - PhosphoSite Protein - - PhosphoSitePlus - - PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. - - urn:miriam:phosphosite.protein - http://identifiers.org/phosphosite.protein/ - urn:miriam:phosphosite - - phosphosite.protein - - urn:miriam:pubmed:12478304 - - - - http://www.phosphosite.org/homeAction.do - 12300 - http://www.phosphosite.org/proteinAction.do?id=$id - PhosphoSite - Cell Signaling Technology, Inc. - USA - - - - mammalian - protein - - - - - species - - - - - - - GeneDB - GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed. - - urn:miriam:genedb - http://identifiers.org/genedb/ - - genedb - - urn:miriam:pubmed:14681429 - - - - http://www.genedb.org/ - Cj1536c - http://www.genedb.org/gene/$id - GeneDB at Sanger Institute - Pathogen Genomics, Sanger Institute and European Bioinformatics Institute - UK - - - - genome - sequence - - - - - species - - - - - - - TEDDY - The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. - - urn:miriam:biomodels.teddy - http://identifiers.org/biomodels.teddy/ - urn:miriam:teddy - - biomodels.teddy - - http://teddyontology.sourceforge.net/ - - - - http://teddyontology.sourceforge.net/ - TEDDY_0000066 - http://purl.bioontology.org/ontology/TEDDY/$id - TEDDY through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/teddy - TEDDY_0000066 - https://www.ebi.ac.uk/ols/ontologies/teddy/terms?short_form=$id - TEDDY though OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - - - - - KiSAO - - Kinetic Simulation Algorithm Ontology - - The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. - - urn:miriam:biomodels.kisao - http://identifiers.org/biomodels.kisao/ - - biomodels.kisao - - http://www.ebi.ac.uk/compneur-srv/kisao/ - - - - http://bioportal.bioontology.org/ontologies/KISAO - KISAO_0000057 - http://purl.bioontology.org/ontology/KISAO/kisao:$id - KiSAO via NCBO's Bioportal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/kisao - KISAO_0000057 - https://www.ebi.ac.uk/ols/ontologies/kisao/terms?short_form=$id - KiSAO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - Molecular Interactions Ontology - - MI - - The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. - - urn:miriam:psimi - http://identifiers.org/psimi/ - http://identifiers.org/obo.mi/ - urn:miriam:obo.mi - - psimi - - urn:miriam:pubmed:14755292 - - - - https://www.ebi.ac.uk/ols/ontologies/mi - MI:0308 - https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=$id - Molecular Interactions Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/PPIO - MI:0308 - http://purl.bioontology.org/ontology/PPIO/$id - PSI Molecular Interactions Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - - This collection is a subset of the information in the 'Protein Affinity Reagents' (PSI-PAR) collection [MIR:00000533], which should be used in preference. - http://www.psidev.info/psi-par#cv - - - - interaction - ontology - protein - - - - - event - - - - - - - Cell Type Ontology - - Cell Ontology - CL - - The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. - - urn:miriam:cl - http://identifiers.org/cl/ - http://purl.obolibrary.org/obo/CL - http://identifiers.org/obo.clo/ - urn:miriam:obo.clo - - cl - - urn:miriam:pubmed:15693950 - - - - https://www.ebi.ac.uk/ols/ontologies/cl - CL:0000232 - https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=$id - Cell Type Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/CL - CL:0000232 - http://purl.bioontology.org/ontology/CL/$id - Cell Type Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - species - model - - - - - - - Brenda Tissue Ontology - - BTO - - The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. - - urn:miriam:bto - http://identifiers.org/bto/ - http://purl.obolibrary.org/obo/BTO - http://identifiers.org/obo.bto/ - urn:miriam:obo.bto - - bto - - http://www.brenda-enzymes.info/ - - - - https://www.ebi.ac.uk/ols/ontologies/bto - BTO:0000146 - https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=$id - Brenda Tissue Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/BTO - BTO:0000146 - http://purl.bioontology.org/ontology/BTO/$id - Brenda Tissue Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - model - compartment - species - - - - - - - PATO - PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. - - urn:miriam:pato - http://identifiers.org/pato/ - http://purl.obolibrary.org/obo/PATO - http://purl.org/obo/owl/PATO - http://identifiers.org/obo.pato/ - urn:miriam:obo.pato - - pato - - http://obofoundry.org/wiki/index.php/PATO:About - - - - https://www.ebi.ac.uk/ols/ontologies/pato - PATO:0001998 - https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=$id - PATO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/PATO - PATO:0001998 - http://purl.bioontology.org/ontology/PATO/$id - PATO through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - phenotype - - - - - parameter - model - species - - - - - - - Chemical Component Dictionary - - PDBeChem - PDB-CCD - - The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. - - urn:miriam:pdb-ccd - http://identifiers.org/pdb-ccd/ - - pdb-ccd - - urn:miriam:pubmed:14634627 - - - - http://www.ebi.ac.uk/pdbe-srv/pdbechem/ - AB0 - http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id - Protein Data Bank Chemical Component Dictionary at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - chemical - classification - - - - - species - - - - - - - GlycomeDB - GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links. - - urn:miriam:glycomedb - http://identifiers.org/glycomedb/ - - glycomedb - - urn:miriam:pubmed:19759275 - - - - http://www.glycome-db.org/showMenu.action?major=database - 1 - http://www.glycome-db.org/database/showStructure.action?glycomeId=$id - GlycomeDB carbohydrate structure database - German Cancer Research Center, Heidelberg - Germany - - - - structure - - - - - species - - - - - - - LipidBank - LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. - - urn:miriam:lipidbank - http://identifiers.org/lipidbank/ - - lipidbank - - urn:miriam:pubmed:12058481 - - - - http://lipidbank.jp/index.html - BBA0001 - http://lipidbank.jp/cgi-bin/detail.cgi?id=$id - LipidBank the Lipid database - Department of Computational Biology, University of Tokyo, Tokyo - Japan - - - - lipid - structure - - - - - species - - - - - - - KEGG Orthology - - - - KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms. - - urn:miriam:kegg.orthology - http://identifiers.org/kegg.orthology/ - - kegg.orthology - - http://www.genome.jp/kegg/ko.html - - - - http://www.genome.jp/kegg/ko.html - K00001 - http://www.kegg.jp/entry/$id - KEGG Orthology Database - Department of Computational Biology, University of Tokyo, Tokyo - Japan - - - - clustering - pathway - - - - - species - - - - - - - ProDom - ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. - - urn:miriam:prodom - http://identifiers.org/prodom/ - - prodom - - urn:miriam:pubmed:15608179 - - - - http://prodom.prabi.fr/prodom/current/html/home.php - PD10000 - http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$id - ProDom Protein Domain Database - Laboratoire des Interactions Plantes-Microorganismes, INRA/CNRS - France - - - - domain - protein - - - - - species - - - - - - - SMART - The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures. - - urn:miriam:smart - http://identifiers.org/smart/ - - smart - - urn:miriam:pubmed:9847187 - - - - http://smart.embl-heidelberg.de/ - SM00015 - http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$id - SMART (Simple Modular Architecture Research Tool) - EMBL, Heidelberg - Germany - - - - domain - gene - protein - - - - - species - - - - - - - Conserved Domain Database - - CDD - - The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. - - urn:miriam:cdd - http://identifiers.org/cdd/ - - cdd - - urn:miriam:pubmed:18984618 - - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd - cd00400 - http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$id - Conserved Domain Database at NCBI - National Library of Medicine, National Institutes of Health, Maryland - USA - - - - domain - protein - - - - - species - - - - - - - Relation Ontology - The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. - - urn:miriam:ro - http://identifiers.org/ro/ - http://identifiers.org/obo.ro/ - urn:miriam:obo.ro - - ro - - urn:miriam:pubmed:15892874 - - - - http://obofoundry.org/ontology/ro.html - RO_0002533 - http://purl.obolibrary.org/obo/$id - OBO Relation Ontology through OntoBee - University of Michigan Medical School (MI), Lawrence Berkeley National Laboratory (CA) and Science Commons (MA) - USA - - - https://www.ebi.ac.uk/ols/ontologies/ro - RO_0002533 - https://www.ebi.ac.uk/ols/ontologies/ro/terms?short_form=$id - OBO Relation Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.obofoundry.org/ro/ - OBO_REL:is_a - http://www.obofoundry.org/ro/#$id - OBO Relation Ontology - Institute for Formal Ontology and Medical Information Science, Saarbrücken - Germany - - - - ontology - - - - - Molecular Modeling Database - - MMDB - Entrez Structure - - The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. - - urn:miriam:mmdb - http://identifiers.org/mmdb/ - - mmdb - - urn:miriam:pubmed:17135201 - - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure - 50885 - http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$id - MMDB at NCBI - National Library of Medicine, National Institutes of Health, Maryland - USA - - - - domain - protein - structure - - - - - species - - - - - - - IMEx - The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources. - - urn:miriam:imex - http://identifiers.org/imex/ - - imex - - urn:miriam:pubmed:17893861 - - - - http://www.imexconsortium.org/ - IM-19210-3 - http://www.ebi.ac.uk/intact/imex/main.xhtml?query=$id - IMEx Consortium running at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.ebi.ac.uk/intact/ - IM-19210-3 - https://imexcentral.org/icentral/imex/rec/$id - IMEx Consortium though Intact - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - interaction - protein - - - - - species - - - - - - - iRefWeb - iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived. - - urn:miriam:irefweb - http://identifiers.org/irefweb/ - - irefweb - - urn:miriam:doi:10.1186%2F1471-2105-9-405 - http://irefindex.uio.no/wiki/iRefIndex - - - - http://wodaklab.org/iRefWeb/ - 617102 - http://wodaklab.org/iRefWeb/interaction/show/$id - iRefWeb Protein Interaction Reference Index - Wodak Lab, Hospital for Sick Children, Toronto - Canada - - - - interaction - protein - - - - - species - - - - - - - Microbial Protein Interaction Database - - MPID - - The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. - - urn:miriam:mpid - http://identifiers.org/mpid/ - - mpid - - urn:miriam:pubmed:18556668 - - - - http://www.jcvi.org/mpidb/about.php - 172 - http://www.jcvi.org/mpidb/experiment.php?interaction_id=$id - Microbial Protein Interaction Database - J. Craig Venter Institute, Maryland - USA - - - http://www.ebi.ac.uk/intact/ - 1776 - http://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$id - Microbial Protein Interaction Database subset through IntAct - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - interaction - microbial - protein - - - - - species - - - - - - - PhosphoSite Residue - PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence. - - urn:miriam:phosphosite.residue - http://identifiers.org/phosphosite.residue/ - - phosphosite.residue - - urn:miriam:pubmed:12478304 - - - - http://www.phosphosite.org/homeAction.do - 2842 - http://www.phosphosite.org/siteAction.do?id=$id - PhosphoSite Residue - Cell Signaling Technology, Inc. - USA - - - - - - NeuroLex - - BIRNLex - NIFSTD - - The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex). - - urn:miriam:neurolex - http://identifiers.org/neurolex/ - - neurolex - - urn:miriam:pubmed:18975148 - - - - http://www.neurolex.org/wiki/Main_Page - Birnlex_721 - http://www.neurolex.org/wiki/$id - NeuroLex Neuroscience Lexicon - Department of Neuroscience, University of California, San Diego - USA - - - http://bioportal.bioontology.org/ontologies/BIRNLEX - birnlex_1672 - http://purl.bioontology.org/ontology/BIRNLEX/$id - NeuroLex through NCBO's BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - controlled vocabulary - neuroscience - ontology - - - - - species - - - - - - - Ontology for Biomedical Investigations - - OBI - - The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). - - urn:miriam:obi - http://identifiers.org/obi/ - urn:miriam:obo.obi - http://identifiers.org/obo.obi/ - - obi - - http://www.jbiomedsem.com/content/1/S1/S7 - http://purl.obolibrary.org/obo/obi - - - - http://www.ontobee.org/ - OBI_0000070 - http://purl.obolibrary.org/obo/$id - OBI through Ontobee - University of Michigan Medical School (MI), awrence Berkeley National Laboratory (CA) and Science Commons (MA) - USA - - - http://bioportal.bioontology.org/ontologies/OBI - OBI:0000070 - http://purl.bioontology.org/ontology/OBI/$id - Ontology for Biomedical Investigations through Bioportal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/obi - OBI:0000070 - https://www.ebi.ac.uk/ols/ontologies/obi/terms?obo_id=$id - OBI through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://obi-ontology.org/page/Main_Page - OBI:0000225 - http://ashby.csail.mit.edu/cgi-bin/obiterm?ref=$id - OBI at MIT - Massachusetts Institute of Technology (MIT) - USA - - - https://www.ebi.ac.uk/ols/beta/ontologies/obi - OBI:0000070 - https://www.ebi.ac.uk/ols/beta/ontologies/obi/terms?obo_id=$id - OBI through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - SABIO-RK EC Record - - SABIO-RK Enzyme Classification Record - - SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. - - urn:miriam:sabiork.ec - http://identifiers.org/sabiork.ec/ - - sabiork.ec - - urn:miriam:pubmed:17822389 - urn:miriam:doi:10.2390%2Fbiecoll-jib-2007-49 - urn:miriam:doi:10.1186%2F1752-0509-1-S1-S6 - urn:miriam:doi:10.1007%2F11799511_9 - urn:miriam:doi:10.1186%2F1752-0509-1-S1-P4 - - - - http://sabiork.h-its.org/ - 2.7.1.1 - http://sabiork.h-its.org/newSearch?q=ecnumber:$id - SABIO-RK Reaction Kinetics Database - Enzyme Classification (EC) - Heidelberg Institute for Theoretical Studies (HITS gGmbH) - Germany - - - - classification - enzyme - kinetics - - - - - reaction - event - - - - - - - Ontology of Physics for Biology - - OPB - - The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. - - urn:miriam:opb - http://identifiers.org/opb/ - - opb - - http://sig.biostr.washington.edu/projects/biosim/opb-intro.html - - - - http://bioportal.bioontology.org/ontologies/OPB - OPB_00573 - http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23$id - Ontology of Physics for Biology through Bioportal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - parameter - species - - - - - - - JWS Online - - JWS - - JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser. - - urn:miriam:jws - http://identifiers.org/jws/ - - jws - - urn:miriam:pubmed:15072998 - - - - http://jjj.biochem.sun.ac.za/models/ - curien - http://jjj.biochem.sun.ac.za/models/$id/ - JWS Online Model Repository at Stellenbosch - Department of Biochemistry, Stellenbosch University - South Africa - - - http://jjj.bio.vu.nl/models/ - curien - http://jjj.bio.vu.nl/models/$id/ - JWS Online Model Repository at Amsterdam - University of Amsterdam - Netherlands - - - http://jjj.mib.ac.uk/index.html - curien - http://jjj.mib.ac.uk/models/$id - JWS Online Model Repository at Manchester - Manchester Interdisciplinary Biocentre, University of Manchester - UK - - - - model - - - - - model - - - - - - - ModelDB - ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. - - urn:miriam:modeldb - http://identifiers.org/modeldb/ - - modeldb - - urn:miriam:pubmed:15055399 - - - - http://senselab.med.yale.edu/ModelDB/ - 45539 - http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$id - ModelDB at SenseLab - Yale University School of Medicine - USA - - - - model - neuroscience - - - - - model - - - - - - - SubtiWiki - SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. -Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon. - - urn:miriam:subtiwiki - http://identifiers.org/subtiwiki/ - - subtiwiki - - urn:miriam:pubmed:19959575 - urn:miriam:pubmed:20157485 - - - - http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page - BSU29180 - http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$id - SubtiWiki website - University of Göttingen, Department for General Microbiology - Germany - - - - gene - genome - microbial - protein - - - - - species - - - - - - - NCI Pathway Interaction Database: Pathway - - NCI_Nature - PID - Pathway Interaction Database NCI-Nature Curated Data - NCI-Nature PID - NCI-Nature Pathway Interaction Database - NCI_Nature curated - - The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information. - - urn:miriam:pid.pathway - http://identifiers.org/pid.pathway/ - - pid.pathway - - urn:miriam:pubmed:18832364 - - - - http://pid.nci.nih.gov/ - pi3kcipathway - http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$id - NCI Pathway Interaction Database (Pathway) - National Cancer Institute, Rockville, Maryland - USA - - - - human - interaction - pathway - - - - - Database of Quantitative Cellular Signaling: Model - - DOQCS Model - - The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. - - urn:miriam:doqcs.model - http://identifiers.org/doqcs.model/ - - doqcs.model - - urn:miriam:pubmed:12584128 - - - - http://doqcs.ncbs.res.in/ - 57 - http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$id - Database of Quantitative Cellular Signaling (DOQCS) - Model Access - National Centre for Biological Sciences, Bangalore - India - - - - model - - - - - model - - - - - - - Database of Quantitative Cellular Signaling: Pathway - - DOQCS Pathway - - The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. - - urn:miriam:doqcs.pathway - http://identifiers.org/doqcs.pathway/ - - doqcs.pathway - - urn:miriam:pubmed:12584128 - - - - http://doqcs.ncbs.res.in/ - 131 - http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$id - Database of Quantitative Cellular Signaling (DOQCS) - Pathway Access - National Centre for Biological Sciences, Bangalore - India - - - - pathway - - - - - model - - - - - - - Unit Ontology - - UO - - Ontology of standardized units - - urn:miriam:uo - http://identifiers.org/uo/ - http://purl.obolibrary.org/obo/UO - http://identifiers.org/unit/ - urn:miriam:unit - urn:miriam:obo.unit - http://identifiers.org/obo.unit/ - - uo - - - https://www.ebi.ac.uk/ols/ontologies/uo - UO:0000080 - https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=$id - Unit Ontology via Ontology Lookup Service - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/UO - UO:0000080 - http://purl.bioontology.org/ontology/UO/$id - Unit Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - ClinicalTrials.gov - - NCT - - ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries - - urn:miriam:clinicaltrials - http://identifiers.org/clinicaltrials/ - http://bio2rdf.org/clinicaltrials - - clinicaltrials - - http://clinicaltrials.gov/ct2/info/about - - - - http://clinicaltrials.gov/ - NCT00222573 - http://clinicaltrials.gov/ct2/show/$id - ClinicalTrials.gov at NIH - National Library of Medicine and ClinicalTrials.gov, Maryland - USA - - - http://clinicaltrials.bio2rdf.org/fct - NCT00222573 - http://clinicaltrials.bio2rdf.org/describe/?url=http://bio2rdf.org/clinicaltrials:$id - Bio2RDF - Bio2RDF.org - - - - - disease - disorder - human - pharmacogenomics - - - - - ChemSpider - ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. - - urn:miriam:chemspider - http://identifiers.org/chemspider/ - - chemspider - - http://www.chemspider.com/About.aspx - - - - http://www.chemspider.com/ - 56586 - http://www.chemspider.com/Chemical-Structure.$id.html - ChemSpider at RSC - Royal Society of Chemistry, Cambridge - UK - - - - chemical - structure - - - - - species - - - - - - - NCIt - - NCI thesaurus - National Cancer Institute Thesaurus - - NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. - - urn:miriam:ncit - http://identifiers.org/ncit/ - - ncit - - urn:miriam:pubmed:19789731 - http://ncit.nci.nih.gov/ncitbrowser/pages/help.jsf - - - - http://ncit.nci.nih.gov/ - C80519 - http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$id - NCIt at National Cancer Institute - National Cancer Institute, Center for Bioinformatics, Maryland - USA - - - https://www.ebi.ac.uk/ols/ontologies/ncit - C16353 - https://www.ebi.ac.uk/ols/ontologies/ncit/terms?short_form=NCIT_$id - NCIt through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - controlled vocabulary - ontology - - - - - compartment - species - model - - - - - - - BioCatalogue - The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. - - urn:miriam:biocatalogue.service - http://identifiers.org/biocatalogue.service/ - - biocatalogue.service - - urn:miriam:pubmed:20484378 - http://www.biocatalogue.org/wiki/ - - - - http://www.biocatalogue.org/ - 614 - https://www.biocatalogue.org/services/$id - BioCatalogue at EMBL-EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - registry - - - - - Protein Ontology - The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. - - urn:miriam:pr - http://identifiers.org/pr/ - http://identifiers.org/obo.pr/ - urn:miriam:obo.pr - - pr - - urn:miriam:pubmed:18047702 - https://pir5.georgetown.edu/wiki/PRO - - - - http://pir.georgetown.edu/pro/pro.shtml - PR:000000024 - http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=$id - Protein Ontology at Georgetown - Georgetown University Medical Center, Washington - USA - - - http://bioportal.bioontology.org/ontologies/PR - PR:000000024 - http://purl.bioontology.org/ontology/PR/$id - Protein Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/pr - PR:000000024 - https://www.ebi.ac.uk/ols/ontologies/pr/terms?obo_id=$id - Protein Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - protein - - - - - species - speciesType - - - - - physicalEntity - - - - - - - OMIA - - Online Mendelian Inheritance in Animals - - Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). - - urn:miriam:omia - http://identifiers.org/omia/ - - omia - - http://omia.angis.org.au/ - - - - http://omia.angis.org.au/ - 1000 - http://omia.angis.org.au/$id/ - OMIA at University of Sydney - Reprogen, Faculty of Veterinary Science, University of Sydney - Australia - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=omia - 1000 - http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=omia&dopt=Detailed&list_uids=$id - OMIA at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - disorder - phenotype - - - - - model - - - - - - - ChemBank - ChemBank stores small molecule information, as well as measurements derived from cells and other biological assay systems treated with small molecules. - - urn:miriam:chembank - http://identifiers.org/chembank/ - - chembank - - urn:miriam:pubmed:17947324 - - - - http://chembank.broadinstitute.org/ - 1000000 - http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$id - ChemBank at Broad Institute - Broad Institute of Harvard and MIT, Cambridge, MA - USA - - - - chemical - metabolite - - - - - species - - - - - - - CSA - - Catalytic Site Atlas - - The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. - - urn:miriam:csa - http://identifiers.org/csa/ - - csa - - urn:miriam:pubmed:14681376 - - - - http://www.ebi.ac.uk/thornton-srv/databases/CSA/ - 1a05 - http://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$id - CSA at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - structure - - - - - species - - - - - - - Candida Genome Database - - CGD - - The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. - - urn:miriam:cgd - http://identifiers.org/cgd/ - - cgd - - urn:miriam:pubmed:15608216 - - - - http://www.candidagenome.org/ - CAL0003079 - http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$id - Candida Genome Database at Stanford University - Stanford University, - USA - - - - eukaryotic - genome - nucleotide - - - - - species - parameter - - - - - - - AntWeb - AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. - - urn:miriam:antweb - http://identifiers.org/antweb/ - - antweb - - urn:miriam:pubmed:12867945 - - - - http://www.antweb.org/ - casent0106247 - http://www.antweb.org/specimen.do?name=$id - AntWeb at California Academy of Sciences - California Academy of Sciences, Goldengate Park, San Francisco - USA - - - - classification - - - - - model - - - - - - - PMC International - - PubMed Central - PMCI - - PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. - - urn:miriam:pmc - http://identifiers.org/pmc/ - - pmc - - - http://www.ncbi.nlm.nih.gov/pmc/ - PMC3084216 - http://www.ncbi.nlm.nih.gov/pmc/articles/$id/?tool=pubmed - PubMed Central - NCBI - USA - - - http://europepmc.org/ - PMC3084216 - http://europepmc.org/articles/$id - Europe PMC - Europe PubMed Central partners - UK - - - http://pubmedcentralcanada.ca/pmcc - PMC3084216 - http://pubmedcentralcanada.ca/pmcc/articles/$id - PubMedCentral Canada - Canadian Institute of Health, Ottawa - Canada - - - http://ukpmc.ac.uk/ - PMC3084216 - http://ukpmc.ac.uk/articles/$id - PMC through UK PubMed Central - UKPMC Funders Group - UK - - - - bibliography - schema.org - - - - - model - parameter - reaction - species - - - - - - - AmoebaDB - AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:amoebadb - http://identifiers.org/amoebadb/ - - amoebadb - - urn:miriam:pubmed:19914931 - - - - http://amoebadb.org/amoeba/ - EDI_244000 - http://amoebadb.org/amoeba/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - AmoebaDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - - - - - CryptoDB - CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:cryptodb - http://identifiers.org/cryptodb/ - - cryptodb - - urn:miriam:pubmed:16381902 - - - - http://cryptodb.org/cryptodb/ - cgd7_230 - http://cryptodb.org/cryptodb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - CryptoDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - genome - - - - - model - - - - - - - PlasmoDB - AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:plasmodb - http://identifiers.org/plasmodb/ - - plasmodb - - urn:miriam:pubmed:18957442 - - - - http://plasmodb.org/plasmo/ - PF11_0344 - http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - PlasmoDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - genome - - - - - model - - - - - - - GiardiaDB - GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:giardiadb - http://identifiers.org/giardiadb/ - - giardiadb - - urn:miriam:pubmed:18824479 - - - - http://giardiadb.org/giardiadb/ - GL50803_102438 - http://giardiadb.org/giardiadb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - GiardiaDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - genome - - - - - model - - - - - - - MicrosporidiaDB - MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:microsporidia - http://identifiers.org/microsporidia/ - - microsporidia - - urn:miriam:pubmed:19914931 - - - - http://microsporidiadb.org/micro/ - ECU03_0820i - http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - MicrosporidiaDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - genome - - - - - model - - - - - - - ToxoDB - ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:toxoplasma - http://identifiers.org/toxoplasma/ - - toxoplasma - - urn:miriam:pubmed:18003657 - - - - http://toxodb.org/toxo/ - TGME49_053730 - http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - ToxoDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - genome - - - - - model - - - - - - - TrichDB - TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:trichdb - http://identifiers.org/trichdb/ - - trichdb - - urn:miriam:pubmed:18824479 - - - - http://trichdb.org/trichdb/ - TVAG_386080 - http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - TrichDB at EuPathDB - Center for Tropical & Emerging Global Diseases, University of Georgia - USA - - - - eukaryotic - genome - - - - - model - - - - - - - TriTrypDB - - Kinetoplastid Genomics Resource - - TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:tritrypdb - http://identifiers.org/tritrypdb/ - - tritrypdb - - urn:miriam:pubmed:19843604 - - - - http://tritrypdb.org/tritrypdb/ - Tb927.8.620 - http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - TriTrypDB at EuPathDB - Wellcome Trust Sanger Institute, Hinxton - UK - - - - eukaryotic - genome - - - - - model - - - - - - - BDGP insertion DB - - BDGP gene disruption - - BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element. - - urn:miriam:bdgp.insertion - http://identifiers.org/bdgp.insertion/ - - bdgp.insertion - - urn:miriam:pubmed:15238527 - - - - http://flypush.imgen.bcm.tmc.edu/pscreen/ - KG09531 - http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$id - BDGP Gene Disruption Project - Baylor College of Medicine, Texas - USA - - - - gene - sequence - - - - - species - - - - - - - BeetleBase - BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications. - - urn:miriam:beetlebase - http://identifiers.org/beetlebase/ - - beetlebase - - urn:miriam:pubmed:19820115 - - - - http://beetlebase.org/ - TC010103 - http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$id - BeetleBase at Kansas State University - Bioinformatics Center, Kansas State University - USA - - - - classification - - - - - model - - - - - - - BOLD Taxonomy - The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. - - urn:miriam:bold.taxonomy - http://identifiers.org/bold.taxonomy/ - - bold.taxonomy - - urn:miriam:pubmed:18784790 - - - - http://www.boldsystems.org/ - 27267 - http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$id - BOLD taxonomy browser - Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario - Canada - - - - classification - - - - - model - - - - - - - dbEST - - Database of Expressed Sequence Tags - NCBI EST - - The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. - - urn:miriam:dbest - http://identifiers.org/dbest/ - - dbest - - urn:miriam:pubmed:8401577 - - - - http://www.ncbi.nlm.nih.gov/nucest - BP100000 - http://www.ncbi.nlm.nih.gov/nucest/$id - dbEST at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://www.ebi.ac.uk/ena - BP100000.1 - http://www.ebi.ac.uk/ena/data/view/$id - dbEST through European Nucleotide Archive (ENA) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.ddbj.nig.ac.jp/ - BP100000 - http://getentry.ddbj.nig.ac.jp/getentry/na/$id - dbEST through DNA Data Bank of Japan (DDBJ) - DNA Data Bank of Japan, Mishima, Shizuoka - Japan - - - - expression - gene - - - - - species - - - - - - - dbProbe - The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. - - urn:miriam:dbprobe - http://identifiers.org/dbprobe/ - - dbprobe - - http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/UsingProbeDB.shtml - - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe - 1000000 - http://www.ncbi.nlm.nih.gov/probe/?term=$id - dbProbe at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - nucleotide - - - - - species - - - - - - - dbSNP - The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. - - urn:miriam:dbsnp - http://identifiers.org/dbsnp/ - - dbsnp - - urn:miriam:pubmed:11125122 - - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp - 121909098 - http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$id - dbSNP at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - gene - nucleotide - - - - - species - - - - - - - UniSTS - - dbSTS - - UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. - - urn:miriam:unists - http://identifiers.org/unists/ - - unists - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists - - - - http://www.ncbi.nlm.nih.gov/sites/entrez?db=unists - 456789 - http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$id - UniSTS at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - gene - sequence - - - - - species - - - - - - - EcoGene - The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. - - urn:miriam:ecogene - http://identifiers.org/ecogene/ - - ecogene - - urn:miriam:pubmed:10592181 - urn:miriam:pubmed:23197660 - - - - http://ecogene.org/ - EG10173 - http://www.ecogene.org/gene/$id - EcoGene at University of Miami - Miller School of Medicine, University of Miami - USA - - - http://maxd.cs.purdue.edu:9455 - EG10173 - http://maxd.cs.purdue.edu:9455/geneInfo.php?eg_id=$id - EcoGene at Purdue University - Purdue University - USA - - - - genome - microbial - - - - - species - - - - - - - GABI - - GABI PD - - GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. - - urn:miriam:gabi - http://identifiers.org/gabi/ - - gabi - - urn:miriam:pubmed:18812395 - - - - http://www.gabipd.org/ - 2679240 - http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$id&Mode=ShowBioObject - GABI at Max Planck - Max Planck Institute of Molecular Plant Physiology, Berlin - Germany - - - - gene - genome - plant - - - - - model - species - - - - - - - GreenGenes - A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. - - urn:miriam:greengenes - http://identifiers.org/greengenes/ - - greengenes - - urn:miriam:pubmed:16820507 - - - - http://greengenes.lbl.gov/ - 100000 - http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$id - GreenGenes at Lawrence Berkeley - Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, California - USA - - - - sequence - - - - - species - - - - - - - GRIN Plant Taxonomy - - GRIN Taxonomy for Plants - Germplasm Resources Information Network Plant Taxonomy - - GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact. - - urn:miriam:grin.taxonomy - http://identifiers.org/grin.taxonomy/ - - grin.taxonomy - - http://www.ars-grin.gov/cgi-bin/npgs/html/paper.pl?language=en - - - - http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en - 19333 - http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$id - GRIN at Maryland - National Germplasm Resources Laboratory, Beltsville, Maryland - USA - - - - plant - taxonomy - - - - - model - - - - - - - H-InvDb Locus - H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view. - - urn:miriam:hinv.locus - http://identifiers.org/hinv.locus/ - - hinv.locus - - urn:miriam:pubmed:19933760 - - - - http://h-invitational.jp/hinv/ahg-db/index.jsp - HIX0004394 - http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$id - H-Invitational Locus View at BIRC - BIRC, Tokyo - Japan - - - - gene - human - - - - - species - - - - - - - H-InvDb Transcript - H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view. - - urn:miriam:hinv.transcript - http://identifiers.org/hinv.transcript/ - - hinv.transcript - - urn:miriam:pubmed:19933760 - - - - http://h-invitational.jp/hinv/ahg-db/index.jsp - HIT000195363 - http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$id - H-Invitational Transcript View at BIRC - BIRC, Tokyo - Japan - - - - expression - human - - - - - species - - - - - - - H-InvDb Protein - H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view. - - urn:miriam:hinv.protein - http://identifiers.org/hinv.protein/ - - hinv.protein - - urn:miriam:pubmed:19933760 - - - - http://h-invitational.jp/hinv/ahg-db/index.jsp - HIP000030660 - http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$id - H-Invitational Protein View at BIRC - BIRC, Tokyo - Japan - - - - human - protein - - - - - species - - - - - - - HOMD Sequence Metainformation - - Human Oral Microbiome Database - - The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. - - urn:miriam:homd.seq - http://identifiers.org/homd.seq/ - - homd.seq - - urn:miriam:pubmed:20624719 - - - - http://www.homd.org/index.php - SEQF1003 - http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$id - HOMD sequence metainformation at The Forsyth Institute - The Forsyth Institute, Boston - USA - - - - genome - microbial - - - - - species - - - - - - - HOMD Taxonomy - The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. - - urn:miriam:homd.taxon - http://identifiers.org/homd.taxon/ - - homd.taxon - - urn:miriam:pubmed:20624719 - - - - http://www.homd.org/index.php - 811 - http://www.homd.org/modules.php?op=modload&name=HOMD&file=index&oraltaxonid=$id&view=dynamic - HOMD taxon information at The Forsyth Institute - The Forsyth Institute, Boston - USA - - - - microbial - taxonomy - - - - - model - - - - - - - IRD Segment Sequence - - Influenza Research Database Segment - - Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). - - urn:miriam:ird.segment - http://identifiers.org/ird.segment/ - - ird.segment - - urn:miriam:pubmed:17965094 - - - - http://www.fludb.org/ - CY077097 - http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$id - IRD at BioHealthBase - Southwestern Medical Center, University of Texas, Dallas - USA - - - - gene - protein - - - - - ISFinder - - Insertion Sequence Finder - - ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available. - - urn:miriam:isfinder - http://identifiers.org/isfinder/ - - isfinder - - urn:miriam:pubmed:16381877 - - - - http://www-is.biotoul.fr/i - ISA1083-2 - https://www-is.biotoul.fr/scripts/ficheIS.php?name=$id - IS Finder at CNRS - Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, Toulouse - France - - - - gene - sequence - - - - - Japan Collection of Microorganisms - - JCM - - The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2. - - urn:miriam:jcm - http://identifiers.org/jcm/ - - jcm - - http://www.jcm.riken.go.jp/JCM/aboutJCM.shtml - - - - http://www.jcm.riken.go.jp/ - 17254 - http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$id - JCM at RIKEN BioResource Center - RIKEN BioResource Center, Ibaraki - Japan - - - - microbial - strain - - - - - Integrated Microbial Genomes Taxon - - IMG Taxon - - The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. - - urn:miriam:img.taxon - http://identifiers.org/img.taxon/ - - img.taxon - - urn:miriam:pubmed:17933782 - - - - http://img.jgi.doe.gov/ - 648028003 - http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$id - Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory - Lawrence Berkeley National Laboratory, Berkeley - USA - - - - - Access to this collection requires registration for an account. - https://img.jgi.doe.gov/cgi-bin/submit/request.cgi - - - - genome - taxonomy - - - - - model - - - - - - - Integrated Microbial Genomes Gene - The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information. - - urn:miriam:img.gene - http://identifiers.org/img.gene/ - - img.gene - - urn:miriam:pubmed:17933782 - - - - http://img.jgi.doe.gov/ - 638309541 - http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$id - Integrated Microbial Genomes Taxon at Lawrence Berkeley National Laboratory - Lawrence Berkeley National Laboratory, Berkeley - USA - - - - - Access to this collection requires registration for an account. - https://img.jgi.doe.gov/cgi-bin/submit/request.cgi - - - - gene - genome - - - - - species - - - - - - - MaizeGDB Locus - MaizeGDB is the maize research community's central repository for genetics and genomics information. - - urn:miriam:maizegdb.locus - http://identifiers.org/maizegdb.locus/ - - maizegdb.locus - - urn:miriam:pubmed:18769488 - - - - http://www.maizegdb.org/ - 25011 - http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$id - MaizeGDB at Missouri - Division of Plant Sciences, Missouri - USA - - - - genome - plant - - - - - model - - - - - - - MycoBank - MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations. - - urn:miriam:mycobank - http://identifiers.org/mycobank/ - - mycobank - - http://www.mycobank.org/Help.aspx - - - - http://www.mycobank.org/ - 349124 - http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$id - MycoBank at Fungal Biodiversity Centre - CBS-KNAW Fungal Biodiversity Centre, Utrecht - Netherlands - - - - classification - - - - - model - - - - - - - NITE Biological Research Center Catalogue - - NBRC Catalogue - - NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. - - urn:miriam:nbrc - http://identifiers.org/nbrc/ - - nbrc - - http://www.bio.nite.go.jp/pamphlet/e/nbrc-e.html - - - - http://www.nbrc.nite.go.jp/e/index.html - 00001234 - http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$id - NBRC Catalogue at National Institute of Technology Evaluation - National Institute of Technology Evaluation, Tokyo - Japan - - - - microbial - strain - - - - - model - - - - - - - Pseudomonas Genome Database - - PGD - Pseudocap - - The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. - - urn:miriam:pseudomonas - http://identifiers.org/pseudomonas/ - - pseudomonas - - urn:miriam:pubmed:18978025 - - - - http://www.pseudomonas.com/ - PSEEN0001 - http://v2.pseudomonas.com/getAnnotation.do?locusID=$id - Pseudomonas Genome Database at Simon Fraser University - Simon Fraser University, British Columbia - Canada - - - - gene - microbial - protein - - - - - species - - - - - - - Gramene protein - Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene. - - urn:miriam:gramene.protein - http://identifiers.org/gramene.protein/ - - gramene.protein - - urn:miriam:pubmed:21076153 - - - - http://www.gramene.org/ - 78073 - http://www.gramene.org/db/protein/protein_search?protein_id=$id - Gramene Protein at Cold Spring Harbor - Cold Spring Harbor Laboratory, New York - USA - - - - expression - genome - plant - sequence - - - - - Gramene genes - Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. - - urn:miriam:gramene.gene - http://identifiers.org/gramene.gene/ - - gramene.gene - - urn:miriam:pubmed:21076153 - - - - http://www.gramene.org/ - GR:0080039 - http://www.gramene.org/db/genes/search_gene?acc=$id - Gramene Genes at Cold Spring Harbor - Cold Spring Harbor Laboratory, New York - USA - - - - gene - genome - plant - - - - - species - - - - - - - Gramene Taxonomy - Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene. - - urn:miriam:gramene.taxonomy - http://identifiers.org/gramene.taxonomy/ - - gramene.taxonomy - - urn:miriam:pubmed:21076153 - - - - http://www.gramene.org/ - GR_tax:013681 - http://www.gramene.org/db/ontology/search?id=$id - Gramene Taxonomy at Cold Spring Harbor - Cold Spring Harbor Laboratory, New York - USA - - - - plant - taxonomy - - - - - model - - - - - - - Gramene QTL - Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene. - - urn:miriam:gramene.qtl - http://identifiers.org/gramene.qtl/ - - gramene.qtl - - urn:miriam:pubmed:21076153 - - - - http://www.gramene.org/ - CQG5 - http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$id - Gramene Quantitative Trait Loci at Cold Spring Harbor - Cold Spring Harbor Laboratory, New York - USA - - - - gene - genome - phenotype - plant - - - - - Sol Genomics Network - - SGN - - The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. - - urn:miriam:sgn - http://identifiers.org/sgn/ - - sgn - - urn:miriam:pubmed:20935049 - - - - http://solgenomics.net/ - 0001 - http://solgenomics.net/phenome/locus_display.pl?locus_id=$id - Sol Genomics Network at Boyce Thompson Institute for Plant Research - Boyce Thompson Institute for Plant Research, New York - USA - - - - genome - plant - - - - - model - - - - - - - Xenbase - Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. - - urn:miriam:xenbase - http://identifiers.org/xenbase/ - - xenbase - - urn:miriam:pubmed:19884130 - - - - http://www.xenbase.org/ - 922462 - http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=$id - Xenbase at University of Calgary - Department of Biological Sciences, University of Calgary, Alberta - Canada - - - - expression - genome - - - - - model - parameter - species - - - - - - - BioPortal - BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. - - urn:miriam:bioportal - http://identifiers.org/bioportal/ - - bioportal - - urn:miriam:pubmed:19483092 - - - - http://bioportal.bioontology.org/ - 1046 - http://bioportal.bioontology.org/ontologies/$id - BioPortal at National Center for Biomedical Ontology - National Center for Biomedical Ontology, Stanford University - USA - - - - ontology - registry - - - - - MIRIAM Registry resource - MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. - - urn:miriam:miriam.resource - http://identifiers.org/miriam.resource/ - - miriam.resource - - urn:miriam:pubmed:18078503 - - - - http://www.ebi.ac.uk/miriam/ - MIR:00100005 - http://www.ebi.ac.uk/miriam/main/resources/$id - MIRIAM Registry (resources) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - schema.org - - - - - EDAM Ontology - - EMBRACE Data and Methods Ontology - - EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications). - - urn:miriam:edam - http://identifiers.org/edam/ - http://edamontology.org/ - - edam - - urn:miriam:pubmed:23479348 - http://edamontology.sourceforge.net/ - - - - http://bioportal.bioontology.org/ontologies/EDAM - data_1664 - http://purl.bioontology.org/ontology/EDAM/$id - EDAM through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/edam - data_1664 - https://www.ebi.ac.uk/ols/ontologies/edam/terms?short_form=$id - EDAM through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.ebi.ac.uk/ontology-lookup/ - 1664 - https://www.ebi.ac.uk/ontology-lookup/?termId=EDAM_data:$id - EDAM via OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - - - - - Protein Model Database - - PMDB - - The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. - - urn:miriam:pmdb - http://identifiers.org/pmdb/ - - pmdb - - urn:miriam:doi:10.1093%2Fnar%2Fgkj105 - - - - https://bioinformatics.cineca.it/PMDB/ - PM0012345 - https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$id - Protein Model Database at University of Rome - CASPUR and Biocomputing group, Department of Biochemical Sciences, University of Rome, Rome - Italy - - - - protein - structure - - - - - species - - - - - - - This collection is no longer maintained. - 2D-PAGE protein - - 2D-PAGE E. coli - - 2DBase of Escherichia coli stores 2D polyacrylamide gel electrophoresis and mass spectrometry proteome data for E. coli. This collection references a subset of Uniprot, and contains general information about the protein record. - - urn:miriam:2d-page.protein - http://identifiers.org/2d-page.protein/ - - 2d-page.protein - - urn:miriam:pubmed:17904107 - - - - http://2dbase.techfak.uni-bielefeld.de/ - P39172 - http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?ac=$id - 2D-Page at Bielefeld - Graduate School in Bioinformatics and Genome Research, University of Bielefeld, - Germany - - - - - The long term stability of this collection is questionable. Users are advised to find an alternative source of information. - - - - protein - - - - - species - - - - - - - This service is obsolete and has been dismissed. - AGD - - Ashbya Genome Database - - AGD 3.0 is a genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from the fungi Ashbya gossypii and Saccharomyces cerevisiae. - - urn:miriam:agd - http://identifiers.org/agd/ - - agd - - urn:miriam:pubmed:15001715 - - - - http://agd.vital-it.ch/ - AGR144C - http://agd.vital-it.ch/Ashbya_gossypii/geneview?gene=$id - AGD at Basel - Biozentrum der Universität Basel, Basel - Switzerland - - - - expression - microarray - nucleotide - - - - - species - - - - - - - ArachnoServer - ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. - - urn:miriam:arachnoserver - http://identifiers.org/arachnoserver/ - - arachnoserver - - urn:miriam:pubmed:21036864 - - - - http://www.arachnoserver.org/ - AS000060 - http://www.arachnoserver.org/toxincard.html?id=$id - ArachnoServer at Brisbane - Institute for Molecular Bioscience, The University of Queensland, Brisbane - Australia - - - - drug - sequence - structure - - - - - species - - - - - - - BioCyc - BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. - - urn:miriam:biocyc - http://identifiers.org/biocyc/ - - biocyc - - urn:miriam:pubmed:16246909 - - - - http://biocyc.org - ECOLI:CYT-D-UBIOX-CPLX - http://biocyc.org/getid?id=$id - BioCyc at SRI International - Bioinformatics Research Group, SRI International, California - USA - - - - - BioCyc is a collection of 1690 Pathway/Genome Databases. - http://biocyc.org/intro.shtml - - - - chemical - genome - pathway - reaction - sequence - - - - - species - reaction - - - - - - - CAZy - - Carbohydrate-Active enzYmes - - The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features. - - urn:miriam:cazy - http://identifiers.org/cazy/ - - cazy - - urn:miriam:pubmed:18838391 - - - - http://www.cazy.org/ - GT10 - http://www.cazy.org/$id.html - CAZy at CNRS - Architecture et Fonction des Macromolécules Biologiques, CNRS, Marseille - France - - - - classification - polysaccharide - - - - - species - - - - - - - GOA - - Gene Ontology Annotation - UniProtKB-GOA - - The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. - - urn:miriam:goa - http://identifiers.org/goa/ - - goa - - urn:miriam:pubmed:18957448 - - - - http://www.ebi.ac.uk/GOA/ - P12345 - http://www.ebi.ac.uk/QuickGO/GProtein?ac=$id - GOA through QuickGO - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - annotation - ontology - protein - - - - - PaleoDB - - Paleobiology database - - The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data. - - urn:miriam:paleodb - http://identifiers.org/paleodb/ - - paleodb - - http://paleodb.org/cgi-bin/bridge.pl?a=displayPage&page=paleodbFAQ - - - - http://paleodb.org/ - 83088 - http://fossilworks.org/?a=taxonInfo&taxon_no=$id - PaleoDB at Macquarie University - Macquarie University, Sydney - Australia - - - http://museumu03.museumwww.naturkundemuseum-berlin.de/ - 83088 - http://museumu03.museumwww.naturkundemuseum-berlin.de/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id - PaleoDB at Museum für Naturkunde - Museum für Naturkunde, Berlin - Germany - - - http://paleodb.geology.wisc.edu/ - 83088 - http://paleodb.geology.wisc.edu/cgi-bin/bridge.pl?a=basicTaxonInfo&taxon_no=$id - PaleoDB at University of Wisconsin - University of Wisconsin, Madison - USA - - - - taxonomy - - - - - Compulyeast - - Compluyeast-2D-DB - - Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record. - - urn:miriam:compulyeast - http://identifiers.org/compulyeast/ - - compulyeast - - urn:miriam:pubmed:18617148 - - - - http://compluyeast2dpage.dacya.ucm.es/ - O08709 - http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$id - Compluyeast database at Universidad Complutense Madrid - Department Microbiology II, Universidad Complutense Madrid, Madrid - Spain - - - - protein - - - - - species - - - - - - - DisProt - The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. - - urn:miriam:disprot - http://identifiers.org/disprot/ - - disprot - - urn:miriam:pubmed:17145717 - - - - http://www.disprot.org/ - DP00003 - http://www.disprot.org/$id - DisProt at Indiana University - Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis - USA - - - - protein - structure - - - - - species - - - - - - - EchoBASE - EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. - - urn:miriam:echobase - http://identifiers.org/echobase/ - - echobase - - urn:miriam:pubmed:15608209 - - - - http://www.york.ac.uk/ - EB0170 - http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$id - EchoBASE at the University of York - Department of Biology (Area 10), University of York, York - UK - - - - gene - genome - protein - - - - - species - - - - - - - eggNOG - eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). - - urn:miriam:eggnog - http://identifiers.org/eggnog/ - - eggnog - - urn:miriam:pubmed:19900971 - - - - http://eggnog.embl.de/version_3.0/ - veNOG12876 - http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$id - eggNOG Version 3 at European Molecular Biology Laboratory - European Molecular Biology Laboratory, Heidelberg - Germany - - - http://eggnog.embl.de/version_2/ - veNOG12876 - http://eggnog.embl.de/cgi_bin/display_single_node.pl?node=$id - eggNOG Version 2 at European Molecular Biology Laboratory - European Molecular Biology Laboratory, Heidelberg - Germany - - - - clustering - gene - - - - - species - - - - - - - Ensembl Bacteria - - Ensembl Genomes Bacteria - - Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes. - - urn:miriam:ensembl.bacteria - http://identifiers.org/ensembl.bacteria/ - - ensembl.bacteria - - urn:miriam:pubmed:19884133 - - - - http://bacteria.ensembl.org/ - MU9_3181 - http://bacteria.ensembl.org/id/$id - Ensembl Bacteria at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - nucleotide - sequence - - - - - species - - - - - - - Ensembl Protists - - Ensembl Genomes Protists - - Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. - - urn:miriam:ensembl.protist - http://identifiers.org/ensembl.protist/ - - ensembl.protist - - urn:miriam:pubmed:19884133 - - - - http://protists.ensembl.org - PFC0120w - http://protists.ensembl.org/id/$id - Ensembl Protists at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - nucleotide - sequence - - - - - species - - - - - - - Ensembl Metazoa - - Ensembl Genomes Metazoa - - Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes. - - urn:miriam:ensembl.metazoa - http://identifiers.org/ensembl.metazoa/ - - ensembl.metazoa - - urn:miriam:pubmed:19884133 - - - - http://metazoa.ensembl.org/ - FBtr0084214 - http://metazoa.ensembl.org/id/$id - Enzembl Metazoa at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - nucleotide - sequence - - - - - species - - - - - - - Ensembl Plants - - Ensembl Genomes Plants - - Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes. - - urn:miriam:ensembl.plant - http://identifiers.org/ensembl.plant/ - - ensembl.plant - - urn:miriam:pubmed:19884133 - - - - http://plants.ensembl.org/ - AT1G73965 - http://plants.ensembl.org/id/$id - Enzembl Plants at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - nucleotide - sequence - - - - - species - - - - - - - Ensembl Fungi - - Ensembl Genomes Fungi - - Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes. - - urn:miriam:ensembl.fungi - http://identifiers.org/ensembl.fungi/ - - ensembl.fungi - - urn:miriam:pubmed:19884133 - - - - http://fungi.ensembl.org/ - CADAFLAT00006211 - http://fungi.ensembl.org/id/$id - Enzembl Fungi at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - nucleotide - sequence - - - - - species - - - - - - - HCVDB - - euHCVDB - - the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses. - - urn:miriam:hcvdb - http://identifiers.org/hcvdb/ - - hcvdb - - urn:miriam:pubmed:17142229 - - - - http://euhcvdb.ibcp.fr/euHCVdb/ - M58335 - https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$id - HCVDB at CNRS - Institut de Biologie et Chimie des Protéines, CNRS, University of Lyon , Lyon-Gerland - France - - - - genome - sequence - - - - - species - - - - - - - Genatlas - GenAtlas is a database containing information on human genes, markers and phenotypes. - - urn:miriam:genatlas - http://identifiers.org/genatlas/ - - genatlas - - urn:miriam:pubmed:9835018 - - - - http://genatlas.medecine.univ-paris5.fr/ - HBB - http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$id - Genatlas at Paris Descartes University - Paris Descartes University, Paris - France - - - - disorder - gene - human - - - - - species - - - - - - - CATH superfamily - The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. - - urn:miriam:cath.superfamily - http://identifiers.org/cath.superfamily/ - - cath.superfamily - - urn:miriam:pubmed:9309224 - - - - http://www.cathdb.info/ - 1.10.10.200 - http://www.cathdb.info/cathnode/$id - CATH superfamily at UCL - Institute of Structural and Molecular Biology, University College London - United Kingdom - - - - classification - protein - schema.org - structure - - - - - species - - - - - - - CATH domain - The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains. - - urn:miriam:cath.domain - http://identifiers.org/cath.domain/ - - cath.domain - - urn:miriam:pubmed:9309224 - - - - http://www.cathdb.info/ - 1cukA01 - http://www.cathdb.info/domain/$id - CATH domain at UCL - Institute of Structural and Molecular Biology, University College London - UK - - - - classification - protein - schema.org - structure - - - - - species - - - - - - - GeneFarm - GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. - - urn:miriam:genefarm - http://identifiers.org/genefarm/ - - genefarm - - urn:miriam:pubmed:15608279 - - - - http://urgi.versailles.inra.fr/Genefarm/ - 4892 - https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$id - GeneFarm at Unité de Recherche en Génomique Végétale - Unité de Recherche en Génomique Végétale, Evry - France - - - - expression - genome - nucleotide - sequence - - - - - species - - - - - - - GPCRDB - - G protein-coupled receptor database - - The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models. - - urn:miriam:gpcrdb - http://identifiers.org/gpcrdb/ - - gpcrdb - - urn:miriam:pubmed:21045054 - - - - http://www.gpcrdb.org/ - RL3R1_HUMAN - http://www.gpcrdb.org/protein/$id/ - GPCRDB at Radboud University - Radboud University Nijmegen Medical Centre, Nijmegen, - Holland - - - - protein - - - - - species - - - - - - - HOGENOM - HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. - - urn:miriam:hogenom - http://identifiers.org/hogenom/ - - hogenom - - urn:miriam:pubmed:19534752 - - - - http://pbil.univ-lyon1.fr/databases/hogenom/ - HBG284870 - http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$id - HOGENOM at CNRS - Laboratoire de Biométrie et Biologie Evolutive, CNRS, Lyon - France - - - - classification - sequence - - - - - species - - - - - - - GeneTree - - Ensembl GeneTree - - Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. - - urn:miriam:genetree - http://identifiers.org/genetree/ - - genetree - - urn:miriam:pubmed:16381931 - - - - http://www.ensembl.org/ - ENSGT00550000074763 - http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$id - GeneTree at Ensembl - Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - classification - gene - protein - schema.org - - - - - species - - - - - - - HSSP - - Homology-derived Structure of Proteins - - HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. - - urn:miriam:hssp - http://identifiers.org/hssp/ - - hssp - - urn:miriam:pubmed:7937066 - - - - http://swift.cmbi.kun.nl/swift/hssp/ - 102l - ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$id.hssp.bz2 - HSSP at EMBL - Protein Design Group, European Molecular Biology Laboratory, Heidelberg - Germany - - - ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/ - 102l - ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$id.hssp.bz2 - HSSP at CMBI - Nijmegen Centre for Molecular Life Sciences, CMBI, Nijmegen - Holland - - - - clustering - protein - sequence - - - - - species - - - - - - - MycoBrowser tuberculosis - - TubercuList - - Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information. - - urn:miriam:myco.tuber - http://identifiers.org/myco.tuber/ - - myco.tuber - - urn:miriam:pubmed:20980200 - - - - http://tuberculist.epfl.ch/ - Rv1908c - http://tuberculist.epfl.ch/quicksearch.php?gene+name=$id - MycoBrowser tuberculosis at Global Health Institute - Global Health Institute, Lausanne - Switzerland - - - - genome - sequence - - - - - species - - - - - - - MycoBrowser leprae - - Leproma - - Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information. - - urn:miriam:myco.lepra - http://identifiers.org/myco.lepra/ - - myco.lepra - - urn:miriam:pubmed:20980200 - - - - http://mycobrowser.epfl.ch/leprosy.html - ML0224 - http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$id - MycoBrowser leprae at Global Health Institute - Global Health Institute, Lausanne - Switzerland - - - - genome - sequence - - - - - species - - - - - - - MycoBrowser marinum - - marinolist - - Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information. - - urn:miriam:myco.marinum - http://identifiers.org/myco.marinum/ - - myco.marinum - - urn:miriam:pubmed:20980200 - - - - http://mycobrowser.epfl.ch/marinolist.html - MMAR_2462 - http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$id - MycoBrowser marinum at Global Health Institute - Global Health Institute, Lausanne - Switzerland - - - - genome - sequence - - - - - species - - - - - - - MycoBrowser smegmatis - - smegmalist - - Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information. - - urn:miriam:myco.smeg - http://identifiers.org/myco.smeg/ - - myco.smeg - - urn:miriam:pubmed:20980200 - - - - http://mycobrowser.epfl.ch/smegmalist.html - MSMEG_3769 - http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$id - MycoBrowser smegmatis at Global Health Institute - Global Health Institute, Lausanne - Switzerland - - - - genome - sequence - - - - - species - - - - - - - Orphanet - - Orpha - - Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. - - urn:miriam:orphanet - http://identifiers.org/orphanet/ - http://bio2rdf.org/orphanet - - orphanet - - urn:miriam:pubmed:19058507 - - - - http://www.orpha.net/consor/ - 85163 - http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$id - Orphanet at Inserm - Inserm, Hôpital Broussais, Paris - France - - - http://orphanet.bio2rdf.org/fct - 85163 - http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$id - Bio2RDF - Bio2RDF.org - - - - - disease - drug - human - - - - - model - - - - - - - OrthoDB - OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups - - urn:miriam:orthodb - http://identifiers.org/orthodb/ - - orthodb - - urn:miriam:pubmed:20972218 - - - - http://cegg.unige.ch/orthodb4 - Q9P0K8 - http://cegg.unige.ch/orthodb/results?searchtext=$id - OrthoDB at Swiss Institute of Bioinformatics - Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, Geneva - Switzerland - - - - eukaryotic - protein - sequence - - - - - species - - - - - - - Peroxibase - Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences. - - urn:miriam:peroxibase - http://identifiers.org/peroxibase/ - - peroxibase - - urn:miriam:pubmed:19112168 - - - - http://peroxibase.toulouse.inra.fr/ - 5282 - http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$id - Peroxibase at University of Geneva - Department of Plant Biology, University of Geneva, Geneva - Switzerland - - - - enzyme - sequence - - - - - species - - - - - - - PhylomeDB - PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins. - - urn:miriam:phylomedb - http://identifiers.org/phylomedb/ - - phylomedb - - urn:miriam:pubmed:17962297 - - - - http://phylomedb.org/ - Phy000CLXM_RAT - http://phylomedb.org/?seqid=$id - PhylomeDB at Centro de Investigación Príncipe Felipe - Bioinformatics Department,Centro de Investigación Príncipe Felipe, Valencia - Spain - - - - genome - protein - taxonomy - - - - - species - - - - - - - SubstrateDB - - PMAP substrateDB - - The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. - - urn:miriam:pmap.substratedb - http://identifiers.org/pmap.substratedb/ - - pmap.substratedb - - urn:miriam:pubmed:18842634 - - - - http://substrate.burnham.org/ - 1915 - http://substrate.burnham.org/protein/annotation/$id/html - SubstrateDB at The Burnham Institute for Medical Research - The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California - USA - - - - domain - protein - reaction - - - - - species - - - - - - - CutDB - - PMAP cutDB - - The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). - - urn:miriam:pmap.cutdb - http://identifiers.org/pmap.cutdb/ - - pmap.cutdb - - urn:miriam:pubmed:17142225 - - - - http://cutdb.burnham.org - 25782 - http://cutdb.burnham.org/relation/show/$id - CutDB at The Burnham Institute for Medical Research - The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, California - USA - - - - domain - protein - reaction - - - - - species - - - - - - - ProtClustDB - - Protein Clusters Database - Entrez ProtClustDB - - ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. - - urn:miriam:protclustdb - http://identifiers.org/protclustdb/ - - protclustdb - - urn:miriam:pubmed:18940865 - - - - http://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters - O80725 - http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$id - ProtClustDB at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - clustering - protein - - - - - species - - - - - - - PMP - - Protein Model Portal - - The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. - - urn:miriam:pmp - http://identifiers.org/pmp/ - - pmp - - urn:miriam:pubmed:19037750 - - - - http://www.proteinmodelportal.org/ - Q0VCA6 - http://www.proteinmodelportal.org/query/uniprot/$id - PMP at University of Basel - Biozentrum, University of Basel, Basel - Switzerland - - - - protein - structure - - - - - species - - - - - - - ProtoNet ProteinCard - ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. - - urn:miriam:protonet.proteincard - http://identifiers.org/protonet.proteincard/ - - protonet.proteincard - - urn:miriam:pubmed:16672244 - - - - http://www.protonet.cs.huji.ac.il/ - 16941567 - http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$id - ProtoNet at Hebrew University - Hebrew University, Jerusalem - Israel - - - - protein - - - - - species - - - - - - - ProtoNet Cluster - ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. - - urn:miriam:protonet.cluster - http://identifiers.org/protonet.cluster/ - - protonet.cluster - - urn:miriam:pubmed:16672244 - - - - http://www.protonet.cs.huji.ac.il/ - 4349895 - http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$id - ProtoNet at Hebrew University - Hebrew University, Jerusalem - Israel - - - - classification - clustering - protein - - - - - species - - - - - - - REBASE - - Restriction Enzyme Database - - REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. - - urn:miriam:rebase - http://identifiers.org/rebase/ - - rebase - - urn:miriam:pubmed:19846593 - - - - http://rebase.neb.com/rebase/ - 101 - http://rebase.neb.com/rebase/enz/$id.html - REBASE at New England Biolabs - New England Biolabs, Ipswich, Massachusetts - USA - - - - enzyme - reaction - - - - - species - - - - - - - SWISS-MODEL - The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT. - - urn:miriam:swiss-model - http://identifiers.org/swiss-model/ - - swiss-model - - urn:miriam:pubmed:18931379 - - - - http://swissmodel.expasy.org/ - P23298 - http://swissmodel.expasy.org/repository/smr.php?sptr_ac=$id - SWISS-MODEL at SIB Swiss Institute of Bioinformatics - Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel - Switzerland - - - - - Identifiers to individual models are not stable, since they can change between releases. - http://swissmodel.expasy.org/?pid=smd06 - - - - protein - structure - - - - - species - - - - - - - VectorBase - VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. - - urn:miriam:vectorbase - http://identifiers.org/vectorbase/ - - vectorbase - - urn:miriam:pubmed:19028744 - - - - http://www.vectorbase.org/ - ISCW007415 - https://www.vectorbase.org/search/site/$id?&site="Genome" - Vectorbase at EMBL-EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - gene - genome - protein - - - - - species - - - - - - - Human Disease Ontology - - DO - - The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. - - urn:miriam:doid - http://identifiers.org/doid/ - urn:miriam:obo.do - http://identifiers.org/obo.do/ - - doid - - urn:miriam:doi:10.1093%2Fnar%2Fgkr972 - http://www.disease-ontology.org/ - - - - http://bioportal.bioontology.org/ontologies/DOID - DOID:11337 - http://purl.bioontology.org/ontology/DOID/$id - Human Disease Ontology through BioPortal - National Center for Biomedical Ontology, Stanford University - USA - - - https://www.ebi.ac.uk/ols/ontologies/doid - DOID:11337 - https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=$id - Human Disease Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://disease-ontology.org/ - DOID:11337 - http://disease-ontology.org/term/$id - Human Disease Ontology at Northwestern University - University of Maryland (Maryland) and Northwestern University (Illinois) - USA - - - - disease - human - ontology - - - - - model - species - - - - - - - Cell Cycle Ontology - The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. - - urn:miriam:cco - http://identifiers.org/cco/ - - cco - - urn:miriam:pubmed:19480664 - - - - https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=CCO - CCO:P0000023 - https://www.ebi.ac.uk/ontology-lookup/?termId=$id - Cell Cycle Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ - CCO:P0000023 - http://bioportal.bioontology.org/ontologies/1507?p=terms&conceptid=$id - Cell Cycle Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - model - species - - - - - - - miRBase mature sequence - The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. - - urn:miriam:mirbase.mature - http://identifiers.org/mirbase.mature/ - - mirbase.mature - - urn:miriam:doi:10.1093%2Fnar%2Fgkq1027 - - - - http://www.mirbase.org/ - MIMAT0000001 - http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=$id - miRBase - Faculty of Life Sciences, University of Manchester - UK - - - - nucleotide - sequence - - - - - nextProt - neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. - - urn:miriam:nextprot - http://identifiers.org/nextprot/ - - nextprot - - urn:miriam:pubmed:22139911 - http://www.nextprot.org/db/open/page/about-nextprot - - - - http://www.nextprot.org/ - NX_O00165 - http://www.nextprot.org/db/entry/$id - nextProt at Swiss Institute of Bioinformatics - Swiss Institute of Bioinformatics, Geneva - Switzerland - - - - human - protein - - - - - species - - - - - - - CAS - - Chemical Abstracts Service - CAS Registry Number - CAS Number - CASRN - - CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. - - urn:miriam:cas - http://identifiers.org/cas/ - - cas - - http://www.cas.org/index.html - - - - http://commonchemistry.org - 50-00-0 - http://commonchemistry.org/ChemicalDetail.aspx?ref=$id - CAS through Common Chemistry - American Chemistry Society, Washington, DC - USA - - - http://www.ncbi.nlm.nih.gov/pccompound - 50-00-0 - http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=$id - CAS through PubChem Compound - National Center for Biotechnology Information (NCBI) - USA - - - - - CAS provides fee-based services. - http://cas.org/aboutcas/faq.html#cost - - - - chemical - structure - - - - - species - - - - - - - KEGG Genome - - KEGG Organism - - - KEGG Genome is a collection of organisms whose genomes have been completely sequenced. - - urn:miriam:kegg.genome - http://identifiers.org/kegg.genome/ - - kegg.genome - - urn:miriam:pubmed:22080510 - - - - http://www.genome.jp/kegg/catalog/org_list.html - eco - http://www.kegg.jp/entry/$id - KEGG Genome Database - Kyoto University Bioinformatics Center, Kyoto - Japan - - - - genome - - - - - model - - - - - - - KEGG Metagenome - - - - The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. - - urn:miriam:kegg.metagenome - http://identifiers.org/kegg.metagenome/ - - kegg.metagenome - - urn:miriam:pubmed:22080510 - - - - http://www.genome.jp/kegg/catalog/org_list3.html - T30002 - http://www.kegg.jp/entry/$id - KEGG Metagenome Database - Kyoto University Bioinformatics Center, Kyoto - Japan - - - - genome - - - - - model - - - - - - - NARCIS - - National Academic Research and Collaborations Information System - - NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. - - urn:miriam:narcis - http://identifiers.org/narcis/ - - narcis - - http://www.narcis.nl/about/Language/en - - - - http://www.narcis.nl/?Language=en - oai:cwi.nl:4725 - http://www.narcis.nl/publication/RecordID/$id - NARCIS at The Hague - NARCIS, Royal Netherlands Academy of Science and Arts - Holland - - - http://persistent-identifier.nl/ - oai:cwi.nl:4725 - http://oai.cwi.nl/oai?verb=GetRecord&metadataPrefix=nl_didl&identifier=oai:cwi.nl:$id - Dutch publication NBN through Persistent-identifier (redirection) - Dans, The Hague - Holland - - - - bibliography - - - - - model - - - - - - - Japan Chemical Substance Dictionary - The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST). - - urn:miriam:jcsd - http://identifiers.org/jcsd/ - - jcsd - - http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp - - - - http://jglobal.jst.go.jp/en/ - J55.713G - http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$id - Japan Chemical Substance Dictionary - Japan Science and Technology Agency - Japan - - - - chemical - structure - - - - - species - - - - - - - Pathway Ontology - The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions. - - urn:miriam:pw - http://identifiers.org/pw/ - http://identifiers.org/obo.pw/ - urn:miriam:obo.pw - - pw - - urn:miriam:pubmed:21478484 - - - - http://rgd.mcw.edu/rgdweb/ontology/search.html - PW:0000208 - http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=$id - Pathway Ontology at Rat Genome Database - Medical College of Wisconsin, Wisconsin - USA - - - https://www.ebi.ac.uk/ols/ontologies/pw - PW:0000208 - https://www.ebi.ac.uk/ols/ontologies/pw/terms?obo_id=$id - Pathway Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/PW - PW:0000208 - http://purl.bioontology.org/ontology/PW/$id - Pathway Ontology through BioPortal - National Center for Biomedical Ontology, Stanford, California - USA - - - - human - mammalian - ontology - pathway - - - - - model - reaction - - - - - - - Sequence Read Archive - The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database. - - urn:miriam:insdc.sra - http://identifiers.org/insdc.sra/ - - insdc.sra - - urn:miriam:pubmed:22009675 - - - - http://www.ncbi.nlm.nih.gov/sra - SRX000007 - http://www.ncbi.nlm.nih.gov/sra/$id?&report=full - Sequence Read Archive at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://www.ebi.ac.uk/ena - SRX000007 - http://www.ebi.ac.uk/ena/data/view/$id - European Nucleotide Archive (ENA) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://trace.ddbj.nig.ac.jp/dra/ - SRX000007 - http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$id - DDBJ Sequence Read Archive (DRA) - DNA Data Bank of Japan, Mishima, Shizuoka - Japan - - - - sequence - - - - - species - - - - - - - ScerTF - ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor. - - urn:miriam:scretf - http://identifiers.org/scretf/ - - scretf - - urn:miriam:pubmed:22140105 - - - - http://stormo.wustl.edu/ScerTF/ - RSC3 - http://stormo.wustl.edu/ScerTF/details/$id/ - ScerTF at Washington University - Department of Genetics, Washington University Medical School, St Louis, Missouri - USA - - - - domain - nucleotide - sequence - - - - - species - - - - - - - PharmGKB Gene - The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. - - urn:miriam:pharmgkb.gene - http://identifiers.org/pharmgkb.gene/ - - pharmgkb.gene - - urn:miriam:pubmed:22103613 - - - - http://www.pharmgkb.org/ - PA131 - http://www.pharmgkb.org/gene/$id - PharmGKB Gene at Stanford - Department of Genetics, School of Medicine, Stanford University, Stanford, California - USA - - - - - The data may be used for research purposes only. - http://www.pharmgkb.org/home/policies/web-data.jsp - - - - gene - pharmacogenomics - - - - - species - - - - - - - miRNEST - miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. - - urn:miriam:mirnest - http://identifiers.org/mirnest/ - - mirnest - - urn:miriam:pubmed:22135287 - - - - http://rhesus.amu.edu.pl/mirnest/copy/ - MNEST029358 - http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$id - miRNEST at Adam Mickiewicz University - Institute of Molecular Biology, Adam Mickiewicz University, Poznan - Poland - - - - expression - - - - - species - - - - - - - NAPP - - Nucleic Acid Phylogenetic Profiling - - NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters. - - urn:miriam:napp - http://identifiers.org/napp/ - - napp - - - http://napp.u-psud.fr/ - 351 - http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$id - NAPP at CNRS - Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, Paris - France - - - - clustering - nucleotide - - - - - species - - - - - - - NONCODE v3 - NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. - - urn:miriam:noncodev3 - http://identifiers.org/noncodev3/ - urn:miriam:noncode - http://identifiers.org/noncode/ - - noncodev3 - - urn:miriam:pubmed:22135294 - - - - http://www.noncode.org/ - 377550 - http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$id - NONCODE at Chinese Academy of Sciences - Bioinformatics Research Group, Chinese Academy of Sciences, Beijing - China - - - - expression - nucleotide - - - - - species - - - - - - - VIRsiRNA - - Virus siRNA database - VIRsiRNAdb - - The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region. - - urn:miriam:virsirna - http://identifiers.org/virsirna/ - - virsirna - - urn:miriam:pubmed:22139916 - - - - http://crdd.osdd.net/servers/virsirnadb - virsi1909 - http://crdd.osdd.net/servers/virsirnadb/record.php?details=$id - VIRsiRNA at Institute of Microbial Technology - Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India - India - - - - mammalian - nucleotide - - - - - species - - - - - - - ELM - - Eukaryotic Linear Motifs - - Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. - - urn:miriam:elm - http://identifiers.org/elm/ - - elm - - urn:miriam:pubmed:22110040 - - - - http://elm.eu.org/ - CLV_MEL_PAP_1 - http://elm.eu.org/elms/elmPages/$id.html - ELM at EMBL (Germany) - Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg - Germany - - - - domain - eukaryotic - protein - - - - - species - - - - - - - MimoDB - - Mimotope Database - BDB - Biopanning Data Bank - - MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank. - - urn:miriam:mimodb - http://identifiers.org/mimodb/ - - mimodb - - urn:miriam:pubmed:22053087 - - - - http://immunet.cn/bdb/ - 1 - http://immunet.cn/bdb/index.php/mimoset/$id - BDB at University of Electronic Science and Technology of China - Key Laboratory for Neuroinformation of Ministry of Education, University of Electronic Science and Technology of China, Sichuan - China - - - - interaction - protein - - - - - species - - - - - - - SitEx - SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments. - - urn:miriam:sitex - http://identifiers.org/sitex/ - - sitex - - urn:miriam:pubmed:22139920 - - - - http://www-bionet.sscc.ru/sitex/ - 1000 - http://www-bionet.sscc.ru/sitex/index.php?siteid=$id - SitEx at Novosibirsk State University - Novosibirsk State University, Novosibirsk - Russia - - - - domain - eukaryotic - sequence - structure - - - - - species - - - - - - - BYKdb - - Bacterial protein tYrosine Kinase database - - The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. - - urn:miriam:bykdb - http://identifiers.org/bykdb/ - - bykdb - - urn:miriam:pubmed:22080550 - - - - http://bykdb.ibcp.fr/BYKdb/ - A0A010GJI9 - https://bykdb.ibcp.fr/data/html/annotated/$id.html - BYKdb at CNRS - Unité Bases Moléculaires et Structurales des Systèmes Infectieux; CNRS - Université Claude Bernard, Lyon - France - - - - domain - microbial - sequence - - - - - species - - - - - - - Conoserver - ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails. - - urn:miriam:conoserver - http://identifiers.org/conoserver/ - - conoserver - - urn:miriam:pubmed:18065428 - urn:miriam:pubmed:22058133 - - - - http://www.conoserver.org/ - 2639 - http://www.conoserver.org/?page=card&table=protein&id=$id - ConoServer at University of Queensland - Institute for Molecular Bioscience, The University of Queensland, Brisbane - Australia - - - - - Conoserver can only be used for academic research. - http://www.conoserver.org/ - - - - drug - protein - - - - - species - - - - - - - TopFind - TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. - - urn:miriam:topfind - http://identifiers.org/topfind/ - - topfind - - urn:miriam:pubmed:22102574 - - - - http://clipserve.clip.ubc.ca/topfind - Q9UKQ2 - http://clipserve.clip.ubc.ca/topfind/proteins/$id - TopFind at University of British Columbia - Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver - Canada - - - - domain - protein - - - - - species - - - - - - - MIPModDB - MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures. - - urn:miriam:mipmod - http://identifiers.org/mipmod/ - - mipmod - - urn:miriam:pubmed:22080560 - - - - http://bioinfo.iitk.ac.in/MIPModDB - HOSAPI0399 - http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$id - MIPModDB at Indian Institute of Technology Kanpur - Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur - India - - - - protein - structure - - - - - species - - - - - - - Cell Image Library - - CIL - The Cell: An Image Library-CCDB - The Cell: An Image Library-Cell Centered Database - - The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. - - urn:miriam:cellimage - http://identifiers.org/cellimage/ - - cellimage - - urn:miriam:doi:10.1017%2FS1551929511000034 - http://cellimagelibrary.org/pages/about - - - - http://cellimagelibrary.org/ - 24801 - http://cellimagelibrary.org/images/$id - Cell Image Library at American Society for Cell Biology - American Society for Cell Biology, Bethesda, Maryland and The National Center for Microscopy and Imaging Research, San Diego, California - USA - - - - - Each image may be individually associated with its own copyright restriction, which should be consulted for appropriateness by users. - http://cellimagelibrary.org/pages/license - - - - image library - - - - - COMBINE specifications - The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. - - urn:miriam:combine.specifications - http://identifiers.org/combine.specifications/ - - combine.specifications - - http://co.mbine.org/about - - - - http://co.mbine.org/standards/ - sbgn.er.level-1.version-1.2 - http://co.mbine.org/specifications/$id - COMBINE at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - ZFIN Phenotype - ZFIN serves as the zebrafish model organism database. This collection references the phenotypes observed for any given genotype. - - urn:miriam:zfin.phenotype - http://identifiers.org/zfin.phenotype/ - - zfin.phenotype - - urn:miriam:pubmed:17991680 - - - - http://zfin.org - ZDB-GENO-980202-899 - http://zfin.org/$id - ZFIN Phenotype at University of Oregon - Zebrafish Information Network, University of Oregon, USA - USA - - - - gene - phenotype - - - - - model - - - - - - - ZFIN Expression - ZFIN serves as the zebrafish model organism database. This collection references the set of expressed genes for any given genotype. - - urn:miriam:zfin.expression - http://identifiers.org/zfin.expression/ - - zfin.expression - - urn:miriam:pubmed:17991680 - - - - http://zfin.org - ZDB-GENO-980202-899 - http://zfin.org/$id - ZFIN Expression at University of Oregon - Zebrafish Information Network, University of Oregon, USA - USA - - - - expression - gene - - - - - model - - - - - - - CABRI - CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it. - - urn:miriam:cabri - http://identifiers.org/cabri/ - - cabri - - http://www.cabri.org/guidelines.html - - - - http://www.cabri.org/ - dsmz_mutz-id:ACC 291 - http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] - CABRI Cell Lines catalogue in Genova (SRS) - National Cancer Research Institute of Genova, Genova - Italy - - - http://www.be.cabri.org/ - dsmz_mutz-id:ACC 291 - http://www.be.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] - CABRI Cell Lines catalogue in Brussels (SRS) - BCCM, Brussels - Belgium - - - http://www.fr.cabri.org/ - dsmz_mutz-id:ACC 291 - http://www.fr.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] - CABRI Cell Lines catalogue in Paris (SRS) - nstitut Pasteur, Paris - France - - - - catalogue - eukaryotic - microbial - - - - - model - - - - - - - CYGD - The MIPS Comprehensive Yeast Genome Database (CYGD) provides information on the molecular structure and functional network of the entirely sequenced the budding yeast, Saccharomyces cerevisiae, as well as on related yeasts which are used for comparative analysis. - - urn:miriam:cygd - http://identifiers.org/cygd/ - - cygd - - urn:miriam:pubmed:15608217 - http://mips.gsf.de/ - - - - http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Method=start_method&Db=p3_p13838_Sac_cerev - YFL039c - http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Db=p3_p13838_Sac_cerev&Method=ReportGene&GeneticelemCode=$id - CYGD PEDANT Interface at Biomax Informatics - Biomax Informatics AG, Planegg - Germany - - - http://mips.gsf.de/genre/proj/yeast/ - YFL039c - http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=$id - CYGD at MIPS - Institute for Bioinformatics (MIPS) - Germany - - - http://mips.helmholtz-muenchen.de/genre/proj/yeast/ - YFL039c - http://mips.helmholtz-muenchen.de/genre/proj/yeast/singleGeneReport.html?entry=$id - CYGD at MIPS (GmbH) - Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, GmbH, Neuherberg - Germany - - - - - Accompanying disclaimer on each page states that data and services are for academic, non-commercial use only. - http://mips.helmholtz-muenchen.de/genre/proj/yeast/About/index.html - - - - gene - genome - protein - - - - - species - - - - - - - HUGE - The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. - - urn:miriam:huge - http://identifiers.org/huge/ - - huge - - urn:miriam:pubmed:14681467 - - - - http://www.kazusa.or.jp/huge/ - KIAA0001 - http://www.kazusa.or.jp/huge/gfpage/$id/ - HUGE at Kazusa DNA Research Institute - Kazusa DNA Research Institute, Chiba - Japan - - - - - The information provided is for research purposes only. - http://www.kazusa.or.jp/disclaimers.html - - - - DNA - protein - - - - - species - - - - - - - BindingDB - BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. - - urn:miriam:bindingDB - http://identifiers.org/bindingDB/ - - bindingDB - - urn:miriam:pubmed:17145705 - - - - http://www.bindingdb.org/bind/index.jsp - 22360 - http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=$id - BindingDB At Skaggs School of Pharmacy & Pharmaceutical Sciences - Skaggs School of Pharmacy & Pharmaceutical Sciences, La Jolla, California - USA - - - - drug - interaction - protein - - - - - STRING - - Search Tool for Retrieval of Interacting Genes/Proteins - - STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions. -The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. - - urn:miriam:string - http://identifiers.org/string/ - - string - - urn:miriam:pubmed:18940858 - - - - http://string.embl.de/ - P53350 - http://string.embl.de/interactions/$id - STRING at Heidelberg - European Molecular Biology Laboratory, Heidelberg - Germany - - - http://string-db.org/ - P53350 - http://string-db.org/interactions/$id - STRING Mirror at Heidelberg - European Molecular Biology Laboratory, Heidelberg - Germany - - - - - Identifiers are regenerated each time a new STRING version is released, hence the specific information recorded between versions may differ. - - - - interaction - protein - - - - - STITCH - STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. - - urn:miriam:stitch - http://identifiers.org/stitch/ - - stitch - - urn:miriam:pubmed:18084021 - - - - http://stitch.embl.de/ - BQJCRHHNABKAKU - http://stitch.embl.de/interactions/$id - STITCH - European Molecular Biology Laboratory, Heidelberg - Germany - - - - - Identifiers are regenerated each time a new version is released. The best way to reference this information is to use the first segment (14 characters) of an InChi key. - http://www.inchi.info/inchikey_overview_en.html - - - - chemical - interaction - protein - - - - - model - - - - - - - Anatomical Therapeutic Chemical Vetinary - The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. - - urn:miriam:atcvet - http://identifiers.org/atcvet/ - - atcvet - - http://www.whocc.no/atcvet/atcvet_methodology/purpose_of_the_atcvet_system/ - - - - http://www.whocc.no/atcvet/atcvet_index/ - QJ51RV02 - http://www.whocc.no/atcvet/atcvet_index/?code=$id - Anatomical Therapeutic Chemical Vet Index at WHO - World Health Organisation - Switzerland - - - - classification - drug - - - - - species - - - - - - - Phenol-Explorer - Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. - - urn:miriam:phenolexplorer - http://identifiers.org/phenolexplorer/ - - phenolexplorer - - urn:miriam:doi:10.1093%2Fdatabase%2Fbap024 - - - - http://www.phenol-explorer.eu/foods/ - 75 - http://phenol-explorer.eu/foods/$id - Phenol-Explorer Database on Phenol content of foods - INRA and University of Alberta - France and Canada - - - - chemical - - - - - SNOMED CT - SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc. - - urn:miriam:snomedct - http://identifiers.org/snomedct/ - - snomedct - - http://www.connectingforhealth.nhs.uk/systemsandservices/data/snomed/ - - - - http://www.snomedbrowser.com/ - 284196006 - http://www.snomedbrowser.com/Codes/Details/$id - SNOMED-CT at The National Pathology Exchange - The Health Informatics Service, NHS, West Yorkshire - UK - - - http://vtsl.vetmed.vt.edu/ - 284196006 - http://vtsl.vetmed.vt.edu/TerminologyMgt/Browser/ISA.cfm?SCT_ConceptID=$id - SNOMED CT at Virginia - Virginia Maryland Regional College of Veterinary Medicine, Virginia - USA - - - http://www.ihtsdo.org/snomed-ct/ - 284196006 - http://unknown/$id - SNOMED CT at The International Health Terminology Standards Development Organization. - IHTSDO, Copenhagen - Denmark - - - - - Access to data may require a license, depending on whether or not it is used in a member country, and for a particular purpose. - http://www.ihtsdo.org/join-us/ - - - - controlled vocabulary - - - - - MeSH 2012 - - Medical Subject Headings 2012 - - MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012. - - urn:miriam:mesh.2012 - http://identifiers.org/mesh.2012/ - - mesh.2012 - - http://www.nlm.nih.gov/pubs/factsheets/mesh.html - - - - http://www.nlm.nih.gov/mesh/ - 17186 - http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$id&view=expanded - MeSH at National Library of Medicine - U.S. National Library of Medicine, National Institute of Health, Maryland - USA - - - http://bioportal.bioontology.org/ - D018377 - http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=$id - MeSH at BioPortal - National Center for Biomedical Ontology, Stanford University - USA - - - - - Records accessed through MESH may include content that itself has some copyright restriction when reproduced. - http://www.nlm.nih.gov/copyright.html - - - Access to Mesh 2012 uses identifiers that could potentially change. We recommend the use of the stable MeSH collection (http://identifiers.org/mesh/). If you have issues accessing Mesh 2012, you may wish to try the ftp service. - ftp://nlmpubs.nlm.nih.gov/online/mesh/.asciimesh/c2012.bin - - - - controlled vocabulary - - - - - KnapSack - Knapsack provides information on metabolites and the taxonomic class with which they are associated. - - urn:miriam:knapsack - http://identifiers.org/knapsack/ - - knapsack - - urn:miriam:pubmed:22123792 - http://kanaya.aist-nara.ac.jp/KNApSAcK/Manual/KNApSAcKManual.html - - - - http://kanaya.aist-nara.ac.jp/KNApSAcK/ - C00000001 - http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=$id - KnapSack at Nara Institute - Nara Institute of Science and Technology - Japan - - - - metabolite - - - - - Canadian Drug Product Database - - DPD - - The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). - - urn:miriam:cdpd - http://identifiers.org/cdpd/ - - cdpd - - http://www.hc-sc.gc.ca/dhp-mps/prodpharma/databasdon/terminolog-eng.php - - - - http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp - 63250 - http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$id - Canadian Drug Identification Number at Health Canada - Health Canada, Ottawa, Ontario - Canada - - - - - Need an active session to access information (timeout set at 29 mins). - - - - drug - registry - - - - - species - - - - - - - MassBank - MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). - - urn:miriam:massbank - http://identifiers.org/massbank/ - - massbank - - urn:miriam:pubmed:20623627 - - - - http://www.massbank.jp - PB000166 - http://www.massbank.jp/jsp/FwdRecord.jsp?id=$id - MassBank in Japan - The MassBank Consortium - Japan - - - http://www.massbank.eu/ - PB000166 - http://www.massbank.eu/MassBank/jsp/FwdRecord.jsp?id=$id - MassBank in Europe - NORMAN Network and The MassBank Consortium - Germany - - - http://msbi.ipb-halle.de/MassBank/ - PB000166 - http://msbi.ipb-halle.de/MassBank/jsp/FwdRecord.jsp?id=$id - MassBank in Germany - The MassBank Consortium - Germany - - - - - Downloading, copying, saving, or printing out of materials for purposes other than academic research or education is prohibited. - http://www.massbank.jp/en/regulation.html - - - - chemical - mass spectrometry - metabolite - - - - - species - - - - - - - Golm Metabolome Database - - GMD - - Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena. - - urn:miriam:gmd - http://identifiers.org/gmd/ - - gmd - - urn:miriam:pubmed:15613389 - urn:miriam:pubmed:20526350 - - - - http://gmd.mpimp-golm.mpg.de/ - 68513255-fc44-4041-bc4b-4fd2fae7541d - http://gmd.mpimp-golm.mpg.de/Metabolites/$id.aspx - Golm Metabolome Database at Max Planck Institute of Molecular Plant Physiology - Max Planck Institute of Molecular Plant Physiology, Potsdam - Germany - - - - - Data in this collection is restricted for non-academic users. - http://gmd.mpimp-golm.mpg.de/termsconditions.aspx - - - - metabolite - - - - - species - - - - - - - HomoloGene - HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. - - urn:miriam:homologene - http://identifiers.org/homologene/ - http://bio2rdf.org/homologene - - homologene - - urn:miriam:pubmed:21097890 - - - - http://www.ncbi.nlm.nih.gov/homologene/ - 1000 - http://www.ncbi.nlm.nih.gov/homologene/$id - Homologene at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://homologene.bio2rdf.org/fct - 1000 - http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$id - Bio2RDF - Bio2RDF.org - - - - - clustering - eukaryotic - gene - - - - - species - - - - - - - UM-BBD Compound - - University of Minnesota Biocatalysis/Biodegradation Database (Compound) - - The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information. - - urn:miriam:umbbd.compound - http://identifiers.org/umbbd.compound/ - - umbbd.compound - - urn:miriam:pubmed:19767608 - - - - http://umbbd.ethz.ch/ - c0001 - http://umbbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$id - Biocatalysis/Biodegradation Database Mirror (Compound) at ETH Zurich - ETH, Zurich - Switzerland - - - http://umbbd.msi.umn.edu/index.html - c0001 - http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=c&compID=$id - Biocatalysis/Biodegradation Database (Compound) at University of Minnesota - Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota - USA - - - - metabolite - microbial - - - - - species - - - - - - - ABS - - Annotated regulatory Binding Sites database - - The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. - - urn:miriam:abs - http://identifiers.org/abs/ - - abs - - urn:miriam:pubmed:16381947 - - - - http://genome.crg.es/datasets/abs2005/ - A0014 - http://genome.crg.es/datasets/abs2005/entries/$id.html - ABS at IMIM - Institut Municipal d'Investigaci&oacute; M&egrave;dica, Barcelona - Spain - - - - gene - interaction - - - - - APD - - Antimicrobial Peptide Database - - The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. - - urn:miriam:apd - http://identifiers.org/apd/ - - apd - - urn:miriam:pubmed:14681488 - - - - http://aps.unmc.edu/AP/ - 01001 - http://aps.unmc.edu/AP/database/query_output.php?ID=$id - APD at Nebraska - Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha - USA - - - - drug - protein - - - - - species - - - - - - - ChemDB - ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. - - urn:miriam:chemdb - http://identifiers.org/chemdb/ - - chemdb - - urn:miriam:pubmed:17599932 - - - - http://cdb.ics.uci.edu/ - 3966782 - http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$id - ChemDB at UC Irvine - University of California, Irvine - USA - - - - - Commercial access may require acquisition of a license. - http://cdb.ics.uci.edu/index.htm - - - - chemical - - - - - species - - - - - - - DPV - - Description of Plant Viruses - DPVweb - - Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. - - urn:miriam:dpv - http://identifiers.org/dpv/ - - dpv - - urn:miriam:pubmed:16381892 - - - - http://www.dpvweb.net/ - 100 - http://www.dpvweb.net/dpv/showdpv.php?dpvno=$id - DPV at Rothamsted - Plant-Pathogen Interactions Division, Wheat Pathogenesis Programme, Rothamsted Research Harpenden, Hertfordshire - UK - - - - - Information on this site may be subject to copyright. - http://www.dpvweb.net/index.php - - - - plant - - - - - model - - - - - - - IUPHAR receptor - - International Union of Basic and Clinical Pharmacology - IUPHAR-DB - - The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits. - - urn:miriam:iuphar.receptor - http://identifiers.org/iuphar.receptor/ - - iuphar.receptor - - urn:miriam:pubmed:23087376 - - - - http://www.guidetopharmacology.org/targets.jsp - 101 - http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$id - IUPHAR Receptor at University of Edinburgh - Centre for Cardiovascular Science, University of Edinburgh, Edinburgh - UK - - - - - Material from this site may be downloaded for personal, non-commercial use. - http://www.iuphar-db.org/copyright.jsp - - - - mammalian - - - - - model - - - - - - - Aceview Worm - - AceView WormGenes - - AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. - - urn:miriam:aceview.worm - http://identifiers.org/aceview.worm/ - - aceview.worm - - urn:miriam:pubmed:16925834 - - - - http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm - aap-1 - http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$id - AceView Worm at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - eukaryotic - gene - - - - - species - - - - - - - ASAP - ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. - - urn:miriam:asap - http://identifiers.org/asap/ - - asap - - urn:miriam:pubmed:12519969 - - - - http://asap.ahabs.wisc.edu/asap/home.php - ABE-0009634 - http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$id - ASAP at University of Wisconsin - Animal Health and Biomedical Sciences, University of Wisconsin, Madison - USA - - - - - May require the acceptance of terms and conditions. - http://asap.ahabs.wisc.edu/asap/ASAP-DataReleasePolicy.htm - - - - gene - genome - microbial - - - - - species - - - - - - - ATCC - - American Type Culture Collection - - The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. - - urn:miriam:atcc - http://identifiers.org/atcc/ - - atcc - - http://www.atcc.org/About/tabid/138/Default.aspx - - - - http://www.atcc.org/ - 11303 - http://www.lgcstandards-atcc.org/Products/All/$id.aspx - ATCC in Virginia - American Type Culture Collection, Manassas, Virginia - USA - - - - catalogue - eukaryotic - microbial - - - - - model - - - - - - - BDGP EST - - Berkeley Drosophila Genome Project EST - - The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). - - urn:miriam:bdgp.est - http://identifiers.org/bdgp.est/ - - bdgp.est - - urn:miriam:pubmed:12537569 - - - - http://www.ncbi.nlm.nih.gov/dbEST/index.html - EY223054.1 - http://www.ncbi.nlm.nih.gov/nucest/$id - BDGP EST at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - - Data is a subset of a larger collection. - http://www.fruitfly.org/EST/EST.shtml#ck_est - - - - eukaryotic - expression - - - - - species - - - - - - - Dictybase Gene - The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. - - urn:miriam:dictybase.gene - http://identifiers.org/dictybase.gene/ - - dictybase.gene - - urn:miriam:pubmed:21087999 - - - - http://dictybase.org/ - DDB_G0267522 - http://dictybase.org/gene/$id - Dictybase Gene at Northwestern University - Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois - USA - - - - gene - plant - - - - - species - - - - - - - IMGT LIGM - - IMGT/LIGM-DB - - IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. - - urn:miriam:imgt.ligm - http://identifiers.org/imgt.ligm/ - - imgt.ligm - - urn:miriam:pubmed:16381979 - - - - http://genius.embnet.dkfz-heidelberg.de/ - M94112 - http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$id'] - IMGT LIGM through DKFZ (SRS) - DKFZ TP3, Heidelberg - Germany - - - http://www.imgt.org/ - M94112 - http://www.imgt.org/ligmdb/view?id=$id - IMGT LIGM at CNRS - CNRS, Montpellier University, Montpellier - France - - - http://www.ebi.ac.uk/imgt/ - M94112 - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fmSL1g8Xvs+-e+[IMGTLIGM:'$id'] - IMGT LIGM through EBI (SRS) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - The data are provided as a service to the scientific community to be used only for research and educational purposes. - http://www.imgt.org/Warranty.html - - - - immunogenetics - mammalian - - - - - Worfdb - - Worm Orf DB - - WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends). - - urn:miriam:worfdb - http://identifiers.org/worfdb/ - - worfdb - - urn:miriam:pubmed:15489327 - - - - http://worfdb.dfci.harvard.edu/ - T01B6.1 - http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$id - Worm Orf DB at Harvard - Center for Cancer Systems Biology, Harvard Medical School, Massachusetts - USA - - - - eukaryotic - gene - - - - - species - - - - - - - NEXTDB - - Nematode Expression Pattern Database - - NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones. - - urn:miriam:nextdb - http://identifiers.org/nextdb/ - - nextdb - - http://nematode.lab.nig.ac.jp/method/index.php - - - - http://nematode.lab.nig.ac.jp/ - 6b1 - http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$id - NEXTDB at Shizuoka - National Institute of Genetics, Shizuoka - Japan - - - - - The information does not appear to have been updated in a number of years. - http://nematode.lab.nig.ac.jp/ - - - - eukaryotic - expression - - - - - species - - - - - - - As of November 2013, this collection is no longer accessible. - Plant Genome Network - The Plant Genome Network (PGN) is a resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. All data are directly derived from chromatograms with original and intermediate data stored in the database. - - urn:miriam:pgn - http://identifiers.org/pgn/ - - pgn - - http://pgn.cornell.edu/help/about.pl - - - - http://pgn.cornell.edu/ - 196828 - http://pgn.cornell.edu/unigene/unigene_assembly_contigs.pl?unigene_id=$id - PGN at Cornell University - Cornell University, Ithaca, New York - USA - - - - expression - plant - - - - - species - - - - - - - SoyBase - SoyBase is a repository for curated genetics, genomics and related data resources for soybean. - - urn:miriam:soybase - http://identifiers.org/soybase/ - - soybase - - urn:miriam:pubmed:20008513 - - - - http://soybase.org/ - BARC-013845-01256 - http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$id - SoyBase at Iowa State University - USDA-ARS-CICGRU, Iowa State University, Iowa - USA - - - - gene - plant - - - - - species - - - - - - - HAMAP - - High-quality Automated and Manual Annotation of microbial Proteomes - - HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. - - urn:miriam:hamap - http://identifiers.org/hamap/ - - hamap - - urn:miriam:pubmed:12798039 - - - - http://hamap.expasy.org/ - MF_01400 - http://hamap.expasy.org/unirule/$id - HAPMAP at Swiss Institute of Bioinformatics - Swiss Institute of Bioinformatics, Geneva - Switzerland - - - - annotation - microbial - - - - - Rouge - - Rodent Unidentified Gene-Encoded Large Proteins - - The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. - - urn:miriam:rouge - http://identifiers.org/rouge/ - - rouge - - urn:miriam:pubmed:15368895 - - - - http://www.kazusa.or.jp/rouge/ - mKIAA4200 - http://www.kazusa.or.jp/rouge/gfpage/$id/ - Rouge at Kazusa DNA Research Institute - Kazusa DNA Research Institute, Chiba - Japan - - - - - The information provided is for research purposes only. - http://www.kazusa.or.jp/disclaimers.html - - - - gene - mammalian - protein - - - - - species - - - - - - - ArrayExpress Platform - ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. - - urn:miriam:arrayexpress.platform - http://identifiers.org/arrayexpress.platform/ - - arrayexpress.platform - - urn:miriam:pubmed:12519949 - - - - http://www.ebi.ac.uk/arrayexpress/ - A-GEOD-50 - http://www.ebi.ac.uk/arrayexpress/arrays/$id - ArrayExpress Platform at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - microarray - - - - - CGSC Strain - - Coli Genetic Stock Center - - The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. - - urn:miriam:cgsc - http://identifiers.org/cgsc/ - - cgsc - - urn:miriam:pubmed:1475178 - - - - http://cgsc.biology.yale.edu/index.php - 11042 - http://cgsc.biology.yale.edu/Strain.php?ID=$id - CGSC at Yale university - Dept. of Molecular, Cellular, and Developmental Biology, Yale University, Conneticut - USA - - - - microbial - strain - - - - - model - - - - - - - As of September 2013, this collection is no longer maintained. Various archives are available at: ftp://ftp.ncbi.nih.gov/pub/COG/. - COGs - - Clusters of Orthologous Groups - - Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. - - urn:miriam:cogs - http://identifiers.org/cogs/ - - cogs - - urn:miriam:pubmed:12969510 - - - - http://www.ncbi.nlm.nih.gov/COG/ - COG0001 - http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?$id - COGs at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - clustering - genome - protein - - - - - species - - - - - - - DragonDB DNA - DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. - - urn:miriam:dragondb.dna - http://identifiers.org/dragondb.dna/ - - dragondb.dna - - - http://www.antirrhinum.net/ - 3hB06 - http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id;class=DNA - DragonDB DNA at University of British Columbia - University of British Columbia, Vancouver - Canada - - - - DNA - plant - - - - - species - - - - - - - DragonDB Protein - DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. - - urn:miriam:dragondb.protein - http://identifiers.org/dragondb.protein/ - - dragondb.protein - - - http://www.antirrhinum.net/ - AMDEFA - http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id;class=Peptide - DragonDB Protein at University of British Columbia - University of British Columbia, Vancouver - Canada - - - - plant - protein - - - - - species - - - - - - - DragonDB Locus - DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. - - urn:miriam:dragondb.locus - http://identifiers.org/dragondb.locus/ - - dragondb.locus - - - http://www.antirrhinum.net/ - DEF - http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id&amp;class=Locus - DragonDB Locus at University of British Columbia - University of British Columbia, Vancouver - Canada - - - - DNA - plant - - - - - species - - - - - - - DragonDB Allele - DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. - - urn:miriam:dragondb.allele - http://identifiers.org/dragondb.allele/ - - dragondb.allele - - - http://www.antirrhinum.net/ - cho - http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$id&amp;class=Allele - DragonDB Allele at University of British Columbia - University of British Columbia, Vancouver - Canada - - - - - Images are subject to copyright. - http://www.antirrhinum.net/ - - - - gene - plant - - - - - species - - - - - - - ISSN - The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books. - - urn:miriam:issn - http://identifiers.org/issn/ - - issn - - http://catalog.loc.gov/help/number.htm - - - - http://catalog.loc.gov/webvoy.htm - 0745-4570 - https://catalog.loc.gov/vwebv/search?searchCode=STNO&searchArg=$id&searchType=1&recCount=25 - ISSN at Library of Congress - Library of Congress Online Catalogue, Washington DC - USA - - - - - Session time out prevents direct links. - http://catalog.loc.gov/help/timeout.htm - - - - bibliography - - - - - model - - - - - - - MEROPS Family - The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families. - - urn:miriam:merops.family - http://identifiers.org/merops.family/ - - merops.family - - urn:miriam:pubmed:17991683 - - - - http://merops.sanger.ac.uk/index.htm - S1 - http://merops.sanger.ac.uk/cgi-bin/famsum?family=$id - Merops Family at Sanger Institute - Wellcome Trust Sanger Institute, Hinxton - UK - - - - enzyme - interaction - protein - - - - - species - - - - - - - MGED Ontology - - MO - - The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. - - urn:miriam:mo - http://identifiers.org/mo/ - - mo - - urn:miriam:pubmed:16428806 - http://mged.sourceforge.net/ontologies/index.php - - - - http://bioportal.bioontology.org/ - ArrayGroup - http://purl.bioontology.org/ontology/MO/$id - MGED Ontology at BioPortal - National Center for Biomedical Ontology, Stanford University - USA - - - http://mged.sourceforge.net/ontologies/MGEDontology.php - ArrayGroup - http://mged.sourceforge.net/ontologies/MGEDontology.php#$id - MGED Ontology at SourceForge - (Ontology Working Group), European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - - - - - species - - - - - - - NASC code - - The Nottingham Arabidopsis Stock Centre - - The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. - - urn:miriam:nasc - http://identifiers.org/nasc/ - - nasc - - - http://arabidopsis.info/ - N1899 - http://arabidopsis.info/StockInfo?NASC_id=$id - NASC at University of Nottingham - The Nottingham Arabidopsis Stock Centre, University of Nottingham - UK - - - - plant - strain - - - - - NIAEST - A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. - - urn:miriam:niaest - http://identifiers.org/niaest/ - - niaest - - urn:miriam:pubmed:14744099 - http://lgsun.grc.nia.nih.gov/cDNA/ - - - - http://lgsun.grc.nia.nih.gov/cDNA/ - J0705A10 - http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$id - NIAEST at National Institute on Aging - National Institute on Aging, NIH - USA - - - - expression - gene - human - - - - - species - - - - - - - Pazar Transcription Factor - - Pazar Database - - The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. - - urn:miriam:pazar - http://identifiers.org/pazar/ - - pazar - - urn:miriam:pubmed:18971253 - - - - http://www.pazar.info/ - TF0001053 - http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$id - Pazar Transcription Factor at University of British Columbia - Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver - Canada - - - - DNA - interaction - protein - - - - - species - - - - - - - Plant Ontology - - PO - - The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. - - urn:miriam:po - http://identifiers.org/po/ - http://purl.obolibrary.org/obo/PO - urn:miriam:obo.po - http://identifiers.org/obo.po/ - - po - - urn:miriam:pubmed:18194960 - - - - http://www.plantontology.org/ - PO:0009089 - http://www.plantontology.org/amigo/go.cgi?view=details&query=$id - Plant Ontology through Amigo - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York - USA - - - http://bioportal.bioontology.org/ontologies/PO - PO:0009089 - http://purl.bioontology.org/ontology/PO/$id - Plant Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/po - PO:0009089 - https://www.ebi.ac.uk/ols/ontologies/po/terms?obo_id=$id - Plant Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - plant - - - - - species - model - - - - - - - RNA Modification Database - - RNAmods - - The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. - - urn:miriam:rnamods - http://identifiers.org/rnamods/ - - rnamods - - urn:miriam:pubmed:9399834 - http://rna-mdb.cas.albany.edu/RNAmods/rnadesc.htm - - - - http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm - 101 - http://mods.rna.albany.edu/mods/modifications/view/$id - RNA Modification Database at University of Utah - Department of Medicinal Chemistry and Department of Biochemistry, University of Utah, Salt Lake City, Utah - USA - - - - nucleotide - - - - - WARNING: this data collection has been deprecated! - -As of June 2015, this data collection has been archived by the data provider. Archived data is available <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/sites/default/files/adv_page_assets/connections_map_data_20120208.zip'>here</a>. For further information, please see <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/about/help/cm'>this page</a>. - -We recommend usage of the following data collection for pathway related annotation and referencing <a href='http://www.ebi.ac.uk/miriam/cura/collections/MIR:00000018' title='Reactome'>REACTOME</a>. - Science Signaling Pathway-Independent Component - The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway independent component information. - - urn:miriam:sciencesignaling.pic - http://identifiers.org/sciencesignaling.pic/ - - sciencesignaling.pic - - http://www.sciencemag.org/site/help/librarians/sci_signal_faq.xhtml - - - - http://stke.sciencemag.org/ - CMC_15493 - http://stke.sciencemag.org/cgi/cm/stkecm;$id - Science Signaling: Pathway-Independent Component at Science Magazine - Science Mag, Washington DC - USA - - - - - material for personal and noncommercial use - http://www.sciencemag.org/site/help/readers/copyright.xhtml - - - - pathway - - - - - species - - - - - - - WARNING: this data collection has been deprecated! - -As of June 2015, this data collection has been archived by the data provider. Archived data is available <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/sites/default/files/adv_page_assets/connections_map_data_20120208.zip'>here</a>. For further information, please see <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/about/help/cm'>this page</a>. - -We recommend usage of the following data collection for pathway related annotation and referencing <a href='http://www.ebi.ac.uk/miriam/cura/collections/MIR:00000018' title='Reactome'>REACTOME</a>. - Science Signaling Pathway-Dependent Component - The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway-dependent component information. - - urn:miriam:sciencesignaling.pdc - http://identifiers.org/sciencesignaling.pdc/ - - sciencesignaling.pdc - - http://www.sciencemag.org/site/help/librarians/sci_signal_faq.xhtml - - - - http://stke.sciencemag.org/ - CMN_15494 - http://stke.sciencemag.org/cgi/cm/stkecm;$id - Science Signaling: Pathway-dependent Component at Science Magazine - Science Mag, Washington DC - USA - - - - - material for personal and noncommercial use - http://www.sciencemag.org/site/help/readers/copyright.xhtml - - - - interaction - - - - - species - - - - - - - WARNING: this data collection has been deprecated! - -As of June 2015, this data collection has been archived by the data provider. Archived data is available <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/sites/default/files/adv_page_assets/connections_map_data_20120208.zip'>here</a>. For further information, please see <a target='_blank' title='link opens in new window' href='http://stke.sciencemag.org/about/help/cm'>this page</a>. - -We recommend usage of the following data collection for pathway related annotation and referencing <a href='http://www.ebi.ac.uk/miriam/cura/collections/MIR:00000018' title='Reactome'>REACTOME</a>. - Science Signaling Pathway - The Database of Cell Signaling (Science Signaling) contains information on signaling components and their relations. The data are organized into signaling pathways called Connections Maps and are provided by leading authorities in the field. This collection refers to pathway information. - - urn:miriam:sciencesignaling.path - http://identifiers.org/sciencesignaling.path/ - - sciencesignaling.path - - http://www.sciencemag.org/site/help/librarians/sci_signal_faq.xhtml - - - - http://stke.sciencemag.org/ - CMP_18019 - http://stke.sciencemag.org/cgi/cm/stkecm;$id - Science Signaling: Pathway at Science Magazine - Science Mag, Washington DC - USA - - - - - material for personal and noncommercial use - http://www.sciencemag.org/site/help/readers/copyright.xhtml - - - - - - model - - - - - - - TreeBASE - TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. - - urn:miriam:treebase - http://identifiers.org/treebase/ - - treebase - - urn:miriam:pubmed:12801879 - - - - http://treebase.org/ - TB2:S1000 - http://purl.org/phylo/treebase/phylows/study/$id?format=html - TreeBASE (hosted at National Evolutionary Synthesis Center) - Phyloinformatics Research Foundation, Durham, North Carolina - USA - - - - clustering - - - - - Tetrahymena Genome Database - - TGD - - The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. - - urn:miriam:tgd - http://identifiers.org/tgd/ - - tgd - - urn:miriam:pubmed:16381920 - - - - http://ciliate.org/index.php/ - TTHERM_00648910 - http://ciliate.org/index.php/feature/details/$id - TGD at Stanford University - Department of Genetics, School of Medicine, Stanford University, Stanford, California - USA - - - - gene - genome - sequence - - - - - species - - - - - - - CMR is no longer supported by the JCVI and has been taken offline. More information at: http://www.jcvi.org/cms/research/past-projects/cmr/overview/ - CMR Gene - - Comprehensive Microbial Resource Gene Page - - The Comprehensive Microbial Resource (CMR) contains annotation for all complete microbial genomes and allows for a wide variety of data retrievals. This collection refers to the Gene Page which provides information pertaining to a specific gene such as the Locus Name, Gene Symbol, Coordinates, DNA Molecule Name, and Gene Length. - - urn:miriam:cmr.gene - http://identifiers.org/cmr.gene/ - - cmr.gene - - urn:miriam:pubmed:11125067 - - - - http://cmr.jcvi.org/cgi-bin/CMR/CmrHomePage.cgi - NTL15EF2281 - http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=$id - CMR at JCVI - The Institute for Genomic Research, Rockville, Maryland - USA - - - - gene - sequence - - - - - species - - - - - - - TIGRFAMS - TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. - - urn:miriam:tigrfam - http://identifiers.org/tigrfam/ - - tigrfam - - urn:miriam:pubmed:11125067 - - - - http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi - TIGR00010 - http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=$id - TIGRFAM at JCVI - The Institute for Genomic Research, Rockville, Maryland - USA - - - - clustering - protein - - - - - species - - - - - - - Animal TFDB Family - - Animal Transcription Factor Database - - The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. - - urn:miriam:atfdb.family - http://identifiers.org/atfdb.family/ - - atfdb.family - - urn:miriam:pubmed:22080564 - - - - http://www.bioguo.org/AnimalTFDB/family_index.php - CUT - http://www.bioguo.org/AnimalTFDB/family.php?fam=$id - Animal TFDB at Hubei Bioinformatics & Molecular Imaging Key Laboratory - Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan - China - - - - DNA - interaction - protein - - - - - species - - - - - - - IUPHAR family - The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits. - - urn:miriam:iuphar.family - http://identifiers.org/iuphar.family/ - - iuphar.family - - urn:miriam:pubmed:23087376 - - - - http://www.guidetopharmacology.org/ - 78 - http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$id - The IUPHAR/BPS Guide to PHARMACOLOGY - International Union of Pharmacology, Edinburgh - UK - - - http://www.iuphar-db.org/ - 78 - http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=$id - IUPHAR family at University of Edinburgh - Centre for Cardiovascular Science, University of Edinburgh, Edinburgh - UK - - - - - Material from this site may be downloaded for personal, non-commercial use. - http://www.iuphar-db.org/copyright.jsp - - - - mammalian - schema.org - - - - - model - - - - - - - DBG2 Introns - - Database for Bacterial Group II Introns - - The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. - - urn:miriam:dbg2introns - http://identifiers.org/dbg2introns/ - - dbg2introns - - urn:miriam:pubmed:22080509 - - - - http://webapps2.ucalgary.ca/~groupii/ - Cu.me.I1 - http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$id - Bacterial Group II Introns at University of Calgary - Department of Biological Sciences, University of Calgary, Calgary, Alberta - Canada - - - - - Some introns from previous versions have been removed. - http://webapps2.ucalgary.ca/~groupii/ - - - - DNA - sequence - - - - - species - - - - - - - Spectral Database for Organic Compounds - - SDBS - - The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra. - - urn:miriam:sdbs - http://identifiers.org/sdbs/ - - sdbs - - http://riodb01.ibase.aist.go.jp/sdbs/LINKS/Introduction_eng.html - http://riodb01.ibase.aist.go.jp/sdbs/ - - - - http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi - 4544 - http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$id - SDBS at AIST - National Institute of Advanced Industrial Science and Technology (AIST) - Japan - - - - - Not for commercial use - http://riodb01.ibase.aist.go.jp/sdbs/LINKS/disclaimer_eng.html - - - Requires acceptance of terms and conditions - http://riodb01.ibase.aist.go.jp/sdbs/LINKS/disclaimer_eng.html - - - - chemical - mass spectrometry - - - - - species - - - - - - - Vbase2 - The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. - - urn:miriam:vbase2 - http://identifiers.org/vbase2/ - - vbase2 - - urn:miriam:pubmed:15608286 - - - - http://www.vbase2.org/vbase2.php - humIGHV025 - http://www.vbase2.org/vgene.php?id=$id - Vbase2 at German Research Centre for Biotechnology - Department of Experimental Immunology, German Research Centre for Biotechnology, Braunschweig - Germany - - - - - Non-commercial use only - http://www.vbase2.org/vbdisclaimer.php - - - The date given for last database update is 2006, hence information may be outdated. - http://www.vbase2.org/vbase2.php - - - - human - immunogenetics - sequence - - - - - species - - - - - - - SPIKE Map - - Signaling Pathways Integrated Knowledge Engine - - SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. - - urn:miriam:spike.map - http://identifiers.org/spike.map/ - - spike.map - - urn:miriam:pubmed:18289391 - urn:miriam:pubmed:21097778 - - - - http://www.cs.tau.ac.il/~spike/ - spike00001 - http://www.cs.tau.ac.il/~spike/maps/$id.html - SPIKE database at Tel Aviv University - School of Computer Sciences and School of Medicine, Tel Aviv University - Israel - - - - pathway - - - - - model - - - - - - - METLIN - - Metabolite and Tandem Mass Spectrometry Database - - The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. - - urn:miriam:metlin - http://identifiers.org/metlin/ - - metlin - - urn:miriam:pubmed:16404815 - - - - http://masspec.scripps.edu/ - 1455 - http://metlin.scripps.edu/metabo_info.php?molid=$id - METLIN at Scripps Center, Molecular Biology and Center for Mass Spectrometry, La Jolla - Scripps Research Institute, San Diego - USA - - - - - METLIN services may not be used in commercial applications. - http://metlin.scripps.edu/terms.php - - - - mass spectrometry - metabolite - - - - - GeneCards - The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. - - urn:miriam:genecards - http://identifiers.org/genecards/ - - genecards - - urn:miriam:pubmed:20689021 - - - - http://www.genecards.org/ - ABL1 - http://www.genecards.org/cgi-bin/carddisp.pl?gene=$id - GeneCards at Weizmann Institute - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot - Israel - - - http://genecards.bii.a-star.edu.sg/ - ABL1 - http://genecards.bii.a-star.edu.sg/cgi-bin/carddisp.pl?gene=$id - Genecards at A*STAR - Bioinformatics Institute, A*STAR - Singapore - - - http://p570e70p1.ophid.utoronto.ca/genecards/index.php - ABL1 - http://p570e70p1.ophid.utoronto.ca/genecards/cgi-bin/carddisp.pl?gene=$id - Genecards at University of Toronto - University Health Network, University of Toronoto, Toronto - Canada - - - http://bioinformatics.mdanderson.org/genecards/ - ABL1 - http://bioinformatics.mdanderson.org/genecards/cgi-bin/carddisp.pl?gene=$id - GeneCards at University of Texas - Univ of Texas M.D. Anderson Cancer Center, Houston, Texas - USA - - - http://www6.unito.it/cards/ - ABL1 - http://www6.unito.it/cards/cgi-bin/carddisp.pl?gene=$id - GeneCards at University of Torino - Dept. of Clinical and Biological Sciences , Univ of Torino - Italy - - - http://genecards.bioinformatics.nl/ - ABL1 - http://genecards.bioinformatics.nl/cgi-bin/carddisp.pl?gene=$id - GeneCards at Wageningen - Laboratory of Bioinformatics, Wageningen UR, Wageningen - Holland - - - http://genecards_v3.hgc.jp/ - ABL1 - http://genecards_v3.hgc.jp/cgi-bin/carddisp.pl?gene=$id - GeneCards at University of Tokyo - Human Genome Center, Institute of Medical Science, Univ of Tokyo - Japan - - - - - Commercial use requires a license. - http://www.genecards.org/AcademicTermsOfUse.shtml?noHdrFtr - - - - gene - human - - - - - species - - - - - - - MMRRC - - Mutant Mouse Regional Resource Centers - - The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. - - urn:miriam:mmrrc - http://identifiers.org/mmrrc/ - - mmrrc - - http://www.mmrrc.org/about/generalInfo.php - - - - http://www.mmrrc.org/ - 70 - http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$id - MMRRC at University of North Carolina - University of North Carolina - USA - - - - - restriction due to embedded MGI data - http://www.mmrrc.org/about/data_download.php - - - - catalogue - mammalian - strain - - - - - UM-BBD Reaction - - University of Minnesota Biocatalysis/Biodegradation Database (Reaction) - - The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information. - - urn:miriam:umbbd.reaction - http://identifiers.org/umbbd.reaction/ - - umbbd.reaction - - urn:miriam:pubmed:19767608 - - - - http://umbbd.ethz.ch/ - r0001 - http://umbbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$id - Biocatalysis/Biodegradation Database Mirror (Reaction) at ETH Zurich - ETH, Zurich - Switzerland - - - http://umbbd.msi.umn.edu/index.html - r0001 - http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=$id - Biocatalysis/Biodegradation Database (Reaction) at University of Minnesota - Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota - USA - - - - microbial - reaction - - - - - reaction - - - - - - - UM-BBD Enzyme - - University of Minnesota Biocatalysis/Biodegradation Database (Enzyme) - - The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information. - - urn:miriam:umbbd.enzyme - http://identifiers.org/umbbd.enzyme/ - - umbbd.enzyme - - urn:miriam:pubmed:19767608 - - - - http://umbbd.ethz.ch/ - e0333 - http://umbbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$id - Biocatalysis/Biodegradation Database Mirror (Enzyme) at ETH Zurich - ETH, Zurich - Switzerland - - - http://umbbd.msi.umn.edu/index.html - e0333 - http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=$id - Biocatalysis/Biodegradation Database (Enzyme) at University of Minnesota - Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota - USA - - - - enzyme - microbial - - - - - species - - - - - - - UM-BBD Pathway - - University of Minnesota Biocatalysis/Biodegradation Database (Pathway) - - The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information. - - urn:miriam:umbbd.pathway - http://identifiers.org/umbbd.pathway/ - - umbbd.pathway - - urn:miriam:pubmed:19767608 - - - - http://umbbd.ethz.ch/ - ala - http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$id - Biocatalysis/Biodegradation Database Mirror (Pathway) at ETH Zurich - ETH, Zurich - Switzerland - - - http://umbbd.msi.umn.edu/index.html - ala - http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=p&pathway_abbr=$id - Biocatalysis/Biodegradation Database (Pathway) at University of Minnesota - Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota - USA - - - - microbial - pathway - - - - - model - - - - - - - UM-BBD Biotransformation Rule - The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules. - - urn:miriam:umbbd.rule - http://identifiers.org/umbbd.rule/ - - umbbd.rule - - urn:miriam:pubmed:19767608 - http://sivabio.50webs.com/pps.htm - - - - http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules - bt0001 - http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$id - Biocatalysis/Biodegradation Database Mirror (Biotransformation Rule) at ETH Zurich - ETH, Zurich - Switzerland - - - http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allrules - bt0001 - http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=$id - Biocatalysis/Biodegradation Database Mirror (Biotransformation Rules) at University of Minnesota - Department of Laboratory Medicine and Pathology, University of Minnesota, Minnesota - USA - - - - microbial - reaction - - - - - reaction - - - - - - - mirEX - mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages. - - urn:miriam:mirex - http://identifiers.org/mirex/ - - mirex - - urn:miriam:pubmed:22013167 - - - - http://comgen.pl/mirex/?page=home - 165a - http://comgen.pl/mirex1/?page=results/record&name=$id&exref=pp2a&limit=yes - mirEX at Adam Mickiewicz University - Institute of Molecular Biology, Adam Mickiewicz University, Poznan - Poland - - - - expression - gene - plant - - - - - species - - - - - - - Dictybase EST - The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. - - urn:miriam:dictybase.est - http://identifiers.org/dictybase.est/ - - dictybase.est - - urn:miriam:pubmed:21087999 - - - - http://dictybase.org/ - DDB0016567 - http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$id - Dictybase Gene at Northwestern University - Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, Chicago, Illinois - USA - - - - DNA - plant - sequence - - - - - species - - - - - - - IMGT HLA - - IPD IMGT/HLA - - IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. - - urn:miriam:imgt.hla - http://identifiers.org/imgt.hla/ - - imgt.hla - - urn:miriam:pubmed:16381979 - - - - http://www.ebi.ac.uk/imgt/hla/allele.html - A*01:01:01:01 - http://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$id - IMGT HLA at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - human - immunogenetics - - - - - species - - - - - - - Flystock - - Bloomington Drosophila Stock Center at Indiana University - - The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research. - - urn:miriam:flystock - http://identifiers.org/flystock/ - - flystock - - http://flystocks.bio.indiana.edu/Inst/history.htm - - - - http://flystocks.bio.indiana.edu/bloomhome.htm - 33159 - http://flystocks.bio.indiana.edu/Reports/$id.html - Flystock at Indiana University - BDSC, Department of Biology, Indiana University, Bloomington - USA - - - - eukaryotic - strain - - - - - OPM - - Orientations of Proteins in Membranes - - The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. - - urn:miriam:opm - http://identifiers.org/opm/ - - opm - - urn:miriam:pubmed:21890895 - - - - http://opm.phar.umich.edu/ - 1h68 - http://opm.phar.umich.edu/protein.php?pdbid=$id - OPM at University of Michigan - Department of Medicinal Chemistry, College of Pharmacy, University of Michigan - USA - - - - - Based upon, and uses identifiers from, a subset of PDB entries. - http://opm.phar.umich.edu/ - - - - protein - structure - - - - - species - - - - - - - Allergome - Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. - - urn:miriam:allergome - http://identifiers.org/allergome/ - - allergome - - urn:miriam:pubmed:17434469 - - - - http://www.allergome.org/ - 1948 - http://www.allergome.org/script/dettaglio.php?id_molecule=$id - Allergome at Rome - Center for Clinical and Experimental Allergology, Rome - Italy - - - - - Non-commercial license associated. - http://creativecommons.org/licenses/by-nc-sa/2.5/deed.en - - - - chemical - human - - - - - species - - - - - - - PomBase - PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. - - urn:miriam:pombase - http://identifiers.org/pombase/ - - pombase - - urn:miriam:pubmed:22039153 - - - - http://www.pombase.org/ - SPCC13B11.01 - http://www.pombase.org/spombe/result/$id - PomBase at University of Cambridge - Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge - UK - - - - eukaryotic - genome - nucleotide - - - - - species - - - - - - - HPA - - Human Protein Atlas - - The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. - - urn:miriam:hpa - http://identifiers.org/hpa/ - - hpa - - urn:miriam:pubmed:18669619 - - - - http://www.proteinatlas.org/ - ENSG00000026508 - http://www.proteinatlas.org/$id - Human Protein Atlas at AlbaNova University - Department of Proteomics, School of Biotechnology, AlbaNova University Center, Stockholm - Sweden - - - - - May not be suitable for commercial use. - http://www.proteinatlas.org/about/datausage - - - - disease - image library - protein - schema.org - - - - - species - - - - - - - JAX Mice - JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory. - - urn:miriam:jaxmice - http://identifiers.org/jaxmice/ - - jaxmice - - http://www.jax.org/about/index.html - - - - http://jaxmice.jax.org/ - 005012 - http://jaxmice.jax.org/strain/$id.html - JAX Mice at Jackson Laboratory - The Jackson Laboratory, Sacremento, California - USA - - - - - free for non-commercial or personal use - http://www.jax.org/about/legal.html - - - - mammalian - schema.org - strain - - - - - uBio NameBank - - Universal Biological Indexer and Organizer (NameBank) - - NameBank is a "biological name server" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context. - - urn:miriam:ubio.namebank - http://identifiers.org/ubio.namebank/ - - ubio.namebank - - urn:miriam:pubmed:16861205 - - - - http://www.ubio.org - 2555646 - http://www.ubio.org/browser/details.php?namebankID=$id - uBio NameBank at The Marine Biological Laboratory - Marine Biological Laboratory, Woods Hole, Massachusetts - USA - - - - controlled vocabulary - taxonomy - - - - - species - - - - - - - YeTFasCo - - Yeast Transcription Factor Specificity Compendium - - The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. - - urn:miriam:yetfasco - http://identifiers.org/yetfasco/ - - yetfasco - - urn:miriam:pubmed:22102575 - - - - http://yetfasco.ccbr.utoronto.ca/ - YOR172W_571.0 - http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$id - YeTFasCo at University of Toronto - Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto - Canada - - - - eukaryotic - gene - interaction - - - - - species - - - - - - - TarBase - TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. - - urn:miriam:tarbase - http://identifiers.org/tarbase/ - - tarbase - - urn:miriam:pubmed:22135297 - - - - http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index - hsa-let-7a-2-3p - http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$id - TarBase v7 at University of Thessaly - DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly - Greece - - - http://diana.cslab.ece.ntua.gr/DianaToolsNew/index.php?r=tarbase - hsa-let-7 - http://diana.cslab.ece.ntua.gr/DianaToolsNew/index.php?r=tarbase/index&mirnas=$id - TarBase v6 at IMIS Institute - IMIS Institute, Athena Research Center, Athens - Greece - - - - gene - interaction - nucleotide - - - - - species - - - - - - - CharProt - CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. - - urn:miriam:charprot - http://identifiers.org/charprot/ - - charprot - - urn:miriam:pubmed:22140108 - - - - http://www.jcvi.org/charprotdb - CH_001923 - http://www.jcvi.org/charprotdb/index.cgi/view/$id - CharProt at JCVI - J Craig Venter institute, Rockville, Maryland - USA - - - - annotation - controlled vocabulary - gene - - - - - species - - - - - - - OMA Protein - - Orthologous MAtrix - - OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. - - urn:miriam:oma.protein - http://identifiers.org/oma.protein/ - - oma.protein - - urn:miriam:pubmed:21113020 - - - - http://omabrowser.org/cgi-bin/gateway.pl - HUMAN16963 - http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$id - OMA Protein through OMA browser at ETH Zurich - ETH Zurich, Computer Science, Zurich - Switzerland - - - - - Terms of service under a noncommercial license. - http://omabrowser.org/about.html - - - - clustering - protein - - - - - species - - - - - - - OMA Group - OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. - - urn:miriam:oma.grp - http://identifiers.org/oma.grp/ - - oma.grp - - urn:miriam:pubmed:21113020 - - - - http://omabrowser.org/cgi-bin/gateway.pl - LCSCCPN - http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$id - OMA Group through OMA browser at ETH Zurich - ETH Zurich, Computer Science, Zurich - Switzerland - - - - - Terms of service under a noncommercial license. - http://omabrowser.org/about.html - - - - clustering - protein - - - - - NCBI Protein - The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. - - urn:miriam:ncbiprotein - http://identifiers.org/ncbiprotein/ - - ncbiprotein - - http://www.ncbi.nlm.nih.gov/protein - - - - http://www.ncbi.nlm.nih.gov/protein - CAA71118.1 - http://www.ncbi.nlm.nih.gov/protein/$id - NCBI Protein at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - - This collection is an aggregation of a variety of data sources. - http://www.ncbi.nlm.nih.gov/protein - - - - protein - sequence - - - - - species - - - - - - - GenPept - - protein genbank identifier - - The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. - - urn:miriam:genpept - http://identifiers.org/genpept/ - - genpept - - http://www.ncbi.nlm.nih.gov/protein - - - - http://www.ncbi.nlm.nih.gov/protein - CAA71118.1 - http://www.ncbi.nlm.nih.gov/protein/$id?report=genpept - GenPept at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - - This collection is a subset of the information found in the NCBI protein database. - http://www.ncbi.nlm.nih.gov/guide/all/ - - - - genome - protein - sequence - - - - - species - - - - - - - UniGene - A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. - - urn:miriam:unigene - http://identifiers.org/unigene/ - - unigene - - http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch21 - - - - http://www.ncbi.nlm.nih.gov/unigene - 4900 - http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$id - UniGene at NCBI - National Center for Biotechnology , Maryland - USA - - - - - It is not possible to directly specify a cluster ID without providing an organism abbreviation. - http://www.ncbi.nlm.nih.gov/UniGene/help.cgi?item=FAQ#q12 - - - - - - BitterDB Receptor - BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors. - - urn:miriam:bitterdb.rec - http://identifiers.org/bitterdb.rec/ - - bitterdb.rec - - urn:miriam:pubmed:21940398 - - - - http://bitterdb.agri.huji.ac.il/dbbitter.php - 1 - http://bitterdb.agri.huji.ac.il/Receptor.php?id=$id - BitterDB Receptor at The Hebrew University of Jerusalem - The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot - Israel - - - - chemical - human - protein - - - - - species - - - - - - - BitterDB Compound - BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds. - - urn:miriam:bitterdb.cpd - http://identifiers.org/bitterdb.cpd/ - - bitterdb.cpd - - urn:miriam:pubmed:21940398 - - - - http://bitterdb.agri.huji.ac.il/dbbitter.php - 46 - http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$id - BitterDB Compound at The Hebrew University of Jerusalem - The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot - Israel - - - - chemical - human - - - - - species - - - - - - - BioProject - BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories. - - urn:miriam:bioproject - http://identifiers.org/bioproject/ - - bioproject - - urn:miriam:pubmed:22110025 - urn:miriam:pubmed:22139929 - - - - http://trace.ddbj.nig.ac.jp/bioproject/ - PRJDB3 - http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$id - BioProject at DNA Data Bank of Japan - DNA Data Bank of Japan, Shizuoka - Japan - - - http://www.ncbi.nlm.nih.gov/bioproject - PRJDB3 - http://www.ncbi.nlm.nih.gov/bioproject?term=$id - BioProject at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://www.ebi.ac.uk/ena/ - PRJDB3 - http://www.ebi.ac.uk/ena/data/view/$id - BioProject at European Nucleotide Archive (ENA) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - annotation - - - - - model - - - - - - - BioSample - - BioSDe - BioSdn - - The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation. - - urn:miriam:biosample - http://identifiers.org/biosample/ - - biosample - - urn:miriam:pubmed:22096232 - - - - http://www.ebi.ac.uk/biosamples/ - SAMEA2397676 - http://www.ebi.ac.uk/biosamples/sample/$id - BioSample Database at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.ncbi.nlm.nih.gov/biosample - SAMN00000002 - http://www.ncbi.nlm.nih.gov/biosample?term=$id - BioSample at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://trace.ddbj.nig.ac.jp/biosample/ - SAMD00005257 - http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$id - BioSample at DNA Data Bank of Japan - Institution DNA Data Bank of Japan, Shizuoka - Japan - - - - annotation - - - - - model - - - - - - - PiroplasmaDB - PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. - - urn:miriam:piroplasma - http://identifiers.org/piroplasma/ - - piroplasma - - urn:miriam:pubmed:19914931 - - - - http://piroplasmadb.org/ - TA14985 - http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$id - PiroplasmaBD at EuPathDB - Center for Tropical &amp; Emerging Global Diseases, University of Georgia, Georgia - USA - - - - eukaryotic - genome - - - - - species - - - - - - - Unite - UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. - - urn:miriam:unite - http://identifiers.org/unite/ - - unite - - urn:miriam:pubmed:20409185 - - - - http://unite.ut.ee/ - UDB000691 - http://unite.ut.ee/bl_forw.php?nimi=$id - Unite at University of Tartu - Institute of Botany, University of Tartu, Tartu - Estonia - - - - nucleotide - sequence - - - - - species - - - - - - - NCIm - - National Cancer Institute Metathesaurus - NCI metathesaurus - - NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. - - urn:miriam:ncim - http://identifiers.org/ncim/ - - ncim - - http://ncim.nci.nih.gov/ncimbrowser/pages/help.jsf - - - - http://ncim.nci.nih.gov/ - C0026339 - http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$id - NCIm at National Cancer Institue - National Cancer Institute, Center for Bioinformatics, Maryland - USA - - - - - Some proprietary terminologies are included, with permission, and have restrictions on their use. - http://ncimeta.nci.nih.gov/ncimbrowser/pages/source_help_info.jsf - - - - controlled vocabulary - ontology - - - - - species - compartment - model - - - - - - - ProGlycProt - ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. - - urn:miriam:proglyc - http://identifiers.org/proglyc/ - - proglyc - - urn:miriam:pubmed:22039152 - - - - http://www.proglycprot.org/ - AC119 - http://www.proglycprot.org/detail.aspx?ProId=$id - ProGlycProt at IMT - Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh - India - - - - protein - sequence - - - - - species - - - - - - - PolBase - Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. - - urn:miriam:polbase - http://identifiers.org/polbase/ - - polbase - - urn:miriam:pubmed:21993301 - - - - http://polbase.neb.com/ - 19-T4 - https://polbase.neb.com/polymerases/$id#sequences - PolBase at New England BioLabs - New England Biolabs, Ipswich, Massachusetts - USA - - - - DNA - enzyme - - - - - species - - - - - - - NucleaRDB - NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. - - urn:miriam:nuclearbd - http://identifiers.org/nuclearbd/ - - nuclearbd - - urn:miriam:pubmed:22064856 - - - - http://www.receptors.org/nucleardb/ - prgr_human - http://www.receptors.org/nucleardb/proteins/$id - NucleaRDB at Radboud University Nijmegen Medical Centre - CMBI, Radboud University Nijmegen Medical Centre, Dreijenplein, Wageningen - Holland - - - - interaction - protein - sequence - - - - - species - - - - - - - SUPFAM - - SUPERFAMILY - - SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. - - urn:miriam:supfam - http://identifiers.org/supfam/ - - supfam - - urn:miriam:pubmed:19036790 - - - - http://supfam.org/SUPERFAMILY/ - SSF57615 - http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$id - SUPFAM at MRC and University of Bristol - MRC Laboratory of Molecular Biology, Cambridge - UK - - - - protein - structure - - - - - species - - - - - - - Rice Genome Annotation Project - The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines. - - urn:miriam:ricegap - http://identifiers.org/ricegap/ - - ricegap - - urn:miriam:pubmed:17145706 - - - - http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml - LOC_Os02g13300 - http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$id - Rice Genome Annotation Project at TIGR - The Institute for Genomic Research, Rockville, Maryland - USA - - - - genome - sequence - - - - - species - - - - - - - PINA - - Protein Interaction Network Analysis - - Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms. - - urn:miriam:pina - http://identifiers.org/pina/ - - pina - - urn:miriam:pubmed:19079255 - - - - http://cbg.garvan.unsw.edu.au/pina/ - Q13485 - http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?ac=$id&showExtend=null - Protein Interaction Network Analysis (PINA) at Garvan Institute - Garvan Institute of Medical Research, Sydney - Australia - - - - - Protein-protein interaction data from IntAct, MINT, BioGRID, DIP, HPRD, MIPS/MPact, and Protein annotations from UniProt, Ensembl, WormBase. - http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do - - - - interaction - protein - - - - - species - - - - - - - Tissue List - The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified. - - urn:miriam:tissuelist - http://identifiers.org/tissuelist/ - - tissuelist - - http://www.expasy.org/cgi-bin/lists?tisslist.txt - - - - http://www.uniprot.org/docs/tisslist.txt - TS-0285 - http://www.uniprot.org/tissues/$id - Tissue List at Swiss Institute of Bioinformatics - Swiss Institute of Bioinformatics (SIB), Geneva - Switzerland - - - - controlled vocabulary - - - - - model - - - - - - - BacMap Biography - BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information. - - urn:miriam:bacmap.biog - http://identifiers.org/bacmap.biog/ - - bacmap.biog - - urn:miriam:pubmed:22135301 - - - - http://bacmap.wishartlab.com/ - 1050 - http://bacmap.wishartlab.com/organisms/$id - BacMap Biography at University of Alberta - Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton - Canada - - - - genome - microbial - - - - - species - - - - - - - HGNC Symbol - - HUGO Gene Nomenclature Committee Symbol - - The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol. - - urn:miriam:hgnc.symbol - http://identifiers.org/hgnc.symbol/ - - hgnc.symbol - - urn:miriam:pubmed:17984084 - urn:miriam:pubmed:20929869 - urn:miriam:pubmed:23161694 - - - - http://www.genenames.org/ - DAPK1 - http://www.genenames.org/cgi-bin/gene_symbol_report?match=$id - HGNC Symbol at HUGO Genome Nomenclature Committee - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - The main HGNC collection [MIR:00000080] should be used in preference as it has more robust identifiers. - http://www.genenames.org/guidelines.html/#symbolstatus - - - - gene - human - schema.org - - - - - species - - - - - - - PANTHER Pathway - The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. - - urn:miriam:panther.pathway - http://identifiers.org/panther.pathway/ - - panther.pathway - - urn:miriam:pubmed:12952881 - - - - http://www.pantherdb.org/ - P00024 - http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$id - PANTHER Pathway at USC (Los Angeles) - Keck School of Medicine, University of Southern California - USA - - - - - - reaction - model - - - - - - - FAIRsharing - The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. - - urn:miriam:fairsharing - http://identifiers.org/fairsharing/ - urn:miriam:biosharing - - fairsharing - - urn:miriam:pubmed:21304729 - - - - https://fairsharing.org/ - bsg-000052 - https://fairsharing.org/$id - FAIRSharing at University of Oxford - Oxford e-Research Centre, University of Oxford, Oxford - UK - - - - registry - schema.org - - - - - FungiDB - FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina. - - urn:miriam:fungidb - http://identifiers.org/fungidb/ - - fungidb - - urn:miriam:pubmed:22064857 - - - - http://FungiDB.org - CNBG_0001 - http://fungidb.org/gene/$id - FungiDB at University of California - Department of Plant Pathology & Microbiology, University of California, Riverside, California - USA - - - - - Provides access to information from multiple fungal species. - http://fungidb.org/fungidb.b2/showXmlDataContent.do?name=XmlQuestions.GenomeDataType - - - - gene - genome - - - - - species - - - - - - - DARC - - Database of Aligned Ribosomal Complexes - - DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. - - urn:miriam:darc - http://identifiers.org/darc/ - - darc - - urn:miriam:pubmed:22009674 - - - - http://darcsite.genzentrum.lmu.de/darc/index.php - 1250 - http://darcsite.genzentrum.lmu.de/darc/view.php?id=$id - DARC at University of Munich - Gene Center and Department for Biochemistry and Center for integrated Protein Science Munich, University of Munich, Munich - Germany - - - - protein - structure - - - - - species - - - - - - - DRSC - - FlyRNAi - Drosophila RNAi Screening Cente - - The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. - - urn:miriam:drsc - http://identifiers.org/drsc/ - - drsc - - urn:miriam:pubmed:22067456 - - - - http://flyrnai.org/ - DRSC05221 - http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$id - DRSC at Harvard Medical School - Department of Genetics, Harvard Medical School, Boston, Massachusetts - USA - - - - eukaryotic - expression - gene - - - - - species - - - - - - - OriDB Schizosaccharomyces - OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. - - urn:miriam:oridb.schizo - http://identifiers.org/oridb.schizo/ - - oridb.schizo - - urn:miriam:pubmed:22121216 - - - - http://pombe.oridb.org/index.php - 1 - http://pombe.oridb.org/details.php?id=$id - OriDB Schizosaccharomyces at University of Nottingham - Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham - UK - - - - eukaryotic - genome - - - - - species - - - - - - - OriDB Saccharomyces - OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. - - urn:miriam:oridb.sacch - http://identifiers.org/oridb.sacch/ - - oridb.sacch - - urn:miriam:pubmed:22121216 - - - - http://cerevisiae.oridb.org/index.php - 1 - http://cerevisiae.oridb.org/details.php?id=$id - OriDB Saccharomyces at University of Nottingham - Centre for Genetics and Genomics, The University of Nottingham, Queen's Medical Centre, Nottingham - UK - - - - eukaryotic - genome - - - - - species - - - - - - - PSCDB - - Protein Structural Change DataBase - - The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. - - urn:miriam:pscdb - http://identifiers.org/pscdb/ - - pscdb - - urn:miriam:pubmed:22080505 - - - - http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html - 051 - http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$id.html - PSCDB at Nagoya University - Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku - Japan - - - - interaction - protein - structure - - - - - species - - - - - - - SCOP - - Structural Classification of Proteins - - The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes. - - urn:miriam:scop - http://identifiers.org/scop/ - - scop - - - http://scop.mrc-lmb.cam.ac.uk/scop/ - 47419 - http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$id - SCOP at MRC - MRC Laboratory of Molecular Biology, Centre for Protein Engineering, Hills Road, Cambridge - UK - - - http://scop.berkeley.edu/ - 47419 - http://scop.berkeley.edu/sunid=$id - SCOP at Berkeley - University of California, Berkeley - USA - - - http://scop.bic.nus.edu.sg/ - 47419 - http://scop.bic.nus.edu.sg/search.cgi?sunid=$id - SCOP at National University Singapore - National University Singapore - Singapore - - - - classification - protein - structure - - - - - species - - - - - - - ENA - - European Nucleotide Archive - Embl-Bank - - The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers. - - urn:miriam:ena.embl - http://identifiers.org/ena.embl/ - - ena.embl - - http://www.ebi.ac.uk/ena/about/embl_bank_format - - - - http://www.ebi.ac.uk/ena/ - BN000065 - http://www.ebi.ac.uk/ena/data/view/$id - ENA at European Bioinformatics Institute - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - nucleotide - sequence - - - - - species - - - - - - - DOMMINO - - Database of Macromolecular Interactions - - DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. - - urn:miriam:dommino - http://identifiers.org/dommino/ - - dommino - - urn:miriam:pubmed:22135305 - - - - http://dommino.org/ - 2GC4 - http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$id - DOMMINO at University of Missouri - Informatics Institute and Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia - USA - - - - interaction - protein - - - - - species - - - - - - - PANTHER Node - The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes. - - urn:miriam:panther.node - http://identifiers.org/panther.node/ - - panther.node - - urn:miriam:pubmed:12952881 - - - - http://pantree.org/ - PTN000000026 - http://www.pantree.org/node/annotationNode.jsp?id=$id - PANTHER Node at USC (Los Angeles) - Keck School of Medicine, University of Southern California - USA - - - - - - Consensus CDS - - CCDS - - The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations. - - urn:miriam:ccds - http://identifiers.org/ccds/ - - ccds - - urn:miriam:pubmed:19498102 - - - - http://www.ncbi.nlm.nih.gov/CCDS/ - CCDS13573.1 - http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$id - Consensus CDS at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - genome - mammalian - protein - sequence - - - - - species - - - - - - - Locus Reference Genomic - - LRG - - Locus Reference Genomic (LRG) provides identifiers to stable genomic DNA sequences for regions of the human genome, providing a recognized reference-sequence standard for reporting sequence variants. LRG is maintained by the NCBI and the European Bioinformatics Institute (EBI). - - urn:miriam:lrg - http://identifiers.org/lrg/ - - lrg - - urn:miriam:pubmed:20398331 - - - - http://www.lrg-sequence.org/ - LRG_1 - ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$id.xml - Locus Reference Genomic at University of Leicester - Department of Genetics, University of Leicester, Leicester - UK - - - http://www.ensembl.org/ - LRG_1 - http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id - Locus Reference Genomic through Ensembl - EnSembl, Sanger Institute and European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://asia.ensembl.org/ - LRG_1 - http://asia.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id - Locus Reference Genomic through Ensembl mirror (asia) - - Singapore - - - http://uswest.ensembl.org/ - LRG_1 - http://uswest.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id - Locus Reference Genomic through Ensembl mirror (US west) - - USA - - - http://useast.ensembl.org/ - LRG_1 - http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$id - Locus Reference Genomic through Ensembl mirror (US east) - - USA - - - - DNA - genome - human - schema.org - sequence - - - - - species - - - - - - - HPRD - - Human Protein Reference Database - - The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. - - urn:miriam:hprd - http://identifiers.org/hprd/ - - hprd - - urn:miriam:pubmed:18988627 - - - - http://www.hprd.org/ - 00001 - http://www.hprd.org/protein/$id - Human Protein Reference Database - Institute of Bioinformatics, International Tech Park, Bangalore - India - - - - - HPRD is free for non-commercial, where it may incur a license fee. - http://www.hprd.org/FAQ - - - - human - protein - - - - - species - - - - - - - GXA Gene - - Gene Expression Atlas Gene - - The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. - - urn:miriam:gxa.gene - http://identifiers.org/gxa.gene/ - - gxa.gene - - urn:miriam:pubmed:22064864 - - - - http://www.ebi.ac.uk/gxa/ - AT4G01080 - http://www.ebi.ac.uk/gxa/genes/$id - GXA Gene at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - expression - gene - microarray - - - - - species - - - - - - - GXA Expt - - Gene Expression Atlas Experiment - - The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. - - urn:miriam:gxa.expt - http://identifiers.org/gxa.expt/ - - gxa.expt - - urn:miriam:pubmed:22064864 - - - - http://www.ebi.ac.uk/gxa/ - E-MTAB-2037 - http://www.ebi.ac.uk/gxa/experiments/$id - GXA Expt at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.omicsdi.org/ - E-MTAB-2037 - https://www.omicsdi.org/dataset/atlas-experiments/$id - GXA Expt through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - This collection is a curated subset of ArrayExpress [MIR:00000036]. - - - - expression - microarray - - - - - model - - - - - - - MetaboLights - MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies. - - urn:miriam:metabolights - http://identifiers.org/metabolights/ - - metabolights - - http://www.ebi.ac.uk/metabolights/about - - - - http://www.ebi.ac.uk/metabolights/ - MTBLS1 - http://www.ebi.ac.uk/metabolights/$id - MetaboLights at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.omicsdi.org/ - MTBLS1 - https://www.omicsdi.org/dataset/metabolights_dataset/$id - MataboLights through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - metabolite - - - - - species - - - - - - - National Bibliography Number - - NBN - - The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. - - urn:miriam:nbn - http://identifiers.org/nbn/ - - nbn - - http://tools.ietf.org/html/rfc3188 - http://www.dnb.de/EN/Service/DigitaleDienste/URNService/urnservice_node.html - - - - http://nbn-resolving.org/resolve_urn.htm - urn:nbn:fi:tkk-004781 - http://nbn-resolving.org/resolver?identifier=$id&verb=redirect - NBN through URN Resolver at German National Library - Deutsche Nationalbibliothek, Frankfurt - Germany - - - - bibliography - - - - - model - parameter - reaction - species - - - - - - - ORCID - - Open Researcher and Contributor ID - - ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. - - urn:miriam:orcid - http://identifiers.org/orcid/ - - orcid - - https://about.orcid.org/about/what-is-orcid/our-principles - https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier - - - - https://orcid.org - 0000-0002-6309-7327 - https://orcid.org/$id - ORCID at Bethesda - ORCID Inc, Bethesda, Mayrland - USA - - - - bibliography - - - - - model - - - - - - - InChI - - IUPAC International Chemical Identifier - - The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. - - urn:miriam:inchi - http://identifiers.org/inchi/ - - inchi - - http://www.iupac.org/inchi/ - http://www.inchi-trust.org/ - - - - http://rdf.openmolecules.net/ - InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 - http://rdf.openmolecules.net/?$id - InChI through RDF Open Molecules - BiGCaT, Department of Bioinformatics, Maastricht - Netherlands - - - http://www.chemspider.com/ - InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 - http://www.chemspider.com/$id - InChI through Chemspider - Royal Society of Chemistry, Cambridge - UK - - - http://webbook.nist.gov/chemistry - InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 - http://webbook.nist.gov/cgi/cbook.cgi?$id - InChI through NIST - National Institute of Standards and Technology, Gaithersburg, Maryland - USA - - - http://www.ebi.ac.uk/chebi/ - InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 - http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$id - InChI through ChEBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - Identifiers are the structural representation of a substance. - http://www.iupac.org/home/publications/e-resources/inchi.html - - - Identifiers are not restricted to a specific data collection. - http://www.iupac.org/home/publications/e-resources/inchi.html - - - - chemical - structure - - - - - species - - - - - - - Wikipedia (En) - Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay. - - urn:miriam:wikipedia.en - http://identifiers.org/wikipedia.en/ - - wikipedia.en - - http://en.wikipedia.org/wiki/Wikipedia:About - http://wiki.dbpedia.org/Publications - - - - http://en.wikipedia.org/wiki/Main_Page - SM_UB-81 - http://en.wikipedia.org/wiki/$id - Wikipedia (English) - Wikimedia Foundation, San Francisco, California - USA - - - http://wiki.dbpedia.org/ - SM_UB-81 - http://dbpedia.org/page/$id - Wikipedia structured content through DBpedia - OpenLink Software, Burlington, Massachusetts - USA - - - - - Identifiers are formed of descriptive text, and may not be unique, in which case a disambiguation page is returned. - http://en.wikipedia.org/wiki/Wikipedia:Disambiguation - - - - encyclopedia - - - - - PhosphoPoint Kinase - PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. - - urn:miriam:phosphopoint.kinase - http://identifiers.org/phosphopoint.kinase/ - - phosphopoint.kinase - - urn:miriam:pubmed:18689816 - - - - http://kinase.bioinformatics.tw/ - AURKA - http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$id&drawing=0&sorting=0&kinome=1 - PhosphoPoint Kinase at National Taiwan University - Department of Computer Science and Information Engineering, National Taiwan University - Republic of China - - - - human - interaction - protein - - - - - species - - - - - - - PhosphoPoint Phosphoprotein - PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. - - urn:miriam:phosphopoint.protein - http://identifiers.org/phosphopoint.protein/ - - phosphopoint.protein - - urn:miriam:pubmed:18689816 - - - - http://kinase.bioinformatics.tw/ - AURKA - http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$id&drawing=0&sorting=0&kinome=0 - PhosphoPoint Phosphoprotein at National Taiwan University - Department of Computer Science and Information Engineering, National Taiwan University - Republic of China - - - - human - interaction - protein - - - - - species - - - - - - - InChIKey - - hashed InChI - - The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. - - urn:miriam:inchikey - http://identifiers.org/inchikey/ - - inchikey - - http://en.wikipedia.org/wiki/International_Chemical_Identifier - http://www.inchi-trust.org/technical-faq/ - - - - http://www.chemspider.com/ - RYYVLZVUVIJVGH-UHFFFAOYSA-N - http://www.chemspider.com/inchikey=$id - InChIKey through ChemSpider - Royal Society of Chemistry, Cambridge - UK - - - http://cactus.nci.nih.gov/chemical/structure - RYYVLZVUVIJVGH-UHFFFAOYSA-N - http://cactus.nci.nih.gov/chemical/structure/$id/names - InChiKey resolver at NCI - National Cancer Institute, Rockville, Maryland - USA - - - - - Identifiers are composed of non-standard characters and do not follow recommended practices. - http://www.ebi.ac.uk/miriam/main/mdb?section=faq#RegistryRequirements - - - Identifiers are not restricted to a specific data collection, and are applicable universally. - http://www.iupac.org/home/publications/e-resources/inchi.html - - - - chemical - structure - - - - - species - - - - - - - UniProt Isoform - - UniProtKB Isoform - - The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information. - - urn:miriam:uniprot.isoform - http://identifiers.org/uniprot.isoform/ - - uniprot.isoform - - urn:miriam:pubmed:16381842 - http://www.uniprot.org/faq/30 - - - - http://www.uniprot.org/ - Q5BJF6-3 - http://www.uniprot.org/uniprot/$id - UniProt Isoform through Universal Protein Resource - UniProt Consortium - USA, UK and Switzerland - - - http://purl.uniprot.org/ - Q5BJF6-3 - http://purl.uniprot.org/uniprot/$id - UniProt Isoform through Universal Protein Resource using Persistent URL system - UniProt Consortium - USA, UK and Switzerland - - - http://www.uniprot.org/uniparc/ - Q5BJF6-3 - http://www.uniprot.org/uniparc/?query=$id - UniProt Isoform through UniParc - UniProt Consortium - USA, UK and Switzerland - - - - - UniProt Isoform is a subset of the information available from a standard UniProt record. - http://www.uniprot.org/faq/30 - - - - protein - sequence - - - - - species - - - - - - - KEGG Environ - - KEGG - - KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable. - - urn:miriam:kegg.environ - http://identifiers.org/kegg.environ/ - - kegg.environ - - http://www.genome.jp/kegg/drug/environ.html - - - - http://www.genome.jp/kegg/drug/environ.html - ev:E00032 - http://www.kegg.jp/entry/$id - KEGG ENVIRON Database - Kyoto University Bioinformatics Center - Japan - - - - chemical - drug - - - - - species - - - - - - - CLDB - - Cell Line Data Base - - The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. - - urn:miriam:cldb - http://identifiers.org/cldb/ - - cldb - - urn:miriam:pubmed:18927105 - - - - http://bioinformatics.hsanmartino.it/hypercldb/indexes.html - cl3603 - http://bioinformatics.hsanmartino.it/hypercldb/$id.html - CLDB at Genova - Bioinformatics, Cell Bank, National Cancer Research Institute, Genova - Italy - - - - catalogue - mammalian - strain - - - - - species - - - - - - - Experimental Factor Ontology - - EFO - - The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team. - - urn:miriam:efo - http://identifiers.org/efo/ - - efo - - urn:miriam:pubmed:20200009 - - - - https://www.ebi.ac.uk/ols/ontologies/efo - 0004859 - https://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=EFO:$id - EFO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://bioportal.bioontology.org/ontologies/EFO - 0004859 - http://purl.bioontology.org/ontology/EFO/efo:EFO_$id - EFO through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - http://www.ebi.ac.uk/efo/ - 0004859 - http://www.ebi.ac.uk/efo/EFO_$id - EFO through Functional Genomics Group (EBI) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - - - - - parameter - species - model - - - - - - - HGMD - - Human Gene Mutation Database - - The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. - - urn:miriam:hgmd - http://identifiers.org/hgmd/ - - hgmd - - urn:miriam:pubmed:22948725 - - - - http://www.hgmd.cf.ac.uk/ac/index.php - CALM1 - http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$id - HGMD at Cardiff University - Cardiff University, Cardiff - Wales - - - - - A copyright notice is in place. - http://www.hgmd.cf.ac.uk/docs/copyright.html - - - Requires registration to access data. - http://www.hgmd.cf.ac.uk/docs/register.html - - - - disease - gene - human - - - - - species - - - - - - - AphidBase Transcript - AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. - - urn:miriam:aphidbase.transcript - http://identifiers.org/aphidbase.transcript/ - - aphidbase.transcript - - urn:miriam:pubmed:20482635 - - - - http://www.aphidbase.com/aphidbase - ACYPI000159 - http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$id - AphidBase at INRA - INRA UMR, Le Rheu - France - - - - - The use of information for commercial or publicity purposes is forbidden. - http://www.aphidbase.com/aphidbase/legal_mentions - - - - genome - sequence - - - - - species - - - - - - - Affymetrix Probeset - An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. - - urn:miriam:affy.probeset - http://identifiers.org/affy.probeset/ - http://bio2rdf.org/affymetrix - - affy.probeset - - http://www.affymetrix.com - - - - http://www.affymetrix.com/ - 243002_at - https://www.affymetrix.com/LinkServlet?probeset=$id - Affymetrix ProbeSet in Santa Clara - Affymetrix, Santa Clara, California - USA - - - http://cu.affymetrix.bio2rdf.org/fct/ - 243002_at - http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$id - Bio2RDF - Bio2RDF.org - - - - - - Site is for personal non-commercial use - http://www.affymetrix.com/estore/browse/terms.jsp - - - Requires registration and user log in. - https://www.affymetrix.com/estore/user/login.jsp?toURL=/estore/ - - - - genome - nucleotide - - - - - species - - - - - - - TreeFam - TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. - - urn:miriam:treefam - http://identifiers.org/treefam/ - - treefam - - urn:miriam:pubmed:16381935 - - - - http://www.treefam.org/ - TF101014 - http://www.treefam.org/family/$id - TreeFam database - Beijing Genomics Institute, Beijing - China - - - - - - species - - - - - - - CAPS-DB - CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. - - urn:miriam:caps - http://identifiers.org/caps/ - - caps - - urn:miriam:pubmed:22021380 - - - - http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home - 434 - http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$id - CAPS-DB at Leeds Institute of Molecular Medicine - Leeds Institute of Molecular Medicine, Section of Experimental Therapeutics, University of Leeds, Leeds - UK - - - - domain - protein - structure - - - - - Cube db - Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. - - urn:miriam:cubedb - http://identifiers.org/cubedb/ - - cubedb - - urn:miriam:pubmed:22139934 - - - - http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html - AKR - http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$id/ - Cube db at Bioinformatics Institute (Singapore) - Bioinformatics Institute, Singapore - China - - - - - To identify specific results, it is necessary to also specify a 'cluster'. - - - - domain - human - protein - - - - - species - - - - - - - IDEAL - - Intrinsically Disordered proteins with Extensive Annotations and Literature - - IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. - - urn:miriam:ideal - http://identifiers.org/ideal/ - - ideal - - urn:miriam:pubmed:22067451 - - - - http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/ - IID00001 - http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/idealItem.php?id=$id - IDEAL at Maebashi Institute of Technology - Faculty of Engineering, Maebashi Institute of Technology, Maebashi - Japan - - - - protein - - - - - species - - - - - - - STAP - - Statistical Torsional Angles Potentials of NMR - - STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). - - urn:miriam:stap - http://identifiers.org/stap/ - - stap - - urn:miriam:pubmed:22102572 - - - - http://psb.kobic.re.kr/STAP/refinement/ - 1a24 - http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$id - STAP at Korean Bioinformation Center - Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon - South Korea - - - - protein - structure - - - - - species - - - - - - - Pocketome - Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. - - urn:miriam:pocketome - http://identifiers.org/pocketome/ - - pocketome - - urn:miriam:pubmed:22080553 - - - - http://www.pocketome.org/sfSearch.cgi?act=browseall - 1433C_TOBAC_1_252 - http://www.pocketome.org/files/$id.html - Pocketome at UCSD Skaggs School - UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, California - USA - - - - interaction - protein - structure - - - - - species - - - - - - - GOLD genome - The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes. - - urn:miriam:gold.genome - http://identifiers.org/gold.genome/ - - gold.genome - - urn:miriam:pubmed:22135293 - - - - http://www.genomesonline.org/cgi-bin/GOLD/index.cgi - Gi07796 - http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$id - GOLD genome at Department of Energy Joint Genome Institute - Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California - USA - - - - genome - registry - - - - - species - - - - - - - GOLD metadata - The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples. - - urn:miriam:gold.meta - http://identifiers.org/gold.meta/ - - gold.meta - - urn:miriam:pubmed:22135293 - - - - http://www.genomesonline.org/cgi-bin/GOLD/index.cgi - Gm00047 - http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$id - GOLD metadata at Department of Energy Joint Genome Institute - Department of Energy Joint Genome Institute, Microbial Genomics and Metagenomics Program, California - USA - - - - annotation - genome - - - - - species - - - - - - - BugBase Protocol - BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. - - urn:miriam:bugbase.protocol - http://identifiers.org/bugbase.protocol/ - - bugbase.protocol - - urn:miriam:pubmed:21948792 - - - - http://bugs.sgul.ac.uk/E-BUGS - 67 - http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$id&amp;action=view - BugBase Protocol at University of London - Bacterial Microarray Group, St George's, University of London - UK - - - - - Must accept terms and conditions to enter site, or register an account. - http://bugs.sgul.ac.uk/bugsbase/index.php - - - - expression - microarray - microbial - - - - - species - - - - - - - BugBase Expt - BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. - - urn:miriam:bugbase.expt - http://identifiers.org/bugbase.expt/ - - bugbase.expt - - urn:miriam:pubmed:21948792 - - - - http://bugs.sgul.ac.uk/E-BUGS - 288 - http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$id&action=view - BugBase Expt at University of London - Bacterial Microarray Group, St George's, University of London - UK - - - - - Must accept terms and conditions to enter site, or register an account. - http://bugs.sgul.ac.uk/bugsbase/index.php - - - - expression - microarray - microbial - - - - - species - - - - - - - Tree of Life - The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). - -Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things. - - urn:miriam:tol - http://identifiers.org/tol/ - - tol - - http://tolweb.org - - - - http://tolweb.org/tree/ - 98034 - http://tolweb.org/$id - Tree of Life Web - University of Arizona - USA - - - - classification - - - - - species - - - - - - - VariO - - Variation Ontology - - The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. - - urn:miriam:vario - http://identifiers.org/vario/ - - vario - - http://variationontology.org/ - - - - http://www.variationontology.org/ - VariO:0294 - http://www.variationontology.org/cgi-bin/amivario/term-details.cgi?term=$id - VariO at Lund University - Department of Experimental Medical Science, Lund University - Sweden - - - http://bioportal.bioontology.org/ontologies/VARIO - VariO:0294 - http://purl.bioontology.org/ontology/VARIO/$id - VariO through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/vario - VariO:0294 - https://www.ebi.ac.uk/ols/ontologies/vario/terms?obo_id=$id - VariO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - DNA - ontology - protein - - - - - species - - - - - - - ViPR Strain - - Virus Pathogen Resource Strain - - The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. - - urn:miriam:vipr - http://identifiers.org/vipr/ - - vipr - - urn:miriam:pubmed:23202522 - - - - http://www.viprbrc.org/brc/home.do?decorator=vipr - BeAn 70563 - http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$id&decorator=arena - ViPR Strain at J. Craig Venter Institute - J. Craig Venter Institute, San Diego, California - USA - - - - strain - viral - - - - - species - - - - - - - EPD - - Eukaryotic Promoter Database - - The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. - - urn:miriam:epd - http://identifiers.org/epd/ - - epd - - urn:miriam:pubmed:23193273 - - - - http://epd.vital-it.ch/ - TA_H3 - http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$id - EPD at Swiss Institute of Bioinformatics - Swiss Institute of Bioinformatics (SIB), Geneva - Switzerland - - - http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+EPD - TA_H3 - http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fmSL1hlE31+-e+[EPD:'$id'] - EPD through EBI (SRS) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - DNA - eukaryotic - expression - sequence - - - - - species - - - - - - - RFAM - - RNA Family Database - - The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. - - urn:miriam:rfam - http://identifiers.org/rfam/ - - rfam - - urn:miriam:pubmed:23125362 - - - - http://rfam.xfam.org/ - RF00230 - http://rfam.xfam.org/family/$id - Rfam at EMBL-EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://rfam.sanger.ac.uk/ - RF00230 - http://rfam.sanger.ac.uk/family/$id - RFAM at Sanger Institute - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge - UK - - - http://janelia.org/ - RF00230 - http://rfam.janelia.org/family/$id - RFAM at Janelia Farm Research - Janelia Farm Research Campus, Ashburn, Virginia - USA - - - - domain - nucleotide - - - - - species - - - - - - - Fungal Barcode - - International Fungal Working Group - FBOL - Fungal Barcode of Life - - DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. - - urn:miriam:fbol - http://identifiers.org/fbol/ - - fbol - - urn:miriam:pubmed:21564968 - - - - http://www.fungalbarcoding.org/ - 2224 - http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$id&Fields=All&ExactMatch=T - Fungal Barcode at Fungal Biodiversity Centre - Fungal Biodiversity Centre, Utrecht - Netherlands - - - - classification - eukaryotic - - - - - species - - - - - - - AFTOL - - Assembling the Fungal Tree of Life - - The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. - - urn:miriam:aftol.taxonomy - http://identifiers.org/aftol.taxonomy/ - - aftol.taxonomy - - - http://aftol.org/data.php - 959 - http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$id - AFTOL at University of Minnesota - Department of Plant Biology, University of Minnesota, Minnesota - USA - - - - - Requires acceptance of terms and conditions. - http://wasabi.lutzonilab.net/pub/disclaimer - - - - - - AspGD Locus - - Aspergillus Genome Database Locus - - The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information. - - urn:miriam:aspgd.locus - http://identifiers.org/aspgd.locus/ - - aspgd.locus - - urn:miriam:pubmed:22080559 - - - - http://www.aspgd.org/ - ASPL0000349247 - http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$id - AspGD at Stanford Medical School - Department of Genetics, Stanford University Medical School, Stanford, California - USA - - - - - - AspGD Protein - The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information. - - urn:miriam:aspgd.protein - http://identifiers.org/aspgd.protein/ - - aspgd.protein - - urn:miriam:pubmed:22080559 - - - - http://www.aspgd.org/ - ASPL0000349247 - http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$id - AspGD Protein at Stanford Medical School - Department of Genetics, Stanford University Medical School, Stanford, California - USA - - - - - - Access to this legacy data is no longer supported. - DrugBank Target v3 - The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 3 of the database. - - urn:miriam:drugbank.target - http://identifiers.org/drugbank.target/ - - drugbank.target - - urn:miriam:pubmed:16381955 - - - - http://v3.drugbank.ca/ - 54 - http://v3.drugbank.ca/molecules/$id?as=target - DrugBank Target information version 3 - Departments of Computing Science, Biological Sciences, University of Alberta - Canada - - - - interaction - protein - - - - - species - - - - - - - AutDB - - Autism Database - - AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. - - urn:miriam:autdb - http://identifiers.org/autdb/ - - autdb - - urn:miriam:pubmed:19015121 - - - - http://autism.mindspec.org/autdb/ - ADA - http://autism.mindspec.org/GeneDetail/$id - AutDB at MindSpec - MindSpec Inc., Fairfax, Virginia - USA - - - - disorder - gene - human - - - - - species - - - - - - - BacMap Map - BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information. - - urn:miriam:bacmap.map - http://identifiers.org/bacmap.map/ - - bacmap.map - - urn:miriam:pubmed:22135301 - - - - http://bacmap.wishartlab.com/ - AP011135 - http://bacmap.wishartlab.com/maps/$id/index.html - BacMap Genome Map at University of Alberta - Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton - Canada - - - - genome - microbial - - - - - species - - - - - - - Bgee family - Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. - - urn:miriam:bgee.family - http://identifiers.org/bgee.family/ - - bgee.family - - urn:miriam:doi:10.1007%2F978-3-540-69828-9_12 - - - - http://bgee.unil.ch/bgee/bgee - ENSFM00500000270089 - http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$id - Bgee at Lausanne - Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - clustering - expression - gene - - - - - species - - - - - - - Bgee gene - Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression within anatomical structures within a species. - - urn:miriam:bgee.gene - http://identifiers.org/bgee.gene/ - - bgee.gene - - urn:miriam:doi:10.1007%2F978-3-540-69828-9_12 - - - - http://bgee.unil.ch/bgee/bgee - ENSDARG00000013057 - http://bgee.unil.ch/bgee/bgee?page=gene&action=summary&gene_id=$id - Bgee at Lausanne - Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - expression - gene - - - - - species - - - - - - - Bgee stage - Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages. - - urn:miriam:bgee.stage - http://identifiers.org/bgee.stage/ - - bgee.stage - - urn:miriam:doi:10.1007%2F978-3-540-69828-9_12 - - - - http://bgee.unil.ch/bgee/bgee - HsapDO:0000004 - http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_id=$id&stage_children=on - Bgee at Lausanne - Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - expression - gene - - - - - species - - - - - - - Bgee organ - Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. - - urn:miriam:bgee.organ - http://identifiers.org/bgee.organ/ - - bgee.organ - - urn:miriam:doi:10.1007%2F978-3-540-69828-9_12 - - - - http://bgee.unil.ch/bgee/bgee - EHDAA:2185 - http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_id=$id&organ_children=on - Bgee at Lausanne - Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - controlled vocabulary - expression - gene - - - - - species - - - - - - - BioCarta Pathway - BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. - - urn:miriam:biocarta.pathway - http://identifiers.org/biocarta.pathway/ - - biocarta.pathway - - http://www.biocarta.com/about/index.asp - - - - http://www.biocarta.com/ - h_aktPathway - http://cgap.nci.nih.gov/Pathways/BioCarta/$id - BioCarta Pathway at NCI - National Cancer Institute, Center for Bioinformatics, Maryland - USA - - - - - Since Sept 2015, BioCarta is hosted by NCI, and no new pathways are being added. - http://www.genecarta.com/ - - - - image library - pathway - - - - - model - species - - - - - - - PANTHER Pathway Component - The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway -components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation. - - urn:miriam:panther.pthcmp - http://identifiers.org/panther.pthcmp/ - - panther.pthcmp - - urn:miriam:pubmed:12952881 - - - - http://www.pantherdb.org/ - P00266 - http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$id - PANTHER Pathway Component at USC (Los Angeles) - Keck School of Medicine, University of Southern California - USA - - - - classification - pathway - protein - - - - - species - - - - - - - Golm Metabolome Database Profile - Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. - - urn:miriam:gmd.profile - http://identifiers.org/gmd.profile/ - - gmd.profile - - urn:miriam:pubmed:15613389 - urn:miriam:pubmed:20526350 - - - - http://gmd.mpimp-golm.mpg.de/ - 10b38aaf-b977-4950-85b8-f4775f66658d - http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$id - Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology - Max Planck Institute of Molecular Plant Physiology, Potsdam - Germany - - - - - Data in this collection is restricted for non-academic users. - http://gmd.mpimp-golm.mpg.de/termsconditions.aspx - - - - assay - metabolite - - - - - species - - - - - - - Golm Metabolome Database GC-MS spectra - Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra. - - urn:miriam:gmd.gcms - http://identifiers.org/gmd.gcms/ - - gmd.gcms - - urn:miriam:pubmed:15613389 - urn:miriam:pubmed:20526350 - - - - http://gmd.mpimp-golm.mpg.de/ - 53d583d8-40c6-40e1-9296-23f821cd77a5 - http://gmd.mpimp-golm.mpg.de/Spectrums/$id - Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology - Max Planck Institute of Molecular Plant Physiology, Potsdam - Germany - - - - - Data in this collection is restricted for non-academic users. - http://gmd.mpimp-golm.mpg.de/termsconditions.aspx - - - - mass spectrometry - metabolite - - - - - species - - - - - - - Golm Metabolome Database Reference Substance - Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. - - urn:miriam:gmd.ref - http://identifiers.org/gmd.ref/ - - gmd.ref - - urn:miriam:pubmed:15613389 - urn:miriam:pubmed:20526350 - - - - http://gmd.mpimp-golm.mpg.de/ - 8cf84adb-b4db-4807-ac98-0004247c35df - http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$id - Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology - Max Planck Institute of Molecular Plant Physiology, Potsdam - Germany - - - - - Data in this collection is restricted for non-academic users. - http://gmd.mpimp-golm.mpg.de/termsconditions.aspx - - - - catalogue - metabolite - structure - - - - - species - - - - - - - Golm Metabolome Database Analyte - Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes. - - urn:miriam:gmd.analyte - http://identifiers.org/gmd.analyte/ - - gmd.analyte - - urn:miriam:pubmed:15613389 - urn:miriam:pubmed:20526350 - - - - http://gmd.mpimp-golm.mpg.de/ - 4f0fa9b6-514f-4ff4-98cc-0009bc08eb80 - http://gmd.mpimp-golm.mpg.de/Analytes/$id - Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology - Max Planck Institute of Molecular Plant Physiology, Potsdam - Germany - - - - - Data in this collection is restricted for non-academic users. - http://gmd.mpimp-golm.mpg.de/termsconditions.aspx - - - - mass spectrometry - metabolite - structure - - - - - species - - - - - - - IntAct Molecule - IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. - - urn:miriam:intact.molecule - http://identifiers.org/intact.molecule/ - - intact.molecule - - urn:miriam:pubmed:14681455 - urn:miriam:pubmed:17145710 - - - - http://www.ebi.ac.uk/intact/ - EBI-366083 - http://www.ebi.ac.uk/intact/molecule/$id - IntAct Molecule at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - interaction - protein - - - - - species - - - - - - - DEPOD - - human DEPhOsphorylation Database - - The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources. - - urn:miriam:depod - http://identifiers.org/depod/ - - depod - - urn:miriam:pubmed:25332398 - urn:miriam:doi:10.1126%2Fscisignal.2003203 - - - - http://www.koehnlab.de/depod/ - PTPN1 - http://www.koehnlab.de/depod/showp.php?gene=$id - DEPOD at EMBL - European Molecular Biology Laboratory EMBL, Heidelberg - Germany - - - - human - interaction - structure - - - - - species - - - - - - - Cell Signaling Technology Pathways - Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways. - - urn:miriam:cst - http://identifiers.org/cst/ - - cst - - http://www.cellsignal.com/about/index.html - - - - http://www.cellsignal.com/pathways/index.html - Akt_PKB - http://www.cellsignal.com/reference/pathway/$id.html - CST Pathways at Cell Signaling Technology - Cell Signaling Technology, Inc., Danvers, Massachusetts - USA - - - - catalogue - immunogenetics - pathway - - - - - species - - - - - - - Cell Signaling Technology Antibody - Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products. - - urn:miriam:cst.ab - http://identifiers.org/cst.ab/ - - cst.ab - - http://www.cellsignal.com/about/index.html - - - - http://www.cellsignal.com/catalog/index.html - 3305 - http://www.cellsignal.com/products/$id.html - CST Antibody at Cell Signaling Technology - Cell Signaling Technology, Inc., Danvers, Massachusetts - USA - - - - catalogue - immunogenetics - interaction - - - - - species - - - - - - - National Drug Code - - NDC - - The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. - - urn:miriam:ndc - http://identifiers.org/ndc/ - http://bio2rdf.org/ndc - - ndc - - http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm - - - - http://www.accessdata.fda.gov/scripts/cder/ndc/ - 0002-1975-61 - http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$id - National Drug Code at Food and Drug Administration - U.S. Food and Drug Administration, Maryland - USA - - - http://ndc.bio2rdf.org/fct - 0002-1975-61 - http://ndc.bio2rdf.org/describe/?url=http://bio2rdf.org/ndc:$id - Bio2RDF - Bio2RDF.org - - - - http://healthprovidersdata.com/ - 0002-1975 - http://healthprovidersdata.com/hipaa/codes/NDC_$id.aspx - National Drug Code at Health Providers Data - Health Providers Data, Fargo, North Dakota - USA - - - - catalogue - drug - - - - - species - - - - - - - Phytozome Locus - Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information. - - urn:miriam:phytozome.locus - http://identifiers.org/phytozome.locus/ - - phytozome.locus - - urn:miriam:pubmed:22110026 - - - - http://www.phytozome.net/ - Glyma0021s00410 - http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$id - Phytozome Locus at Joint Genome Institute - Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne - USA and Switzerland - - - - - - SubtiList - SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. -SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments. - - urn:miriam:subtilist - http://identifiers.org/subtilist/ - - subtilist - - urn:miriam:pubmed:11752255 - - - - http://genolist.pasteur.fr/SubtiList/ - BG11523 - http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$id - SubtiList at Pasteur Institute - Pasteur Institute, Paris - France - - - - - - DailyMed - DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. - - urn:miriam:dailymed - http://identifiers.org/dailymed/ - - dailymed - - http://dailymed.nlm.nih.gov/dailymed/help.cfm - - - - http://dailymed.nlm.nih.gov/dailymed/ - 8889bcd7-d0e9-434b-b09d-30132bd033b0 - http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=$id - DailyMed at NLM - U.S. National Library of Medicine, Bethesda, Maryland - USA - - - - catalogue - drug - - - - - species - - - - - - - SIDER Drug - - Side Effect Resource - - SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. - - urn:miriam:sider.drug - http://identifiers.org/sider.drug/ - - sider.drug - - urn:miriam:pubmed:20087340 - - - - http://sideeffects.embl.de/ - 2244 - http://sideeffects.embl.de/drugs/$id/ - SIDER Drug v2 at EMBL (Heidelberg) - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg - Germany - - - - - This data is not free to commercial users. - http://creativecommons.org/licenses/by-nc-sa/3.0/ - - - - drug - phenotype - - - - - species - - - - - - - SIDER Side Effect - SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. - - urn:miriam:sider.effect - http://identifiers.org/sider.effect/ - - sider.effect - - urn:miriam:pubmed:20087340 - - - - http://sideeffects.embl.de/ - C0017565 - http://sideeffects.embl.de/se/$id/ - SIDER Side Effect v2 at EMBL (Heidelberg) - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg - Germany - - - - - This data is not free to commercial users. - http://creativecommons.org/licenses/by-nc-sa/3.0/ - - - - drug - phenotype - - - - - model - - - - - - - WikiGenes - WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process. - - urn:miriam:wikigenes - http://identifiers.org/wikigenes/ - - wikigenes - - urn:miriam:pubmed:18728691 - - - - http://www.wikigenes.org/ - 3771877 - http://www.wikigenes.org/e/gene/e/$id.html - WikiGenes at Massachusetts Institute of Technology - Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts - USA - - - - disease - gene - interaction - - - - - species - - - - - - - Broad Fungal Genome Initiative - - Magnaporthe comparative genomics database - - Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. - - urn:miriam:broad - http://identifiers.org/broad/ - - broad - - http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/Info.html - - - - http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ - S7000002168151102 - http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$id - Broad Fungal Genome Initiative at Broad Institute - Broad Institute of MIT and Harvard, Cambridge, Massachuchetts - USA - - - - disease - fungal - genome - - - - - model - - - - - - - Coriell Cell Repositories - The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. - - urn:miriam:coriell - http://identifiers.org/coriell/ - - coriell - - http://ccr.coriell.org/Default.aspx?public=true - - - - http://ccr.coriell.org/ - GM17027 - http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$id - Coriell Cell Repositories at Coriell Institute - Coriell Institute for Medical Research, New Jersey - USA - - - - catalogue - human - mammalian - - - - - model - - - - - - - CORUM - The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded. - - urn:miriam:corum - http://identifiers.org/corum/ - - corum - - urn:miriam:pubmed:19884131 - - - - http://mips.helmholtz-muenchen.de/genre/proj/corum/ - 100 - http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=$id - CORUM at Institute for Bioinformatics and Systems Biology (Germany) - Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum M&amp;uuml;nchen-German Research Center for Environmental Health, Neuherberg - Germany - - - - - The associated data and services are for academic, non-commercial use only. - http://mips.helmholtz-muenchen.de/genre/proj/corum/about/corum.html - - - - mammalian - protein - - - - - species - - - - - - - As of September 2013, this collection is no longer maintained. Various archives are available at: ftp://ftp.ncbi.nih.gov/pub/COG/. - COGs Function - - Clusters of Orthologous Groups Function - - Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. This collection references functional groups. - - urn:miriam:cogs.function - http://identifiers.org/cogs.function/ - - cogs.function - - urn:miriam:pubmed:12969510 - - - - http://www.ncbi.nlm.nih.gov/COG/ - A - http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?fun=$id - COGs Function at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - clustering - protein - - - - - species - - - - - - - EcoliWiki - EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. - - urn:miriam:ecoliwiki - http://identifiers.org/ecoliwiki/ - - ecoliwiki - - urn:miriam:pubmed:22064863 - - - - http://ecoliwiki.net/colipedia/ - aaeA - http://ecoliwiki.net/colipedia/index.php/$id:Gene - EcoliWiki at Texas Agrilife Research - Texas Agrilife Research, Texas A&amp;M University College Station - USA - - - - genome - microbial - - - - - species - - - - - - - Genome Properties (CMR) is no longer supported by the JCVI and has been taken offline. More information at: http://www.jcvi.org/cms/research/past-projects/cmr/overview/ - Genome Properties - The Genome Properties system captures key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties, expressed using controlled vocabulary, reflect gene content, phenotype, phylogeny and computational analyses. Additional properties are derived from curation, published reports and other forms of evidence. - - urn:miriam:genprop - http://identifiers.org/genprop/ - - genprop - - urn:miriam:pubmed:15347579 - - - - http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropertiesHomePage.cgi - GenProp0151 - http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenomePropDefinition.cgi?prop_acc=$id - Genome Properties at JCVI - J Craig Venter institute, Rockville, Maryland - USA - - - - controlled vocabulary - microbial - - - - - model - - - - - - - JSTOR - - Journal Storage - - JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration. - - urn:miriam:jstor - http://identifiers.org/jstor/ - - jstor - - http://en.wikipedia.org/wiki/JSTOR - http://about.jstor.org/individuals-faq - - - - http://www.jstor.org/ - 3075966 - http://www.jstor.org/stable/$id - JSTOR Online - Ithaka Harbors, Inc., New York - USA - - - - bibliography - - - - - model - parameter - reaction - species - - - - - - - Mouse Adult Gross Anatomy - A structured controlled vocabulary of the adult anatomy of the mouse (Mus) - - urn:miriam:ma - http://identifiers.org/ma/ - - ma - - http://www.obofoundry.org/cgi-bin/detail.cgi?id=adult_mouse_anatomy - http://www.informatics.jax.org/searches/AMA_form.shtml - - - - http://bioportal.bioontology.org/ontologies/MA - MA:0002502 - http://purl.bioontology.org/ontology/MA/$id - Mouse Adult Gross Anatomy through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/ma - MA:0002502 - https://www.ebi.ac.uk/ols/ontologies/ma/terms?obo_id=$id - Mouse Adult Gross Anatomy through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://www.informatics.jax.org/ - MA:0002502 - http://www.informatics.jax.org/searches/AMA.cgi?id=$id - Mouse Adult Gross Anatomy at The Jackson Laboratory - The Jackson Laboratory, Bar Harbor, Maine - USA - - - - ontology - - - - - compartment - model - - - - - - - UBERON - - Uber Anatomy Ontology - - Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. - - urn:miriam:uberon - http://identifiers.org/uberon/ - http://purl.obolibrary.org/obo/UBERON - - uberon - - urn:miriam:pubmed:22293552 - - - - http://bioportal.bioontology.org/ontologies/UBERON - UBERON:0008203 - http://purl.bioontology.org/ontology/UBERON/$id - UBERON through bioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/uberon - UBERON:0008203 - https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=$id - UBERON through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - ontology - - - - - compartment - model - - - - - - - Unimod - Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide). - - urn:miriam:unimod - http://identifiers.org/unimod/ - - unimod - - urn:miriam:pubmed:15174123 - - - - http://www.unimod.org/ - 1200 - http://www.unimod.org/modifications_view.php?editid1=$id - Unimod at Matrix Sciences Ltd. - Matrix Science Ltd., London - UK - - - - - This site requires a login, but can be accessed as guest. - http://www.unimod.org/register_disabled.html - - - - mass spectrometry - protein - - - - - species - - - - - - - VBRC - - Viral Bioinformatics Resource Center - - The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. - - urn:miriam:vbrc - http://identifiers.org/vbrc/ - - vbrc - - http://vbrc.org/about.asp - - - - http://vbrc.org/ - 35742 - http://vbrc.org/gene_detail.asp?gene_id=$id - VBRC at University of Alabama - University of Alabama, Birmingham and the University of Victoria, British Columbia - USA and Canada - - - - genome - viral - - - - - species - - - - - - - ViralZone - ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures. - - urn:miriam:viralzone - http://identifiers.org/viralzone/ - - viralzone - - urn:miriam:pubmed:20947564 - - - - http://www.expasy.org/viralzone/ - 992 - http://viralzone.expasy.org/all_by_protein/$id.html - ViralZone at SIB - Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva - Switzerland - - - - image library - viral - - - - - model - - - - - - - Gene Ontology Reference - - GO reference collection - - The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of "GO content" meetings at which substantial changes in the ontologies are discussed and made. - - urn:miriam:go.ref - http://identifiers.org/go.ref/ - - go.ref - - urn:miriam:pubmed:14681407 - http://www.geneontology.org/GO.consortiumlist.shtml - - - - http://www.geneontology.org/cgi-bin/references.cgi - GO_REF:0000041 - http://www.geneontology.org/cgi-bin/references.cgi#$id - Gene Ontology Reference at The Gene Ontology Consortium - The Gene Ontology Consortium - USA - - - - controlled vocabulary - - - - - Rat Genome Database qTL - Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes. - - urn:miriam:rgd.qtl - http://identifiers.org/rgd.qtl/ - - rgd.qtl - - urn:miriam:pubmed:17151068 - - - - http://rgd.mcw.edu/ - 1354581 - http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$id - Rat Genome Database qTL at Medical College of Wisconsin - Medical College of Wisconsin, Milwaukee, Wisconsin - USA - - - - gene - phenotype - - - - - species - - - - - - - Rat Genome Database strain - Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology. - - urn:miriam:rgd.strain - http://identifiers.org/rgd.strain/ - - rgd.strain - - urn:miriam:pubmed:17151068 - - - - http://rgd.mcw.edu/ - 5688061 - http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$id - Rat Genome Database strain at Medical College of Wisconsin - Medical College of Wisconsin, Milwaukee, Wisconsin - USA - - - - - - DOOR - - Database for prOkaryotic OpeRons - - DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. - - urn:miriam:door - http://identifiers.org/door/ - - door - - urn:miriam:pubmed:18988623 - - - - http://csbl1.bmb.uga.edu/OperonDB/DOOR.php - 60101 - http://csbl1.bmb.uga.edu/OperonDB/genedetail.php?id=$id - DOOR v1 at University of Georgia - Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia - USA - - - - - Not suitable for commercial use. - http://csbl1.bmb.uga.edu/OperonDB/ - - - - - - Degradome Database - The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. - - urn:miriam:degradome - http://identifiers.org/degradome/ - - degradome - - urn:miriam:pubmed:18776217 - - - - http://degradome.uniovi.es/ - Ax1 - http://degradome.uniovi.es/cgi-bin/protease/$id - Degradome Database at - Departamento de Bioqu&amp;amp;iacute;mica y Biolog&amp;amp;iacute;a Molecular, Facultad de Medicina, Universidad de Oviedo - Spain - - - - - - DBD - - Transcription Factor Database - - The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins. - - urn:miriam:dbd - http://identifiers.org/dbd/ - - dbd - - urn:miriam:pubmed:18073188 - - - - http://www.transcriptionfactor.org/ - 0045310 - http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$id+cat:DBD - DBD at MRC Laboratory of Molecular Biology - MRC Laboratory of Molecular Biology, Cambridge - UK - - - - - - DATF - - Database of Arabidopsis transcription factors - - DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals. - - urn:miriam:datf - http://identifiers.org/datf/ - - datf - - urn:miriam:pubmed:15731212 - - - - http://datf.cbi.pku.edu.cn/ - AT1G01030.1 - http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$id - DATF through PlantTFDB - Center for Bioinformatics, Peking - Peoples Republic of China. - - - - - - IUPHAR ligand - The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands. - - urn:miriam:iuphar.ligand - http://identifiers.org/iuphar.ligand/ - - iuphar.ligand - - urn:miriam:pubmed:23087376 - - - - http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all - 1755 - http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$id - IUPHAR ligand at University of Edinburgh - Centre for Cardiovascular Science, University of Edinburgh, Edinburgh - UK - - - - - - Molbase - Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. - - urn:miriam:molbase - http://identifiers.org/molbase/ - - molbase - - http://www.molbase.com/en/index.php?app=article&act=view&article_id=112 - - - - http://www.molbase.com/ - 128796-39-4 - http://www.molbase.com/en/index.php?app=search&search_keyword=$id - Molbase at Chinese Academy of Sciences - Chinese Academy of Sciences, Xuhui District Shanghai - China - - - - - - YRC PDR - - Yeast Resource Center Public Data Repository - - The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. - - urn:miriam:yrcpdr - http://identifiers.org/yrcpdr/ - - yrcpdr - - urn:miriam:pubmed:15608220 - - - - http://www.yeastrc.org/pdr/ - 2673500 - http://yeastrc.org/pdr/viewProtein.do?id=$id - YRC PDR at University of Washington - Department of Biochemistry, University of Washington, Seattle - USA - - - - - - Yeast Intron Database v3 - The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. - - urn:miriam:yid - http://identifiers.org/yid/ - - yid - - urn:miriam:pubmed:12073325 - - - - http://compbio.soe.ucsc.edu/yeast_introns.html - SNR17A - http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$id - Yeast Intron Database version 3 at Baskin School of Engineering - Baskin School of Engineering, Center for Molecular Biology of RNA, University of California, Santa Cruz, California - USA - - - - DNA - eukaryotic - sequence - - - - - species - - - - - - - FuncBase Fly - Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data. - - urn:miriam:funcbase.fly - http://identifiers.org/funcbase.fly/ - - funcbase.fly - - urn:miriam:pubmed:20495000 - - - - http://func.mshri.on.ca/fly - 10194 - http://func.mshri.on.ca/fly/genes/list_functional_scores/$id - FuncBase Fly at Harvard Medical School - Harvard Medical School, Boston, Massachusetts - USA - - - - - - FuncBase Human - Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data. - - urn:miriam:funcbase.human - http://identifiers.org/funcbase.human/ - - funcbase.human - - urn:miriam:pubmed:20495000 - - - - http://func.mshri.on.ca/human/ - 119514 - http://func.mshri.on.ca/human/genes/list_functional_scores/$id - FuncBase Human at Harvard Medical School - Harvard Medical School, Boston, Massachusetts - USA - - - - - - FuncBase Mouse - Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse. - - urn:miriam:funcbase.mouse - http://identifiers.org/funcbase.mouse/ - - funcbase.mouse - - urn:miriam:pubmed:20495000 - - - - http://func.mshri.on.ca/mouse/ - 1351341 - http://func.mshri.on.ca/mouse/genes/list_functional_scores/$id - FuncBase Mouse at Harvard Medical School - Harvard Medical School, Boston, Massachusetts - USA - - - - - - FuncBase Yeast - Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast. - - urn:miriam:funcbase.yeast - http://identifiers.org/funcbase.yeast/ - - funcbase.yeast - - urn:miriam:pubmed:20495000 - - - - http://func.mshri.on.ca/yeast - 2701 - http://func.mshri.on.ca/yeast/genes/list_functional_scores/$id - FuncBase Yeast at Harvard Medical School - Harvard Medical School, Boston, Massachusetts - USA - - - - - - YDPM - - Yeast Deletion Project and Proteomics of Mitochondria Database - - The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. - - urn:miriam:ydpm - http://identifiers.org/ydpm/ - - ydpm - - urn:miriam:pubmed:12134146 - - - - http://www-deletion.stanford.edu/YDPM/ - YAL001C - http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$id - YDPM at Stanford University School of Medicine - Stanford University School of Medicine, Stanford, California - USA - - - - - - WormBase RNAi - WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. - - urn:miriam:wormbase.rnai - http://identifiers.org/wormbase.rnai/ - - wormbase.rnai - - urn:miriam:pubmed:11125056 - urn:miriam:pubmed:17099234 - - - - http://www.wormbase.org/ - WBRNAi00086878 - http://www.wormbase.org/species/c_elegans/rnai/$id - WormBase RNAi at Cold Spring Harbor Laboratory - Cold Spring Harbor Laboratory, Cold Spring, Harbor New York - USA - - - - - - FunCat - - MIPS Functional Catalogue Database - - The Functional Catalogue (FunCat) is a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. It has been applied for the manual annotation of prokaryotes, fungi, plants and animals. - - urn:miriam:funcat - http://identifiers.org/funcat/ - - funcat - - urn:miriam:pubmed:15486203 - - - - http://mips.helmholtz-muenchen.de/funcatDB/ - 32.01.01 - http://mips.helmholtz-muenchen.de/funcatDB/cgi-bin/search_advanced.pl?action=2&wert=$id - FunCat at MIPS (Neuherberg) - Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Neuherberg - Germany - - - - - - PASS2 - - Protein Alignments organised as Structural Superfamilies - - The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. - - urn:miriam:pass2 - http://identifiers.org/pass2/ - - pass2 - - urn:miriam:pubmed:22123743 - - - - http://caps.ncbs.res.in/pass2/ - 46977 - http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$id - PASS2 at National centre for Biological Sciences (India) - National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka - India - - - - - - ICEberg element - ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. - - urn:miriam:iceberg.element - http://identifiers.org/iceberg.element/ - - iceberg.element - - urn:miriam:pubmed:22009673 - - - - http://db-mml.sjtu.edu.cn/ICEberg/ - 100 - http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$id - ICEberg element at Shanghai Jiaotong University - State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai - China - - - - - - ICEberg family - ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. - - urn:miriam:iceberg.family - http://identifiers.org/iceberg.family/ - - iceberg.family - - urn:miriam:pubmed:22009673 - - - - http://db-mml.sjtu.edu.cn/ICEberg/ - 1 - http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$id - ICEberg family at Shanghai Jiaotong University - State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai - China - - - - - - VFDB Genus - - Virulence Factor Database genus - - VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. - - urn:miriam:vfdb.genus - http://identifiers.org/vfdb.genus/ - - vfdb.genus - - urn:miriam:pubmed:22067448 - - - - http://www.mgc.ac.cn/VFs/ - Chlamydia - http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$id - VFDB Genus at Institute of Pathogen Biology - State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing - China - - - - - - VFDB Gene - VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. - - urn:miriam:vfdb.gene - http://identifiers.org/vfdb.gene/ - - vfdb.gene - - urn:miriam:pubmed:22067448 - - - - http://www.mgc.ac.cn/VFs/ - VFG2154 - http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$id - VFDB Gene at Institute of Pathogen Biology - State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing - China - - - - - - MeSH 2013 - MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013. - - urn:miriam:mesh.2013 - http://identifiers.org/mesh.2013/ - - mesh.2013 - - http://www.nlm.nih.gov/pubs/factsheets/mesh.html - - - - http://www.nlm.nih.gov/mesh/ - 17165 - http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$id&view=expanded - MeSH 2013 at National Library of Medicine - U.S. National Library of Medicine, National Institute of Health, Maryland - USA - - - - - Records accessed through MESH may include content that itself has some copyright restriction when reproduced. - http://www.nlm.nih.gov/copyright.html - - - Access to Mesh 2013 uses identifiers that could potentially change. We recommend the use of the stable MeSH collection (http://identifiers.org/mesh/). If you have issues accessing Mesh 2013, you may wish to try the ftp service. - ftp access for MeSH 2013 records - - - - - - KEGG Module - - - - KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules. - - urn:miriam:kegg.module - http://identifiers.org/kegg.module/ - - kegg.module - - http://www.kegg.jp/kegg/module.html - - - - http://www.kegg.jp/kegg/module.html - M00002 - http://www.kegg.jp/entry/$id - KEGG Module at Kyoto University Bioinformatics Center - Department of Computational Biology, University of Tokyo, Tokyo - Japan - - - - clustering - - - - - species - - - - - - - KEGG Disease - - - - The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system. - - urn:miriam:kegg.disease - http://identifiers.org/kegg.disease/ - - kegg.disease - - http://www.genome.jp/kegg/disease/ - - - - http://www.genome.jp/kegg/disease/ - H00076 - http://www.kegg.jp/entry/$id - KEGG Disease at Kyoto University Bioinformatics Center - Kyoto University Bioinformatics Center, Kyoto - Japan - - - - disease - - - - - model - - - - - - - MedlinePlus - MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language. - - urn:miriam:medlineplus - http://identifiers.org/medlineplus/ - - medlineplus - - http://www.nlm.nih.gov/medlineplus/aboutmedlineplus.html - - - - http://www.nlm.nih.gov/medlineplus/ - 002804 - http://www.nlm.nih.gov/medlineplus/ency/article/$id.htm - MedlinePlus at NCBI - NCBI, NIH, Bethesda, Maryland - USA - - - - encyclopedia - human - schema.org - - - - - species - model - - - - - - - LigandBox - LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. - - urn:miriam:ligandbox - http://identifiers.org/ligandbox/ - - ligandbox - - https://www.jstage.jst.go.jp/article/biophysics/9/0/9_113/_article - - - - http://ligandbox.protein.osaka-u.ac.jp/ligandbox//cgi-bin/index.cgi?LANG=en - D00001 - http://ligandbox.protein.osaka-u.ac.jp/ligandbox/cgi-bin/liginf.cgi?id=$id - LigandBox at - nstitute for Protein Research, Osaka University and Fujitsu Kyushu R&amp;D Center, Life Science Systems Dept., Fujitsu - Japan - - - - chemical - structure - - - - - species - - - - - - - GlycoEpitope - GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes. - - urn:miriam:glycoepitope - http://identifiers.org/glycoepitope/ - - glycoepitope - - http://www.glycoepitope.jp/GlycoEpitope_guide_E.pdf - - - - http://www.glycoepitope.jp/epitopes/ - EP0311 - http://www.glycoepitope.jp/epitopes/$id - GlycoEpitope at Ritsumeikan University - Kawasaki laboratory, Research Center for Glycobiotechnology, Ritsumeikan University - Japan - - - - immunogenetics - interaction - - - - - species - - - - - - - JCGGDB - - Japan Consortium for Glycobiology and Glycotechnology DataBase - - JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc. - - urn:miriam:jcggdb - http://identifiers.org/jcggdb/ - - jcggdb - - http://jcggdb.jp/seturitu_en.html - - - - http://jcggdb.jp/index_en.html - JCGG-STR008690 - http://jcggdb.jp/idb/jcggdb/$id - JCGGDB at Advanced Science Institute (Japan) - Advanced Science Institute(ASI), Chemical Biology Department Systems Glycobiology research Group, Saitama - Japan - - - - lipid - polysaccharide - protein - structure - - - - - species - - - - - - - NONCODE v4 Gene - NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. - - urn:miriam:noncodev4.gene - http://identifiers.org/noncodev4.gene/ - - noncodev4.gene - - urn:miriam:pubmed:22135294 - - - - http://www.bioinfo.org/NONCODEv4/ - NONHSAG00001 - http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$id - NONCODE v4 Gene at Chinese Academy of Sciences - Bioinformatics Research Group, Chinese Academy of Sciences, Beijing - China - - - - expression - gene - sequence - - - - - species - - - - - - - NONCODE v4 Transcript - NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. - - urn:miriam:noncodev4.rna - http://identifiers.org/noncodev4.rna/ - - noncodev4.rna - - urn:miriam:pubmed:22135294 - - - - http://www.bioinfo.org/NONCODEv4/ - NONHSAT000001 - http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$id - NONCODE v4 Transcript at Chinese Academy of Sciences - Bioinformatics Research Group, Chinese Academy of Sciences, Beijing - China - - - - expression - nucleotide - - - - - species - - - - - - - Oryzabase Gene - Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information. - - urn:miriam:oryzabase.gene - http://identifiers.org/oryzabase.gene/ - - oryzabase.gene - - urn:miriam:pubmed:16403737 - - - - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ - 117 - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$id - Oryzabase v4 Gene at National Institute of Genetics (Japan) - Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka - Japan - - - - gene - plant - - - - - species - - - - - - - Oryzabase Mutant - Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information. - - urn:miriam:oryzabase.mutant - http://identifiers.org/oryzabase.mutant/ - - oryzabase.mutant - - urn:miriam:pubmed:16403737 - - - - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ - 21393 - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$id - Oryzabase v4 Mutant at National Institute of Genetics (Japan) - Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka - Japan - - - - phenotype - plant - - - - - species - - - - - - - Oryzabase Strain - Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. - - urn:miriam:oryzabase.strain - http://identifiers.org/oryzabase.strain/ - - oryzabase.strain - - urn:miriam:pubmed:16403737 - - - - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ - 1 - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$id - Oryzabase v4 Strain at National Institute of Genetics (Japan) - Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka - Japan - - - - plant - strain - - - - - species - - - - - - - Oryzabase Stage - Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information. - - urn:miriam:oryzabase.stage - http://identifiers.org/oryzabase.stage/ - - oryzabase.stage - - urn:miriam:pubmed:16403737 - - - - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ - 34 - http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$id - Oryzabase v4 Stage at National Institute of Genetics (Japan) - Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka - Japan - - - - phenotype - plant - - - - - model - - - - - - - Oryza Tag Line - - OTL - - Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. - - urn:miriam:otl - http://identifiers.org/otl/ - - otl - - urn:miriam:pubmed:17947330 - - - - http://oryzatagline.cirad.fr/ - AADB12 - http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$id - Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI - CIRAD-INRA-SUPAGRO-UMII, Biological Systems Department, Montpellier - France - - - - phenotype - plant - - - - - species - - - - - - - Gene Wiki - The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. - - urn:miriam:genewiki - http://identifiers.org/genewiki/ - - genewiki - - urn:miriam:pubmed:18613750 - - - - http://en.wikipedia.org/wiki/Gene_Wiki - 1017 - http://plugins.biogps.org/cgi-bin/wp.cgi?id=$id - Gene Wiki through BioGPS - Wikimedia Foundation, San Francisco, California - USA - - - - - This collection is a subset of NCBI gene (MIR:00000069), accessed through BioGPS. - http://biogps.org/ - - - - encyclopedia - gene - human - - - - - species - - - - - - - PaxDb Organism - PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. - - urn:miriam:paxdb.organism - http://identifiers.org/paxdb.organism/ - - paxdb.organism - - urn:miriam:pubmed:22535208 - - - - http://pax-db.org/ - 9606 - http://pax-db.org/#!species/$id - PaxDb v3 at University of Zurich - Institute of Molecular Life Sciences, University of Zurich, Zurich - Switzerland - - - - expression - genome - protein - - - - - model - - - - - - - PaxDb Protein - PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. - - urn:miriam:paxdb.protein - http://identifiers.org/paxdb.protein/ - - paxdb.protein - - urn:miriam:pubmed:22535208 - - - - http://pax-db.org/ - 977869 - http://pax-db.org/#!protein/$id - PaxDb v3 at University of Zurich - Institute of Molecular Life Sciences, University of Zurich, Zurich - Switzerland - - - - expression - protein - - - - - species - - - - - - - Protein Data Bank Ligand - The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. - - urn:miriam:pdb.ligand - http://identifiers.org/pdb.ligand/ - - pdb.ligand - - urn:miriam:pubmed:17142228 - urn:miriam:pubmed:10592235 - - - - http://www.pdb.org/ - TRQ - http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$id - PDB Ligand at RCSB - Rutgers, The State University of New Jersey - USA - - - http://www.pdbe.org/ - TRQ - http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$id - PDB Ligand at Protein Databank in Europe (PDBe) - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - structure - - - - - species - - - - - - - MEROPS Inhibitor - The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors. - - urn:miriam:merops.inhibitor - http://identifiers.org/merops.inhibitor/ - - merops.inhibitor - - urn:miriam:pubmed:17991683 - - - - http://merops.sanger.ac.uk/index.htm - I31.952 - http://merops.sanger.ac.uk/cgi-bin/pepsum?id=$id - MEROPS Inhibitor at Sanger Institute - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge - UK - - - - enzyme - interaction - protein - - - - - Animal Diversity Web - Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. - - urn:miriam:adw - http://identifiers.org/adw/ - - adw - - http://www.lsa.umich.edu/ummz/default.asp - - - - http://animaldiversity.ummz.umich.edu/ - Lycalopex_vetulus - http://animaldiversity.ummz.umich.edu/accounts/$id/ - Animal Diversity Web at University of Michigan - University of Michigan Museum of Zoology, Ann Arbor, Michigan - USA - - - - classification - - - - - species - model - - - - - - - GLIDA GPCR - - GPCR-LIgand DAtabase GPCR - - The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors. - - urn:miriam:glida.gpcr - http://identifiers.org/glida.gpcr/ - - glida.gpcr - - urn:miriam:pubmed:16381956 - urn:miriam:pubmed:17986454 - - - - http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ - ACM1_HUMAN - http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$id - GLIDA GPCR at Kyoto University - Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto - Japan - - - - chemical - interaction - - - - - species - - - - - - - GLIDA Ligand - - GPCR-LIgand DAtabase Ligand - - The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands. - - urn:miriam:glida.ligand - http://identifiers.org/glida.ligand/ - - glida.ligand - - urn:miriam:pubmed:16381956 - urn:miriam:pubmed:17986454 - - - - http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ - L000001 - http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$id - GLIDA Ligand at Kyoto University - Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto - Japan - - - - chemical - interaction - - - - - species - - - - - - - GRSDB - - G-Rich Sequences DataBase - - GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. - - urn:miriam:grsdb - http://identifiers.org/grsdb/ - - grsdb - - urn:miriam:pubmed:16381828 - - - - http://bioinformatics.ramapo.edu/GRSDB2/ - 10142 - http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$id - GRSDB v2 at Ramapo College of New Jersey - Bioinformatics Group, School of Theoretical and Applied Science, Ramapo College of New Jersey, Mahwah - USA - - - - eukaryotic - nucleotide - - - - - species - - - - - - - F-SNP - - Functional Single Nucleotide Polymorphism - - The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. - - urn:miriam:fsnp - http://identifiers.org/fsnp/ - - fsnp - - urn:miriam:pubmed:17986460 - - - - http://compbio.cs.queensu.ca/F-SNP/ - rs17852708 - http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&amp;id_type=snp_id&amp;id_val=$id - F-SNP at Queen's University (Canada) - Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, Ontario - Canada - - - - nucleotide - - - - - species - - - - - - - Homeodomain Research - The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders. - - urn:miriam:hdr - http://identifiers.org/hdr/ - - hdr - - urn:miriam:pubmed:20157477 - - - - http://research.nhgri.nih.gov/apps/homeodomain/web/ - 63 - http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&amp;view=proteins&amp;id=$id - Homeodomain Research at National Human Genome Research Institute (NIH) - Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland - USA - - - - domain - interaction - protein - - - - - species - - - - - - - NORINE - Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings. - - urn:miriam:norine - http://identifiers.org/norine/ - - norine - - urn:miriam:pubmed:17913739 - - - - http://bioinfo.lifl.fr/norine/ - NOR00681 - http://bioinfo.lifl.fr/norine/result.jsp?ID=$id - NORINE at Computer Science Laboratory of Lille - Computer Science Laboratory of Lille, INRIA and ProBioGEM, University of Sciences and Technologies of Lille, Lille - France - - - - fungal - microbial - protein - - - - - species - - - - - - - Olfactory Receptor Database - - OrDB - - The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). - - urn:miriam:ordb - http://identifiers.org/ordb/ - - ordb - - urn:miriam:pubmed:23585030 - - - - http://senselab.med.yale.edu/OrDB/ - 8497 - http://senselab.med.yale.edu/ORDB/Data/$id - Olfactory Receptor Database at Yale University School of Medicine - Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut - USA - - - - nucleotide - sequence - - - - - species - - - - - - - Odor Molecules DataBase - - OdorDB - - OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors - - urn:miriam:odor - http://identifiers.org/odor/ - - odor - - urn:miriam:pubmed:23585030 - - - - http://senselab.med.yale.edu/OdorDB - 74 - http://senselab.med.yale.edu/OdorDB/Data/$id/?db=5 - Odor Molecules DataBase at Yale University School of Medicine - Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut - USA - - - - chemical - - - - - species - - - - - - - P3DB Protein - Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. - - urn:miriam:p3db.protein - http://identifiers.org/p3db.protein/ - - p3db.protein - - urn:miriam:pubmed:22973285 - - - - http://www.p3db.org/ - 70 - http://www.p3db.org/protein.php?id=$id&amp;ref=0 - P3DB Protein at University of Missouri - Department of Computer Science, University of Missouri, Columbia, Missouri - USA - - - - plant - protein - - - - - species - - - - - - - P3DB Site - Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. - - urn:miriam:p3db.site - http://identifiers.org/p3db.site/ - - p3db.site - - urn:miriam:pubmed:22973285 - - - - http://www.p3db.org/ - 65 - http://www.p3db.org/phosphosite.php?id=$id&ref=0 - P3DB Site at University of Missouri - Department of Computer Science, University of Missouri, Columbia, Missouri - USA - - - - plant - protein - - - - - species - - - - - - - TOPDB - The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. - - urn:miriam:topdb - http://identifiers.org/topdb/ - - topdb - - urn:miriam:pubmed:17921502 - - - - http://topdb.enzim.hu/ - AP00378 - http://topdb.enzim.hu/?m=show&id=$id - TOPDB at Hungarian Academy of Sciences - Institute of Enzymology, Hungarian Academy of Sciences, Budapest - Hungary - - - - protein - - - - - species - - - - - - - Animal Genome Cattle QTL - The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs. - - urn:miriam:cattleqtldb - http://identifiers.org/cattleqtldb/ - - cattleqtldb - - urn:miriam:pubmed:23180796 - - - - http://www.animalgenome.org/cgi-bin/QTLdb/BT/index - 4685 - http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=$id - Animal QTL Cattle at Iowa State University - Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa - USA - - - - gene - phenotype - - - - - species - - - - - - - Animal Genome Chicken QTL - The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. - - urn:miriam:chickenqtldb - http://identifiers.org/chickenqtldb/ - - chickenqtldb - - urn:miriam:pubmed:23180796 - - - - http://www.animalgenome.org/cgi-bin/QTLdb/GG/index - 14362 - http://www.animalgenome.org/cgi-bin/QTLdb/GG/qdetails?QTL_ID=$id - Animal QTL Chicken at Iowa State University - Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa - USA - - - - gene - phenotype - - - - - species - - - - - - - Animal Genome Pig QTL - The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs. - - urn:miriam:pigqtldb - http://identifiers.org/pigqtldb/ - - pigqtldb - - urn:miriam:pubmed:23180796 - - - - http://www.animalgenome.org/cgi-bin/QTLdb/SS/index - 14 - http://www.animalgenome.org/cgi-bin/QTLdb/SS/qdetails?QTL_ID=$id - Animal QTL Pig at Iowa State University - Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa - USA - - - - gene - phenotype - - - - - species - - - - - - - Animal Genome Sheep QTL - The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. - - urn:miriam:sheepqtldb - http://identifiers.org/sheepqtldb/ - - sheepqtldb - - urn:miriam:pubmed:23180796 - - - - http://www.animalgenome.org/cgi-bin/QTLdb/OA/index - 19803 - http://www.animalgenome.org/cgi-bin/QTLdb/OA/qdetails?QTL_ID=$id - Animal QTL Sheep at Iowa State University - Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Iowa - USA - - - - gene - phenotype - - - - - species - - - - - - - Gramene Growth Stage Ontology - Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene. - - urn:miriam:gramene.growthstage - http://identifiers.org/gramene.growthstage/ - - gramene.growthstage - - urn:miriam:pubmed:21076153 - - - - http://www.gramene.org/ - GRO:0007133 - http://www.gramene.org/db/ontology/search?id=$id - Gramene Growth Stage Ontology at Cold Spring Harbor - Cold Spring Harbor Laboratory, New York - USA - - - - ontology - - - - - species - compartment - - - - - - - NCBI GI - The NCBI GI (or "gi") identifier is the original form of identifier for sequence records processed by the NCBI. This 'GenInfo' identifier system was used to access GenBank and related databases, and was assigned to both protein and nucleotide sequences. - - urn:miriam:ncbigi - http://identifiers.org/ncbigi/ - - ncbigi - - http://www.ncbi.nlm.nih.gov/protein - - - - http://www.ncbi.nlm.nih.gov/protein/ - GI:9082283 - http://www.ncbi.nlm.nih.gov/protein/$id - NCBI GI at NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - - Historical subset of NCBI gene and protein (MIR:00000069, MIR:00000344), which continue to be the recommended manner in which to reference nucelotide and protein sequence information. - http://www.ebi.ac.uk/miriam/main/mdb?section=faq#CollectionsRestrictions - - - It is not possible to discriminate protein or nucleotide entities based on the identifier. - http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html - - - - - - EBI Metagenomics Sample - The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. - - urn:miriam:ebimetagenomics.samp - http://identifiers.org/ebimetagenomics.samp/ - http://identifiers.org/ebimetagenomics/ - urn:miriam:ebimetagenomics - - ebimetagenomics.samp - - urn:miriam:doi:10.1093%2Fnar%2Fgkt961 - - - - http://www.ebi.ac.uk/metagenomics - SRS086444 - http://www.ebi.ac.uk/metagenomics/samples/$id - EBI Metagenomics at European Bioinformatics Institute - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - - - - - European Genome-phenome Archive Study - - EGA Study - - The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. - - urn:miriam:ega.study - http://identifiers.org/ega.study/ - - ega.study - - https://www.ebi.ac.uk/ega/about/introduction - - - - https://www.ebi.ac.uk/ega/studies - EGAS00000000001 - https://www.ebi.ac.uk/ega/studies/$id - EGA Study at European Bioinformatics Institute - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.omicsdi.org/ - EGAS00000000001 - https://www.omicsdi.org/dataset/ega/$id - EGA Study through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - gene - human - phenotype - - - - - European Genome-phenome Archive Dataset - - EGA Dataset - - The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. - - urn:miriam:ega.dataset - http://identifiers.org/ega.dataset/ - - ega.dataset - - https://www.ebi.ac.uk/ega/about/introduction - - - - https://www.ebi.ac.uk/ega/dataset - EGAD00000000001 - https://www.ebi.ac.uk/ega/datasets/$id - EGA Dataset at European Bioinformatics Institute - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.omicsdi.org/ - EGAD00000000001 - https://www.omicsdi.org/dataset/ega/$id - EGA Dataset through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - gene - human - phenotype - - - - - ProteomeXchange - The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. - - urn:miriam:px - http://identifiers.org/px/ - urn:miriam:proteomexchange - - px - - http://www.proteomexchange.org/faq - - - - http://www.proteomexchange.org/ - PXD000500 - http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$id - ProteomeXchange at Seattle - Institute for Systems Biology, Seattle, WA, USA - USA - - - - mass spectrometry - protein - - - - - SBML RDF Vocabulary - Vocabulary used in the RDF representation of SBML models. - - urn:miriam:biomodels.vocabulary - http://identifiers.org/biomodels.vocabulary/ - - biomodels.vocabulary - - https://github.com/sarala/ricordo-rdfconverter/wiki - - - - http://biomodels.net/rdf/vocabulary.rdf - rateRule - http://biomodels.net/rdf/vocabulary.rdf#$id - Vocabulary via BioModels.net - BioModels.net - UK - - - - - - PRIDE Project - The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. - - urn:miriam:pride.project - http://identifiers.org/pride.project/ - - pride.project - - urn:miriam:pubmed:16381953 - urn:miriam:pubmed:16041671 - urn:miriam:pubmed:18033805 - urn:miriam:pubmed:18428683 - - - - http://www.ebi.ac.uk/pride/ - PXD000440 - http://www.ebi.ac.uk/pride/archive/projects/$id - PRIDE Project at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.omicsdi.org/ - PXD000440 - https://www.omicsdi.org/dataset/pride/$id - PRIDE Project through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - protein - - - - - Antibody Registry - The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. - - urn:miriam:antibodyregistry - http://identifiers.org/antibodyregistry/ - - antibodyregistry - - http://antibodyregistry.org/ - - - - http://antibodyregistry.org/ - 493771 - http://antibodyregistry.org/AB_$id - Antibody Registry at University of California - Neuroscience Information Framework, University of California, San Diego, California - USA - - - - immunogenetics - registry - - - - - Mathematical Modelling Ontology - - MAMO - - The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. - - urn:miriam:mamo - http://identifiers.org/mamo/ - - mamo - - http://sourceforge.net/projects/mamo-ontology/ - - - - http://bioportal.bioontology.org/ontologies/MAMO - MAMO_0000026 - http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/$id - MAMO through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/mamo - MAMO_0000026 - https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form=$id - MaMO through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - model - - - - - - - Plant Environment Ontology - - Plant Environment Conditions - - The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. - - urn:miriam:eo - http://identifiers.org/eo/ - urn:miriam:peo - - eo - - http://wiki.plantontology.org/index.php/Plant_Environment_Ontology_Wiki - - - - http://archive.gramene.org/db/ontology/search_term?id=EO:0007359 - EO:0007404 - http://archive.gramene.org/db/ontology/search?query=$id - Plant Environment Ontology through Gramene - Cold Spring Harbor Laboratory, New York - USA - - - http://bioportal.bioontology.org/ontologies/PECO - EO:0007404 - http://purl.bioontology.org/ontology/PECO/$id - Plant Environment Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://www.ebi.ac.uk/ols/ontologies/eo - EO:0007404 - https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=$id - Plant Environment Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - controlled vocabulary - plant - - - - - species - model - - - - - - - Identifiers.org Terms - - IdoT - - Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. - - urn:miriam:idot - http://identifiers.org/idot/ - - idot - - http://biomodels.net/vocab/idot.rdf - - - - http://identifiers.org/ - identifierPattern - http://biomodels.net/vocab/idot.rdf#$id - IdoT via biomodels.net - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - schema.org - - - - - HGNC Family - The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides symbols for both structural and functional gene families. This collection refers to records using the HGNC family symbol. - - urn:miriam:hgnc.family - http://identifiers.org/hgnc.family/ - - hgnc.family - - urn:miriam:pubmed:17984084 - urn:miriam:pubmed:20929869 - urn:miriam:pubmed:23161694 - - - - http://www.genenames.org/ - PADI - http://www.genenames.org/genefamilies/$id - HGNC Family at HUGO Genome Nomenclature Committee - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - HGNC Family has been reimplemented using numerical identifiers, and is not directly related to this version. We suggest the use of the new version: http://identifiers.org/hgnc.genefamily/ - http://www.genenames.org/newer-gene-family-resource-available - - - - classification - gene - human - schema.org - - - - - species - - - - - - - Yeast Intron Database v4.3 - The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]. - - urn:miriam:yeastintron - http://identifiers.org/yeastintron/ - - yeastintron - - urn:miriam:pubmed:12073325 - - - - http://intron.ucsc.edu/yeast4.3/ - SNR17A - http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&amp;orfName=$id - Yeast Intron Database version 4.3 at Baskin School of Engineering - Baskin School of Engineering, Center for Molecular Biology of RNA, University of California, Santa Cruz, California - USA - - - - DNA - eukaryotic - sequence - - - - - species - - - - - - - Antibiotic Resistance Genes Database - - ARDB - - The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. - - urn:miriam:ardb - http://identifiers.org/ardb/ - - ardb - - urn:miriam:pubmed:18832362 - - - - http://ardb.cbcb.umd.edu/ - CAE46076 - http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&amp;field=ni&amp;term=$id - ARDB at University of Maryland - Center for Bioinformatics and Computational Biology, University of Maryland, Maryland - USA - - - - drug - gene - - - - - Pathema is no longer supported and has been taken offline. See more at: http://www.jcvi.org/cms/research/past-projects/pathema/overview/ - Pathema - The over-arching goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica — involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics. - - urn:miriam:pathema - http://identifiers.org/pathema/ - - pathema - - urn:miriam:pubmed:19843611 - - - - http://pathema.jcvi.org/ - http://pathema.jcvi.org/$id - - - - - - - - - ProteomicsDB Protein - ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins. - - urn:miriam:proteomicsdb.protein - http://identifiers.org/proteomicsdb.protein/ - - proteomicsdb.protein - - urn:miriam:pubmed:24870543 - - - - https://www.proteomicsdb.org/#human - 53504 - https://www.proteomicsdb.org/#human/proteinDetails/$id/summary - Proteomics DB Protein at Center for Integrated Protein Science - Center for Integrated Protein Science, Munich, - Germany - - - - human - protein - - - - - ProteomicsDB Peptide - ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. - - urn:miriam:proteomicsdb.peptide - http://identifiers.org/proteomicsdb.peptide/ - - proteomicsdb.peptide - - urn:miriam:pubmed:24870543 - - - - https://www.proteomicsdb.org/#peptideSearch - 53504 - https://www.proteomicsdb.org/#human/proteinDetails/$id/peptides/ - Proteomics DB Peptide at Center for Integrated Protein Science - Center for Integrated Protein Science, Munich - Germany - - - - human - protein - - - - - Human Proteome Map Protein - - HPM - - The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. - - urn:miriam:hpm.protein - http://identifiers.org/hpm.protein/ - - hpm.protein - - urn:miriam:pubmed:24870542 - - - - http://www.humanproteomemap.org/index.php - 1968 - http://www.humanproteomemap.org/protein.php?hpm_id=$id - Human Proteome Map Protein at Institute of Bioinformatics (Bangalore) - Institute of Bioinformatics, International Tech Park, Bangalore - India - - - - human - protein - - - - - Human Proteome Map Peptide - The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. - - urn:miriam:hpm.peptide - http://identifiers.org/hpm.peptide/ - - hpm.peptide - - urn:miriam:pubmed:24870542 - - - - http://www.humanproteomemap.org/index.php - 9606117 - http://www.humanproteomemap.org/spectrum.php?pep_id=$id - Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore) - Institute of Bioinformatics, International Tech Park, Bangalore - India - - - - human - protein - - - - - DrugBank Target v4 - The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database. - - urn:miriam:drugbankv4.target - http://identifiers.org/drugbankv4.target/ - - drugbankv4.target - - urn:miriam:pubmed:24203711 - - - - http://www.drugbank.ca/targets - BE0000048 - http://www.drugbank.ca/biodb/bio_entities/$id - DrugBank Target information version 4 - Departments of Computing Science, Biological Sciences, University of Alberta - Canada - - - - chemical - interaction - protein - - - - - ZINC - ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. - - urn:miriam:zinc - http://identifiers.org/zinc/ - - zinc - - urn:miriam:pubmed:22587354 - http://wiki.bkslab.org/index.php/ZINC_Database - - - - http://zinc15.docking.org/ - ZINC1084 - http://zinc15.docking.org/substances/$id - ZINC at University of California (San Francisco) - Shoichet Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco - USA - - - - chemical - structure - - - - - species - - - - - - - FooDB Compound - FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. - - urn:miriam:foodb.compound - http://identifiers.org/foodb.compound/ - - foodb.compound - - http://foodb.ca/about - - - - http://foodb.ca/foods - FDB002100 - http://foodb.ca/compounds/$id - FooDB database of food additives at University of Alberta - University of Alberta, Edmonton, AB - Canada - - - - chemical - structure - - - - - species - - - - - - - UNII - - Substance Registration System - Unique ingredient identifier - - The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information. - - urn:miriam:unii - http://identifiers.org/unii/ - - unii - - http://www.fda.gov/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/default.htm - - - - http://fdasis.nlm.nih.gov/srs/ - 3G6A5W338E - http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$id - UNII at U.S. Food and Drug Administration - U.S. Food and Drug Administration, Maryland - USA - - - - chemical - drug - - - - - species - - - - - - - Orphanet Rare Disease Ontology - - ORDO - - The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. -It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10). - - urn:miriam:orphanet.ordo - http://identifiers.org/orphanet.ordo/ - http://www.orpha.net/ORDO/ - - orphanet.ordo - - http://www.orphadata.org/cgi-bin/inc/ordo_orphanet.inc.php - - - - https://www.ebi.ac.uk/ols/ontologies/ordo - Orphanet_C023 - https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form=$id - ORDO via OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - disease - ontology - - - - - Protein Affinity Reagents - - PSI-PAR - - Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. - - urn:miriam:psipar - http://identifiers.org/psipar/ - - psipar - - urn:miriam:pubmed:19674966 - - - - https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR - PAR:0116 - https://www.ebi.ac.uk/ontology-lookup/?termId=$id - Protein Affinity Reagents through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - ClinVar Record - ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. - - urn:miriam:clinvar.record - http://identifiers.org/clinvar.record/ - - clinvar.record - - urn:miriam:doi:10.1093%2Fnar%2Fgkt1113 - - - - http://www.ncbi.nlm.nih.gov/clinvar/ - RCV000033555.3 - http://www.ncbi.nlm.nih.gov/clinvar/$id/ - ClinVar Record at NCBI - National Center for Biotechnology Information (NCBI), NIH, Maryland - USA - - - - gene - human - phenotype - - - - - EBI Metagenomics Project - The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references projects. - - urn:miriam:ebimetagenomics.proj - http://identifiers.org/ebimetagenomics.proj/ - - ebimetagenomics.proj - - urn:miriam:doi:10.1093%2Fnar%2Fgkt961 - urn:miriam:doi:10.1093%2Fnar%2Fgkt961 - - - - https://www.ebi.ac.uk/metagenomics - ERP004492 - https://www.ebi.ac.uk/metagenomics/projects/$id - EBI metagenomics projects at EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - genome - - - - - EU Clinical Trials - - EU Clinical Trials Register - - The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. -It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population. - - urn:miriam:euclinicaltrials - http://identifiers.org/euclinicaltrials/ - - euclinicaltrials - - urn:miriam:doi:10.1093%2Fnar%2Fgkt961 - urn:miriam:doi:10.1093%2Fnar%2Fgkt961 - https://www.clinicaltrialsregister.eu/about.html - - - - https://www.clinicaltrialsregister.eu/ - 2008-005144-16 - https://www.clinicaltrialsregister.eu/ctr-search/search?query=$id - EU Clinical Trials at European Medicines Agency - European Medicines Agency, London - UK - - - - disease - disorder - human - pharmacogenomics - - - - - Google Patents - Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. - - urn:miriam:google.patent - http://identifiers.org/google.patent/ - - google.patent - - https://support.google.com/faqs/answer/2539193?hl=en - - - - https://www.google.com/patents/ - US4145692 - https://www.google.com/patents/$id - Google Patents at Google - Google Incorporated - - - - - registry - - - - - USPTO - - United States Patent and Trademark Office - - The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. - - urn:miriam:uspto - http://identifiers.org/uspto/ - - uspto - - http://patft.uspto.gov/netahtml/PTO/help/helpfaq.htm - - - - http://patft.uspto.gov/netahtml/PTO/index.html - 4145692 - http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$id - USPTO patents at USPTO - United States Patent and Trademark Office - USA - - - - registry - - - - - Cooperative Patent Classification - - CPC - - The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. - - urn:miriam:cpc - http://identifiers.org/cpc/ - - cpc - - http://worldwide.espacenet.com/help?quickHelpPage=classificationsearchCPC.1&amp;locale=en_EP&amp;method=handleQuickHelp - - - - http://worldwide.espacenet.com/classification - A01M1/026 - http://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$id - Cooperative Patent Classification at Espace - Espace, European Patent Office - - - - - classification - - - - - GWAS Central Study - GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. - - urn:miriam:gwascentral.study - http://identifiers.org/gwascentral.study/ - - gwascentral.study - - urn:miriam:pubmed:24301061 - - - - http://www.gwascentral.org/studies - HGVST1828 - http://www.gwascentral.org/study/$id - GWAS Central Study at University of Leicester - Department of Genetics, University of Leicester, Leicester - UK - - - - genome - human - phenotype - - - - - ExAC Variant - The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. - - urn:miriam:exac.variant - http://identifiers.org/exac.variant/ - - exac.variant - - http://exac.broadinstitute.org/faq - - - - http://exac.broadinstitute.org/ - 22-46615880-T-C - http://exac.broadinstitute.org/variant/$id - ExAC Variant at Exome Aggregation Consortium - Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts - USA - - - - genome - human - phenotype - - - - - GWAS Central Marker - GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker. - - urn:miriam:gwascentral.marker - http://identifiers.org/gwascentral.marker/ - - gwascentral.marker - - urn:miriam:pubmed:24301061 - - - - http://www.gwascentral.org/markers/ - HGVM15354 - http://www.gwascentral.org/marker/$id - GWAS Central Marker at University of Leicester - Department of Genetics, University of Leicester, Leicester - UK - - - - genome - human - phenotype - - - - - GWAS Central Phenotype - GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype. - - urn:miriam:gwascentral.phenotype - http://identifiers.org/gwascentral.phenotype/ - - gwascentral.phenotype - - urn:miriam:pubmed:24301061 - - - - http://www.gwascentral.org/phenotypes - HGVPM623 - http://www.gwascentral.org/phenotype/$id - GWAS Central Phenotype at University of Leicester - Department of Genetics, University of Leicester, Leicester - UK - - - - genome - human - phenotype - - - - - LINCS Cell - The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease. - - urn:miriam:lincs.cell - http://identifiers.org/lincs.cell/ - - lincs.cell - - http://www.lincsproject.org/LINCS/data/standards - http://bd2k-lincs.org/#/ - https://biosharing.org/bsg-s000651 - - - - http://lincsportal.ccs.miami.edu/cells/ - LCL-2085 - http://lincsportal.ccs.miami.edu/cells/#/view/$id - LINCS Portal - University of Miami, BD2K-LINCS DCIC - USA - - - - human - - - - - LINCS Protein - The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. - - urn:miriam:lincs.protein - http://identifiers.org/lincs.protein/ - - lincs.protein - - http://lincs.hms.harvard.edu/resources/tutorials-presentations/ - - - - http://lincs.hms.harvard.edu/db/proteins/ - 200282 - http://lincs.hms.harvard.edu/db/proteins/$id/ - LINCS Protein at Harvard Medical School - Harvard Medical School, Boston, Massachusetts - USA - - - - human - - - - - LINCS Small Molecule - The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). - - urn:miriam:lincs.smallmolecule - http://identifiers.org/lincs.smallmolecule/ - urn:miriam:lincs.molecule - - lincs.smallmolecule - - http://www.lincsproject.org/LINCS/data/standards - http://bd2k-lincs.org/#/ - https://biosharing.org/bsg-s000655 - - - - http://lincsportal.ccs.miami.edu/SmallMolecules/ - LSM-6306 - http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$id - LINCS Portal - University of Miami, BD2K-LINCS DCIC, USA - USA - - - - human - - - - - ExAC Transcript - The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. - - urn:miriam:exac.transcript - http://identifiers.org/exac.transcript/ - - exac.transcript - - http://exac.broadinstitute.org/faq - - - - http://exac.broadinstitute.org/ - ENST00000407236 - http://exac.broadinstitute.org/transcript/$id - ExAC Transcript at Exome Aggregation Consortium - Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts - USA - - - - genome - human - phenotype - - - - - ExAC Gene - The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. - - urn:miriam:exac.gene - http://identifiers.org/exac.gene/ - - exac.gene - - http://exac.broadinstitute.org/faq - - - - http://exac.broadinstitute.org/ - ENSG00000169174 - http://exac.broadinstitute.org/gene/$id - ExAC Gene at Exome Aggregation Consortium - Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts - USA - - - - genome - human - phenotype - - - - - Wikidata - Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic. - - urn:miriam:wikidata - http://identifiers.org/wikidata/ - - wikidata - - https://www.wikidata.org/wiki/Help:Contents - - - - https://www.wikidata.org/ - Q2207226 - https://www.wikidata.org/wiki/$id - Wikidata at Wikimedia Foundation - Wikimedia Foundation, San Francisco, California - USA - - - - encyclopedia - - - - - SwissLipids - SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. - - urn:miriam:swisslipid - http://identifiers.org/swisslipid/ - - swisslipid - - http://www.swisslipids.org/#/about - - - - http://www.swisslipids.org/#/ - SLM:000048885 - http://www.swisslipids.org/#/entity/$id/ - SwissLipids at Swiss Institute of Bioinformatics - Swiss Institute of Bioinformatics, Basel - Switzerland - - - - lipid - metabolite - - - - - UniPathway Compound - UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds. - - urn:miriam:unipathway.compound - http://identifiers.org/unipathway.compound/ - - unipathway.compound - - urn:miriam:pubmed:22102589 - - - - http://www.grenoble.prabi.fr/obiwarehouse/unipathway - UPC04349 - http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$id - UniPathway Compound at Swiss Institute of Bioinformatics (SIB) - Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control - Switzerland - - - - - This collection re-uses a modified version of the identifiers associated with KEGG Compound. - http://identifiers.org/kegg.compound/ - - - - chemical - metabolite - structure - - - - - SEED Subsystem - This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. - - urn:miriam:seed - http://identifiers.org/seed/ - - seed - - urn:miriam:pubmed:16214803 - - - - http://seed-viewer.theseed.org/seedviewer.cgi - Biotin_biosynthesis - http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$id - SEED Subsystem at Argonne National Laboratory - Argonne National Laboratory, University of Chicago, Argonne, Illinois - USA - - - - pathway - - - - - SEED Compound - This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. - - urn:miriam:seed.compound - http://identifiers.org/seed.compound/ - - seed.compound - - urn:miriam:pubmed:16214803 - - - - http://modelseed.org/ - cpd15380 - http://modelseed.org/biochem/compounds/$id - SEED Compound at Argonne National Laboratory - Argonne National Laboratory, University of Chicago, Argonne, Illinois - USA - - - - chemical - metabolite - structure - - - - - BiGG Model - BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. - - urn:miriam:bigg.model - http://identifiers.org/bigg.model/ - - bigg.model - - urn:miriam:pubmed:20426874 - - - - http://bigg.ucsd.edu/models - iECABU_c1320 - http://bigg.ucsd.edu/models/$id - BiGG Model at University of California - Systems Biology Research Group at the University of California, San Diego - USA - - - - - The data may be used freely for research purposes only. - http://bigg.ucsd.edu/# - - - - model - - - - - BiGG Compartment - BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments. - - urn:miriam:bigg.compartment - http://identifiers.org/bigg.compartment/ - - bigg.compartment - - urn:miriam:pubmed:20426874 - - - - http://bigg.ucsd.edu/compartments/ - c - http://bigg.ucsd.edu/compartments/$id - BiGG Compartment at University of California - Systems Biology Research Group at the University of California, San Diego - USA - - - - - The data may be used freely for research purposes only. - http://bigg.ucsd.edu/# - - - - model - - - - - BiGG Metabolite - BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. - - urn:miriam:bigg.metabolite - http://identifiers.org/bigg.metabolite/ - - bigg.metabolite - - urn:miriam:pubmed:20426874 - - - - http://bigg.ucsd.edu/universal/metabolites - 12dgr161 - http://bigg.ucsd.edu/models/universal/metabolites/$id - BiGG Metabolite at University of Cakifornia - Systems Biology Research Group at the University of California, San Diego - USA - - - - - The data may be used freely for research purposes only. - http://bigg.ucsd.edu/# - - - - model - - - - - BiGG Reaction - BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. - - urn:miriam:bigg.reaction - http://identifiers.org/bigg.reaction/ - - bigg.reaction - - urn:miriam:pubmed:20426874 - - - - http://bigg.ucsd.edu/universal/reactions - 13GS - http://bigg.ucsd.edu/models/universal/reactions/$id - BiGG Reaction at University of California - Systems Biology Research Group at the University of California, San Diego - USA - - - - - The data may be used freely for research purposes only. - http://bigg.ucsd.edu/# - - - - model - - - - - RRID - - Research Resource IDentifier - - The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. -The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch. - - urn:miriam:rrid - http://identifiers.org/rrid/ - - rrid - - https://scicrunch.org/page/scicrunch - - - - https://scicrunch.org/resolver - RRID:AB_262044 - https://scicrunch.org/resolver/$id - RRID at SciCrunch - University of California, San Diego - USA - - - - registry - - - - - UMLS - - Unified Medical Language System - - The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. - - urn:miriam:umls - http://identifiers.org/umls/ - - umls - - urn:miriam:pubmed:14681409 - http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=nlmumls - - - - http://linkedlifedata.com/ - C0021390 - http://linkedlifedata.com/resource/umls/id/$id - Unified Medical Language System at LinkedLifeData - Linkedlifedata, Ontotext, Sofia - Bulgaria - - - - - While data is free to use in many circumstances under terms and conditions presented, these must be agreed to in the process of account creation. - http://www.nlm.nih.gov/databases/umls.html - - - - controlled vocabulary - - - - - MeSH - - Medical Subject Headings - - MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc. - - urn:miriam:mesh - http://identifiers.org/mesh/ - - mesh - - http://www.nlm.nih.gov/pubs/factsheets/mesh.html - - - - http://id.nlm.nih.gov/mesh/ - C000100 - http://id.nlm.nih.gov/mesh/$id - MeSH Linked Data at National Library of Medicine - U.S. National Library of Medicine, National Institute of Health, Maryland - USA - - - - - - Electron Microscopy Data Bank - - EMDB - - The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. - - urn:miriam:emdb - http://identifiers.org/emdb/ - - emdb - - urn:miriam:pubmed:20935055 - - - - http://www.ebi.ac.uk/pdbe/emdb/ - EMD-1001 - http://www.ebi.ac.uk/pdbe/entry/emdb/$id - EMDB at Protein Data Bank in Europe - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - mass spectrometry - - - - - miRTarBase - miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. - - urn:miriam:mirtarbase - http://identifiers.org/mirtarbase/ - - mirtarbase - - urn:miriam:pubmed:26590260 - - - - http://mirtarbase.mbc.nctu.edu.tw/ - MIRT000002 - http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$id - miRTarBase at National Chiao Tung University - Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu - Taiwan - - - - interaction - nucleotide - - - - - MedDRA - - Medical Dictionary for Regulatory Activities - - The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). - - urn:miriam:meddra - http://identifiers.org/meddra/ - - meddra - - http://www.meddra.org/basics - - - - http://bioportal.bioontology.org/ontologies/MEDDRA - 10015919 - http://purl.bioontology.org/ontology/MEDDRA/$id - MedDRA through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - controlled vocabulary - ontology - - - - - DASHR - - Database of small human noncoding RNAs - - DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records. - - urn:miriam:dashr - http://identifiers.org/dashr/ - - dashr - - urn:miriam:pubmed:26553799 - - - - http://lisanwanglab.org/DASHR/ - hsa-mir-200a - http://lisanwanglab.org/DASHR/entry/$id - DASHR at University of Pennsylvania - Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia - USA - - - - human - nucleotide - sequence - - - - - DASHR expression - DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression. - - urn:miriam:dashr.expression - http://identifiers.org/dashr.expression/ - - dashr.expression - - urn:miriam:pubmed:26553799 - - - - http://lisanwanglab.org/DASHR/show-expression-table.php?start=0 - hsa-mir-200a - http://lisanwanglab.org/DASHR/entry/$id#exprPerTissueTable - DASHR expression at University of Pennsylvania - Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia - USA - - - - expression - human - nucleotide - sequence - - - - - SPLASH - The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. - - urn:miriam:splash - http://identifiers.org/splash/ - - splash - - http://splash.fiehnlab.ucdavis.edu/ - - - - http://mona.fiehnlab.ucdavis.edu/ - splash10-0zq2000000-77302b0326a418630a84 - http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$id - Mass Bank of North America (MoNA) - University of Californai, Davis, California - USA - - - - chemical - mass spectrometry - metabolite - - - - - MetaNetX chemical - MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components. - - urn:miriam:metanetx.chemical - http://identifiers.org/metanetx.chemical/ - - metanetx.chemical - - urn:miriam:pubmed:26527720 - urn:miriam:pubmed:23172809 - - - - http://www.metanetx.org/ - MNXM1723 - http://www.metanetx.org/chem_info/$id - MetaNetX chemical at SIB Swiss Institute of Bioinformatics - Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - chemical - model - - - - - MetaNetX reaction - MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. - - urn:miriam:metanetx.reaction - http://identifiers.org/metanetx.reaction/ - - metanetx.reaction - - urn:miriam:pubmed:26527720 - urn:miriam:pubmed:23172809 - - - - http://www.metanetx.org/ - MNXR101574 - http://www.metanetx.org/equa_info/$id - MetaNetX reaction at SIB Swiss Institute of Bioinformatics - Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - model - reaction - - - - - MetaNetX compartment - MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments. - - urn:miriam:metanetx.compartment - http://identifiers.org/metanetx.compartment/ - - metanetx.compartment - - urn:miriam:pubmed:26527720 - urn:miriam:pubmed:23172809 - - - - http://www.metanetx.org/ - MNXC15 - http://www.metanetx.org/comp_info/$id - MetaNetX compartment at SIB Swiss Institute of Bioinformatics - Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne - Switzerland - - - - model - - - - - UniPathway Reaction - UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions. - - urn:miriam:unipathway.reaction - http://identifiers.org/unipathway.reaction/ - - unipathway.reaction - - urn:miriam:pubmed:22102589 - - - - http://www.grenoble.prabi.fr/obiwarehouse/unipathway - UCR00226 - http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$id - UniPathway Reaction at Swiss Institute of Bioinformatics (SIB) - Swiss Institute of Bioinformatics (SIB) and French National Institute for Research in Computer Science and Control - Switzerland - - - - - This collection re-uses a modified version of the identifiers associated with KEGG Reaction. - http://identifiers.org/kegg.reaction/ - - - - reaction - - - - - Human Phenotype Ontology - - HPO - - The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. - - urn:miriam:hp - http://identifiers.org/hp/ - http://purl.obolibrary.org/obo/HP - urn:miriam:hpo - - hp - - urn:miriam:pubmed:24217912 - - - - http://human-phenotype-ontology.github.io/ - HP:0000118 - http://compbio.charite.de/hpoweb/showterm?id=$id - Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics - Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin - Germany - - - https://www.ebi.ac.uk/ols/ontologies/hp - HP:0000118 - https://www.ebi.ac.uk/ols/ontologies/hp/terms?obo_id=$id - Human Phenotype Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - human - ontology - phenotype - - - - - SASBDB - - Small Angle Scattering Biological Data Bank - - Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. - - urn:miriam:sasbdb - http://identifiers.org/sasbdb/ - - sasbdb - - urn:miriam:pubmed:25352555 - - - - http://www.sasbdb.org/ - SASDAX8 - http://www.sasbdb.org/data/$id - SASBDB at European Molecular Biology Laboratory - Biological Small Angle Scattering Group, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg - Germany - - - - domain - structure - - - - - HGNC gene family - The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families. - - urn:miriam:hgnc.genefamily - http://identifiers.org/hgnc.genefamily/ - - hgnc.genefamily - - urn:miriam:pubmed:26842383 - urn:miriam:pubmed:25361968 - - - - http://www.genenames.org/ - 141 - http://www.genenames.org/cgi-bin/genefamilies/set/$id - HGNC gene family at HUGO Genome Nomenclature Committee - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - human - schema.org - - - - - MDM - - Medical Data Models - - The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. - - urn:miriam:mdm - http://identifiers.org/mdm/ - - mdm - - urn:miriam:pubmed:26868052 - - - - https://medical-data-models.org/ - 4776 - https://medical-data-models.org/forms/$id - MDM at University of Muenster - Institute of Medical Informatics, University of Muenster - Germany - - - - human - registry - - - - - ProbOnto - - Probability Distribution Ontology - - ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. - - urn:miriam:probonto - http://identifiers.org/probonto/ - - probonto - - urn:miriam:pubmed:27153608 - - - - https://www.ebi.ac.uk/ols/ontologies/probonto - PROB_c0000005 - https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$id - ProbOnto through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - APID Interactomes - - Agile Protein Interactomes DataServer - - APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. - - urn:miriam:apid.interactions - http://identifiers.org/apid.interactions/ - - apid.interactions - - urn:miriam:pubmed:27131791 - - - - http://cicblade.dep.usal.es:8080/APID/ - P01116 - http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$id - APID at Salamanca - Cancer Research Center (CiC-IBMCC), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca - Spain - - - - interaction - protein - - - - - STOREDB - STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. - - urn:miriam:storedb - http://identifiers.org/storedb/ - - storedb - - https://www.storedb.org/store_v3/help.jsp - - - - https://www.storedb.org/ - STOREDB:STUDY1040 - https://www.storedb.org/?$id - STOREDB at University of Cambridge - University of Cambridge, Department of Physiology, Downing Street, Cambridge - UK - - - - - - Kyoto Encyclopedia of Genes and Genomes - - KEGG - - Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. - - urn:miriam:kegg - http://identifiers.org/kegg/ - - kegg - - urn:miriam:pubmed:22700311 - - - - http://www.kegg.jp/ - hsa00190 - http://www.kegg.jp/entry/$id - KEGG at Kyoto University Bioinformatics Center - Kyoto University Bioinformatics Center - Japan - - - - - KEGG provides a variety of 'Data-oriented entry points', which are also represented separately in this Registry. For instance, kegg disease (http://identifiers.org/kegg.disease), kegg pathway (http://identifiers.org/kegg.pathway/), etc. - http://www.kegg.jp/ - - - - chemical - genome - pathway - - - - - Plant Transcription Factor Database - - PlantTFDB - - The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. - - urn:miriam:planttfdb - http://identifiers.org/planttfdb/ - - planttfdb - - urn:miriam:pubmed:24174544 - - - - http://planttfdb.cbi.pku.edu.cn - Ath_AT1G01030.1 - http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$id - PlantTFDB at Peking University - Center for Bioinformatics, Peking University, Beijing - Peoples Republic of China - - - - DNA - interaction - protein - - - - - Mammalian Phenotype Ontology - The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. - - urn:miriam:mp - http://identifiers.org/mp/ - - mp - - urn:miriam:pubmed:20052305 - urn:miriam:pubmed:20052305 - - - - http://www.informatics.jax.org/ - MP:0005452 - http://www.informatics.jax.org/searches/Phat.cgi?id=$id - Mammalian Phenotype Ontology at The Jackson Lab - The Jackson Laboratory, Bar Harbor, Maine - USA - - - https://www.ebi.ac.uk/ols/ontologies/mp/ - MP:0005452 - https://www.ebi.ac.uk/ols/ontologies/mp/terms?obo_id=$id - Mammalian Phenotype Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://bioportal.bioontology.org/ontologies/MP - MP:0005452 - https://bioportal.bioontology.org/ontologies/MP/$id - Mammalian Phenotype Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - mammalian - ontology - phenotype - - - - - World Register of Marine Species - - WoRMS - - The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. - - urn:miriam:worms - http://identifiers.org/worms/ - urn:lsid:marinespecies.org:taxname:146421 - - worms - - http://www.marinespecies.org/aphia.php?p=manual - - - - http://www.marinespecies.org/ - 146421 - http://www.marinespecies.org/aphia.php?p=taxdetails&id=$id - World Register of Marine Species - Flanders Marine Institute, Ostend - Belgium - - - - classification - taxonomy - - - - - MultiCellDS collection - MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections). - - urn:miriam:multicellds.collection - http://identifiers.org/multicellds.collection/ - - multicellds.collection - - http://multicellds.org/ - http://multicellds.org/ - http://multicellds.org/ - - - - http://multicellds.org/MultiCellDB.php - MCDS_C_0000000001 - http://multicellds.org/MultiCellDB/$id - MultiCellDScollection at Keck School of Medicine - Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California - USA - - - - model - - - - - MultiCellDS Digital snapshot - MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data. - - urn:miriam:multicellds.snapshot - http://identifiers.org/multicellds.snapshot/ - - multicellds.snapshot - - - http://multicellds.org/MultiCellDB.php - MCDS_S_0000000001 - http://multicellds.org/MultiCellDB/$id - MultiCellDS snapshot at Keck School of Medicine - Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California - USA - - - - model - - - - - MultiCellDS Digital Cell Line - MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. - - urn:miriam:multicellds.cell_line - http://identifiers.org/multicellds.cell_line/ - - multicellds.cell_line - - - http://multicellds.org/MultiCellDB.php - MCDS_L_0000000001 - http://multicellds.org/MultiCellDB/$id - MultiCellDS Digital Cell Line at Keck School of Medicine - Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, California - USA - - - - model - - - - - E-cyanobacterium entity - E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. - - urn:miriam:ecyano.entity - http://identifiers.org/ecyano.entity/ - - ecyano.entity - - http://e-cyanobacterium.org/support/ - https://sybila.fi.muni.cz/_media/wiki/cmsb2016.pdf - - - - http://www.e-cyanobacterium.org/bcs/entity/ - 23 - http://e-cyanobacterium.org/bcs/entity/$id/ - e-cyanobacterium entity at Masaryk University Brno - Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno - Czech Republic - - - - metabolite - model - - - - - E-cyanobacterium model - E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. - - urn:miriam:ecyano.model - http://identifiers.org/ecyano.model/ - - ecyano.model - - http://e-cyanobacterium.org/support/ - https://sybila.fi.muni.cz/_media/wiki/cmsb2016.pdf - - - - http://e-cyanobacterium.org/models/ - 26 - http://e-cyanobacterium.org/models/model/$id/ - e-cyanobacterium entity at Masaryk University Brno - Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno - Czech Republic - - - - microbial - model - - - - - E-cyanobacterium rule - E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules. - - urn:miriam:ecyano.rule - http://identifiers.org/ecyano.rule/ - - ecyano.rule - - http://e-cyanobacterium.org/support/ - https://sybila.fi.muni.cz/_media/wiki/cmsb2016.pdf - - - - http://www.e-cyanobacterium.org/bcs/rule/ - 56 - http://e-cyanobacterium.org/bcs/rule/$id/ - e-cyanobacterium entity at Masaryk University Brno - Systems Biology Laboratory, Faculty of Informatics, Masaryk University Brno - Czech Republic - - - - model - reaction - - - - - LINCS Data - The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level). - - urn:miriam:lincs.data - http://identifiers.org/lincs.data/ - - lincs.data - - http://www.lincsproject.org/ - - - - http://lincsportal.ccs.miami.edu/datasets/ - LDS-1110 - http://lincsportal.ccs.miami.edu/datasets/#/view/$id - LINCS Data at University of Miami - University of Miami, BD2K-LINCS DCIC - USA - - - https://www.omicsdi.org/ - LDS-1110 - https://www.omicsdi.org/dataset/lincs/$id - Lincs through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - human - - - - - AGRICOLA - - Agricultural Online Access - - AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century. - - urn:miriam:agricola - http://identifiers.org/agricola/ - urn:miriam:argicola - - agricola - - http://www.nal.usda.gov/help/ - - - - http://agricola.nal.usda.gov/ - 50018 - http://ddr.nal.usda.gov/dspace/handle/10113/$id - AGRICOLA at National Agricultural Library - National Agricultural Library, United States Department of Agriculture - USA - - - - - - Mass Spectrometry Controlled Vocabulary - The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. - - urn:miriam:ms - http://identifiers.org/ms/ - - ms - - urn:miriam:pubmed:23482073 - - - - https://www.ebi.ac.uk/ols/ontologies/ms - MS:1000001 - https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=$id - Mass Spectrometry Controlled Vocabulary through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://bioportal.bioontology.org/ontologies/MS - MS:1000001 - http://purl.bioontology.org/ontology/MS/$id - Mass Spectrometry Controlled Vocabulary through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - controlled vocabulary - mass spectrometry - - - - - Environment Ontology - - ENVO - - The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. - - urn:miriam:envo - http://identifiers.org/envo/ - - envo - - urn:miriam:pubmed:27664130 - - - - https://www.ebi.ac.uk/ols/ontologies/envo - ENVO:09200010 - https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=$id - The Environment Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - http://purl.bioontology.org/ontology/ENVO/ - ENVO:09200010 - http://purl.bioontology.org/ontology/ENVO/$id - The Environment Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - ontology - - - - - ARK - - Archival Resource Key - - An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. - - urn:miriam:ark - http://identifiers.org/ark/ - - ark - - https://en.wikipedia.org/wiki/Archival_Resource_Key - - - - http://n2t.net/ - ark:/12345/fk1234 - http://n2t.net/$id - ARK via the Name-to-Thing resolver. - California Digital Library, University of California Office of the President - USA - - - - - - GRID - - Global Research Identifier Database - - International coverage of the world's leading research organisations, indexing 92% of funding allocated globally. - - urn:miriam:grid - http://identifiers.org/grid/ - - grid - - https://gridac.freshdesk.com/support/solutions - - - - https://www.grid.ac/ - grid.225360.0 - https://www.grid.ac/institutes/$id - GRID at Digital Science & Research Ltd. - Digital Science &amp;amp; Research Ltd, London - UK - - - - schema.org - - - - - MedGen - MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. - - urn:miriam:medgen - http://identifiers.org/medgen/ - - medgen - - https://www.ncbi.nlm.nih.gov/medgen/docs/help/#start - - - - https://www.ncbi.nlm.nih.gov/medgen/ - 760050 - https://www.ncbi.nlm.nih.gov/medgen/$id - MedGen at NCBI - National Center for Biotechnology Information (NCBI), NIH, Maryland - USA - - - - gene - human - phenotype - - - - - ClinVar Submission - ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. - - urn:miriam:clinvar.submission - http://identifiers.org/clinvar.submission/ - urn:miriam:clinvar.sub - - clinvar.submission - - urn:miriam:doi:10.1093%2Fnar%2Fgkt1113 - - - - http://www.ncbi.nlm.nih.gov/clinvar/ - SCV000151292 - http://www.ncbi.nlm.nih.gov/clinvar?term=$id - ClinVar Submission at NCBI - National Center for Biotechnology Information (NCBI), NIH, Maryland - USA - - - - - - ClinVar Variant - ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier. - - urn:miriam:clinvar - http://identifiers.org/clinvar/ - - clinvar - - urn:miriam:doi:10.1093%2Fnar%2Fgkt1113 - - - - http://www.ncbi.nlm.nih.gov/clinvar/ - 12345 - https://www.ncbi.nlm.nih.gov/clinvar/variation/$id - ClinVar Variant at NCBI - National Center for Biotechnology Information (NCBI), NIH, Maryland - USA - - - - - - BioAssay Ontology - The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. - - urn:miriam:bao - http://identifiers.org/bao/ - - bao - - - http://bioportal.bioontology.org/ontologies/BAO/ - 0002989 - http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$id - BioAssay Ontology through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - https://bioportal.bioontology.org/ontologies/BAO/ - 0002989 - https://www.ebi.ac.uk/ols/ontologies/bao/terms?obo_id=BAO:$id - BioAssay Ontology through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - model - - - - - - - Cellosaurus - The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines. - - urn:miriam:cellosaurus - http://identifiers.org/cellosaurus/ - - cellosaurus - - http://web.expasy.org/cellosaurus/description.html - - - - http://web.expasy.org/cellosaurus/ - CVCL_0030 - http://web.expasy.org/cellosaurus/$id - Cellosaurus through SIB - Swiss Institute of Bioinformatics - Swizerland - - - - - - Identifiers.org Registry - The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or "PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources. - - urn:miriam:mir - http://identifiers.org/mir/ - - mir - - http://biorxiv.org/content/early/2017/01/18/101279 - - - - http://identifiers.org/registry - MIR:00100037 - http://identifiers.org/registry?query="$id" - Identifiers.org Registry through EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - Progenetix - - Cancer Genome Knowledge Resource - - The Progenetix database provides an overview of copy number abnormalities in human cancer from currently 32317 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1026 articles and represents 364 different cancer types, according to the International classification of Diseases in Oncology (ICD-O). - - urn:miriam:pgx - http://identifiers.org/pgx/ - - pgx - - http://europepmc.org/abstract/MED/24225322 - http://europepmc.org/abstract/MED/11751233 - - - - http://progenetix.org/ - icdom:8500_3 - http://progenetix.org/pgx:$id - Progenetix - University of Zurich - Switzerland - - - - - - COSMIC Gene - - Catalogue of Somatic Mutations in Cancer Gene - - COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes. - - urn:miriam:cosmic - http://identifiers.org/cosmic/ - - cosmic - - urn:miriam:pubmed:18428421 - - - - http://cancer.sanger.ac.uk/cosmic/ - BRAF - http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$id - COSMIC Gene at Sanger - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge - UK - - - - schema.org - - - - - dbGaP - - Database of Genotypes and Phenotypes - - The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. - - urn:miriam:dbgap - http://identifiers.org/dbgap/ - - dbgap - - urn:miriam:doi:10.1038%2Fng1007-1181 - - - - https://www.ncbi.nlm.nih.gov/projects/gap - phs000768.v2.p1 - https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$id - dbGaP through NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - - - Information Artifact Ontology - An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. - - urn:miriam:iao - http://identifiers.org/iao/ - - iao - - https://github.com/information-artifact-ontology/IAO - - - - http://www.ontobee.org/ontology/IAO - 0000030 - http://purl.obolibrary.org/obo/IAO_$id - IAO through Ontobee - University of Pennsylvania - USA - - - - - - Genomic Data Commons Data Portal - The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. - - urn:miriam:gdc - http://identifiers.org/gdc/ - - gdc - - urn:miriam:doi:10.1056%2FNEJMp1607591 - - - - https://gdc.cancer.gov - ae8c77fe-e6c8-44d5-8265-4a38c637bbef - https://portal.gdc.cancer.gov/cases/$id - Genomic Data Commons - National Cancer Institute Genomic Data Commons, NIH - - USA - - - - - - OMIT - - Ontology for miRNA Target - - The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). - - urn:miriam:omit - http://identifiers.org/omit/ - - omit - - - https://www.ebi.ac.uk/ols/ontologies/omit/ - 0005506 - https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$id - Ontology for miRNA Target (OMIT) through OLS - European Bioinformatics Institute, Hinxton, Cambridge - - UK - - - - - - INSDC CDS - The coding sequence or protein identifiers as maintained in INSDC. - - urn:miriam:insdc.cds - http://identifiers.org/insdc.cds/ - - insdc.cds - - - http://www.ebi.ac.uk/ena - AAA35559 - http://www.ebi.ac.uk/ena/data/view/$id - INSDC CDS through ENA - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.ncbi.nlm.nih.gov/protein/ - AAA35559 - https://www.ncbi.nlm.nih.gov/protein/$id - INSDC CDS through NCBI - National Center for Biotechnology Information (NCBI) - USA - - - http://getentry.ddbj.nig.ac.jp - AAA35559 - http://getentry.ddbj.nig.ac.jp/getentry/dad/$id - INSDC CDS through DDBJ - DNA Data Bank of Japan, Mishima, Shizuoka - Japan - - - - - - Genome assembly database - The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. - - urn:miriam:insdc.gca - http://identifiers.org/insdc.gca/ - - insdc.gca - - - http://www.ebi.ac.uk/ena/browse/genome-assembly-database - GCA_000155495.1 - http://www.ebi.ac.uk/ena/data/view/$id - Genome assembly database through ENA - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - https://www.ncbi.nlm.nih.gov/assembly/ - GCA_000155495.1 - https://www.ncbi.nlm.nih.gov/assembly/$id - Genome assembly database NCBI - National Center for Biotechnology Information (NCBI) - USA - - - - - - GlyTouCan - GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data. - - urn:miriam:glytoucan - http://identifiers.org/glytoucan/ - - glytoucan - - urn:miriam:doi:10.1093%2Fglycob%2Fcwx066 - urn:miriam:doi:10.1093%2Fnar%2Fgkv1041 - - - - https://glytoucan.org - G00054MO - https://glytoucan.org/Structures/Glycans/$id - The Glycan Repository - Soka University, Hachioji, Tokyo - Japan - - - - schema.org - - - - - MetaCyc Compound - - MetaCyc Metabolic Pathway Database - - MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. - - urn:miriam:metacyc.compound - http://identifiers.org/metacyc.compound/ - - metacyc.compound - - urn:miriam:doi:10.1093%2Fnar%2Fgkv1164 - - - - https://metacyc.org - CPD-10330 - https://metacyc.org/compound?orgid=META&id=$id - MetaCyc Metabolic Pathway Database - Bioinformatics Research Group at SRI International, CA - USA - - - - - - MetaCyc Reaction - MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. - - urn:miriam:metacyc.reaction - http://identifiers.org/metacyc.reaction/ - - metacyc.reaction - - urn:miriam:doi:10.1093%2Fnar%2Fgkv1164 - - - - https://metacyc.org - RXN-14904 - https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$id - MetaCyc Metabolic Pathway Database - Reaction - Bioinformatics Research Group at SRI International, CA - USA - - - - - - DataONE - DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. - - urn:miriam:d1id - http://identifiers.org/d1id/ - - d1id - - urn:miriam:doi:10.5060%2FD2251G48 - - - - https://www.dataone.org - 00030692-0FE1-4A1B-955E-A2E55D659267 - https://cn.dataone.org/cn/v2/resolve/{$id} - DataONE - DataONE, Albuquerque, NM - USA - - - - - - CATH Protein Structural Domain Superfamily - CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. - - urn:miriam:cath - http://identifiers.org/cath/ - urn:miriam:cath.node - - cath - - urn:miriam:pubmed:27899584 - - - - http://www.cathdb.info - 1.10.8.10 - http://www.cathdb.info/cathnode/$id - CATH Node through UCL - University College London - UK - - - - schema.org - - - - - MarRef - - Marine Metagenomics Portal - - MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. - - urn:miriam:mmp.ref - http://identifiers.org/mmp.ref/ - - mmp.ref - - - https://mmp.sfb.uit.no/databases/marref/ - MMP3312982.2 - https://mmp.sfb.uit.no/databases/marref/#/records/$id - MarRef through SfB - Center for Bioinformatics (SfB), UiT The Arctic university of Norway - Norway - - - - - - MarDB - - Marine Metagenomics Portal - - MarDB includes all sequenced marine microbial genomes regardless of level of completeness. - - urn:miriam:mmp.db - http://identifiers.org/mmp.db/ - - mmp.db - - - https://mmp.sfb.uit.no/databases/mardb/ - MMP02954345.1 - https://mmp.sfb.uit.no/databases/mardb/#/records/$id - MarDB through SfB - Center for Bioinformatics (SfB), UiT The Arctic university of Norway - Norway - - - - - - MarCat - - Marine Metagenomics Portal - - MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. - - urn:miriam:mmp.cat - http://identifiers.org/mmp.cat/ - - mmp.cat - - - https://mmp.sfb.uit.no/databases/marcat/ - MMP743597.11 - https://mmp.sfb.uit.no/databases/marcat/#/records/$id - MarCat through SfB - Center for Bioinformatics (SfB), UiT The Arctic university of Norway - Norway - - - - - - BioTools - Tool and data services registry. - - urn:miriam:biotools - http://identifiers.org/biotools/ - - biotools - - - https://bio.tools/ - uniprotkb - https://bio.tools/$id - BioTools - Elixir-DK - Denmark - - - - - - AOPWiki - International repository of Adverse Outcome Pathways. - - urn:miriam:aop - http://identifiers.org/aop/ - - aop - - - https://aopwiki.org/ - 98 - https://aopwiki.org/aops/$id - AOPWiki - European Commision - DG Joint Research Centre and U.S Environmental Protection Agency - USA - - - - - - NASA GeneLab - NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. - - urn:miriam:ngl - http://identifiers.org/ngl/ - - ngl - - - https://genelab-data.ndc.nasa.gov/genelab/ - GLDS-141 - https://genelab-data.ndc.nasa.gov/genelab/accession/$id - NASA GeneLab - NASA's Ames Research Center - USA - - - - - - Human Endogenous Retrovirus Database - Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. - - urn:miriam:erv - http://identifiers.org/erv/ - - erv - - urn:miriam:pubmed:14681356 - - - - https://herv.img.cas.cz/ - THE1B - https://herv.img.cas.cz/s/$id - Human Endogenous Retrovirus Database - Institute of Molecular Genetics, Academy of Sciences of the Czech Republic - Czech Republic - - - - genome - human - - - - - Natural Product-Drug Interaction Research Data Repository - The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs). - - urn:miriam:napdi - http://identifiers.org/napdi/ - - napdi - - https://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/extending-dideo-ontology-5.pdf - - - - https://repo.napdi.org/ - 28 - https://repo.napdi.org/study/$id - Natural Product-Drug Interaction Research Data Repository - National Center for Complementary and Integrative Health, National Institutes of Health, Washington D.C. - USA - - - - - - ArrayMap - arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. - - urn:miriam:arraymap - http://identifiers.org/arraymap/ - - arraymap - - urn:miriam:pubmed:25428357 - - - - https://www.arraymap.org - icdom:8500_3 - https://www.arraymap.org/pgx:$id - ArrayMap - Institute of Molecular Life Sciences, University of Zurich, Zurich - Switzerland - - - - genome - human - - - - - Benchmark Energy & Geometry Database - - BEGDB - - The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. - - urn:miriam:begdb - http://identifiers.org/begdb/ - - begdb - - urn:miriam:doi:10.1135%2Fcccc20081261 - http://cccc.uochb.cas.cz/73/10/1261/pdf/ - - - - http://www.begdb.com - 4214 - http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$id - Benchmark Energy & Geometry Database - Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague - Czech Republic - - - - structure - - - - - CAMEO - - Continuous Automated Model EvaluatiOn - - The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. - - urn:miriam:cameo - http://identifiers.org/cameo/ - - cameo - - urn:miriam:pubmed:23624946 - - - - https://cameo3d.org - 2018-03-24_00000030_1 - https://www.cameo3d.org/sp/targets/target/$id - CAMEO - Swiss Institute of Bioinformatics, Biozentrum, University of Basel - Switzerland - - - - structure - - - - - SISu - - Sequence Initiative Suomi - - The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies. - - urn:miriam:sisu - http://identifiers.org/sisu/ - - sisu - - http://www.sisuproject.fi/faq - - - - http://www.sisuproject.fi/ - 17:41223048 - http://search.sisuproject.fi/#/variant/$id - SISu - Sequencing Initiative Suomi project (SISu), Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki - Finland - - - - human - sequence - - - - - Universal Spectrum Identifier - The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it. - - urn:miriam:mzspec - http://identifiers.org/mzspec/ - - mzspec - - https://github.com/HUPO-PSI/UniversalSpectrumIdentifier - - - - https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum - mzspec:PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2 - https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=$id - Universal Spectrum Identifier through Peptide Atlas - Institute for Systems Biology - USA - - - - - - CRISPRdb - Repeated CRISPR ("clustered regularly interspaced short palindromic repeats") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data. - - urn:miriam:crisprdb - http://identifiers.org/crisprdb/ - - crisprdb - - urn:miriam:pubmed:17521438 - - - - http://crispr.i2bc.paris-saclay.fr/ - 551115 - http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$id - CRISPRdb - Université Paris-Sud, Institut de Génétique et Microbiologie, Orsay, - France - - - - microbial - sequence - - - - - GnpIS - GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. - - urn:miriam:gnpis - http://identifiers.org/gnpis/ - - gnpis - - urn:miriam:pubmed:23959375 - - - - https://urgi.versailles.inra.fr/gnpis/ - AY109603 - https://urgi.versailles.inra.fr/gnpis/#result/term=$id - GnpIS - URGI (Research Unit in Genomics-Info), INRA de Versailles, Route de Saint-Cyr, Versailles - France - - - - fungal - genome - plant - - - - - LiceBase - Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. - - urn:miriam:licebase - http://identifiers.org/licebase/ - - licebase - - https://licebase.org/?q=node/760957 - - - - https://licebase.org - EMLSAT00000003403 - https://licebase.org/?q=$id - LiceBase - Sea Lice Research Centre (SLRC), University of Bergen - Norway - - - - genome - sequence - - - - - SugarBind - The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands. - - urn:miriam:sugarbind - http://identifiers.org/sugarbind/ - - sugarbind - - urn:miriam:pubmed:26578555 - - - - http://sugarbind.expasy.org/ - lectins/172 - http://sugarbind.expasy.org/$id - SugarBind - Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva - Switzerland - - - - disease - human - interaction - - - - - RNAcentral - RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. - - urn:miriam:rnacentral - http://identifiers.org/rnacentral/ - - rnacentral - - urn:miriam:pubmed:27794554 - - - - http://rnacentral.org/ - URS0000759CF4 - http://rnacentral.org/rna/$id - RNAcentral through EMBL-EBI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - schema.org - - - - - MicroScope - - Microbial Genome Annotation & Analysis Platform - - MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. - - urn:miriam:microscope - http://identifiers.org/microscope/ - - microscope - - - http://www.genoscope.cns.fr/agc/microscope - 5601141 - http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$id - MicroScope - Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Evry - France - - - - genome - microbial - - - - - SwissRegulon - A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. - - urn:miriam:swissregulon - http://identifiers.org/swissregulon/ - - swissregulon - - - http://swissregulon.unibas.ch - AHR - http://swissregulon.unibas.ch/query/$id - SwissRegulon - Swiss Institute of Bioinformatics - Switzerland - - - - - - ValidatorDB - Database of validation results for ligands and non-standard residues in the Protein Data Bank. - - urn:miriam:validatordb - http://identifiers.org/validatordb/ - - validatordb - - urn:miriam:doi:10.1093%2Fnar%2Fgku1118 - - - - https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ - ByStructure/2h6o - https://webchem.ncbr.muni.cz/Platform/ValidatorDb/$id - ValidatorDB - Central European Institute of Technology - Czech Republic - - - - - - Bio-MINDER Tissue Database - Database of the dielectric properties of biological tissues. - - urn:miriam:biominder - http://identifiers.org/biominder/ - - biominder - - - https://datalab.rwth-aachen.de/MINDER - aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 - https://datalab.rwth-aachen.de/MINDER/resource/$id - Bio-MINDER Tissue Database - RWTH Aachen University / NUIG Galway - Ireland - - - - - - NeuroVault Collection - Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images. - - urn:miriam:neurovault.collection - http://identifiers.org/neurovault.collection/ - urn:miriam:neurovault - - neurovault.collection - - urn:miriam:doi:10.3389%2Ffninf.2015.00008 - - - - http://neurovault.org - 3304 - https://neurovault.org/collections/$id - NeuroVault Collection - Stanford University - USA - - - - - - VMH metabolite - The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. - - urn:miriam:vmhmetabolite - http://identifiers.org/vmhmetabolite/ - - vmhmetabolite - - - http://vmh.uni.lu - h2o - http://vmh.uni.lu/#metabolite/$id - VMH metabolite - Luxembourg Centre for Systems Biomedicine, University of Luxembourg - Luxembourg - - - - - - MobiDB - MobiDB is a database of protein disorder and mobility annotations. - - urn:miriam:mobidb - http://identifiers.org/mobidb/ - - mobidb - - urn:miriam:doi:10.1093%2Fnar%2Fgkx1071 - - - - http://mobidb.bio.unipd.it - P10636 - http://mobidb.bio.unipd.it/$id - MobiDB - University of Padua - Italy - - - - schema.org - - - - - NeuroVault Image - Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images. - - urn:miriam:neurovault.image - http://identifiers.org/neurovault.image/ - - neurovault.image - - urn:miriam:doi:10.3389%2Ffninf.2015.00008 - - - - http://neurovault.org - 58788 - https://neurovault.org/images/$id - NeuroVault - Stanford University - USA - - - - - - Nuclear Magnetic Resonance Controlled Vocabulary - - nmrCV - - nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. - - urn:miriam:nmr - http://identifiers.org/nmr/ - - nmr - - urn:miriam:doi:10.1021%2Facs.analchem.7b02795 - - - - https://www.ebi.ac.uk/ols/ontologies/nmrcv - NMR:1000003 - https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=$id - NMR through OLS - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - VMH reaction - The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. - - urn:miriam:vmhreaction - http://identifiers.org/vmhreaction/ - - vmhreaction - - - https://vmh.uni.lu - HEX1 - https://vmh.uni.lu/#reaction/$id - VMH reaction - Luxembourg Centre for Systems Biomedicine, University of Luxembourg - Luxembourg - - - - - - Astrophysics Source Code Library - The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001). - - urn:miriam:ascl - http://identifiers.org/ascl/ - - ascl - - urn:miriam:doi:10.5334%2Fjors.bv - https://arxiv.org/abs/1611.06219 - - - - http://ascl.net/ - 1801.012 - http://ascl.net/$id - Astrophysics Source Code Library - Astrophysics Source Code Library, Houghton, MI - USA - - - - - - FaceBase Data Repository - FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. - - urn:miriam:fb - http://identifiers.org/fb/ - - fb - - urn:miriam:doi:10.1242%2Fdev.135434 - - - - https://www.facebase.org - FB00000917 - https://www.facebase.org/data/record/#1/isa:dataset/accession=$id - FaceBase Data Repository - University of Southern California - USA - - - - - - GUDMAP - The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. - - urn:miriam:gudmap - http://identifiers.org/gudmap/ - - gudmap - - urn:miriam:doi:10.1242%2Fdev.063594 - - - - http://www.gudmap.org/ - Q-2958 - https://gudmap.org/id/$id - GUDMAP - GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium - USA - - - - - - JRC Data Catalogue - The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. - - urn:miriam:eu89h - http://identifiers.org/eu89h/ - - eu89h - - - http://data.jrc.ec.europa.eu/ - jrc-eurl-ecvam-chemagora - http://data.europa.eu/89h/$id - JRC Data Catalogue - European Commission, Joint Research Centre (JRC) - EU - - - - - - Minimal Identifiers for Transient Data - Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. - - urn:miriam:minid - http://identifiers.org/minid/ - - minid - - urn:miriam:doi:10.1109%2FBigData.2016.7840618 - - - - http://minid.bd2k.org - b97957 - http://n2t.net/ark:/57799/$id - Minimal Identifiers for Transient Data - Big Data for Discovery Science Consortium - USA - - - - - - Metabolomics Workbench Study - Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). - - urn:miriam:mw.study - http://identifiers.org/mw.study/ - - mw.study - - - http://www.metabolomicsworkbench.org/ - ST000900 - http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$id - Metabolomics Workbench Study - University of California San Diego - USA - - - https://www.omicsdi.org/ - ST000900 - https://www.omicsdi.org/dataset/metabolomics_workbench/$id - Metabolomics Workbench Study through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - Metabolomics Workbench Project - Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC). - - urn:miriam:mw.project - http://identifiers.org/mw.project/ - - mw.project - - - http://www.metabolomicsworkbench.org/ - PR000001 - http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$id - Metabolomics Workbench Project - University of California San Diego - USA - - - - - - Metabolome Express - A public place to process, interpret and share GC/MS metabolomics datasets. - - urn:miriam:mex - http://identifiers.org/mex/ - - mex - - - https://www.metabolome-express.org/ - 36 - https://www.metabolome-express.org/datasetview.php?datasetid=$id - Metabolome Express - Australian Research Council Centre of Excellence in Plant Energy Biology - Australia - - - https://www.omicsdi.org/ - 36 - https://www.omicsdi.org/dataset/metabolome_express/MEX$id - Metabolome Express through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - GPMDB - The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. - - urn:miriam:gpmdb - http://identifiers.org/gpmdb/ - - gpmdb - - - http://gpmdb.thegpm.org/ - GPM32310002988 - http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$id - GPMDB - The Global Proteome Machine Organization - Canada - - - https://www.omicsdi.org/ - GPM32310002988 - https://www.omicsdi.org/dataset/gpmdb/$id - GPMDB through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - MassIVE - MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. - - urn:miriam:massive - http://identifiers.org/massive/ - - massive - - - https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp - MSV000082131 - https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$id - MassIVE - University of California, San Diego - USA - - - https://www.omicsdi.org/ - MSV000082131 - https://www.omicsdi.org/dataset/massive/$id - MassIVE through OmicsDI - European Bioinformatics Institute, Hinxton, Cambridge - UK - - - - - - FamPlex - FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. - - urn:miriam:fplx - http://identifiers.org/fplx/ - - fplx - - https://www.biorxiv.org/content/early/2018/03/26/225698 - - - - http://bioportal.bioontology.org/ontologies/FPLX/ - RAS - http://bioportal.bioontology.org/ontologies/FPLX/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFPLX%23_$id - FPLX through BioPortal - National Center for Biomedical Ontology, Stanford - USA - - - - - - AOPWiki (Key Event) - International repository of Adverse Outcome Pathways. - - urn:miriam:aop.events - http://identifiers.org/aop.events/ - - aop.events - - - https://aopwiki.org/ - 3 - https://aopwiki.org/events/$id - AOPWiki (Key Event) - European Commision - DG Joint Research Centre and U.S Environmental Protection Agency - USA - - - - - - AOPWiki (Key Event Relationship) - International repository of Adverse Outcome Pathways. - - urn:miriam:aop.relationships - http://identifiers.org/aop.relationships/ - - aop.relationships - - - https://aopwiki.org/ - 5 - https://aopwiki.org/relationships/$id - AOPWiki (Key Event Relationship) - European Commision - DG Joint Research Centre and U.S Environmental Protection Agency - USA - - - - - - AOPWiki (Stressor) - International repository of Adverse Outcome Pathways. - - urn:miriam:aop.stressor - http://identifiers.org/aop.stressor/ - - aop.stressor - - - https://aopwiki.org/ - 9 - https://aopwiki.org/stressors/$id - AOPWiki (Stressor) - European Commision - DG Joint Research Centre and U.S Environmental Protection Agency - USA - - - - - - Software Heritage - Software Heritage is the universal archive of software source code. - - urn:miriam:swh - http://identifiers.org/swh/ - - swh - - https://hal.archives-ouvertes.fr/hal-01590958 - - - - https://archive.softwareheritage.org - swh:1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d - https://archive.softwareheritage.org/browse/$id - Software Heritage - INRIA - France - - - - - - Data Object Service - Assists in resolving data across cloud resources. - - urn:miriam:dev.ga4ghdos - http://identifiers.org/dev.ga4ghdos/ - - dev.ga4ghdos - - - http://github.com/ga4gh/data-object-service-schemas - 23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00 - https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$id - Data Object Service - University of California - USA - - - - - - - annotation - Descriptive text, usually added by an author or curator, that provides extra information that may be missing or not immediately evident. - - - assay - A collection that specifies direct assay conditions and/or provides experimental results. - - - bibliography - A citation list which supports the information provided. This may include books, publications in journal, or URL links. - - - catalogue - A data collection providing information on commercially available products. - - - chemical - Data collections with this tag reference data pertaining to chemical compounds and substances. - - - classification - A classification scheme which does not necessarily depict a relationship between different groups, but only between individuals within a group. - - - clustering - Data collections with this tag contain data which has been processed in such a way as to generate subsets (clusters) within which some trait should be shared. - - - controlled vocabulary - Controlled vocabularies provide predefined and authorised terms for shared use by a community, providing a means to organise knowledge for subsequent processing. - - - disease - A disease is an abnormal condition of an organism that impairs bodily functions and can be deadly. It is also defined as a way of the body harming itself in an abnormal way, associated with specific symptoms and signs. [wikipedia] - - - disorder - The term "disorder" is often considered more value-neutral than the term "disease" [wikipedia]. Hence it may have no attributable signs or symptoms. - - - DNA - Data collections with this tag reference data pertaining to deoxyribonucleic acid. - - - domain - A domain is a protein subsequence that forms a three-dimensional structure, and can provide specific catalytic or binding sites as found in enzymes or regulatory proteins. A specific domain may appear in a variety of evolutionarily related proteins. - - - drug - A drug, broadly speaking, is any chemical substance that, when absorbed into the body of a living organism, alters normal bodily function [wikipedia].Toxins are included in this category. - - - encyclopedia - A generic knowledge repository not restricted to a particular domain, and which is primarily used for reference purposes. - - - enzyme - An enzyme is a biological catalyst of a chemical reaction. Most enzymes are proteins. - - - eukaryotic - Data collection pertaining to eukaryotic cells, which are differentiated from prokaryotic cells by the presence of a nucleus. This group includes human, plant, and fungal cells. - - - expression - Data collections associated with this tag pertain to the measurement of gene expression, often through the use of microarray techniques, and usually in quantitative fashion. - - - fungal - Data collection pertaining to species of fungi. - - - gene - Genes are discrete subsequences of genomic DNA and correspond to a unit of inheritance [based on wikipedia]. A data collection tagged 'gene' should include gene information in addition to purely sequence-oriented data. - - - genome - A genome is the full compliment of hereditary information (usually DNA) for a given organism, and includes coding and non-coding sequences where applicable. 'Genome' tagged data collections are those whose information is derived from genome level sequencing projects. - - - human - Data collections labelled 'human' should contain human centric data. - - - image library - A repository of static images or animations. - - - immunogenetics - A branch of research focused upon the relationship between one's genetics and immune response. - - - interaction - Data collections tagged 'interaction' should contain information relating to molecular interaction data, often protein-protein. - - - kinetics - Kinetics is the study of rates of reactions or chemical processes. Data collections tagged 'kinetics' should provide information such as rate laws and rate constants. - - - lipid - Data collection pertaining to lipids, which are lipophilic, naturally-occurring molecules. - - - mammalian - Data collections labelled 'mammalian' should contain mammal centric data. - - - mass spectrometry - Mass spectrometry is an analytical technique that identifies the chemical composition of a compound or sample on the basis of the mass-to-charge ratio of charged particles. [Wikipedia] - - - metabolite - Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include antibiotics and pigments. - - - microarray - Microarray is a high-throughput technology often used to measure gene expression. - - - microbial - Datatype relating to bacterial species - - - model - Data collection pertaining to mathematical models, encoded in a form that allows their use in simulation software. - - - neuroscience - Scientific study of the nervous system. - - - nucleotide - Data collections tagged with 'nucleotide' refer to DNA and RNA molecules. - - - ontology - Data collections tagged with 'ontology' reference those ontologies that are used in the life sciences. - - - pathway - Series of sequential chemical reactions that are referred to collectively. - - - pharmacogenomics - Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. [wiki] - - - phenotype - A phenotype is any observable characteristic of an organism, such as its morphology, development, biochemical or physiological properties, or behaviour [wikipedia]. - - - plant - Dataype type should be focused on plant species - - - polysaccharide - Polysaccharides are polymeric carbohydrate structures, formed of repeating units (either mono- or di-saccharides) joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. -[http://en.wikipedia.org/wiki/Polysaccharide] - - - protein - Data collections with this tag reference data pertaining to proteins. - - - reaction - A single chemical reaction which yields products which are, generally, different from the reactants. Data collections tagged 'reaction' focus on individual chemical reactions. - - - registry - A data collection within which information is registered or collated, effectively providing a catalogue for (community) reference purposes. - - - schema.org - Data collection containing Schema.org metadata. - - - sequence - Data collections tagged 'sequence' reference sequence data, such as DNA, RNA or protein. - - - strain - A genetic variant of a particular organism. - - - structure - Data collections with the 'structure' tag should reference chemical or 3-dimensional structure. - - - taxonomy - A classification scheme, arranged in a hierarchical structure, that depicts parent-child relationships between its members. - - - viral - Data collection pertaining to virus information. - - - diff --git a/normalizer/src/main/resources/Miriam.xsd b/normalizer/src/main/resources/Miriam.xsd deleted file mode 100644 index fa956c34b..000000000 --- a/normalizer/src/main/resources/Miriam.xsd +++ /dev/null @@ -1,268 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md new file mode 100644 index 000000000..4606ba090 --- /dev/null +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md @@ -0,0 +1,14 @@ +# XRegistry resources + +## registry.json +Extract the prefix, regexp, name, synonyms, etc. +bioregistry.io/chebi:12345 + +## spellmap.json +An additional mapping from identifier db/type name spelling variants +(non-alphanumeric chars are removed) to the corresponding Prefix. +All the keys and values should be upper case. In addition to the predefined map entries, +each registry prefix, name, synonym (removing non-alphanumeric chars) will be also auto-added. + +## synonymap.json +An additional mapping from names/synonyms to Prefixes. diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json new file mode 100644 index 000000000..fa070208b --- /dev/null +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json @@ -0,0 +1,53017 @@ +{ + "3dmet": { + "description": "3DMET is a database collecting three-dimensional structures of natural metabolites.", + "example": "B00162", + "homepage": "http://www.3dmet.dna.affrc.go.jp/", + "keywords": [ + "chemical", + "life science", + "metabolite", + "metabolomics", + "structure" + ], + "mappings": { + "biocontext": "3DMET", + "edam": "2635", + "fairsharing": "FAIRsharing.5ab0n7", + "miriam": "3dmet", + "n2t": "3dmet", + "prefixcommons": "3dmet", + "wikidata": "P2796" + }, + "name": "3D Metabolites", + "pattern": "^B\\d{5}$", + "preferred_prefix": "3dmet", + "publications": [ + { + "doi": "10.2142/biophysico.15.0_87", + "pmc": "PMC5992871", + "pubmed": "29892514", + "title": "Chemical curation to improve data accuracy: recent development of the 3DMET database.", + "year": 2018 + }, + { + "doi": "10.1021/ci300309k", + "pmc": null, + "pubmed": "23293959", + "title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.", + "year": 2013 + } + ], + "uri_format": "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1" + }, + "4dn.biosource": { + "description": "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases.", + "example": "4DNSR73BT2A2", + "homepage": "https://data.4dnucleome.org/biosources", + "keywords": [ + "dna", + "life science", + "protein" + ], + "mappings": { + "cellosaurus": "4DN", + "fairsharing": "FAIRsharing.CugtbQ", + "miriam": "4dn", + "prefixcommons": "4dn" + }, + "name": "4D Nucleome Data Portal Biosource", + "pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$", + "preferred_prefix": "4dn.biosource", + "publications": [ + { + "doi": "10.1038/nature23884", + "pmc": "PMC5617335", + "pubmed": "28905911", + "title": "The 4D nucleome project.", + "year": 2017 + } + ], + "synonyms": [ + "4DN" + ], + "twitter": "4dn_dcic", + "uri_format": "https://data.4dnucleome.org/biosources/$1" + }, + "4dn.replicate": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": "laylamichan@ciencias.unam.mx", + "github": "lmichan", + "name": "Layla Michán Aguirre", + "orcid": "0000-0002-5798-662X" + }, + { + "email": "mineromero2901@ciencias.unam.mx", + "github": "MinRo60", + "name": "Minerva María Romero Pérez", + "orcid": "0000-0002-6240-9325" + }, + { + "email": "victorinolavida@ciencias.unam.mx", + "github": "Victorinolavida", + "name": "José Victorino Ruiz Lavida", + "orcid": "0000-0001-5130-7705" + } + ], + "description": "Database portal containing replicate experiments of different assays and samples", + "example": "4DNESWX1J3QU", + "homepage": "https://data.4dnucleome.org/experiment-set-replicates/", + "name": "4D Nucleome Data Portal Experiment Replicate", + "preferred_prefix": "4dn.replicate", + "uri_format": "https://data.4dnucleome.org/experiment-set-replicates/$1" + }, + "aaindex": { + "description": "Identifier of an entry from the AAindex database.", + "example": "BUNA790102", + "homepage": "http://www.genome.ad.jp/aaindex/", + "keywords": [ + "protein" + ], + "mappings": { + "edam": "1128", + "prefixcommons": "aaindex" + }, + "name": "AAindex", + "preferred_prefix": "aaindex", + "publications": [ + { + "doi": "10.1093/nar/gkm998", + "pmc": "PMC2238890", + "pubmed": "17998252", + "title": "AAindex: amino acid index database, progress report 2008.", + "year": 2007 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1" + }, + "aao": { + "contact": { + "email": "david.c.blackburn@gmail.com", + "github": null, + "name": "David Blackburn", + "orcid": "0000-0002-1810-9886" + }, + "deprecated": true, + "description": "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon.", + "example": "0000138", + "homepage": "http://github.com/seger/aao", + "keywords": [ + "anatomy", + "obo", + "ontology" + ], + "mappings": { + "biocontext": "AAO", + "fairsharing": "FAIRsharing.mxx5rp", + "obofoundry": "aao", + "prefixcommons": "aao" + }, + "name": "Amphibian gross anatomy", + "pattern": "^\\d{7}$", + "preferred_prefix": "AAO", + "publications": [ + { + "doi": "10.1186/2041-1480-5-21", + "pmc": "PMC4089931", + "pubmed": "25009735", + "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.", + "year": 2014 + }, + { + "doi": "10.1142/9789812772435_0035", + "pmc": null, + "pubmed": "17992749", + "title": "An anatomical ontology for amphibians.", + "year": 2007 + } + ], + "uri_format": "http://purl.obolibrary.org/obo/AAO_$1" + }, + "abcd": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies", + "example": "AD834", + "homepage": "https://web.expasy.org/abcd/", + "keywords": [ + "immunology", + "molecular biology" + ], + "mappings": { + "cellosaurus": "ABCD", + "fairsharing": "FAIRsharing.Z8OKi5", + "uniprot": "DB-0236" + }, + "name": "AntiBodies Chemically Defined database", + "preferred_prefix": "abcd", + "publications": [ + { + "doi": "10.1093/nar/gkz714", + "pmc": "PMC6943046", + "pubmed": "31410491", + "title": "The ABCD database: a repository for chemically defined antibodies.", + "year": 2020 + } + ], + "uri_format": "https://web.expasy.org/abcd/ABCD_$1" + }, + "abm": { + "description": "Cell line collections", + "example": "T0599", + "homepage": "https://www.abmgood.com/Cell-Biology.html", + "mappings": { + "cellosaurus": "ABM" + }, + "name": "Applied Biological Materials cell line products", + "preferred_prefix": "abm", + "uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1" + }, + "abs": { + "contact": { + "email": "enrique.blanco@crg.eu", + "github": null, + "name": "Enrique Blanco", + "orcid": "0000-0001-6261-7370" + }, + "description": "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography.", + "example": "A0014", + "homepage": "http://genome.crg.es/datasets/abs2005/", + "keywords": [ + "biology", + "gene", + "interaction", + "regulation" + ], + "mappings": { + "biocontext": "ABS", + "edam": "2741", + "fairsharing": "FAIRsharing.7mnebr", + "miriam": "abs", + "n2t": "abs", + "prefixcommons": "abs" + }, + "name": "Annotated Regulatory Binding Sites", + "pattern": "^A\\d+$", + "preferred_prefix": "abs", + "publications": [ + { + "doi": "10.1093/nar/gkj116", + "pmc": "PMC1347478", + "pubmed": "16381947", + "title": "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.", + "year": 2006 + } + ], + "uri_format": "http://genome.crg.es/datasets/abs2005/entries/$1.html" + }, + "ac": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities.", + "example": "Add", + "homepage": "http://www.w3.org/ns/activitystreams", + "keywords": [ + "semantic web", + "social media" + ], + "name": "Activity Streams", + "preferred_prefix": "ac", + "uri_format": "http://www.w3.org/ns/activitystreams#$1" + }, + "aceview.worm": { + "description": "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression.", + "example": "aap-1", + "homepage": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm", + "keywords": [ + "dna", + "gene", + "rna" + ], + "mappings": { + "biocontext": "ACEVIEW.WORM", + "miriam": "aceview.worm", + "n2t": "aceview.worm", + "prefixcommons": "aceview.worm" + }, + "name": "Aceview Worm", + "pattern": "^[a-z0-9-]+$", + "preferred_prefix": "aceview.worm", + "publications": [ + { + "doi": "10.1186/gb-2006-7-s1-s12", + "pmc": "PMC1810549", + "pubmed": "16925834", + "title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation.", + "year": 2006 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1" + }, + "addexbio": { + "description": "Cell line collections", + "example": "C0020004/4992", + "homepage": "https://www.addexbio.com/productshow?id=4", + "mappings": { + "cellosaurus": "AddexBio" + }, + "name": "AddexBio cell line products", + "preferred_prefix": "addexbio", + "uri_format": "https://www.addexbio.com/productdetail?pid=$1" + }, + "addgene": { + "description": "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world.", + "example": "50943", + "homepage": "http://addgene.org/", + "keywords": [ + "life science", + "plasmid" + ], + "mappings": { + "fairsharing": "FAIRsharing.8hcczk", + "miriam": "addgene", + "n2t": "addgene", + "prefixcommons": "addgene", + "re3data": "r3d100010741" + }, + "name": "Addgene Plasmid Repository", + "pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$", + "preferred_prefix": "addgene", + "publications": [ + { + "doi": "10.1093/nar/gku893", + "pmc": "PMC4384007", + "pubmed": "25392412", + "title": "The Addgene repository: an international nonprofit plasmid and data resource.", + "year": 2014 + }, + { + "doi": "10.1038/505272a", + "pmc": null, + "pubmed": "24429608", + "title": "Repositories share key research tools.", + "year": 2014 + }, + { + "doi": "10.1038/nbt.2177", + "pmc": null, + "pubmed": "22491276", + "title": "Addgene provides an open forum for plasmid sharing.", + "year": 2012 + } + ], + "twitter": "Addgene", + "uri_format": "http://addgene.org/$1" + }, + "ado": { + "contact": { + "email": "alpha.tom.kodamullil@scai.fraunhofer.de", + "github": "akodamullil", + "name": "Alpha Tom Kodamullil", + "orcid": "0000-0001-9896-3531" + }, + "depends_on": [ + "bfo" + ], + "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", + "download_owl": "http://purl.obolibrary.org/obo/ado.owl", + "example": "0000001", + "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", + "keywords": [ + "health science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ADO", + "bioportal": "ADO", + "fairsharing": "FAIRsharing.ckd4rf", + "obofoundry": "ado", + "ols": "ado", + "ontobee": "ADO" + }, + "name": "Alzheimer's Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ADO", + "publications": [ + { + "doi": "10.1016/j.jalz.2013.02.009", + "pmc": null, + "pubmed": "23830913", + "title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.", + "year": 2013 + } + ], + "repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", + "uri_format": "http://purl.obolibrary.org/obo/ADO_$1", + "version": "2.0.0" + }, + "adw": { + "contact": { + "email": "adw_geeks@umich.edu", + "github": null, + "name": "Animal Diversity Web technical staff", + "orcid": null + }, + "deprecated": true, + "description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.", + "download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl", + "example": "Lycalopex_vetulus", + "homepage": "http://www.animaldiversity.org", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "ADW", + "biocontext": "ADW", + "bioportal": "ADW", + "fairsharing": "FAIRsharing.t9fvdn", + "miriam": "adw", + "n2t": "adw", + "obofoundry": "adw" + }, + "name": "Animal natural history and life history", + "pattern": "^[A-Z_a-z]+$", + "preferred_prefix": "ADW", + "uri_format": "https://animaldiversity.org/accounts/$1" + }, + "aeo": { + "appears_in": [ + "ehdaa2" + ], + "contact": { + "email": "J.Bard@ed.ac.uk", + "github": null, + "name": "Jonathan Bard", + "orcid": null + }, + "deprecated": true, + "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", + "download_obo": "https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo", + "download_owl": "http://purl.obolibrary.org/obo/aeo.owl", + "example": "0001017", + "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "AEO", + "bartoc": "181", + "biocontext": "AEO", + "bioportal": "AEO", + "fairsharing": "FAIRsharing.93ee19", + "obofoundry": "aeo", + "ols": "aeo", + "ontobee": "AEO" + }, + "name": "Anatomical Entity Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "AEO", + "publications": [ + { + "doi": "10.3389/fgene.2012.00018", + "pmc": "PMC3278863", + "pubmed": "22347883", + "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs.", + "year": 2012 + } + ], + "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", + "synonyms": [ + "AEO_RETIRED" + ], + "uri_format": "http://purl.obolibrary.org/obo/AEO_$1", + "version": "2014-12-05" + }, + "aeon": { + "contact": { + "email": "Philip.Stroemert@tib.eu", + "github": "StroemPhi", + "name": "Philip Strömert", + "orcid": "0000-0002-1595-3213" + }, + "contributor": { + "email": "Philip.Stroemert@tib.eu", + "github": "StroemPhi", + "name": "Philip Strömert", + "orcid": "0000-0002-1595-3213" + }, + "description": "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page).", + "download_owl": "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl", + "example": "0000001", + "github_request_issue": 617, + "homepage": "https://tibonto.github.io/aeon/", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "name": "Academic Event Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "aeon", + "repository": "https://github.com/tibonto/aeon", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://purl.obolibrary.org/obo/AEON_$1" + }, + "aero": { + "contact": { + "email": "mcourtot@gmail.com", + "github": null, + "name": "Melanie Courtot", + "orcid": "0000-0002-9551-6370" + }, + "deprecated": true, + "description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events", + "download_owl": "http://purl.obolibrary.org/obo/aero.owl", + "example": "0000125", + "homepage": "http://purl.obolibrary.org/obo/aero", + "keywords": [ + "biomedical science", + "health science", + "medicine", + "obo", + "ontology", + "preclinical studies" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "AERO", + "biocontext": "AERO", + "bioportal": "AERO", + "fairsharing": "FAIRsharing.rycy2x", + "obofoundry": "aero" + }, + "name": "Adverse Event Reporting Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "AERO", + "uri_format": "http://purl.obolibrary.org/obo/AERO_$1" + }, + "affy.probeset": { + "description": "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration.", + "example": "243002_at", + "homepage": "http://www.affymetrix.com/", + "mappings": { + "biocontext": "AFFY.PROBESET", + "miriam": "affy.probeset", + "n2t": "affy.probeset" + }, + "name": "Affymetrix Probeset", + "pattern": "^\\d{4,}((_[asx])?_at)$", + "preferred_prefix": "affy.probeset", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Bio2RDF", + "homepage": "http://cu.affymetrix.bio2rdf.org/fct/", + "name": "Bio2RDF", + "uri_format": "http://cu.affymetrix.bio2rdf.org/describe/?url=http://bio2rdf.org/affymetrix:$1" + } + ], + "uri_format": "https://www.affymetrix.com/LinkServlet?probeset=$1" + }, + "afo": { + "contact": { + "email": "more.info@allotrope.org", + "github": null, + "name": "Allotrope Foundation", + "orcid": null + }, + "description": "Allotrope Merged Ontology Suite", + "download_owl": "http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10", + "homepage": "https://www.allotrope.org/", + "keywords": [ + "agricultural engineering", + "agriculture", + "biology", + "environmental science", + "food chemistry", + "forest management", + "ontology", + "veterinary medicine" + ], + "mappings": { + "aberowl": "AFO", + "bioportal": "AFO", + "fairsharing": "FAIRsharing.595710", + "ols": "afo" + }, + "name": "Allotrope Merged Ontology Suite", + "no_own_terms": true, + "preferred_prefix": "afo", + "version": "2019-05-10" + }, + "aftol.taxonomy": { + "contributor_extras": [ + { + "email": "laylamichan@ciencias.unam.mx", + "github": "lmichan", + "name": "Layla Michán Aguirre", + "orcid": "0000-0002-5798-662X" + } + ], + "description": "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species.", + "example": "959", + "homepage": "https://aftol.umn.edu", + "mappings": { + "biocontext": "AFTOL.TAXONOMY", + "miriam": "aftol.taxonomy", + "n2t": "aftol.taxonomy" + }, + "name": "Assembling the Fungal Tree of Life - Taxonomy", + "pattern": "^\\d+$", + "preferred_prefix": "aftol.taxonomy", + "uri_format": "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1" + }, + "agilent.probe": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699.", + "example": "A_24_P98555", + "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt", + "keywords": [ + "transcriptomics" + ], + "name": "Agilent Probe", + "pattern": "^A_\\d+_.+$", + "preferred_prefix": "agilent.probe", + "references": [ + "http://www.cs.tau.ac.il/cgi-bin/cgiwrap/click/get.cgi/conversionFiles/conversion_human_14850_agilent2entrez.txt" + ] + }, + "agricola": { + "contributor_extras": [ + { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + } + ], + "description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.", + "example": "50018", + "homepage": "http://agricola.nal.usda.gov/", + "mappings": { + "biocontext": "AGRICOLA", + "go": "AGRICOLA_ID", + "miriam": "agricola", + "n2t": "agricola", + "uniprot": "DB-0266" + }, + "name": "Agricultural Online Access", + "pattern": "^\\d+$", + "preferred_prefix": "agricola", + "publications": [ + { + "doi": "10.1093/nar/gkz813", + "pmc": "PMC6943066", + "pubmed": "31552413", + "title": "Alliance of Genome Resources Portal: unified model organism research platform.", + "year": 2020 + } + ], + "synonyms": [ + "AGR", + "AGRICOLA_ID" + ], + "uri_format": "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1" + }, + "agrkb": { + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor": { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + }, + "description": "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)", + "example": "100000000000001", + "github_request_issue": 359, + "homepage": "https://www.alliancegenome.org", + "keywords": [ + "model organism database" + ], + "mappings": { + "biolink": "AGRKB" + }, + "name": "Alliance of Genome Resources Knowledge Base", + "pattern": "^[1-9][0-9]{14}$", + "preferred_prefix": "agrkb", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.alliancegenome.org/accession/$1" + }, + "agro": { + "contact": { + "email": "m.a.laporte@cgiar.org", + "github": "marieALaporte", + "name": "Marie-Angélique Laporte", + "orcid": "0000-0002-8461-9745" + }, + "depends_on": [ + "bfo", + "envo", + "foodon", + "go", + "iao", + "ncbitaxon", + "obi", + "pato", + "peco", + "po", + "ro", + "to", + "uo", + "xco" + ], + "description": "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities", + "download_obo": "https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo", + "download_owl": "http://purl.obolibrary.org/obo/agro.owl", + "example": "00020007", + "homepage": "https://github.com/AgriculturalSemantics/agro", + "keywords": [ + "agriculture", + "agronomy", + "farming systems research", + "obo", + "ontology", + "plant breeding" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "AGRO", + "agroportal": "AGRO", + "biocontext": "AGRO", + "bioportal": "AGRO", + "fairsharing": "FAIRsharing.m40bhw", + "obofoundry": "agro", + "ols": "agro", + "ontobee": "AGRO" + }, + "name": "Agronomy Ontology", + "pattern": "^\\d{8}$", + "preferred_prefix": "AGRO", + "repository": "https://github.com/AgriculturalSemantics/agro", + "uri_format": "http://purl.obolibrary.org/obo/AGRO_$1", + "version": "2021-11-05" + }, + "agrovoc": { + "banana": "c_", + "contact": { + "email": "agrovoc@fao.org", + "github": null, + "name": "AGROVOC Team", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages.", + "example": "2842", + "homepage": "https://data.apps.fao.org/catalog/organization/agrovoc", + "keywords": [ + "agriculture", + "botany", + "data management", + "environmental science", + "fisheries science", + "forest management", + "nutritional science" + ], + "mappings": { + "agroportal": "AGROVOC", + "bartoc": "305", + "ecoportal": "AGROVOC", + "fairsharing": "FAIRsharing.anpj91", + "wikidata": "P8061" + }, + "name": "Agronomy Vocabulary", + "pattern": "^[a-z0-9]+$", + "preferred_prefix": "agrovoc", + "publications": [ + { + "doi": "10.4060/cb2838en", + "pmc": null, + "pubmed": null, + "title": "AGROVOC", + "year": 2021 + }, + { + "doi": "10.3390/engproc2021009017", + "pmc": null, + "pubmed": null, + "title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus", + "year": 2021 + }, + { + "doi": "10.1016/j.compag.2020.105965", + "pmc": null, + "pubmed": null, + "title": "AGROVOC: The linked data concept hub for food and agriculture", + "year": 2022 + } + ], + "references": [ + "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip", + "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip", + "https://en.wikipedia.org/wiki/AGROVOC" + ], + "twitter": "FAOAIMS", + "uri_format": "http://aims.fao.org/aos/agrovoc/c_$1" + }, + "agsd": { + "description": "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.", + "example": "4779", + "homepage": "http://www.genomesize.com", + "keywords": [ + "dna", + "genome", + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.efp5v2", + "prefixcommons": "agsd", + "re3data": "r3d100012517" + }, + "name": "Animal Genome Size Database", + "preferred_prefix": "agsd", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.genomesize.com/result_species.php?id=$1" + }, + "aism": { + "appears_in": [ + "colao", + "lepao" + ], + "contact": { + "email": "entiminae@gmail.com", + "github": "JCGiron", + "name": "Jennifer C. Girón", + "orcid": "0000-0002-0851-6883" + }, + "depends_on": [ + "bfo", + "bspo", + "caro", + "pato", + "ro", + "uberon" + ], + "description": "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.", + "download_json": "http://purl.obolibrary.org/obo/aism.json", + "download_obo": "http://purl.obolibrary.org/obo/aism.obo", + "download_owl": "http://purl.obolibrary.org/obo/aism.owl", + "example": "0000027", + "homepage": "https://github.com/insect-morphology/aism", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "AISM", + "bioportal": "AISM", + "obofoundry": "aism", + "ols": "aism", + "ontobee": "AISM" + }, + "name": "Ontology for the Anatomy of the Insect SkeletoMuscular system", + "pattern": "^\\d{7}$", + "preferred_prefix": "AISM", + "repository": "https://github.com/insect-morphology/aism", + "uri_format": "http://purl.obolibrary.org/obo/AISM_$1", + "version": "2022-06-27" + }, + "alfred": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.", + "example": "LO362836C", + "homepage": "http://alfred.med.yale.edu", + "keywords": [ + "classification", + "genome" + ], + "mappings": { + "prefixcommons": "alfred" + }, + "name": "The ALlele FREquency Database", + "preferred_prefix": "alfred", + "publications": [ + { + "doi": "10.1093/nar/gkg043", + "pmc": "PMC165490", + "pubmed": "12519999", + "title": "ALFRED: the ALelle FREquency Database. Update.", + "year": 2003 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1" + }, + "allergome": { + "description": "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources.", + "example": "1948", + "homepage": "http://www.allergome.org/", + "keywords": [ + "allergen", + "biomedical science", + "health science", + "life science", + "medicine" + ], + "mappings": { + "biocontext": "ALLERGOME", + "fairsharing": "FAIRsharing.w6cxgb", + "miriam": "allergome", + "n2t": "allergome", + "prefixcommons": "allergome", + "uniprot": "DB-0160" + }, + "name": "Allergome", + "pattern": "^\\d+$", + "preferred_prefix": "allergome", + "publications": [ + { + "doi": "10.1007/s11882-009-0055-9", + "pmc": null, + "pubmed": "19671381", + "title": "Allergen databases: current status and perspectives.", + "year": 2009 + }, + { + "doi": "10.1016/j.cellimm.2007.02.012", + "pmc": null, + "pubmed": "17434469", + "title": "Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.", + "year": 2007 + }, + { + "doi": null, + "pmc": null, + "pubmed": "17393720", + "title": "Allergome: a unifying platform.", + "year": 2006 + } + ], + "uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1" + }, + "alzforum.mutation": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease.", + "example": "app-d678n-tottori", + "homepage": "https://www.alzforum.org/mutations", + "keywords": [ + "alzheimer's disease", + "genes", + "variants" + ], + "name": "Alzforum Mutations", + "preferred_prefix": "alzforum.mutation", + "synonyms": [ + "Alzforum_mut" + ], + "uri_format": "https://www.alzforum.org/mutations/$1" + }, + "alzgene": { + "description": "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data.", + "example": "88", + "homepage": "http://www.alzgene.org", + "keywords": [ + "gene" + ], + "mappings": { + "prefixcommons": "alzgene" + }, + "name": "Alzheimer Gene Database", + "preferred_prefix": "alzgene", + "publications": [ + { + "doi": "10.1038/ng1934", + "pmc": null, + "pubmed": "17192785", + "title": "Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database.", + "year": 2007 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.alzgene.org/geneoverview.asp?geneid=$1" + }, + "amoebadb": { + "description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "EDI_244000", + "homepage": "http://amoebadb.org/amoeba/", + "keywords": [ + "functional genomics", + "genomics", + "model organism" + ], + "mappings": { + "biocontext": "AMOEBADB", + "fairsharing": "FAIRsharing.swbypy", + "miriam": "amoebadb", + "n2t": "amoebadb", + "prefixcommons": "amoebadb", + "re3data": "r3d100012457" + }, + "name": "AmoebaDB", + "pattern": "^EDI_\\d+$", + "preferred_prefix": "amoebadb", + "publications": [ + { + "doi": "10.1093/nar/gkp941", + "pmc": "PMC2808945", + "pubmed": "19914931", + "title": "EuPathDB: a portal to eukaryotic pathogen databases.", + "year": 2009 + } + ], + "twitter": "eupathdb", + "uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1" + }, + "amphx": { + "contact": { + "email": "hescriva@obs-banyuls.fr", + "github": "hescriva", + "name": "Hector Escriva", + "orcid": "0000-0001-7577-5028" + }, + "depends_on": [ + "uberon" + ], + "description": "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).", + "download_obo": "http://purl.obolibrary.org/obo/amphx.obo", + "download_owl": "http://purl.obolibrary.org/obo/amphx.owl", + "example": "1000160", + "homepage": "https://github.com/EBISPOT/amphx_ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "AMPHX", + "bioportal": "AMPHX", + "obofoundry": "amphx", + "ols": "amphx", + "ontobee": "AMPHX" + }, + "name": "The Amphioxus Development and Anatomy Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "AMPHX", + "repository": "https://github.com/EBISPOT/amphx_ontology", + "uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1", + "version": "2020-12-18" + }, + "antibodyregistry": { + "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", + "example": "493771", + "homepage": "http://antibodyregistry.org/", + "mappings": { + "biocontext": "ANTIBODYREGISTRY", + "miriam": "antibodyregistry", + "n2t": "antibodyregistry" + }, + "name": "Antibody Registry", + "pattern": "^\\d{6}$", + "preferred_prefix": "antibodyregistry", + "uri_format": "http://antibodyregistry.org/AB_$1" + }, + "antweb": { + "description": "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures.", + "example": "casent0106247", + "homepage": "http://www.antweb.org/", + "keywords": [ + "anatomy", + "classification", + "life science" + ], + "mappings": { + "biocontext": "ANTWEB", + "fairsharing": "FAIRsharing.yk38tw", + "miriam": "antweb", + "n2t": "antweb", + "ncbi": "AntWeb", + "prefixcommons": "antweb", + "wikidata": "P5299" + }, + "name": "AntWeb", + "pattern": "^casent\\d+(\\-D\\d+)?$", + "preferred_prefix": "antweb", + "publications": [ + { + "doi": "10.1038/424242b", + "pmc": null, + "pubmed": "12867945", + "title": "Ants join online colony to boost conservation efforts.", + "year": 2003 + } + ], + "uri_format": "http://www.antweb.org/specimen.do?name=$1" + }, + "aop": { + "description": "International repository of Adverse Outcome Pathways.", + "example": "98", + "homepage": "https://aopwiki.org/", + "mappings": { + "biocontext": "AOP", + "miriam": "aop", + "n2t": "aop" + }, + "name": "AOPWiki", + "pattern": "^\\d+$", + "preferred_prefix": "aop", + "uri_format": "https://aopwiki.org/aops/$1" + }, + "aop.events": { + "description": "International repository of Adverse Outcome Pathways.", + "example": "3", + "homepage": "https://aopwiki.org/", + "mappings": { + "biocontext": "AOP.EVENTS", + "miriam": "aop.events", + "n2t": "aop.events" + }, + "name": "AOPWiki (Key Event)", + "pattern": "^\\d+$", + "preferred_prefix": "aop.events", + "uri_format": "https://aopwiki.org/events/$1" + }, + "aop.relationships": { + "description": "International repository of Adverse Outcome Pathways.", + "example": "5", + "homepage": "https://aopwiki.org/", + "mappings": { + "biocontext": "AOP.RELATIONSHIPS", + "miriam": "aop.relationships", + "n2t": "aop.relationships" + }, + "name": "AOPWiki (Key Event Relationship)", + "pattern": "^\\d+$", + "preferred_prefix": "aop.relationships", + "uri_format": "https://aopwiki.org/relationships/$1" + }, + "aop.stressor": { + "description": "International repository of Adverse Outcome Pathways.", + "example": "9", + "homepage": "https://aopwiki.org/", + "mappings": { + "biocontext": "AOP.STRESSOR", + "miriam": "aop.stressor", + "n2t": "aop.stressor" + }, + "name": "AOPWiki (Stressor)", + "pattern": "^\\d+$", + "preferred_prefix": "aop.stressor", + "uri_format": "https://aopwiki.org/stressors/$1" + }, + "apaonto": { + "contact": { + "email": "awalker@apa.org", + "github": null, + "name": "Alvin Walker", + "orcid": "0000-0003-1082-8760" + }, + "description": "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege.", + "download_owl": "http://aber-owl.net/media/ontologies/APAONTO/4/apaonto.owl", + "example": "Abdomen", + "homepage": "https://bioportal.bioontology.org/ontologies/APAONTO", + "keywords": [ + "ontology", + "ontology and terminology", + "psychology" + ], + "mappings": { + "aberowl": "APAONTO", + "bioportal": "APAONTO", + "fairsharing": "FAIRsharing.gkw1w8" + }, + "name": "Psychology Ontology", + "preferred_prefix": "apaonto", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/528" + ], + "uri_format": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1" + }, + "apd": { + "description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.", + "example": "01001", + "homepage": "http://aps.unmc.edu/AP/", + "keywords": [ + "biology", + "protein" + ], + "mappings": { + "biocontext": "APD", + "fairsharing": "FAIRsharing.ctwd7b", + "miriam": "apd", + "n2t": "apd", + "prefixcommons": "apd", + "re3data": "r3d100012901" + }, + "name": "Antimicrobial Peptide Database", + "pattern": "^\\d{5}$", + "preferred_prefix": "apd", + "publications": [ + { + "doi": "10.1093/nar/gkv1278", + "pmc": "PMC4702905", + "pubmed": "26602694", + "title": "APD3: the antimicrobial peptide database as a tool for research and education.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkn823", + "pmc": "PMC2686604", + "pubmed": "18957441", + "title": "APD2: the updated antimicrobial peptide database and its application in peptide design.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkh025", + "pmc": "PMC308759", + "pubmed": "14681488", + "title": "APD: the Antimicrobial Peptide Database.", + "year": 2004 + } + ], + "uri_format": "http://aps.unmc.edu/AP/database/query_output.php?ID=$1" + }, + "aphidbase.transcript": { + "description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.", + "example": "ACYPI000159", + "homepage": "http://www.aphidbase.com/aphidbase", + "keywords": [ + "genome" + ], + "mappings": { + "biocontext": "APHIDBASE.TRANSCRIPT", + "miriam": "aphidbase.transcript", + "n2t": "aphidbase.transcript", + "prefixcommons": "aphidbase" + }, + "name": "AphidBase Transcript", + "pattern": "^ACYPI\\d{6}(-RA)?$", + "preferred_prefix": "aphidbase.transcript", + "publications": [ + { + "doi": "10.1111/j.1365-2583.2009.00930.x", + "pmc": "PMC4372297", + "pubmed": "20482635", + "title": "AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.", + "year": 2010 + } + ], + "uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1" + }, + "apid.interactions": { + "description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.", + "example": "P01116", + "homepage": "http://cicblade.dep.usal.es:8080/APID/", + "mappings": { + "biocontext": "APID.INTERACTIONS", + "miriam": "apid.interactions", + "n2t": "apid.interactions" + }, + "name": "APID Interactomes", + "pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$", + "preferred_prefix": "apid.interactions", + "provides": "uniprot", + "uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1" + }, + "apo": { + "contact": { + "email": "stacia@stanford.edu", + "github": "srengel", + "name": "Stacia R Engel", + "orcid": "0000-0001-5472-917X" + }, + "description": "A structured controlled vocabulary for the phenotypes of Ascomycete fungi.", + "download_obo": "http://purl.obolibrary.org/obo/apo.obo", + "download_owl": "http://purl.obolibrary.org/obo/apo.owl", + "example": "0000184", + "homepage": "http://www.yeastgenome.org/", + "keywords": [ + "cell biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "APO", + "biocontext": "APO", + "bioportal": "APO", + "fairsharing": "FAIRsharing.dyqz3y", + "obofoundry": "apo", + "ols": "apo", + "ontobee": "APO" + }, + "name": "Ascomycete phenotype ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "APO", + "publications": [ + { + "doi": "10.1093/database/bap001", + "pmc": "PMC2790299", + "pubmed": "20157474", + "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database.", + "year": 2009 + } + ], + "repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology", + "twitter": "yeastgenome", + "uri_format": "https://www.yeastgenome.org/observable/APO:$1", + "version": "2022-07-06" + }, + "apollosv": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "hoganwr@ufl.edu", + "github": "hoganwr", + "name": "William Hogan", + "orcid": "0000-0002-9881-1017" + }, + "description": "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models", + "download_owl": "http://purl.obolibrary.org/obo/apollo_sv.owl", + "example": "00000443", + "homepage": "https://github.com/ApolloDev/apollo-sv", + "keywords": [ + "biomedical science", + "ecology", + "epidemiology", + "obo", + "ontology", + "population genetics" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "APOLLO_SV", + "bioportal": "APOLLO-SV", + "fairsharing": "FAIRsharing.ngv2xx", + "obofoundry": "apollo_sv", + "ols": "apollo_sv", + "ontobee": "APOLLO_SV" + }, + "name": "Apollo Structured Vocabulary", + "pattern": "^\\d{8}$", + "preferred_prefix": "APOLLO_SV", + "providers": [ + { + "code": "conflated", + "description": "This might be resulting from properties in Apollo SV actually trying to use appropriate identifiers", + "homepage": "http://purl.obolibrary.org", + "name": "OBO PURL in Parts", + "uri_format": "http://purl.obolibrary.org/obo/apollo_sv/dev/apollo_sv.owl#APOLLO_SV_$1" + } + ], + "publications": [ + { + "doi": "10.1186/s13326-016-0092-y", + "pmc": "PMC4989460", + "pubmed": "27538448", + "title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.", + "year": 2016 + }, + { + "doi": null, + "pmc": "PMC3900155", + "pubmed": "24551417", + "title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.", + "year": 2013 + } + ], + "repository": "https://github.com/ApolloDev/apollo-sv", + "uri_format": "http://purl.obolibrary.org/obo/APOLLO_SV_$1", + "version": "4.1.1" + }, + "arachnoserver": { + "description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.", + "example": "AS000060", + "homepage": "http://www.arachnoserver.org/", + "keywords": [ + "drug", + "life science", + "protein" + ], + "mappings": { + "biocontext": "ARACHNOSERVER", + "edam": "2578", + "fairsharing": "FAIRsharing.c54ywe", + "miriam": "arachnoserver", + "n2t": "arachnoserver", + "prefixcommons": "arachnoserver", + "re3data": "r3d100012902", + "uniprot": "DB-0145" + }, + "name": "ArachnoServer", + "pattern": "^AS\\d{6}$", + "preferred_prefix": "arachnoserver", + "publications": [ + { + "doi": "10.1093/bioinformatics/btx661", + "pmc": null, + "pubmed": "29069336", + "title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gkq1058", + "pmc": "PMC3013666", + "pubmed": "21036864", + "title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures.", + "year": 2010 + } + ], + "uri_format": "http://www.arachnoserver.org/toxincard.html?id=$1" + }, + "araport": { + "description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer", + "example": "AT5G05330", + "homepage": "https://www.araport.org/", + "mappings": { + "miriam": "tair.name", + "ncbi": "Araport", + "uniprot": "DB-0221" + }, + "name": "Arabidopsis Information Portal", + "pattern": "^AT.G[0-9]{5}$", + "preferred_prefix": "araport", + "publications": [ + { + "doi": "10.1093/nar/gku1200", + "pmc": "PMC4383980", + "pubmed": "25414324", + "title": "Araport: the Arabidopsis information portal.", + "year": 2014 + } + ], + "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" + }, + "archdb": { + "contact": { + "email": "narcis.fernandez@gmail.com", + "github": null, + "name": "Narcis Fernandez-Fuentes", + "orcid": "0000-0002-6421-1080" + }, + "description": "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.", + "example": "39421", + "homepage": "http://sbi.imim.es/archdb", + "keywords": [ + "classification", + "life science", + "protein" + ], + "mappings": { + "fairsharing": "FAIRsharing.tp9z4q", + "prefixcommons": "archdb" + }, + "name": "ArchDB", + "preferred_prefix": "archdb", + "publications": [ + { + "doi": "10.1093/nar/gkt1189", + "pmc": "PMC3964960", + "pubmed": "24265221", + "title": "ArchDB 2014: structural classification of loops in proteins.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkh002", + "pmc": "PMC308737", + "pubmed": "14681390", + "title": "ArchDB: automated protein loop classification as a tool for structural genomics.", + "year": 2004 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1" + }, + "ardb": { + "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", + "example": "CAE46076", + "homepage": "http://ardb.cbcb.umd.edu/", + "mappings": { + "biocontext": "ARDB", + "miriam": "ardb", + "n2t": "ardb" + }, + "name": "Antibiotic Resistance Genes Database", + "pattern": "^[A-Z_]{3}[0-9]{4,}$", + "preferred_prefix": "ardb", + "uri_format": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1" + }, + "ark": { + "banana": "ark", + "contact": { + "email": "jakkbl@gmail.com", + "github": "jkunze", + "name": "John Kunze", + "orcid": "0000-0001-7604-8041" + }, + "contributor_extras": [ + { + "email": "jakkbl@gmail.com", + "github": "jkunze", + "name": "John Kunze", + "orcid": "0000-0001-7604-8041" + }, + { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + ], + "description": "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver.", + "example": "/53355/cl010066723", + "homepage": "https://arks.org", + "keywords": [ + "data management", + "subject agnostic" + ], + "mappings": { + "biocontext": "ARK", + "fairsharing": "FAIRsharing.f928f1", + "miriam": "ark", + "n2t": "ark" + }, + "name": "Archival Resource Key", + "namespace_in_lui": true, + "pattern": "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", + "preferred_prefix": "ark", + "references": [ + "https://n2t.net/e/about.html" + ], + "twitter": "ARKsInTheOpen", + "uri_format": "http://n2t.net/ark:$1" + }, + "aro": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "mcarthua@mcmaster.ca", + "github": "agmcarthur", + "name": "Andrew G. McArthur", + "orcid": "0000-0002-1142-3063" + }, + "description": "Antibiotic resistance genes and mutations", + "download_obo": "http://purl.obolibrary.org/obo/aro.obo", + "download_owl": "http://purl.obolibrary.org/obo/aro.owl", + "example": "1000001", + "homepage": "https://github.com/arpcard/aro", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ARO", + "biocontext": "ARO", + "bioportal": "ARO", + "obofoundry": "aro", + "ols": "aro", + "ontobee": "ARO" + }, + "name": "Antibiotic Resistance Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ARO", + "publications": [ + { + "doi": "10.1093/nar/gkz935", + "pmc": "PMC7145624", + "pubmed": "31665441", + "title": "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.", + "year": 2020 + } + ], + "repository": "https://github.com/arpcard/aro", + "uri_format": "http://purl.obolibrary.org/obo/ARO_$1" + }, + "arrayexpress": { + "description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.", + "example": "E-MEXP-1712", + "homepage": "https://www.ebi.ac.uk/arrayexpress/", + "keywords": [ + "expression", + "functional genomics", + "microarray", + "nucleotide" + ], + "mappings": { + "biocontext": "ARRAYEXPRESS", + "cellosaurus": "ArrayExpress", + "fairsharing": "FAIRsharing.6k0kwd", + "miriam": "arrayexpress", + "n2t": "arrayexpress", + "prefixcommons": "arrayexpress", + "re3data": "r3d100010222" + }, + "name": "ArrayExpress", + "pattern": "^[AEP]-\\w{4}-\\d+$", + "preferred_prefix": "arrayexpress", + "providers": [ + { + "code": "omicsdi", + "description": "ArrayExpress through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "ArrayExpress through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/arrayexpress-repository/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gky964", + "pmc": "PMC6323929", + "pubmed": "30357387", + "title": "ArrayExpress update - from bulk to single-cell expression data.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gku1057", + "pmc": "PMC4383899", + "pubmed": "25361974", + "title": "ArrayExpress update--simplifying data submissions.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkg091", + "pmc": "PMC165538", + "pubmed": "12519949", + "title": "ArrayExpress--a public repository for microarray gene expression data at the EBI.", + "year": 2003 + } + ], + "twitter": "ArrayExpressEBI", + "uri_format": "https://www.ebi.ac.uk/arrayexpress/experiments/$1" + }, + "arrayexpress.platform": { + "description": "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results.", + "example": "A-GEOD-50", + "homepage": "https://www.ebi.ac.uk/arrayexpress/", + "mappings": { + "biocontext": "ARRAYEXPRESS.PLATFORM", + "miriam": "arrayexpress.platform", + "n2t": "arrayexpress.platform" + }, + "name": "ArrayExpress Platform", + "pattern": "^[AEP]-\\w{4}-\\d+$", + "preferred_prefix": "arrayexpress.platform", + "uri_format": "https://www.ebi.ac.uk/arrayexpress/arrays/$1" + }, + "arraymap": { + "contact": { + "email": "mbaudis@me.com", + "github": "mbaudis", + "name": "Michael Baudis", + "orcid": "0000-0002-9903-4248" + }, + "description": "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome.", + "example": "icdom:8500_3", + "homepage": "https://www.arraymap.org", + "keywords": [ + "bioinformatics", + "biomedical science", + "genomics", + "life science" + ], + "mappings": { + "biocontext": "ARRAYMAP", + "fairsharing": "FAIRsharing.1fbc5y", + "miriam": "arraymap", + "n2t": "arraymap", + "re3data": "r3d100012630" + }, + "name": "ArrayMap", + "pattern": "^[\\w\\-:,]{3,64}$", + "preferred_prefix": "arraymap", + "publications": [ + { + "doi": "10.1093/nar/gkv1310", + "pmc": "PMC4702916", + "pubmed": "26615188", + "title": "The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gku1123", + "pmc": "PMC4383937", + "pubmed": "25428357", + "title": "arrayMap 2014: an updated cancer genome resource.", + "year": 2014 + }, + { + "doi": "10.1186/1471-2164-15-82", + "pmc": "PMC3909908", + "pubmed": "24476156", + "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.", + "year": 2014 + }, + { + "doi": "10.1371/journal.pone.0036944", + "pmc": "PMC3356349", + "pubmed": "22629346", + "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies.", + "year": 2012 + } + ], + "twitter": "progenetix", + "uri_format": "https://www.arraymap.org/pgx:$1" + }, + "arxiv": { + "description": "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology.", + "example": "0807.4956v1", + "homepage": "https://arxiv.org/", + "keywords": [ + "bibliography" + ], + "mappings": { + "biocontext": "ARXIV", + "miriam": "arxiv", + "n2t": "arxiv", + "prefixcommons": "arxiv", + "wikidata": "P818" + }, + "name": "arXiv", + "pattern": "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$", + "preferred_prefix": "arxiv", + "providers": [ + { + "code": "ar5iv", + "description": "Articles from arXiv.org as responsive HTML5 web pages.", + "homepage": "https://ar5iv.labs.arxiv.org/", + "name": "ar5iv", + "uri_format": "https://ar5iv.org/abs/$1" + }, + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/arxiv/$1" + } + ], + "uri_format": "https://arxiv.org/abs/$1" + }, + "asap": { + "description": "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources.", + "example": "ABE-0009634", + "homepage": "http://asap.ahabs.wisc.edu/asap/home.php", + "keywords": [ + "comparative genomics", + "developmental biology", + "gene expression", + "genome", + "life science" + ], + "mappings": { + "biocontext": "ASAP", + "fairsharing": "FAIRsharing.anpa6", + "go": "ASAP", + "miriam": "asap", + "n2t": "asap", + "ncbi": "ASAP", + "prefixcommons": "asap", + "re3data": "r3d100010666" + }, + "name": "A Systematic Annotation Package for Community Analysis of Genomes", + "pattern": "^[A-Za-z0-9-]+$", + "preferred_prefix": "asap", + "publications": [ + { + "doi": "10.1093/nar/gkj164", + "pmc": "PMC1347526", + "pubmed": "16381899", + "title": "ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.", + "year": 2006 + }, + { + "doi": "10.1093/nar/gkg125", + "pmc": "PMC165572", + "pubmed": "12519969", + "title": "ASAP, a systematic annotation package for community analysis of genomes.", + "year": 2003 + } + ], + "uri_format": "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1" + }, + "ascl": { + "description": "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001).", + "example": "1801.012", + "homepage": "http://ascl.net/", + "keywords": [ + "astrophysics and astronomy" + ], + "mappings": { + "biocontext": "ASCL", + "fairsharing": "FAIRsharing.wb0txg", + "miriam": "ascl", + "n2t": "ascl", + "re3data": "r3d100011865" + }, + "name": "Astrophysics Source Code Library", + "pattern": "^[0-9\\.]+$", + "preferred_prefix": "ascl", + "publications": [ + { + "doi": "10.5334/jors.bv", + "pmc": null, + "pubmed": null, + "title": "Looking before Leaping: Creating a Software Registry", + "year": 2015 + } + ], + "twitter": "asclnet", + "uri_format": "http://ascl.net/$1" + }, + "asin": { + "description": "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue.", + "example": "0471491039", + "homepage": "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182", + "mappings": { + "biocontext": "ASIN", + "miriam": "asin", + "n2t": "asin" + }, + "name": "Amazon Standard Identification Number", + "pattern": "^[0-9]{10}$", + "preferred_prefix": "asin", + "uri_format": "https://amzn.com/$1" + }, + "aspgd.locus": { + "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information.", + "example": "ASPL0000349247", + "homepage": "http://www.aspgd.org/", + "mappings": { + "biocontext": "ASPGD.LOCUS", + "biolink": "AspGD", + "go": "AspGD_LOCUS", + "miriam": "aspgd.locus", + "n2t": "aspgd.locus" + }, + "name": "Aspergillus Genome Database", + "pattern": "^[A-Za-z_0-9]+$", + "preferred_prefix": "aspgd.locus", + "uri_format": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1" + }, + "aspgd.protein": { + "description": "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information.", + "example": "ASPL0000349247", + "homepage": "http://www.aspgd.org/", + "mappings": { + "biocontext": "ASPGD.PROTEIN", + "miriam": "aspgd.protein", + "n2t": "aspgd.protein" + }, + "name": "AspGD Protein", + "pattern": "^[A-Za-z_0-9]+$", + "preferred_prefix": "aspgd.protein", + "uri_format": "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1" + }, + "asrp": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes.", + "example": "ASRP1423", + "homepage": "https://asrp.danforthcenter.org/", + "keywords": [ + "genome", + "regulation", + "rna" + ], + "mappings": { + "prefixcommons": "asrp" + }, + "name": "Arabidopsis Small RNA Project", + "preferred_prefix": "asrp", + "publications": [ + { + "doi": "10.1093/nar/gkm997", + "pmc": "PMC2238918", + "pubmed": "17999994", + "title": "Update of ASRP: the Arabidopsis Small RNA Project database.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gki127", + "pmc": "PMC540081", + "pubmed": "15608278", + "title": "ASRP: the Arabidopsis Small RNA Project Database.", + "year": 2005 + } + ], + "uri_format": "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1" + }, + "astd": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "Identifier of an object from the ASTD database.", + "example": "ENSG00000136147", + "homepage": "http://www.ebi.ac.uk/astd/", + "keywords": [ + "alternative splicing", + "gene", + "transcript" + ], + "mappings": { + "edam": "2367", + "prefixcommons": "astd" + }, + "name": "ASTD", + "preferred_prefix": "astd", + "provides": "ensembl", + "publications": [ + { + "doi": "10.1016/j.ygeno.2008.11.003", + "pmc": null, + "pubmed": "19059335", + "title": "ASTD: The Alternative Splicing and Transcript Diversity database.", + "year": 2008 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.ebi.ac.uk/astd/geneview.html?acc=$1" + }, + "atc": { + "contact": { + "email": "whocc@fhi.no", + "github": null, + "name": "WHO Collaborating Centre for Drug Statistics Methodology", + "orcid": null + }, + "description": "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels.", + "example": "A10BA02", + "homepage": "http://www.whocc.no/atc_ddd_index/", + "keywords": [ + "biomedical science", + "chemical", + "chemical biology", + "ontology", + "pharmacology" + ], + "mappings": { + "aberowl": "ATC", + "bartoc": "449", + "biocontext": "ATC", + "bioportal": "ATC", + "edam": "3103", + "fairsharing": "FAIRsharing.1a27h8", + "hl7": "2.16.840.1.113883.6.73", + "miriam": "atc", + "n2t": "atc", + "prefixcommons": "atc", + "wikidata": "P267" + }, + "name": "Anatomical Therapeutic Chemical Classification System", + "pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$", + "preferred_prefix": "atc", + "publications": [ + { + "doi": null, + "pmc": null, + "pubmed": "7368387", + "title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].", + "year": 1980 + }, + { + "doi": "10.1007/s002280000200", + "pmc": null, + "pubmed": "11214783", + "title": "Different versions of the anatomical therapeutic chemical classification system and the defined daily dose--are drug utilisation data comparable?", + "year": 2000 + } + ], + "synonyms": [ + "ATC_code", + "ATTC" + ], + "uri_format": "http://www.whocc.no/atc_ddd_index/?code=$1" + }, + "atcc": { + "description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.", + "example": "11303", + "homepage": "https://www.lgcstandards-atcc.org", + "keywords": [ + "epidemiology", + "life science", + "virology" + ], + "mappings": { + "biocontext": "ATCC", + "cellosaurus": "ATCC", + "fairsharing": "FAIRsharing.j0ezpm", + "hl7": "2.16.840.1.113883.6.77", + "miriam": "atcc", + "n2t": "atcc", + "ncbi": "ATCC" + }, + "name": "American Type Culture Collection", + "pattern": "^([A-Z]+-)?\\d+$", + "preferred_prefix": "atcc", + "synonyms": [ + "ATCC", + "ATCC number", + "ATCC(dna)", + "ATCC(in host)" + ], + "uri_format": "https://www.atcc.org/products/$1" + }, + "atcvet": { + "description": "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use.", + "example": "QJ51RV02", + "homepage": "http://www.whocc.no/atcvet/atcvet_index/", + "mappings": { + "biocontext": "ATCVET", + "miriam": "atcvet", + "n2t": "atcvet" + }, + "name": "Anatomical Therapeutic Chemical Vetinary", + "pattern": "^Q[A-Z0-9]+$", + "preferred_prefix": "atcvet", + "uri_format": "http://www.whocc.no/atcvet/atcvet_index/?code=$1" + }, + "atfdb.family": { + "description": "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found.", + "example": "CUT", + "homepage": "http://www.bioguo.org/AnimalTFDB/family_index.php", + "mappings": { + "biocontext": "ATFDB.FAMILY", + "miriam": "atfdb.family", + "n2t": "atfdb.family" + }, + "name": "Animal TFDB Family", + "pattern": "^\\w+$", + "preferred_prefix": "atfdb.family", + "uri_format": "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1" + }, + "ato": { + "contact": { + "email": "david.c.blackburn@gmail.com", + "github": null, + "name": "David Blackburn", + "orcid": "0000-0002-1810-9886" + }, + "deprecated": true, + "description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource", + "download_obo": "http://aber-owl.net/media/ontologies/ATO/2/ato.obo", + "example": "0000000", + "homepage": "http://www.amphibanat.org", + "keywords": [ + "obo", + "ontology", + "taxonomy" + ], + "mappings": { + "aberowl": "ATO", + "biocontext": "ATO", + "bioportal": "ATO", + "fairsharing": "FAIRsharing.ayjdsm", + "obofoundry": "ato" + }, + "name": "Amphibian taxonomy", + "pattern": "^\\d{7}$", + "preferred_prefix": "ATO", + "uri_format": "http://purl.obolibrary.org/obo/ATO_$1" + }, + "atol": { + "contact": { + "email": "pylebail@rennes.inra.fr", + "github": null, + "name": "Pierre-Yves LeBail", + "orcid": "0000-0002-8310-5195" + }, + "description": "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production.", + "download_owl": "http://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl", + "example": "0002233", + "homepage": "http://www.atol-ontology.com", + "keywords": [ + "agriculture", + "animal husbandry", + "life science", + "ontology" + ], + "mappings": { + "aberowl": "ATOL", + "agroportal": "ATOL", + "bioportal": "ATOL", + "fairsharing": "FAIRsharing.wsfk5z", + "ols": "atol" + }, + "name": "Animal Trait Ontology for Livestock", + "pattern": "^\\d{7}$", + "preferred_prefix": "atol", + "uri_format": "http://opendata.inra.fr/ATOL/ATOL_$1", + "version": "2018-09-13" + }, + "autdb": { + "description": "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder.", + "example": "ADA", + "homepage": "http://autism.mindspec.org/autdb/", + "mappings": { + "biocontext": "AUTDB", + "miriam": "autdb", + "n2t": "autdb" + }, + "name": "AutDB", + "pattern": "^[A-Z]+[A-Z-0-9]{2,}$", + "preferred_prefix": "autdb", + "uri_format": "http://autism.mindspec.org/GeneDetail/$1" + }, + "bacdive": { + "contact": { + "email": "contact@bacdive.de", + "github": null, + "name": "Lorenz Reimer", + "orcid": "0000-0002-7805-0660" + }, + "description": "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity.", + "example": "131392", + "homepage": "https://bacdive.dsmz.de/", + "keywords": [ + "biodiversity", + "life science", + "microbiology" + ], + "mappings": { + "fairsharing": "FAIRsharing.aSszvY", + "miriam": "bacdive", + "n2t": "bacdive", + "re3data": "r3d100013060", + "wikidata": "P2946" + }, + "name": "BacDive", + "pattern": "^[0-9]+$", + "preferred_prefix": "bacdive", + "publications": [ + { + "doi": "10.1093/nar/gky879", + "pmc": "PMC6323973", + "pubmed": "30256983", + "title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.", + "year": 2019 + }, + { + "doi": "10.1016/j.jbiotec.2017.05.004", + "pmc": null, + "pubmed": "28487186", + "title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.", + "year": 2017 + }, + { + "doi": "10.1093/nar/gkv983", + "pmc": "PMC4702946", + "pubmed": "26424852", + "title": "BacDive--The Bacterial Diversity Metadatabase in 2016.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkt1058", + "pmc": "PMC3965005", + "pubmed": "24214959", + "title": "BacDive--the Bacterial Diversity Metadatabase.", + "year": 2013 + } + ], + "uri_format": "https://bacdive.dsmz.de/strain/$1" + }, + "bacmap.biog": { + "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information.", + "example": "1050", + "homepage": "http://bacmap.wishartlab.com/", + "mappings": { + "biocontext": "BACMAP.BIOG", + "miriam": "bacmap.biog", + "n2t": "bacmap.biog" + }, + "name": "BacMap Biography", + "pattern": "^\\d+$", + "preferred_prefix": "bacmap.biog", + "uri_format": "http://bacmap.wishartlab.com/organisms/$1" + }, + "bacmap.map": { + "description": "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information.", + "example": "AP011135", + "homepage": "http://bacmap.wishartlab.com/", + "mappings": { + "biocontext": "BACMAP.MAP", + "miriam": "bacmap.map", + "n2t": "bacmap.map" + }, + "name": "BacMap Map", + "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", + "preferred_prefix": "bacmap.map", + "uri_format": "http://bacmap.wishartlab.com/maps/$1/index.html" + }, + "bactibase": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria.", + "example": "BAC045", + "homepage": "http://bactibase.hammamilab.org", + "keywords": [ + "life science", + "protein" + ], + "mappings": { + "fairsharing": "FAIRsharing.5f5mfm", + "prefixcommons": "bactibase", + "re3data": "r3d100012755" + }, + "name": "Bactibase", + "preferred_prefix": "bactibase", + "publications": [ + { + "doi": "10.1186/1471-2180-10-22", + "pmc": "PMC2824694", + "pubmed": "20105292", + "title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization.", + "year": 2010 + }, + { + "doi": "10.1186/1471-2180-7-89", + "pmc": "PMC2211298", + "pubmed": "17941971", + "title": "BACTIBASE: a new web-accessible database for bacteriocin characterization.", + "year": 2007 + } + ], + "uri_format": "http://bactibase.hammamilab.org/$1" + }, + "bams": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions.", + "homepage": "https://bams1.org", + "name": "Brain Architecture Knowledge Management System Neuroanatomical Ontology", + "preferred_prefix": "bams", + "references": [ + "https://www.frontiersin.org/articles/10.3389/neuro.11.002.2008/full" + ] + }, + "bao": { + "contact": { + "email": "sschurer@med.miami.edu", + "github": null, + "name": "Stephan Schurer", + "orcid": null + }, + "description": "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.", + "download_owl": "http://www.bioassayontology.org/bao/bao_complete.owl", + "example": "0002989", + "homepage": "http://bioassayontology.org", + "keywords": [ + "biochemistry", + "biomedical science", + "life science", + "ontology" + ], + "mappings": { + "aberowl": "BAO", + "biocontext": "BAO", + "bioportal": "BAO", + "fairsharing": "FAIRsharing.mye76w", + "miriam": "bao", + "n2t": "bao", + "ols": "bao", + "ontobee": "BAO" + }, + "name": "BioAssay Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "bao", + "publications": [ + { + "doi": "10.1186/2041-1480-5-s1-s5", + "pmc": "PMC4108877", + "pubmed": "25093074", + "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications.", + "year": 2014 + }, + { + "doi": "10.1371/journal.pone.0049198", + "pmc": "PMC3498356", + "pubmed": "23155465", + "title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).", + "year": 2012 + }, + { + "doi": "10.1186/1471-2105-12-257", + "pmc": "PMC3149580", + "pubmed": "21702939", + "title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.", + "year": 2011 + }, + { + "doi": "10:1371/journal.pone.0049198", + "pmc": null, + "pubmed": "10", + "title": "Digitoxin metabolism by rat liver microsomes.", + "year": 1975 + } + ], + "repository": "https://github.com/BioAssayOntology/BAO/wiki", + "synonyms": [ + "BAO" + ], + "uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1", + "version": "2.7.2" + }, + "bartoc": { + "contact": { + "email": "voss@gbv.de", + "github": "nichtich", + "name": "Jakob Voß", + "orcid": "0000-0002-7613-4123" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": "voss@gbv.de", + "github": "nichtich", + "name": "Jakob Voß", + "orcid": "0000-0002-7613-4123" + } + ], + "description": "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).", + "example": "241", + "homepage": "https://bartoc.org", + "keywords": [ + "knowledge and information systems", + "ontology and terminology" + ], + "license": "PDDL 1.0", + "mappings": { + "bartoc": "2054", + "fairsharing": "FAIRsharing.f1777e", + "wikidata": "P2689" + }, + "name": "Basic Register of Thesauri, Ontologies & Classifications", + "owners": [ + { + "name": "Verbundzentrale des GBV", + "partnered": false, + "ror": "048vdhs48", + "wikidata": null + } + ], + "pattern": "^[1-9][0-9]*$", + "preferred_prefix": "bartoc", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/783" + ], + "repository": "https://github.com/gbv/bartoc.org", + "uri_format": "https://bartoc.org/en/node/$1" + }, + "bbkg": { + "description": "Blue Brain Project's published data as knowledge graphs and Web Studios.", + "example": "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", + "homepage": "https://portal.bluebrain.epfl.ch", + "mappings": { + "miriam": "bbkg" + }, + "name": "Blue Brain Project Knowledge Graph", + "pattern": "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$", + "preferred_prefix": "bbkg", + "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/$1" + }, + "bbtp": { + "description": "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 ).", + "example": "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a", + "homepage": "https://portal.bluebrain.epfl.ch", + "mappings": { + "miriam": "bbtp" + }, + "name": "Blue Brain Project Topological sampling Knowledge Graph", + "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", + "preferred_prefix": "bbtp", + "uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1" + }, + "bcgo": { + "contact": { + "email": "jiezheng@pennmedicine.upenn.edu", + "github": "zhengj2007", + "name": "Jie Zheng", + "orcid": "0000-0002-2999-0103" + }, + "deprecated": true, + "description": "An application ontology built for beta cell genomics studies.", + "download_owl": "https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl", + "example": "0000015", + "homepage": "https://github.com/obi-bcgo/bcgo", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "BCGO", + "biocontext": "BCGO", + "bioportal": "BCGO", + "cellosaurus": "BCGO", + "obofoundry": "bcgo", + "ontobee": "BCGO" + }, + "name": "Beta Cell Genomics Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "BCGO", + "repository": "https://github.com/obi-bcgo/bcgo", + "uri_format": "http://purl.obolibrary.org/obo/BCGO_$1" + }, + "bcio": { + "contact": { + "email": "srodriguez142857@gmail.com", + "github": null, + "name": "Sergio José Rodríguez Méndez", + "orcid": "0000-0001-7203-8399" + }, + "description": "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation.", + "download_owl": "http://humanbehaviourchange.org/ontology/bcio.owl", + "example": "040000", + "homepage": "https://www.humanbehaviourchange.org/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "BCI-O", + "bioportal": "BCI-O", + "ols": "bcio" + }, + "name": "The Behaviour Change Intervention Ontology", + "pattern": "^\\d{6}$", + "preferred_prefix": "bcio", + "uri_format": "https://w3id.org/BCI-ontology#$1" + }, + "bco": { + "appears_in": [ + "fovt" + ], + "contact": { + "email": "rlwalls2008@gmail.com", + "github": "ramonawalls", + "name": "Ramona Walls", 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This collection refers to anatomical structures.", + "example": "EHDAA:2185", + "homepage": "http://bgee.unil.ch/bgee/bgee", + "mappings": { + "biocontext": "BGEE.ORGAN", + "miriam": "bgee.organ", + "n2t": "bgee.organ" + }, + "name": "Bgee organ", + "pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$", + "preferred_prefix": "bgee.organ", + "uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1" + }, + "bgee.stage": { + "description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.", + "example": "HsapDO:0000004", + "homepage": "http://bgee.unil.ch/bgee/bgee", + "mappings": { + "biocontext": "BGEE.STAGE", + "miriam": "bgee.stage", + "n2t": "bgee.stage" + }, + "name": "Bgee stage", + "pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$", + "preferred_prefix": "bgee.stage", + "uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1" + }, + "bibo": { + "contact": { + "email": "fred@fgiasson.com", + "github": "fgiasson", + "name": "Frédérick Giasson", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web.", + "example": "authorList", + "homepage": "https://bibliontology.com/", + "keywords": [ + "bibliometrics" + ], + "name": "The Bibliographic Ontology", + "preferred_prefix": "bibo", + "uri_format": "http://purl.org/ontology/bibo/$1" + }, + "bido": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF.", + "example": "CategorialBibliometricData", + "homepage": "http://www.sparontologies.net/ontologies/bido", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.d7f0a9" + }, + "name": "Bibliometric Data Ontology", + "preferred_prefix": "BiDO", + "repository": "https://github.com/sparontologies/bido", + "twitter": "sparontologies", + "uri_format": "http://purl.org/spar/bido/$1" + }, + "bigg.compartment": { + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments.", + "example": "c", + "homepage": "http://bigg.ucsd.edu/compartments/", + "mappings": { + "biocontext": "BIGG.COMPARTMENT", + "miriam": "bigg.compartment", + "n2t": "bigg.compartment" + }, + "name": "BiGG Compartment", + "pattern": "^[a-z_A-Z]+$", + "preferred_prefix": "bigg.compartment", + "uri_format": "http://bigg.ucsd.edu/compartments/$1" + }, + "bigg.metabolite": { + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.", + "example": "12dgr161", + "homepage": "http://bigg.ucsd.edu/universal/metabolites", + "mappings": { + "biocontext": "BIGG.METABOLITE", + "miriam": "bigg.metabolite", + "n2t": "bigg.metabolite" + }, + "name": "BiGG Metabolite", + "pattern": "^[a-z_A-Z0-9]+$", + "preferred_prefix": "bigg.metabolite", + "uri_format": "http://bigg.ucsd.edu/models/universal/metabolites/$1" + }, + "bigg.model": { + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.", + "example": "iECABU_c1320", + "homepage": "http://bigg.ucsd.edu/models", + "mappings": { + "biocontext": "BIGG.MODEL", + "miriam": "bigg.model", + "n2t": "bigg.model" + }, + "name": "BiGG Model", + "pattern": "^[a-z_A-Z0-9]+$", + "preferred_prefix": "bigg.model", + "uri_format": "http://bigg.ucsd.edu/models/$1" + }, + "bigg.reaction": { + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.", + "example": "13GS", + "homepage": "http://bigg.ucsd.edu/universal/reactions", + "mappings": { + "biocontext": "BIGG.REACTION", + "miriam": "bigg.reaction", + "n2t": "bigg.reaction" + }, + "name": "BiGG Reaction", + "pattern": "^[a-z_A-Z0-9]+$", + "preferred_prefix": "bigg.reaction", + "uri_format": "http://bigg.ucsd.edu/models/universal/reactions/$1" + }, + "bila": { + "contact": { + "email": "henrich@embl.de", + "github": null, + "name": "Thorsten Heinrich", + "orcid": null + }, + "deprecated": true, + "description": "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.", + "download_owl": "http://purl.obolibrary.org/obo/bila.owl", + "example": "0000000", + "homepage": "http://4dx.embl.de/4DXpress", + "keywords": [ + "anatomy", + "gene expression", + "obo", + "ontology" + ], + "mappings": { + "biocontext": "BILA", + "fairsharing": "FAIRsharing.eqgjeq", + "obofoundry": "bila", + "prefixcommons": "4dxpress" + }, + "name": "Bilateria anatomy", + "pattern": "^\\d{7}$", + "preferred_prefix": "BILA", + "publications": [ + { + "doi": "10.1093/nar/gkm797", + "pmc": "PMC2238840", + "pubmed": "17916571", + "title": "4DXpress: a database for cross-species expression pattern comparisons.", + "year": 2007 + } + ], + "uri_format": "http://purl.obolibrary.org/obo/BILA_$1" + }, + "bind": { + "deprecated": true, + "description": "Accession number of an entry from the BIND database.", + "example": "98346", + "homepage": "http://bind.ca", + "keywords": [ + "interaction", + "pathway", + "small molecule" + ], + "mappings": { + "biocontext": "BIND", + "edam": "1129", + "prefixcommons": "bind" + }, + "name": "BIND accession number", + "preferred_prefix": "bind", + "publications": [ + { + "doi": "10.1093/nar/gkg056", + "pmc": "PMC165503", + "pubmed": "12519993", + "title": "BIND: the Biomolecular Interaction Network Database.", + "year": 2003 + }, + { + "doi": "10.1093/bioinformatics/16.5.465", + "pmc": null, + "pubmed": "10871269", + "title": "BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.", + "year": 2000 + } + ], + "uri_format": "http://www.bind.ca/Action?identifier=bindid&idsearch=$1" + }, + "bindingdb": { + "contact": { + "email": "mgilson@health.ucsd.edu", + "github": null, + "name": "Michael K. 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"github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Schema for the export of the Bioregistry as RDF", + "example": "0000001", + "homepage": "https://bioregistry.io/schema", + "keywords": [ + "registry" + ], + "name": "Bioregistry Schema", + "pattern": "^\\d{7}$", + "preferred_prefix": "bioregistry.schema", + "uri_format": "https://bioregistry.io/schema/#$1" + }, + "biorxiv": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The bioRxiv is a preprint server for biology", + "example": "2022.07.08.499378", + "example_extras": [ + "000091", + "000091v1", + "2022.07.08.499378v2" + ], + "homepage": "https://biorxiv.org", + "keywords": [ + "preprints", + "publishing" + ], + "mappings": { + "go": "bioRxiv", + "wikidata": "P3951" + }, + "name": "bioRxiv", + "pattern": "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$", + "preferred_prefix": "biorxiv", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/biorxiv/$1" + } + ], + "uri_format": "https://www.biorxiv.org/content/10.1101/$1" + }, + "biosample": { + "description": "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation.", + "example": "SAMEA2397676", + "homepage": "https://www.ebi.ac.uk/biosamples/", + "keywords": [ + "biology" + ], + "mappings": { + "biocontext": "BIOSAMPLE", + "cellosaurus": "BioSamples", + "fairsharing": "FAIRsharing.qr6pqk", + "miriam": "biosample", + "n2t": "biosample", + "re3data": "r3d100012828" + }, + "name": "BioSample", + "pattern": "^SAM[NED](\\w)?\\d+$", + "preferred_prefix": "biosample", + "providers": [ + { + "code": "ddbj", + "description": "BioSample at DNA Data Bank of Japan", + "homepage": "http://trace.ddbj.nig.ac.jp/biosample/", + "name": "BioSample at DNA Data Bank of Japan", + "uri_format": "http://trace.ddbj.nig.ac.jp/BSSearch/biosample?acc=$1" + }, + { + "code": "ncbi", + "description": "BioSample at NCBI", + "homepage": "http://www.ncbi.nlm.nih.gov/biosample", + "name": "BioSample at NCBI", + "uri_format": "http://www.ncbi.nlm.nih.gov/biosample?term=$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkr1163", + "pmc": "PMC3245069", + "pubmed": "22139929", + "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.", + "year": 2011 + } + ], + "synonyms": [ + "biosamples" + ], + "uri_format": "https://www.ebi.ac.uk/biosamples/sample/$1" + }, + "bioschemas": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]", + "example": "Dataset", + "homepage": "https://bioschemas.org", + "mappings": { + "biolink": "bioschemas" + }, + "name": "BioSchemas", + "preferred_prefix": "bioschemas", + "repository": "https://github.com/BioSchemas/specifications", + "synonyms": [ + "bioschema" + ], + "twitter": "bioschemas", + "uri_format": "https://bioschemas.org/profiles/$1" + }, + "biosimulations": { + "description": "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools.", + "example": "Yeast-cell-cycle-Irons-J-Theor-Biol-2009", + "homepage": "https://icahn.mssm.edu/", + "mappings": { + "miriam": "biosimulations", + "re3data": "r3d100013361" + }, + "name": "biosimulations", + "pattern": "^[a-zA-Z0-9_-]{3,}$", + "preferred_prefix": "biosimulations", + "uri_format": "https://biosimulations.org/projects/$1" + }, + "biosimulators": { + "contact": { + "email": "karr@mssm.edu", + "github": null, + "name": "Jonathan Karr", + "orcid": "0000-0002-2605-5080" + }, + "description": "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML).", + "example": "vcell", + "homepage": "https://biosimulators.org/", + "keywords": [ + "computational biology", + "systems biology" + ], + "mappings": { + "fairsharing": "FAIRsharing.pwEima", + "miriam": "biosimulators", + "re3data": "r3d100013432" + }, + "name": "BioSimulators", + "pattern": "^[a-zA-Z0-9-_]+$", + "preferred_prefix": "biosimulators", + "repository": "https://github.com/biosimulators/Biosimulators/issues/new/choose", + "uri_format": "https://biosimulators.org/simulators/$1" + }, + "biostudies": { + "description": "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.", + "example": "S-EPMC6266652", + "homepage": "https://www.ebi.ac.uk/biostudies/", + "keywords": [ + "biomedical science", + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.mtjvme", + "miriam": "biostudies", + "n2t": "biostudies", + "re3data": "r3d100012627" + }, + "name": "BioStudies database", + "pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$", + "preferred_prefix": "biostudies", + "publications": [ + { + "doi": "10.1093/nar/gkx965", + "pmc": "PMC5753238", + "pubmed": "29069414", + "title": "The BioStudies database-one stop shop for all data supporting a life sciences study.", + "year": 2018 + }, + { + "doi": "10.15252/msb.20156658", + "pmc": "PMC4704487", + "pubmed": "26700850", + "title": "The BioStudies database.", + "year": 2015 + } + ], + "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" + }, + "biosystems": { + "description": "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources.", + "example": "001", + "homepage": "https://www.ncbi.nlm.nih.gov/biosystems/", + "keywords": [ + "biology", + "molecules", + "pathways", + "systems biology" + ], + "mappings": { + "biocontext": "BIOSYSTEMS", + "fairsharing": "FAIRsharing.w2eeqr", + "miriam": "biosystems", + "n2t": "biosystems", + "prefixcommons": "biosystems", + "re3data": "r3d100011033" + }, + "name": "BioSystems", + "pattern": "^\\d+$", + "preferred_prefix": "biosystems", + "publications": [ + { + "doi": "10.1093/nar/gkp858", + "pmc": "PMC2808896", + "pubmed": "19854944", + "title": "The NCBI BioSystems database.", + "year": 2009 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/biosystems/$1" + }, + "biotools": { + "contact": { + "email": "haiiu@dtu.dk", + "github": "hansioan", + "name": "Hans Ienasescu", + "orcid": "0000-0001-9727-2544" + }, + "description": "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.", + "example": "bioregistry", + "homepage": "https://bio.tools/", + "keywords": [ + "bioinformatics", + "biology", + "biomedical science" + ], + "mappings": { + "biocontext": "BIOTOOLS", + "fairsharing": "FAIRsharing.63520c", + "miriam": "biotools", + "n2t": "biotools", + "re3data": "r3d100013668" + }, + "name": "BioTools", + "pattern": "^[-A-Za-z0-9\\_]*$", + "preferred_prefix": "biotools", + "publications": [ + { + "doi": "10.1093/nar/gkv1116", + "pmc": "PMC4702812", + "pubmed": "26538599", + "title": "Tools and data services registry: a community effort to document bioinformatics resources.", + "year": 2015 + } + ], + "repository": "http://github.com/bio-tools/biotoolsregistry/", + "uri_format": "https://bio.tools/$1" + }, + "biozil": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Redistributor of bilogics and biomedical supplies", + "example": "ls-c35719-120", + "homepage": "https://www.biozol.de/en", + "keywords": [ + "biologics", + "life sciences", + "vendor" + ], + "name": "BIOZIL", + "preferred_prefix": "biozil", + "uri_format": "https://www.biozol.de/en/product/$1" + }, + "birnlex": { + "comment": "Part of the NeuroLex namespace now", + "contact": { + "email": "wbug@ncmir.ucsd.edu", + "github": null, + "name": "William Bug", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design.", + "download_owl": "http://aber-owl.net/media/ontologies/BIRNLEX/1/birnlex.owl", + "example": "2023", + "homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX", + "keywords": [ + "biomedical science", + "ontology" + ], + "mappings": { + "aberowl": "BIRNLEX", + "bioportal": "BIRNLEX", + "fairsharing": "FAIRsharing.jedbbt" + }, + "name": "Biomedical Informatics Research Network Lexicon", + "pattern": "^\\d+$", + "preferred_prefix": "birnlex", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/birnlex_$1" + }, + "biro": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively.", + "example": "BibliographicRecord", + "homepage": "http://www.sparontologies.net/ontologies/biro", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.99da5f" + }, + "name": "Bibliographic Reference Ontology", + "preferred_prefix": "BiRO", + "repository": "https://github.com/sparontologies/biro", + "twitter": "sparontologies", + "uri_format": "http://purl.org/spar/biro/$1" + }, + "bitbucket": { + "description": "Bitbucket is a Git-based source code repository hosting service owned by Atlassian.", + "example": "andreadega/systems-biology-compiler", + "homepage": "https://www.atlassian.com/", + "keywords": [ + "knowledge and information systems", + "software engineering", + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.fc3431", + "miriam": "bitbucket", + "re3data": "r3d100013478" + }, + "name": "Bitbucket", + "pattern": "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$", + "preferred_prefix": "bitbucket", + "uri_format": "https://bitbucket.org/$1" + }, + "bitterdb.cpd": { + "description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds.", + "example": "46", + "homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php", + "mappings": { + "biocontext": "BITTERDB.CPD", + "miriam": "bitterdb.cpd", + "n2t": "bitterdb.cpd" + }, + "name": "BitterDB Compound", + "pattern": "^\\d+$", + "preferred_prefix": "bitterdb.cpd", + "uri_format": "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1" + }, + "bitterdb.rec": { + "description": "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors.", + "example": "1", + "homepage": "http://bitterdb.agri.huji.ac.il/dbbitter.php", + "mappings": { + "biocontext": "BITTERDB.REC", + "miriam": "bitterdb.rec", + "n2t": "bitterdb.rec" + }, + "name": "BitterDB Receptor", + "pattern": "^\\d+$", + "preferred_prefix": "bitterdb.rec", + "uri_format": "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1" + }, + "bko": { + "comment": "This resource also uses SBO terms and resolves them, e.g., http://www.sbgnbricks.org/BKO/full/entry/all/SBO:0000177/.", + "contact": { + "email": "adrienrougny@gmail.com", + "github": "adrienrougny", + "name": "Adrien Rougny", + "orcid": "0000-0002-2118-035X" + }, + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.", + "download_owl": "http://aber-owl.net/media/ontologies/BKO/1/bko.owl", + "example": "0000204", + "github_request_issue": 283, + "homepage": "http://www.sbgnbricks.org/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "BKO", + "bioportal": "BKO" + }, + "name": "SBGN Bricks data and ontology", + "pattern": "^\\d+$", + "preferred_prefix": "bko", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1" + }, + "bmrb": { + "description": "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.", + "example": "15000", + "homepage": "http://www.bmrb.wisc.edu/", + "keywords": [ + "structural biology" + ], + "mappings": { + "fairsharing": "FAIRsharing.p06nme", + "miriam": "bmrb", + "re3data": "r3d100010191", + "uniprot": "DB-0256" + }, + "name": "Biological Magnetic Resonance Data Bank", + "pattern": "^(bmr|bmse|bmst)?[0-9]{1,6}$", + "preferred_prefix": "bmrb", + "publications": [ + { + "doi": "10.1007/s10858-008-9221-y", + "pmc": "PMC2268728", + "pubmed": "18288446", + "title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkm957", + "pmc": "PMC2238925", + "pubmed": "17984079", + "title": "BioMagResBank.", + "year": 2007 + } + ], + "uri_format": "http://rest.bmrb.wisc.edu/bmrb/$1/html" + }, + "bmrb.restraint": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively.", + "example": "28789", + "homepage": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet", + "keywords": [ + "chemistry", + "nmr", + "spectrometry" + ], + "name": "NMR Restraints Grid", + "pattern": "^\\d+$", + "preferred_prefix": "bmrb.restraint", + "uri_format": "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1" + }, + "bold.taxonomy": { + "description": "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information.", + "example": "27267", + "homepage": "http://www.boldsystems.org/", + "keywords": [ + "dna" + ], + "mappings": { + "biocontext": "BOLD.TAXONOMY", + "miriam": "bold.taxonomy", + "n2t": "bold.taxonomy", + "ncbi": "BOLD", + "prefixcommons": "bold", + "wikidata": "P3606" + }, + "name": "BOLD Systems taxon", + "pattern": "^\\d+$", + "preferred_prefix": "bold.taxonomy", + "publications": [ + { + "doi": "10.1111/j.1471-8286.2007.01678.x", + "pmc": "PMC1890991", + "pubmed": "18784790", + "title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org).", + "year": 2007 + } + ], + "uri_format": "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1" + }, + "bootstrep": { + "contact": { + "email": "vlee@ebi.ac.uk", + "github": null, + "name": "Vivian Lee", + "orcid": null + }, + "deprecated": true, + "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "BOOTSTREP", + "obofoundry": "bootstrep" + }, + "name": "Gene Regulation Ontology", + "preferred_prefix": "BOOTSTREP", + "uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1" + }, + "bpdb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database of biopesticides maintained by the University of Hertfordshire ", + "example": "2404", + "homepage": "https://sitem.herts.ac.uk/aeru/bpdb/index.htm", + "keywords": [ + "biology", + "biopesticides", + "pesticides" + ], + "name": "Bio-Pesticides DataBase", + "pattern": "^\\d+$", + "preferred_prefix": "bpdb", + "uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm" + }, + "brenda": { + "description": "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data.", + "example": "1.1.1.1", + "homepage": "https://www.brenda-enzymes.org/", + "keywords": [ + "enzyme", + "life science" + ], + "mappings": { + "biocontext": "BRENDA", + "fairsharing": "FAIRsharing.etp533", + "go": "BRENDA", + "miriam": "brenda", + "n2t": "brenda", + "prefixcommons": "brenda", + "re3data": "r3d100010616" + }, + "name": "BRENDA Enzyme", + "pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", + "preferred_prefix": "brenda", + "provides": "eccode", + "publications": [ + { + "doi": "s0168-1656(17)30183-9", + "pmc": null, + "pubmed": "28438579", + "title": "The BRENDA enzyme information system-From a database to an expert system.", + "year": null + }, + { + "doi": "10.1016/j.jbiotec.2017.04.020", + "pmc": null, + "pubmed": "28438579", + "title": "The BRENDA enzyme information system-From a database to an expert system.", + "year": 2017 + }, + { + "doi": "10.1093/nar/gku1068", + "pmc": "PMC4383907", + "pubmed": "25378310", + "title": "BRENDA in 2015: exciting developments in its 25th year of existence.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks1049", + "pmc": "PMC3531171", + "pubmed": "23203881", + "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkq1089", + "pmc": "PMC3013686", + "pubmed": "21062828", + "title": "BRENDA, the enzyme information system in 2011.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkn820", + "pmc": "PMC2686525", + "pubmed": "18984617", + "title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkl972", + "pmc": "PMC1899097", + "pubmed": "17202167", + "title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkh081", + "pmc": "PMC308815", + "pubmed": "14681450", + "title": "BRENDA, the enzyme database: updates and major new developments.", + "year": 2004 + }, + { + "doi": "10.1016/s1096-7176(03)00008-9", + "pmc": null, + "pubmed": "12850129", + "title": "Review of the BRENDA Database.", + "year": 2003 + }, + { + "doi": "10.1016/s0968-0004(01)02027-8", + "pmc": null, + "pubmed": "11796225", + "title": "BRENDA: a resource for enzyme data and metabolic information.", + "year": 2002 + }, + { + "doi": "10.1093/nar/30.1.47", + "pmc": "PMC99121", + "pubmed": "11752250", + "title": "BRENDA, enzyme data and metabolic information.", + "year": 2002 + } + ], + "uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1" + }, + "brenda.ligand": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Information for ligands in the BRENDA database.", + "example": "278", + "homepage": "https://www.brenda-enzymes.de/ligand.php", + "keywords": [ + "chemistry", + "structrual bioinformatics" + ], + "name": "BRENDA Ligand", + "pattern": "^\\d+$", + "preferred_prefix": "brenda.ligand", + "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1" + }, + "brenda.ligandgroup": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Information for ligand groups (chemical classes).", + "example": "18030", + "homepage": "https://www.brenda-enzymes.de/ligand.php", + "keywords": [ + "chemistry", + "grouping", + "structrual bioinformatics" + ], + "name": "BRENDA Ligand Group", + "pattern": "^\\d+$", + "preferred_prefix": "brenda.ligandgroup", + "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1" + }, + "broad": { + "description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. 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As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.", + "example": "S7000002168151102", + "homepage": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/", + "mappings": { + "biocontext": "BROAD", + "miriam": "broad", + "n2t": "broad" + }, + "name": "Broad Fungal Genome Initiative", + "pattern": "^S\\d+$", + "preferred_prefix": "broad", + "uri_format": "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1" + }, + "bs": { + "comment": "An alernative vocabulary that has been aligned and integrated in Sequence Ontology (SO).", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. 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These predictions are regularly compared against reference structures from PDB.", + "example": "2019-08-03_00000089_1", + "homepage": "https://cameo3d.org", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "CAMEO", + "fairsharing": "FAIRsharing.dq34p2", + "miriam": "cameo", + "n2t": "cameo" + }, + "name": "Continuous Automated Model Evaluation", + "pattern": "^[0-9\\-_]+$", + "preferred_prefix": "cameo", + "publications": [ + { + "doi": "10.1093/database/bat031", + "pmc": "PMC3889916", + "pubmed": "23624946", + "title": "The Protein Model Portal--a comprehensive resource for protein structure and model information.", + "year": 2013 + } + ], + "uri_format": "https://www.cameo3d.org/sp/targets/target/$1" + }, + "caps": { + "description": "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps.", + "example": "434", + "homepage": "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home", + "mappings": { + "biocontext": "CAPS", + "miriam": "caps", + "n2t": "caps" + }, + "name": "CAPS-DB", + "pattern": "^\\d+$", + "preferred_prefix": "caps", + "uri_format": "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1" + }, + "caro": { + "appears_in": [ + "aism", + "colao", + "ehdaa2", + "lepao", + "pco" + ], + "contact": { + "email": "haendel@ohsu.edu", + "github": "mellybelly", + "name": "Melissa Haendel", + "orcid": "0000-0001-9114-8737" + }, + "description": "None", + "download_json": "http://purl.obolibrary.org/obo/caro.json", + "download_obo": "http://purl.obolibrary.org/obo/caro.obo", + "download_owl": "http://purl.obolibrary.org/obo/caro.owl", + "example": "0000000", + "homepage": "https://github.com/obophenotype/caro/", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CARO", + "biocontext": "CARO", + "bioportal": "CARO", + "fairsharing": "FAIRsharing.3kcgmr", + "go": "CARO", + "obofoundry": "caro", + "ols": "caro", + "ontobee": "CARO" + }, + "name": "Common Anatomy Reference Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CARO", + "providers": [ + { + "code": "obo.1", + "description": "This incorrect encoding was found inside IDO-COVID-19", + "homepage": "http://purl.obolibrary.org", + "name": "Nonstandard OBO PURL", + "uri_format": "http://purl.obolibrary.org/obo/ido.owl/CARO_$1" + } + ], + "publications": [ + { + "doi": "10.1007/978-1-84628-885-2_16", + "pmc": null, + "pubmed": null, + "title": "CARO – The Common Anatomy Reference Ontology", + "year": 2008 + } + ], + "repository": "https://github.com/obophenotype/caro", + "uri_format": "http://purl.obolibrary.org/obo/CARO_$1", + "version": "2022-02-18" + }, + "cas": { + "description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.", + "example": "50-00-0", + "homepage": "https://commonchemistry.cas.org/", + "keywords": [ + "chemical", + "cheminformatics", + "structure" + ], + "mappings": { + "biocontext": "CAS", + "cheminf": "000446", + "edam": "1002", + "fairsharing": "FAIRsharing.r7Kwy7", + "go": "CAS", + "hl7": "2.16.840.1.113883.6.61", + "miriam": "cas", + "n2t": "cas", + "prefixcommons": "cas", + "wikidata": "P231" + }, + "name": "CAS Registry Number", + "pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$", + "preferred_prefix": "cas", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/cas/$1" + } + ], + "publications": [ + { + "doi": "10.1021/acs.jcim.2c00268", + "pmc": "PMC9199008", + "pubmed": "35559614", + "title": "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community.", + "year": 2022 + } + ], + "synonyms": [ + "CASID", + "CAS_RN", + "SECONDARY_CAS_RN", + "cas_id" + ], + "uri_format": "https://commonchemistry.cas.org/detail?cas_rn=$1" + }, + "casspc": { + "comment": "Jim Balhoff said that Catalog of Fishes does not publish their data in a machine readable format, but a long time ago they sent a CSV dump to help in the development of TTO and VTO. These ontologies are effectively retired and CASSPC terms are only also used in Phenoscape.", + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "contributor_extras": [ + { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + ], + "deprecated": true, + "example": "5359", + "homepage": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp", + "mappings": { + "go": "CASSPC" + }, + "name": "Eschmeyer's Catalog of Fishes", + "pattern": "^\\d+$", + "preferred_prefix": "casspc", + "uri_format": "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1" + }, + "cath": { + "description": "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence.", + "example": "1.10.8.10", + "homepage": "http://www.cathdb.info", + "keywords": [ + "biology", + "classification", + "evolutionary biology", + "protein", + "structure" + ], + "mappings": { + "biocontext": "CATH", + "edam": "2700", + "fairsharing": "FAIRsharing.xgcyyn", + "miriam": "cath", + "n2t": "cath", + "prefixcommons": "cath", + "re3data": "r3d100012629" + }, + "name": "CATH Protein Structural Domain Superfamily", + "pattern": "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$", + "preferred_prefix": "cath", + "publications": [ + { + "doi": "10.1016/s0969-2126(97)00260-8", + "pmc": null, + "pubmed": "9309224", + "title": "CATH--a hierarchic classification of protein domain structures.", + "year": 1997 + }, + { + "doi": "10.1093/nar/gkaa1079", + "pmc": "PMC7778904", + "pubmed": "33237325", + "title": "CATH: increased structural coverage of functional space.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gky1097", + "pmc": "PMC6323983", + "pubmed": "30398663", + "title": "CATH: expanding the horizons of structure-based functional annotations for genome sequences.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkx1069", + "pmc": "PMC5753370", + "pubmed": "29112716", + "title": "Gene3D: Extensive prediction of globular domains in proteins.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gkw1098", + "pmc": "PMC5210570", + "pubmed": "27899584", + "title": "CATH: an expanded resource to predict protein function through structure and sequence.", + "year": 2016 + }, + { + "doi": "10.1093/bioinformatics/btw473", + "pmc": "PMC5018379", + "pubmed": "27477482", + "title": "Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.", + "year": 2016 + }, + { + "doi": "10.1016/j.biochi.2015.08.004", + "pmc": "PMC4678953", + "pubmed": "26253692", + "title": "The history of the CATH structural classification of protein domains.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gku947", + "pmc": "PMC4384018", + "pubmed": "25348408", + "title": "CATH: comprehensive structural and functional annotations for genome sequences.", + "year": 2014 + }, + { + "doi": null, + "pmc": null, + "pubmed": "11788987", + "title": "The CATH protein family database: a resource for structural and functional annotation of genomes.", + "year": 2002 + } + ], + "twitter": "CATHDatabase", + "uri_format": "http://www.cathdb.info/cathnode/$1" + }, + "cath.domain": { + "description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.", + "example": "1cukA01", + "homepage": "http://www.cathdb.info/", + "mappings": { + "biocontext": "CATH.DOMAIN", + "edam": "1040", + "miriam": "cath.domain", + "n2t": "cath.domain" + }, + "name": "CATH domain", + "pattern": "^\\w+$", + "preferred_prefix": "cath.domain", + "uri_format": "http://www.cathdb.info/domain/$1" + }, + "cath.superfamily": { + "description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.", + "example": "1.10.10.200", + "homepage": "http://www.cathdb.info/", + "mappings": { + "biocontext": "CATH.SUPERFAMILY", + "miriam": "cath.superfamily", + "n2t": "cath.superfamily" + }, + "name": "CATH superfamily", + "part_of": "cath", + "pattern": "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$", + "preferred_prefix": "cath.superfamily", + "uri_format": "http://www.cathdb.info/cathnode/$1" + }, + "cattleqtldb": { + "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs.", + "example": "4685", + "homepage": "https://www.animalgenome.org/QTLdb", + "keywords": [ + "dna", + "genome" + ], + "mappings": { + "biocontext": "CATTLEQTLDB", + "miriam": "cattleqtldb", + "n2t": "cattleqtldb", + "prefixcommons": "cattleqtldb" + }, + "name": "Animal Genome Cattle QTL", + "part_of": "qtldb", + "pattern": "^\\d+$", + "preferred_prefix": "cattleqtldb", + "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" + }, + "cazy": { + "description": "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features.", + "example": "GT10", + "homepage": "http://www.cazy.org/", + "keywords": [ + "classification", + "glycomics", + "life science", + "polysaccharide" + ], + "mappings": { + "biocontext": "CAZY", + "fairsharing": "FAIRsharing.ntyq70", + "go": "CAZY", + "miriam": "cazy", + "n2t": "cazy", + "prefixcommons": "cazy", + "re3data": "r3d100012321", + "uniprot": "DB-0136" + }, + "name": "Carbohydrate Active EnZYmes", + "pattern": "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$", + "preferred_prefix": "cazy", + "publications": [ + { + "doi": "10.1093/nar/gkt1178", + "pmc": "PMC3965031", + "pubmed": "24270786", + "title": "The carbohydrate-active enzymes database (CAZy) in 2013.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkn663", + "pmc": "PMC2686590", + "pubmed": "18838391", + "title": "The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.", + "year": 2008 + } + ], + "uri_format": "http://www.cazy.org/$1.html" + }, + "cba": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE.", + "example": "375364", + "homepage": "http://www.cba.ac.cn", + "keywords": [ + "bibliography" + ], + "name": "Chinese Biological Abstracts", + "pattern": "^\\d+$", + "preferred_prefix": "cba", + "uri_format": "https://europepmc.org/article/CBA/$1" + }, + "cbioportal": { + "contact": { + "email": "gaoj@mskcc.org", + "github": "jjgao", + "name": "Jianjiong Gao", + "orcid": "0000-0002-5739-1781" + }, + "description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.", + "example": "laml_tcga_pub", + "homepage": "http://www.cbioportal.org", + "keywords": [ + "biomedical science", + "genomics", + "preclinical studies", + "proteomics" + ], + "mappings": { + "fairsharing": "FAIRsharing.6L6MjA", + "miriam": "cbioportal", + "n2t": "cbioportal" + }, + "name": "The cBioPortal for Cancer Genomics", + "pattern": "^[a-z0-9\\_]+$", + "preferred_prefix": "cbioportal", + "publications": [ + { + "doi": "10.1126/scisignal.2004088", + "pmc": "PMC4160307", + "pubmed": "23550210", + "title": "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.", + "year": 2013 + }, + { + "doi": "10.1158/2159-8290.cd-12-0095", + "pmc": "PMC3956037", + "pubmed": "22588877", + "title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.", + "year": 2012 + } + ], + "repository": "https://github.com/cBioPortal/cbioportal", + "twitter": "cbioportal", + "uri_format": "https://www.cbioportal.org/study/summary?id=$1" + }, + "ccdc": { + "description": "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC.", + "example": "1829126", + "homepage": "https://www.ccdc.cam.ac.uk/", + "mappings": { + "miriam": "ccdc" + }, + "name": "CCDC Number", + "pattern": "^\\d{6,7}$", + "preferred_prefix": "ccdc", + "uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG" + }, + "ccds": { + "description": "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations.", + "example": "CCDS13573.1", + "homepage": "http://www.ncbi.nlm.nih.gov/CCDS/", + "keywords": [ + "gene", + "life science", + "protein" + ], + "mappings": { + "biocontext": "CCDS", + "fairsharing": "FAIRsharing.46s4nt", + "miriam": "ccds", + "n2t": "ccds", + "prefixcommons": "ccds", + "uniprot": "DB-0187" + }, + "name": "Consensus CDS", + "pattern": "^CCDS\\d+\\.\\d+$", + "preferred_prefix": "ccds", + "publications": [ + { + "doi": "10.1101/gr.080531.108", + "pmc": "PMC2704439", + "pubmed": "19498102", + "title": "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.", + "year": 2009 + } + ], + "uri_format": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1" + }, + "ccle": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Datasets around different cancer cell lines generated by the Broad Institute and Novartis", + "example": "BT20_BREAST", + "homepage": "https://www.cbioportal.org/study/summary?id=ccle_broad_2019", + "mappings": { + "cellosaurus": "CCLE" + }, + "name": "Cancer Cell Line Encyclopedia Cells", + "preferred_prefix": "ccle", + "synonyms": [ + "ccle.cell" + ], + "uri_format": "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1" + }, + "cco": { + "banana": "CCO", + "contact": { + "email": "kuiper@bio.ntnu.no", + "github": "makuintnu", + "name": "Martin Kuiper", + "orcid": "0000-0002-1171-9876" + }, + "description": "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process.", + "download_obo": "https://www.bio.ntnu.no/ontology/CCO/cco.obo", + "download_owl": "https://www.bio.ntnu.no/ontology/CCO/cco.owl", + "example": "0000003", + "homepage": "http://www.semantic-systems-biology.org/apo", + "keywords": [ + "cell cycle", + "functional genomics", + "genomics", + "life science", + "obo", + "ontology", + "proteomics" + ], + "mappings": { + "aberowl": "CCO", + "biocontext": "CCO", + "bioportal": "CCO", + "fairsharing": "FAIRsharing.xhwrnr", + "miriam": "cco", + "n2t": "cco", + "ols": "cco", + "prefixcommons": "cco" + }, + "name": "Cell Cycle Ontology", + "namespace_in_lui": true, + "pattern": "^\\w+$", + "preferred_prefix": "cco", + "publications": [ + { + "doi": "10.1186/gb-2009-10-5-r58", + "pmc": "PMC2718524", + "pubmed": "19480664", + "title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.", + "year": 2009 + } + ], + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1", + "version": "2016-03-23" + }, + "ccrid": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Cell line databases/resources", + "example": "4201PAT-CCTCC00348", + "homepage": "http://www.cellresource.cn", + "mappings": { + "cellosaurus": "CCRID" + }, + "name": "National Experimental Cell Resource Sharing Platform", + "preferred_prefix": "ccrid", + "uri_format": "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1" + }, + "cdao": { + "contact": { + "email": "balhoff@renci.org", + "github": "balhoff", + "name": "Jim Balhoff", + "orcid": "0000-0002-8688-6599" + }, + "description": "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.", + "download_owl": "http://purl.obolibrary.org/obo/cdao.owl", + "example": "0000072", + "homepage": "https://github.com/evoinfo/cdao", + "keywords": [ + "bioinformatics", + "biomedical science", + "evolutionary biology", + "life science", + "molecular biology", + "obo", + "ontology", + "phylogenetics", + "taxonomy" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "CDAO", + "agroportal": "CDAO", + "biocontext": "CDAO", + "bioportal": "CDAO", + "fairsharing": "FAIRsharing.kay31r", + "obofoundry": "cdao", + "ols": "cdao", + "ontobee": "CDAO" + }, + "name": "Comparative Data Analysis Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CDAO", + "publications": [ + { + "doi": "10.4137/ebo.s2320", + "pmc": "PMC2747124", + "pubmed": "19812726", + "title": "Initial implementation of a comparative data analysis ontology.", + "year": 2009 + } + ], + "repository": "https://github.com/evoinfo/cdao", + "uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", + "version": "2019-06-26" + }, + "cdd": { + "description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.", + "example": "cd00400", + "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd", + "keywords": [ + "earth science", + "geology", + "protein", + "structure" + ], + "mappings": { + "biocontext": "CDD", + "edam": "2666", + "fairsharing": "FAIRsharing.ea287c", + "go": "CDD", + "miriam": "cdd", + "n2t": "cdd", + "ncbi": "CDD", + "prefixcommons": "cdd", + "re3data": "r3d100012041", + "uniprot": "DB-0214" + }, + "name": "Conserved Domain Database at NCBI", + "pattern": "^(cd)?\\d{5}$", + "preferred_prefix": "cdd", + "publications": [ + { + "doi": "doi", + "pmc": "PMC4383992", + "pubmed": "25414356", + "title": null, + "year": null + }, + { + "doi": "10.1093/nar/gku1221", + "pmc": "PMC4383992", + "pubmed": "25414356", + "title": "CDD: NCBI's conserved domain database.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkn845", + "pmc": "PMC2686570", + "pubmed": "18984618", + "title": "CDD: specific functional annotation with the Conserved Domain Database.", + "year": 2008 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1" + }, + "cdno": { + "contact": { + "email": "l.andres.hernandez.18@student.scu.edu.au", + "github": "LilyAndres", + "name": "Liliana Andres Hernandez", + "orcid": "0000-0002-7696-731X" + }, + "depends_on": [ + "bfo", + "chebi", + "envo", + "pato", + "ro" + ], + "description": "None", + "download_obo": "http://purl.obolibrary.org/obo/cdno.obo", + "download_owl": "http://purl.obolibrary.org/obo/cdno.owl", + "example": "0000013", + "homepage": "https://cdno.info/", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "CDNO", + "bioportal": "CDNO", + "obofoundry": "cdno", + "ols": "cdno", + "ontobee": "CDNO" + }, + "name": "Compositional Dietary Nutrition Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CDNO", + "publications": [ + { + "doi": "10.1002/csc2.20092", + "pmc": null, + "pubmed": null, + "title": "Knowledge representation and data sharing to unlock crop variation for nutritional food security", + "year": 2020 + } + ], + "repository": "https://github.com/Southern-Cross-Plant-Science/cdno", + "uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", + "version": "2022-06-23" + }, + "cdpd": { + "description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).", + "example": "63250", + "homepage": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp", + "mappings": { + "biocontext": "CDPD", + "miriam": "cdpd", + "n2t": "cdpd" + }, + "name": "Canadian Drug Product Database", + "pattern": "^\\d+$", + "preferred_prefix": "cdpd", + "uri_format": "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1" + }, + "cdt": { + "appears_in": [ + "ohd" + ], + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.", + "download_owl": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl", + "example": "1000001", + "homepage": "https://www.ada.org/publications/CDT", + "keywords": [ + "ontology" + ], + "mappings": { + "bartoc": "20299", + "hl7": "2.16.840.1.113883.6.116" + }, + "name": "Current Dental Terminology", + "pattern": "^\\d{7}$", + "preferred_prefix": "cdt" + }, + "cell_biolabs": { + "description": "Cell line collections", + "example": "AKR-270", + "homepage": "https://www.cellbiolabs.com", + "mappings": { + "cellosaurus": "Cell_Biolabs" + }, + "name": "Cell Biolabs cell line products", + "preferred_prefix": "cell_biolabs", + "uri_format": "https://www.cellbiolabs.com/search?keywords=$1" + }, + "cell_model_passport": { + "description": "Cell line databases/resources", + "example": "SIDM01262", + "homepage": "https://cellmodelpassports.sanger.ac.uk/", + "mappings": { + "cellosaurus": "Cell_Model_Passport" + }, + "name": "Sanger Cell Model Passports", + "preferred_prefix": "cell_model_passport", + "uri_format": "https://cellmodelpassports.sanger.ac.uk/passports/$1" + }, + "cellbank.australia": { + "description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.", + "example": "ab-1-ha", + "homepage": "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/", + "mappings": { + "cellosaurus": "CBA" + }, + "name": "CellBank Australia", + "preferred_prefix": "cellbank.australia", + "uri_format": "https://www.cellbankaustralia.com/$1.html" + }, + "cellimage": { + "description": "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes.", + "example": "24801", + "homepage": "http://cellimagelibrary.org/", + "keywords": [ + "cell biology", + "image", + "life science" + ], + "mappings": { + "biocontext": "CELLIMAGE", + "fairsharing": "FAIRsharing.8t18te", + "miriam": "cellimage", + "n2t": "cellimage", + "prefixcommons": "cellimage", + "re3data": "r3d100000023" + }, + "name": "Cell Image Library", + "pattern": "^\\d+$", + "preferred_prefix": "cellimage", + "publications": [ + { + "doi": "10.1093/nar/gks1257", + "pmc": "PMC3531121", + "pubmed": "23203874", + "title": "The cell: an image library-CCDB: a curated repository of microscopy data.", + "year": 2012 + } + ], + "twitter": "CellImageLibrar", + "uri_format": "http://cellimagelibrary.org/images/$1" + }, + "cellopub": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Cellosaurus identifeirs for publications, like Pubmed", + "example": "CLPUB00496", + "homepage": "https://web.expasy.org/cellosaurus/", + "mappings": { + "cellosaurus": "CelloPub" + }, + "name": "Cellosaurus Publication", + "pattern": "^CLPUB\\d+$", + "preferred_prefix": "cellopub", + "uri_format": "https://web.expasy.org/cellosaurus/cellopub/$1" + }, + "cellosaurus": { + "banana": "CVCL", + "banana_peel": "_", + "contact": { + "email": "Amos.Bairoch@sib.swiss", + "github": "AmosBairoch", + "name": "Amos Bairoch", + "orcid": "0000-0003-2826-6444" + }, + "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", + "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", + "example": "0440", + "homepage": "https://cellosaurus.org", + "keywords": [ + "life science", + "ontology" + ], + "mappings": { + "biocontext": "CELLOSAURUS", + "cellosaurus": "Cellosaurus", + "fairsharing": "FAIRsharing.hkk309", + "miriam": "cellosaurus", + "n2t": "cellosaurus", + "re3data": "r3d100013293", + "wikidata": "P3289" + }, + "name": "Cellosaurus", + "pattern": "^[A-Z0-9]{4}$", + "preferred_prefix": "cellosaurus", + "providers": [ + { + "code": "legacy", + "description": "The legacy URI for the Cellosaurus website, updated on August 30, 2022 [ref](https://twitter.com/Cellosaurus/status/1564658792691810305).", + "homepage": "https://web.expasy.org/cellosaurus", + "name": "Legacy Endpoint", + "uri_format": "https://web.expasy.org/cellosaurus/CVCL_$1" + }, + { + "code": "nextprot", + "description": "The neXtProt endpoint for exploring Cellosaurus", + "homepage": "https://www.nextprot.org/", + "name": "neXtProt Cellosaurus Browser", + "uri_format": "https://www.nextprot.org/term/CVCL_$1" + } + ], + "publications": [ + { + "doi": "10.1002/ijc.32639", + "pmc": null, + "pubmed": "31444973", + "title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication.", + "year": 2019 + }, + { + "doi": "10.7171/jbt.18-2902-002", + "pmc": "PMC5945021", + "pubmed": "29805321", + "title": "The Cellosaurus, a Cell-Line Knowledge Resource.", + "year": 2018 + } + ], + "synonyms": [ + "CVCL" + ], + "twitter": "cellosaurus", + "uri_format": "https://www.cellosaurus.org/CVCL_$1" + }, + "cellosaurus.resource": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The set of prefixes used in the Cellosaurus resource", + "example": "4DN", + "homepage": "https://web.expasy.org/cellosaurus/", + "keywords": [ + "cell lines", + "cells", + "registry" + ], + "name": "Cellosaurus Registry", + "preferred_prefix": "cellosaurus.resource", + "uri_format": "https://bioregistry.io/metaregistry/cellosaurus/$1" + }, + "cellrepo": { + "description": "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines", + "example": "82", + "homepage": "https://cellrepo.ico2s.org/", + "mappings": { + "miriam": "cellrepo" + }, + "name": "Cell Version Control Repository", + "pattern": "^[0-9]+$", + "preferred_prefix": "cellrepo", + "uri_format": "https://cellrepo.ico2s.org/repositories/$1" + }, + "cemo": { + "contact": { + "email": "n.queralt_rosinach@lumc.nl", + "github": "NuriaQueralt", + "name": "Núria Queralt Rosinach", + "orcid": "0000-0003-0169-8159" + }, + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response.", + "download_json": "https://raw.githubusercontent.com/cthoyt/covid19-epidemiology-ontology/add-artifacts/owl/cemo.json", + "download_owl": "https://raw.githubusercontent.com/NuriaQueralt/covid19-epidemiology-ontology/main/owl/cemo.owl", + "example": "secondary_attack_rate", + "github_request_issue": 593, + "homepage": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", + "keywords": [ + "ontology" + ], + "license": "CC0-1.0", + "name": "The COVID-19 epidemiology and monitoring ontology", + "pattern": "^[0-9a-z_-]+$", + "preferred_prefix": "cemo", + "providers": [ + { + "code": "obo", + "description": "This represents misconfigured base IRIs, even though this ontology isn't an OBO Foundry ontology", + "homepage": "http://purl.obolibrary.org/obo/", + "name": "Legacy OBO PURL", + "uri_format": "http://purl.obolibrary.org/obo/cemo.owl#$1" + } + ], + "repository": "https://github.com/NuriaQueralt/covid19-epidemiology-ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://biopragmatics.github.io/providers/cemo/$1" + }, + "ceph": { + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "deprecated": true, + "description": "An anatomical and developmental ontology for cephalopods", + "download_obo": "https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo", + "download_owl": "http://purl.obolibrary.org/obo/ceph.owl", + "example": "0000109", + "homepage": "https://github.com/obophenotype/cephalopod-ontology", + "keywords": [ + "anatomy", + "fisheries science", + "obo", + "ontology", + "zoology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "CEPH", + "biocontext": "CEPH", + "bioportal": "CEPH", + "fairsharing": "FAIRsharing.p58bm4", + "obofoundry": "ceph", + "ols": "ceph", + "ontobee": "CEPH" + }, + "name": "Cephalopod Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CEPH", + "repository": "https://github.com/obophenotype/cephalopod-ontology", + "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", + "version": "2016-01-12" + }, + "cgd": { + "description": "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products.", + "example": "CAL0003079", + "homepage": "http://www.candidagenome.org/", + "keywords": [ + "eukaryotic", + "genome", + "life science", + "nucleotide" + ], + "mappings": { + "biocontext": "CGD", + "fairsharing": "FAIRsharing.j7j53", + "go": "CGD", + "miriam": "cgd", + "n2t": "cgd", + "ncbi": "CGD", + "prefixcommons": "cgd", + "re3data": "r3d100010617", + "uniprot": "DB-0126" + }, + "name": "Candida Genome Database", + "pattern": "^CAL\\d{7}$", + "preferred_prefix": "cgd", + "publications": [ + { + "doi": "10.1093/nar/gkw924", + "pmc": "PMC5210628", + "pubmed": "27738138", + "title": "The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkr945", + "pmc": "PMC3245171", + "pubmed": "22064862", + "title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gki003", + "pmc": "PMC539957", + "pubmed": "15608216", + "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.", + "year": 2005 + } + ], + "uri_format": "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1" + }, + "cghdb": { + "description": "Cell line databases/resources", + "example": "300165/p13898_2106T", + "homepage": "http://www.cghtmd.jp/CGHDatabase/index_e.jsp", + "mappings": { + "cellosaurus": "CGH-DB" + }, + "name": "CGH Data Base", + "preferred_prefix": "cghdb", + "uri_format": "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en" + }, + "cgnc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)", + "example": "10087", + "homepage": "http://birdgenenames.org/cgnc/", + "keywords": [ + "gene" + ], + "mappings": { + "prefixcommons": "cgnc", + "re3data": "r3d100012429" + }, + "name": "Chicken Gene Nomenclature Consortium", + "pattern": "^\\d+$", + "preferred_prefix": "cgnc", + "publications": [ + { + "doi": "10.1186/1471-2164-10-s2-s5", + "pmc": "PMC2966335", + "pubmed": "19607656", + "title": "The Chicken Gene Nomenclature Committee report.", + "year": 2009 + } + ], + "synonyms": [ + "BirdBase", + "CGNC" + ], + "uri_format": "http://birdgenenames.org/cgnc/GeneReport?id=$1" + }, + "cgsc": { + "description": "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature.", + "example": "74", + "homepage": "http://cgsc.biology.yale.edu/index.php", + "keywords": [ + "gene", + "life science" + ], + "mappings": { + "biocontext": "CGSC", + "fairsharing": "FAIRsharing.1tbrdz", + "go": "CGSC", + "miriam": "cgsc", + "n2t": "cgsc", + "prefixcommons": "cgsc", + "re3data": "r3d100010585" + }, + "name": "Coli Genetic Stock Center", + "pattern": "^\\d+$", + "preferred_prefix": "cgsc", + "publications": [ + { + "doi": "10.1016/s0076-6879(06)21001-2", + "pmc": null, + "pubmed": "17352909", + "title": "Strain collections and genetic nomenclature.", + "year": 2007 + } + ], + "uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1" + }, + "charprot": { + "description": "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.", + "example": "CH_001923", + "homepage": "http://www.jcvi.org/charprotdb", + "mappings": { + "biocontext": "CHARPROT", + "miriam": "charprot", + "n2t": "charprot" + }, + "name": "CharProt", + "pattern": "^CH_\\d+$", + "preferred_prefix": "charprot", + "uri_format": "http://www.jcvi.org/charprotdb/index.cgi/view/$1" + }, + "chebi": { + "appears_in": [ + "cdno", + "chiro", + "cl", + "ecocore", + "ecto", + "envo", + "fobi", + "foodon", + "genepio", + "maxo", + "mco", + "ons", + "pcl", + "proco", + "scdo", + "uberon", + "xpo" + ], + "banana": "CHEBI", + "contact": { + "email": "amalik@ebi.ac.uk", + "github": "amalik01", + "name": "Adnan Malik", + "orcid": "0000-0001-8123-5351" + }, + "description": "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.", + "download_obo": "http://purl.obolibrary.org/obo/chebi.obo", + "download_owl": "http://purl.obolibrary.org/obo/chebi.owl", + "example": "24867", + "homepage": "http://www.ebi.ac.uk/chebi", + "keywords": [ + "biochemistry", + "chemical", + "chemistry", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CHEBI", + "bartoc": "558", + "biocontext": "CHEBI", + "bioportal": "CHEBI", + "cellosaurus": "ChEBI", + "cheminf": "000407", + "edam": "1174", + "fairsharing": "FAIRsharing.62qk8w", + "go": "CHEBI", + "miriam": "chebi", + "n2t": "chebi", + "obofoundry": "chebi", + "ols": "chebi", + "ontobee": "CHEBI", + "prefixcommons": "chebi", + "re3data": "r3d100012626", + "wikidata": "P683" + }, + "name": "Chemical Entities of Biological Interest", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "CHEBI", + "providers": [ + { + "code": "chebi-img", + "description": "Image server from chebi", + "homepage": "https://www.ebi.ac.uk/chebi/", + "name": "ChEBI", + "uri_format": "https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkv1031", + "pmc": "PMC4702775", + "pubmed": "26467479", + "title": "ChEBI in 2016: Improved services and an expanding collection of metabolites.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gks1146", + "pmc": "PMC3531142", + "pubmed": "23180789", + "title": "The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkp886", + "pmc": "PMC2808869", + "pubmed": "19854951", + "title": "Chemical Entities of Biological Interest: an update.", + "year": 2009 + }, + { + "doi": "10.1002/0471250953.bi1409s26", + "pmc": null, + "pubmed": "19496059", + "title": "ChEBI: an open bioinformatics and cheminformatics resource.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkm791", + "pmc": "PMC2238832", + "pubmed": "17932057", + "title": "ChEBI: a database and ontology for chemical entities of biological interest.", + "year": 2007 + } + ], + "repository": "https://github.com/ebi-chebi/ChEBI", + "synonyms": [ + "CHEBI", + "CHEBIID", + "ChEBI" + ], + "twitter": "chebit", + "uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1", + "version": "211" + }, + "chembank": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG).", + "example": "1000000", + "homepage": "http://chembank.broad.harvard.edu", + "keywords": [ + "chemical", + "metabolite" + ], + "mappings": { + "biocontext": "CHEMBANK", + "biolink": "ChemBank", + "prefixcommons": "chembank" + }, + "name": "ChemBank", + "preferred_prefix": "chembank", + "publications": [ + { + "doi": "10.1093/nar/gkm843", + "pmc": "PMC2238881", + "pubmed": "17947324", + "title": "ChemBank: a small-molecule screening and cheminformatics resource database.", + "year": 2007 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1" + }, + "chembl": { + "contact": { + "email": "dmendez@ebi.ac.uk", + "github": "nclopezo", + "name": "David Mendez Lopez", + "orcid": "0000-0002-0294-5484" + }, + "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", + "example": "CHEMBL4303805", + "homepage": "https://www.ebi.ac.uk/chembl", + "keywords": [ + "biochemistry", + "drug discovery", + "genomics", + "medicinal chemistry", + "molecules" + ], + "mappings": { + "cheminf": "000412", + "fairsharing": "FAIRsharing.m3jtpg", + "miriam": "chembl", + "prefixcommons": "chembl", + "re3data": "r3d100010539", + "uniprot": "DB-0174" + }, + "name": "ChEMBL", + "pattern": "^CHEMBL\\d+$", + "preferred_prefix": "chembl", + "publications": [ + { + "doi": "10.1093/nar/gky1075", + "pmc": "PMC6323927", + "pubmed": "30398643", + "title": "ChEMBL: towards direct deposition of bioassay data.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw1074", + "pmc": "PMC5210557", + "pubmed": "27899562", + "title": "The ChEMBL database in 2017.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkt1031", + "pmc": "PMC3965067", + "pubmed": "24214965", + "title": "The ChEMBL bioactivity database: an update.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkr777", + "pmc": "PMC3245175", + "pubmed": "21948594", + "title": "ChEMBL: a large-scale bioactivity database for drug discovery.", + "year": 2011 + } + ], + "repository": "https://github.com/chembl/GLaDOS", + "synonyms": [ + "ChEMBL", + "ChEMBL_ID", + "chembl" + ], + "twitter": "chembl", + "uri_format": "https://www.ebi.ac.uk/chembl/entity/$1" + }, + "chembl.cell": { + "contact": { + "email": "dmendez@ebi.ac.uk", + "github": "nclopezo", + "name": "David Mendez Lopez", + "orcid": "0000-0002-0294-5484" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Chemistry resources", + "example": "CHEMBL3307800", + "homepage": "https://www.ebi.ac.uk/chembldb", + "keywords": [ + "bioactivities", + "cell lines" + ], + "mappings": { + "cellosaurus": "ChEMBL-Cells" + }, + "name": "ChEMBL database of bioactive drug-like small molecules - Cell lines section", + "part_of": "chembl", + "preferred_prefix": "chembl.cell", + "synonyms": [ + "ChEMBL-Cells" + ], + "uri_format": "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1" + }, + "chembl.compound": { + "contact": { + "email": "dmendez@ebi.ac.uk", + "github": "nclopezo", + "name": "David Mendez Lopez", + "orcid": "0000-0002-0294-5484" + }, + "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", + "example": "CHEMBL465070", + "homepage": "https://www.ebi.ac.uk/chembldb/", + "mappings": { + "biocontext": "CHEMBL.COMPOUND", + "edam": "2646", + "miriam": "chembl.compound", + "n2t": "chembl.compound", + "wikidata": "P592" + }, + "name": "ChEMBL", + "part_of": "chembl", + "pattern": "^CHEMBL\\d+$", + "preferred_prefix": "chembl.compound", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "ChEMBL compound RDF", + "homepage": "https://github.com/egonw/chembl.rdf", + "name": "ChEMBL compound RDF", + "uri_format": "http://linkedchemistry.info/chembl/chemblid/$1" + }, + { + "code": "CURATOR_REVIEW", + "description": "ChEMBL compound RDF through EBI RDF Platform", + "homepage": "https://www.ebi.ac.uk/rdf/services/chembl/", + "name": "ChEMBL compound RDF through EBI RDF Platform", + "uri_format": "https://rdf.ebi.ac.uk/resource/chembl/molecule/$1" + } + ], + "uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1" + }, + "chembl.target": { + "contact": { + "email": "dmendez@ebi.ac.uk", + "github": "nclopezo", + "name": "David Mendez Lopez", + "orcid": "0000-0002-0294-5484" + }, + "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", + "example": "CHEMBL3467", + "homepage": "https://www.ebi.ac.uk/chembldb/", + "mappings": { + "biocontext": "CHEMBL.TARGET", + "cellosaurus": "ChEMBL-Targets", + "miriam": "chembl.target", + "n2t": "chembl.target" + }, + "name": "ChEMBL target", + "part_of": "chembl", + "pattern": "^CHEMBL\\d+$", + "preferred_prefix": "chembl.target", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "ChEMBL target RDF", + "homepage": "https://github.com/egonw/chembl.rdf", + "name": "ChEMBL target RDF", + "uri_format": "http://linkedchemistry.info/chembl/chemblid/$1" + }, + { + "code": "CURATOR_REVIEW", + "description": "ChEMBL target RDF through EBI RDF Platform", + "homepage": "https://rdf.ebi.ac.uk/resource/chembl/", + "name": "ChEMBL target RDF through EBI RDF Platform", + "uri_format": "https://rdf.ebi.ac.uk/resource/chembl/target/$1" + } + ], + "synonyms": [ + "ChEMBL-Targets" + ], + "uri_format": "https://www.ebi.ac.uk/chembl/target/inspect/$1" + }, + "chemdb": { + "description": "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds.", + "example": "3966782", + "homepage": "http://cdb.ics.uci.edu/", + "keywords": [ + "biochemistry", + "biomedical science", + "life science", + "preclinical studies", + "small molecule", + "systems biology" + ], + "mappings": { + "biocontext": "CHEMDB", + "fairsharing": "FAIRsharing.dstf7h", + "miriam": "chemdb", + "n2t": "chemdb", + "prefixcommons": "chemdb" + }, + "name": "ChemDB", + "pattern": "^\\d+$", + "preferred_prefix": "chemdb", + "publications": [ + { + "doi": "10.1093/bioinformatics/btm341", + "pmc": null, + "pubmed": "17599932", + "title": "ChemDB update--full-text search and virtual chemical space.", + "year": 2007 + }, + { + "doi": "10.1093/bioinformatics/bti683", + "pmc": null, + "pubmed": "16174682", + "title": "ChemDB: a public database of small molecules and related chemoinformatics resources.", + "year": 2005 + } + ], + "uri_format": "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1" + }, + "chemidplus": { + "description": "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.", + "example": "57-27-2", + "homepage": "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp", + "keywords": [ + "biomedical science", + "chemistry", + "molecules", + "structure" + ], + "mappings": { + "biocontext": "CHEMIDPLUS", + "edam": "2658", + "fairsharing": "FAIRsharing.5949vn", + "miriam": "chemidplus", + "n2t": "chemidplus", + "prefixcommons": "chemidplus" + }, + "name": "ChemIDplus", + "pattern": "^\\d+\\-\\d+\\-\\d+$", + "preferred_prefix": "chemidplus", + "publications": [ + { + "doi": "10.1300/j115v21n01_04", + "pmc": null, + "pubmed": "11989279", + "title": "ChemIDplus-super source for chemical and drug information.", + "year": 2002 + } + ], + "synonyms": [ + "ChemIDplus" + ], + "uri_format": "https://chem.nlm.nih.gov/chemidplus/rn/$1" + }, + "cheminf": { + "appears_in": [ + "proco" + ], + "contact": { + "email": "egon.willighagen@gmail.com", + "github": "egonw", + "name": "Egon Willighagen", + "orcid": "0000-0001-7542-0286" + }, + "description": "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.", + "download_owl": "https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl", + "example": "000410", + "homepage": "https://github.com/semanticchemistry/semanticchemistry", + "keywords": [ + "biochemistry", + "chemistry", + "life science", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "CHEMINF", + "biocontext": "CHEMINF", + "bioportal": "CHEMINF", + "fairsharing": "FAIRsharing.sjhvyy", + "obofoundry": "cheminf", + "ols": "cheminf", + "ontobee": "CHEMINF" + }, + "name": "Chemical Information Ontology", + "pattern": "^\\d{6}$", + "preferred_prefix": "CHEMINF", + "providers": [ + { + "code": "semanticscience", + "description": "Legacy URLs before conversion of CHEMINF to OBO PURLs", + "homepage": "http://semanticscience.org", + "name": "Semantic Science", + "uri_format": "http://semanticscience.org/resource/CHEMINF_$1" + } + ], + "publications": [ + { + "doi": "10.1371/journal.pone.0025513", + "pmc": "PMC3184996", + "pubmed": "21991315", + "title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.", + "year": 2011 + } + ], + "repository": "https://github.com/semanticchemistry/semanticchemistry", + "uri_format": "https://semanticscience.org/resource/CHEMINF_$1", + "version": "2.0" + }, + "chemrof": { + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof", + "download_owl": "http://aber-owl.net/media/ontologies/CHEMROF/2/chemrof.owl", + "example": "FullySpecifiedAtom", + "homepage": "https://chemkg.github.io/chemrof/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "CHEMROF", + "bioportal": "CHEMROF" + }, + "name": "Chemical Entity Materials and Reactions Ontological Framework", + "preferred_prefix": "ChEMROF", + "uri_format": "https://chemkg.github.io/chemrof/$1" + }, + "chemspider": { + "contact": { + "email": "pencehe@oneonta.edu", + "github": null, + "name": "Harry E. Pence", + "orcid": "0000-0002-0412-9018" + }, + "description": "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.", + "example": "56586", + "homepage": "http://www.chemspider.com/", + "keywords": [ + "chemistry", + "life science", + "molecules", + "structure" + ], + "mappings": { + "biocontext": "CHEMSPIDER", + "cheminf": "000405", + "edam": "1173", + "fairsharing": "FAIRsharing.96f3gm", + "miriam": "chemspider", + "n2t": "chemspider", + "prefixcommons": "chemspider", + "re3data": "r3d100010205", + "wikidata": "P661" + }, + "name": "ChemSpider", + "pattern": "^\\d+$", + "preferred_prefix": "chemspider", + "publications": [ + { + "doi": "10.1021/ed100697w", + "pmc": null, + "pubmed": null, + "title": "ChemSpider: An Online Chemical Information Resource", + "year": 2010 + } + ], + "synonyms": [ + "ChemSpiderID", + "Chemspider" + ], + "twitter": "ChemSpider", + "uri_format": "http://www.chemspider.com/Chemical-Structure.$1.html" + }, + "chickenqtldb": { + "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs.", + "example": "14362", + "homepage": "https://www.animalgenome.org/QTLdb", + "keywords": [ + "dna", + "genome" + ], + "mappings": { + "biocontext": "CHICKENQTLDB", + "miriam": "chickenqtldb", + "n2t": "chickenqtldb", + "prefixcommons": "chickenqtldb" + }, + "name": "Animal Genome Chicken QTL", + "part_of": "qtldb", + "pattern": "^\\d+$", + "preferred_prefix": "chickenqtldb", + "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" + }, + "chiro": { + "contact": { + "email": "vasilevs@ohsu.edu", + "github": "nicolevasilevsky", + "name": "Nicole Vasilevsky", + "orcid": "0000-0001-5208-3432" + }, + "depends_on": [ + "chebi", + "go", + "hp", + "mp", + "ncbitaxon", + "pr", + "uberon" + ], + "description": "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.", + "download_obo": "http://purl.obolibrary.org/obo/chiro.obo", + "download_owl": "http://purl.obolibrary.org/obo/chiro.owl", + "homepage": "https://github.com/obophenotype/chiro", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "CHIRO", + "bioportal": "CHIRO", + "obofoundry": "chiro", + "ols": "chiro", + "ontobee": "CHIRO" + }, + "name": "ChEBI Integrated Role Ontology", + "no_own_terms": true, + "preferred_prefix": "CHIRO", + "publications": [ + { + "doi": "10.26434/chemrxiv.12591221", + "pmc": null, + "pubmed": null, + "title": "Extension of Roles in the ChEBI Ontology", + "year": 2020 + } + ], + "repository": "https://github.com/obophenotype/chiro", + "uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", + "version": "2015-11-23" + }, + "chmo": { + "appears_in": [ + "rbo", + "scdo" + ], + "contact": { + "email": "batchelorc@rsc.org", + "github": "batchelorc", + "name": "Colin Batchelor", + "orcid": "0000-0001-5985-7429" + }, + "description": "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).", + "download_obo": "http://purl.obolibrary.org/obo/chmo.obo", + "download_owl": "http://purl.obolibrary.org/obo/chmo.owl", + "example": "0002902", + "homepage": "https://github.com/rsc-ontologies/rsc-cmo", + "keywords": [ + "chemistry", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CHMO", + "biocontext": "CHMO", + "bioportal": "CHMO", + "fairsharing": "FAIRsharing.9j4wh2", + "obofoundry": "chmo", + "ols": "chmo", + "ontobee": "CHMO" + }, + "name": "Chemical Methods Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CHMO", + "repository": "https://github.com/rsc-ontologies/rsc-cmo", + "uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", + "version": "2022-04-19" + }, + "cido": { + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "description": "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment.", + "download_owl": "https://github.com/CIDO-ontology/cido/raw/master/cido.owl", + "example": "0000005", + "homepage": "https://github.com/cido-ontology/cido", + "keywords": [ + "bioinformatics", + "drug discovery", + "drug repositioning", + "epidemiology", + "obo", + "ontology", + "virology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CIDO", + "bioportal": "CIDO", + "fairsharing": "FAIRsharing.aVmpKl", + "obofoundry": "cido", + "ols": "cido", + "ontobee": "CIDO" + }, + "name": "Coronavirus Infectious Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CIDO", + "publications": [ + { + "doi": "10.1186/s13326-022-00279-z", + "pmc": "PMC9585694", + "pubmed": "36271389", + "title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.", + "year": 2022 + }, + { + "doi": "10.1038/s41597-020-0523-6", + "pmc": "PMC7293349", + "pubmed": "32533075", + "title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.", + "year": 2020 + } + ], + "repository": "https://github.com/cido-ontology/cido", + "uri_format": "http://purl.obolibrary.org/obo/CIDO_$1", + "version": "1.0.337" + }, + "cio": { + "contact": { + "email": "frederic.bastian@unil.ch", + "github": "fbastian", + "name": "Frédéric Bastian", + "orcid": "0000-0002-9415-5104" + }, + "description": "An ontology to capture confidence information about annotations.", + "download_obo": "http://purl.obolibrary.org/obo/cio.obo", + "download_owl": "http://purl.obolibrary.org/obo/cio.owl", + "example": "0000040", + "homepage": "https://github.com/BgeeDB/confidence-information-ontology", + "keywords": [ + "biology", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "CIO", + "biocontext": "CIO", + "bioportal": "CIO", + "fairsharing": "FAIRsharing.e3t0yw", + "obofoundry": "cio", + "ols": "cio", + "ontobee": "CIO" + }, + "name": "Confidence Information Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CIO", + "publications": [ + { + "doi": "10.1093/database/bav043", + "pmc": "PMC4425939", + "pubmed": "25957950", + "title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.", + "year": 2015 + } + ], + "repository": "https://github.com/BgeeDB/confidence-information-ontology", + "uri_format": "http://purl.obolibrary.org/obo/CIO_$1", + "version": "2015-03-10" + }, + "citexplore": { + "contact": { + "email": "maria.taboada@usc.es", + "github": null, + "name": "Maria Taboada", + "orcid": "0000-0002-2353-596X" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes.", + "example": "C6155", + "homepage": "https://www.ebi.ac.uk/citexplore/", + "keywords": [ + "biomedical science", + "genetics", + "preclinical studies" + ], + "mappings": { + "fairsharing": "FAIRsharing.619eqr", + "prefixcommons": "citexplore" + }, + "name": "CiteXplore", + "preferred_prefix": "citexplore", + "publications": [ + { + "doi": "10.1097/mol.0b013e328362df13", + "pmc": null, + "pubmed": "23759795", + "title": "Cerebrotendinous xanthomatosis.", + "year": 2013 + } + ], + "references": [ + "https://www.embl.de/aboutus/communication_outreach/media_relations/2006/061127_hinxton/" + ], + "synonyms": [ + "CTX" + ], + "uri_format": "https://europepmc.org/article/CTX/$1" + }, + "cito": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically.", + "example": "sharesAuthorInstitutionWith", + "homepage": "http://www.sparontologies.net/ontologies/cito", + "keywords": [ + "knowledge and information systems" + ], + "mappings": { + "fairsharing": "FAIRsharing.b220d4" + }, + "name": "Citation Typing Ontology", + "preferred_prefix": "CiTO", + "publications": [ + { + "doi": "10.1016/j.websem.2012.08.001", + "pmc": null, + "pubmed": null, + "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", + "year": 2012 + } + ], + "repository": "https://github.com/sparontologies/cito", + "twitter": "sparontologies", + "uri_format": "http://purl.org/spar/cito/$1" + }, + "civic.aid": { + "description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.", + "example": "3", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.aid" + }, + "name": "CIViC Assertion", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.aid", + "uri_format": "https://civicdb.org/links/assertions/$1" + }, + "civic.did": { + "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", + "example": "46", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.did" + }, + "name": "CIViC Disease", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.did", + "uri_format": "https://civicdb.org/links/diseases/$1" + }, + "civic.eid": { + "description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).", + "example": "1199", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.eid" + }, + "name": "CIViC Evidence", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.eid", + "uri_format": "https://civicdb.org/links/evidence/$1" + }, + "civic.gid": { + "description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis", + "example": "272", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.gid", + "wikidata": "P11277" + }, + "name": "CIViC gene", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.gid", + "uri_format": "https://civicdb.org/links/gene/$1" + }, + "civic.sid": { + "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", + "example": "62", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.sid" + }, + "name": "CIViC Source", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.sid", + "uri_format": "https://civicdb.org/links/sources/$1" + }, + "civic.tid": { + "description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", + "example": "14", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.tid" + }, + "name": "CIViC Therapy", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.tid", + "uri_format": "https://civicdb.org/links/drugs/$1" + }, + "civic.vid": { + "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", + "example": "12", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.vid", + "wikidata": "P3329" + }, + "name": "CIViC variant", + "part_of": "civic", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.vid", + "uri_format": "https://civicdb.org/links/variant/$1" + }, + "cl": { + "appears_in": [ + "clo", + "ecao", + "ehdaa2", + "go", + "mco", + "pcl", + "uberon", + "xpo" + ], + "banana": "CL", + "contact": { + "email": "addiehl@buffalo.edu", + "github": "addiehl", + "name": "Alexander Diehl", + "orcid": "0000-0001-9990-8331" + }, + "depends_on": [ + "chebi", + "go", + "ncbitaxon", + "pato", + "pr", + "ro", + "uberon" + ], + "description": "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi.", + "download_obo": "https://github.com/obophenotype/cell-ontology/raw/master/cl.obo", + "download_owl": "http://purl.obolibrary.org/obo/cl.owl", + "example": "0000062", + "homepage": "https://obophenotype.github.io/cell-ontology/", + "keywords": [ + "anatomy", + "cell", + "cell biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CL", + "agroportal": "CL", + "biocontext": "CL", + "bioportal": "CL", + "cellosaurus": "CL", + "fairsharing": "FAIRsharing.j9y503", + "go": "CL", + "miriam": "cl", + "n2t": "cl", + "obofoundry": "cl", + "ols": "cl", + "ontobee": "CL", + "prefixcommons": "cl", + "wikidata": "P7963" + }, + "name": "Cell Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "CL", + "providers": [ + { + "code": "cellxgene", + "description": "Explore single cell data through the CZ CELLxGENE portal", + "homepage": "https://onto.cellxgene-labs.prod.si.czi.technology", + "name": "CELLxGENE", + "uri_format": "https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/CL/CL:$1" + } + ], + "publications": [ + { + "doi": "10.1186/s13326-016-0088-7", + "pmc": "PMC4932724", + "pubmed": "27377652", + "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.", + "year": 2016 + }, + { + "doi": "10.1186/1471-2105-12-6", + "pmc": "PMC3024222", + "pubmed": "21208450", + "title": "Logical development of the cell ontology.", + "year": 2011 + } + ], + "repository": "https://github.com/obophenotype/cell-ontology", + "twitter": "CellOntology", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1", + "version": "2022-12-15" + }, + "clao": { + "contact": { + "email": "lagonzalezmo@unal.edu.co", + "github": "luis-gonzalez-m", + "name": "Luis González-Montaña", + "orcid": "0000-0002-9136-9932" + }, + "depends_on": [ + "ro" + ], + "description": "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda).", + "download_obo": "http://purl.obolibrary.org/obo/clao.obo", + "download_owl": "http://purl.obolibrary.org/obo/clao.owl", + "example": "0000088", + "homepage": "https://github.com/luis-gonzalez-m/Collembola", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "CLAO", + "bioportal": "CLAO", + "obofoundry": "clao", + "ols": "clao", + "ontobee": "CLAO" + }, + "name": "Collembola Anatomy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CLAO", + "repository": "https://github.com/luis-gonzalez-m/Collembola", + "uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", + "version": "2021-09-27" + }, + "classyfire": { + "banana": "C", + "comment": "There's a mismatch between the MIRIAM URI format string, which has a C prefix in front of class identifiers and the ontology which does not use them.", + "description": "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API.", + "download_obo": "http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip", + "example": "0004828", + "homepage": "http://classyfire.wishartlab.com/", + "keywords": [ + "ontology" + ], + "mappings": { + "miriam": "classyfire" + }, + "name": "ClassyFire", + "pattern": "^\\d{7}$", + "preferred_prefix": "classyfire", + "synonyms": [ + "CHEMONTID" + ], + "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1" + }, + "clb": { + "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", + "example": "1010", + "homepage": "https://www.checklistbank.org", + "mappings": { + "miriam": "clb" + }, + "name": "ChecklistBank", + "pattern": "^[0-9]+(LR)?$", + "preferred_prefix": "clb", + "uri_format": "https://www.checklistbank.org/dataset/$1" + }, + "cldb": { + "description": "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories.", + "example": "cl3603", + "homepage": "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html", + "mappings": { + "biocontext": "CLDB", + "cellosaurus": "CLDB", + "miriam": "cldb", + "n2t": "cldb" + }, + "name": "Cell Line Database", + "pattern": "^(cl|tum)\\d+$", + "preferred_prefix": "cldb", + "uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html" + }, + "clingene": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + } + ], + "description": "The allele registry provides and maintains identifiers for genetic variants", + "example": "CA981206459", + "homepage": "https://reg.clinicalgenome.org", + "keywords": [ + "alleles", + "genetics", + "mutations" + ], + "mappings": { + "biolink": "CAID" + }, + "name": "ClinGen Allele Registry", + "pattern": "^CA\\d+$", + "preferred_prefix": "clingene", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/647" + ], + "synonyms": [ + "CAID" + ], + "uri_format": "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1" + }, + "clinicaltrials": { + "description": "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries", + "example": "NCT00222573", + "homepage": "https://clinicaltrials.gov/", + "keywords": [ + "disease", + "drug", + "human" + ], + "mappings": { + "biocontext": "CLINICALTRIALS", + "miriam": "clinicaltrials", + "n2t": "clinicaltrials", + "prefixcommons": "clinicaltrials", + "wikidata": "P3098" + }, + "name": "ClinicalTrials.gov", + "pattern": "^NCT\\d{8}$", + "preferred_prefix": "clinicaltrials", + "providers": [ + { + "code": "smartpatients", + "description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.", + "homepage": "https://www.smartpatients.com", + "name": "Smart Patients", + "uri_format": "https://www.smartpatients.com/trials/$1" + } + ], + "synonyms": [ + "clinicaltrial" + ], + "uri_format": "https://clinicaltrials.gov/ct2/show/$1" + }, + "clinvar": { + "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", + "example": "12345", + "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", + "keywords": [ + "biomedical science", + "clinical studies", + "genomics", + "preclinical studies" + ], + "mappings": { + "biocontext": "ClinVarVariant", + "biolink": "CLINVAR", + "cellosaurus": "ClinVar", + "fairsharing": "FAIRsharing.wx5r6f", + "hl7": "2.16.840.1.113883.6.319", + "miriam": "clinvar", + "n2t": "clinvar", + "re3data": "r3d100013331", + "wikidata": "P1929" + }, + "name": "ClinVar Variation", + "pattern": "^\\d+$", + "preferred_prefix": "clinvar", + "publications": [ + { + "doi": "10.1093/nar/gkt1113", + "pmc": "PMC3965032", + "pubmed": "24234437", + "title": "ClinVar: public archive of relationships among sequence variation and human phenotype.", + "year": 2013 + } + ], + "synonyms": [ + "clinvar.variant", + "clinvar.variation" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1" + }, + "clinvar.record": { + "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", + "example": "RCV000033555.3", + "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", + "mappings": { + "biocontext": "CLINVAR.RECORD", + "miriam": "clinvar.record", + "n2t": "clinvar.record" + }, + "name": "ClinVar Record", + "part_of": "clinvar", + "pattern": "^RCV\\d+(\\.\\d+)?$", + "preferred_prefix": "clinvar.record", + "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar/$1" + }, + "clinvar.submission": { + "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession.", + "example": "SCV000151292", + "homepage": "http://www.ncbi.nlm.nih.gov/clinvar/", + "mappings": { + "biocontext": "CLINVAR.SUBMISSION", + "miriam": "clinvar.submission", + "n2t": "clinvar.submission" + }, + "name": "ClinVar Submission", + "pattern": "^SCV\\d+(\\.\\d+)?$", + "preferred_prefix": "clinvar.submission", + "uri_format": "http://www.ncbi.nlm.nih.gov/clinvar?term=$1" + }, + "clinvar.submitter": { + "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs).", + "example": "26957", + "homepage": "https://www.ncbi.nlm.nih.gov/clinvar/", + "mappings": { + "miriam": "clinvar.submitter" + }, + "name": "ClinVar Submitter", + "pattern": "^\\d+$", + "preferred_prefix": "clinvar.submitter", + "uri_format": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1" + }, + "clo": { + "appears_in": [ + "mco" + ], + "contact": { + "email": "siiraa@umich.edu", + "github": "siiraa", + "name": "Sirarat Sarntivijai", + "orcid": "0000-0002-2548-641X" + }, + "depends_on": [ + "cl", + "doid", + "ncbitaxon", + "uberon" + ], + "description": "The Cell Line Ontology is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.", + "download_owl": "http://purl.obolibrary.org/obo/clo.owl", + "example": "0000091", + "homepage": "http://www.clo-ontology.org", + "keywords": [ + "cell biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "CLO", + "biocontext": "CLO", + "bioportal": "CLO", + "cellosaurus": "CLO", + "fairsharing": "FAIRsharing.4dvtcz", + "miriam": "clo", + "obofoundry": "clo", + "ols": "clo", + "ontobee": "CLO", + "prefixcommons": "clo", + "wikidata": "P2158" + }, + "name": "Cell Line Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CLO", + "providers": [ + { + "code": "bioportal", + "description": "Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users.", + "homepage": "https://bioportal.bioontology.org", + "name": "Center for Biomedical Informatics Research, Stanford", + "uri_format": "https://bioportal.bioontology.org/ontologies/CLO/?p=classes&conceptid=http://purl.obolibrary.org/obo/CLO_$1" + } + ], + "publications": [ + { + "doi": "10.1186/2041-1480-5-37", + "pmc": "PMC4387853", + "pubmed": "25852852", + "title": "CLO: The cell line ontology.", + "year": 2014 + }, + { + "doi": "10.1186/gb-2005-6-2-r21", + "pmc": "PMC551541", + "pubmed": "15693950", + "title": "An ontology for cell types.", + "year": 2005 + } + ], + "repository": "https://github.com/CLO-Ontology/CLO", + "synonyms": [ + "CLO" + ], + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?short_form=CLO_$1", + "version": "2.1.178" + }, + "cls": { + "description": "Cell line collections", + "example": "300108/p3934_A-172", + "homepage": "https://cls.shop/", + "mappings": { + "cellosaurus": "CLS" + }, + "name": "Cell Lines Service", + "preferred_prefix": "cls", + "uri_format": "https://cls.shop/$1" + }, + "clyh": { + "contact": { + "email": "lucas.leclere@obs-vlfr.fr", + "github": "L-Leclere", + "name": "Lucas Leclere", + "orcid": "0000-0002-7440-0467" + }, + "depends_on": [ + "iao", + "ro", + "uberon" + ], + "description": "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica.", + "download_obo": "http://purl.obolibrary.org/obo/clyh.obo", + "download_owl": "http://purl.obolibrary.org/obo/clyh.owl", + "example": "1000100", + "homepage": "https://github.com/EBISPOT/clyh_ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "CLYH", + "bioportal": "CLYH", + "obofoundry": "clyh", + "ols": "clyh", + "ontobee": "CLYH" + }, + "name": "Clytia hemisphaerica Development and Anatomy Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "CLYH", + "repository": "https://github.com/EBISPOT/clyh_ontology", + "uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", + "version": "2020-05-29" + }, + "cmecs": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.", + "example": "595", + "homepage": "https://cmecscatalog.org/cmecs", + "keywords": [ + "ecology", + "marine ecology" + ], + "name": "Costal and Marine Ecological Classification Standard", + "pattern": "^\\d+$", + "preferred_prefix": "cmecs", + "references": [ + "http://www.natureserve.org/sites/default/files/publications/files/cmecs_version_06-2012_final.pdf" + ], + "uri_format": "https://cmecscatalog.org/cmecs/classification/unit/$1.html" + }, + "cmf": { + "contact": { + "email": "engelsta@ohsu.edu", + "github": null, + "name": "Mark Engelstad", + "orcid": "0000-0001-5889-4463" + }, + "deprecated": true, + "description": "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain", + "homepage": "https://code.google.com/p/craniomaxillofacial-ontology/", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "aberowl": "CMF", + "biocontext": "CMF", + "obofoundry": "cmf", + "ontobee": "CMF" + }, + "name": "CranioMaxilloFacial ontology", + "preferred_prefix": "CMF", + "uri_format": "http://purl.obolibrary.org/obo/CMF_$1" + }, + "cmo": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "jrsmith@mcw.edu", + "github": "jrsjrs", + "name": "Jennifer Smith", + "orcid": "0000-0002-6443-9376" + }, + "description": "Morphological and physiological measurement records generated from clinical and model organism research and health programs.", + "download_obo": "http://purl.obolibrary.org/obo/cmo.obo", + "download_owl": "http://purl.obolibrary.org/obo/cmo.owl", + "example": "0001350", + "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", + "keywords": [ + "biomedical science", + "life science", + "obo", + "ontology", + "preclinical studies" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "CMO", + "biocontext": "CMO", + "bioportal": "CMO", + "fairsharing": "FAIRsharing.dq78pn", + "obofoundry": "cmo", + "ols": "cmo", + "ontobee": "CMO" + }, + "name": "Clinical measurement ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CMO", + "publications": [ + { + "doi": "10.1186/2041-1480-4-26", + "pmc": "PMC3882879", + "pubmed": "24103152", + "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", + "year": 2013 + }, + { + "doi": "10.3389/fgene.2012.00087", + "pmc": "PMC3361058", + "pubmed": "22654893", + "title": "Three ontologies to define phenotype measurement data.", + "year": 2012 + } + ], + "repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology", + "twitter": "ratgenome", + "uri_format": "http://purl.obolibrary.org/obo/CMO_$1", + "version": "2019-02-19" + }, + "cmpo": { + "contact": { + "email": "jupp@ebi.ac.uk", + "github": null, + "name": "Simon Jupp", + "orcid": "0000-0002-0643-3144" + }, + "description": "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations.", + "download_owl": "http://www.ebi.ac.uk/cmpo/releases/2017-12-19/cmpo.owl", + "example": "0000435", + "homepage": "http://www.ebi.ac.uk/cmpo", + "keywords": [ + "cell biology", + "ontology" + ], + "mappings": { + "aberowl": "CMPO", + "bioportal": "CMPO", + "fairsharing": "FAIRsharing.knp11s", + "ols": "cmpo" + }, + "name": "Cellular Microscopy Phenotype Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "cmpo", + "publications": [ + { + "doi": "10.1186/s13326-016-0074-0", + "pmc": "PMC4870745", + "pubmed": "27195102", + "title": "The cellular microscopy phenotype ontology.", + "year": 2016 + } + ], + "repository": "https://github.com/EBISPOT/CMPO", + "twitter": "EBIOLS", + "uri_format": "http://www.ebi.ac.uk/cmpo/CMPO_$1", + "version": "2017-12-19" + }, + "cnrs": { + "comment": "Motivated to add because of appearance in ROR", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "identifier for an academic research group issued by the CNRS", + "example": "UMR7315", + "homepage": "https://annuaire.cnrs.fr", + "mappings": { + "wikidata": "P4550" + }, + "name": "French National Center for Scientific Research - Research Group Identifier", + "pattern": "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$", + "preferred_prefix": "cnrs", + "uri_format": "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u" + }, + "co_320": { + "contact": { + "email": "j.detras@cgiar.org", + "github": null, + "name": "Jeffrey A. Detras", + "orcid": "0000-0002-6680-578X" + }, + "description": "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables", + "download_owl": "https://cropontology.org/ontology/CO_320/Rice/owl", + "example": "0000618", + "homepage": "https://cropontology.org/ontology/CO_320/Rice", + "keywords": [ + "agriculture", + "botany", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_320", + "cropoct": "CO_320", + "fairsharing": "FAIRsharing.2jkxp5", + "ols": "co_320" + }, + "name": "Rice ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_320", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_320:$1", + "version": "2019-10-09" + }, + "co_321": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Rosemary Shrestha", + "orcid": "0000-0002-9399-8003" + }, + "description": "July 2018", + "download_owl": "https://cropontology.org/ontology/CO_321/Wheat/owl", + "example": "0000449", + "homepage": "https://cropontology.org/ontology/CO_321/Wheat", + "keywords": [ + "agriculture", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_321", + "cropoct": "CO_321", + "fairsharing": "FAIRsharing.czzmpg", + "ols": "co_321" + }, + "name": "Wheat ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_321", + "publications": [ + { + "doi": "10.1093/aobpla/plq008", + "pmc": "PMC3000699", + "pubmed": "22476066", + "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.", + "year": 2010 + } + ], + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_321:$1", + "version": "2019-10-09" + }, + "co_322": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "Maize Trait Dictionary in template 5 - CIMMYT- September 2016", + "download_owl": "https://cropontology.org/ontology/CO_322/Maize/owl", + "example": "0000773", + "homepage": "https://cropontology.org/ontology/CO_322/Maize", + "keywords": [ + "agriculture", + "botany", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_322", + "cropoct": "CO_322", + "fairsharing": "FAIRsharing.eeyne8", + "ols": "co_322" + }, + "name": "Maize ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_322", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_322:$1", + "version": "2019-10-09" + }, + "co_323": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Ramesh Verna", + "orcid": null + }, + "description": "ICARDA - TDv5 - Sept 2018", + "download_owl": "https://cropontology.org/ontology/CO_323/Barley/owl", + "example": "0000252", + "homepage": "https://cropontology.org/ontology/CO_323/Barley", + "keywords": [ + "agriculture", + "botany", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_323", + "cropoct": "CO_323", + "fairsharing": "FAIRsharing.f69084", + "ols": "co_323" + }, + "name": "Barley ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_323", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_323:$1", + "version": "2019-11-20" + }, + "co_324": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "Sorghum TDv5 - Oct 2019", + "download_owl": "https://cropontology.org/ontology/CO_324/Sorghum/owl", + "example": "0000111", + "homepage": "https://cropontology.org/ontology/CO_324/Sorghum", + "keywords": [ + "agriculture", + "botany", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_324", + "cropoct": "CO_324", + "fairsharing": "FAIRsharing.dxx0c", + "ols": "co_324" + }, + "name": "Sorghum ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_324", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_324:$1", + "version": "2019-10-09" + }, + "co_325": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Elizabeth Arnaud", + "orcid": "0000-0002-6020-5919" + }, + "description": "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019", + "download_owl": "https://cropontology.org/ontology/CO_325/Banana/owl", + "example": "0000519", + "homepage": "https://cropontology.org/ontology/CO_325/Banana", + "keywords": [ + "agriculture", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_325", + "cropoct": "CO_325", + "fairsharing": "FAIRsharing.gdszhh", + "ols": "co_325" + }, + "name": "Banana ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_325", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_325:$1", + "version": "2019-10-09" + }, + "co_326": { + "description": "Draft version", + "download_owl": "https://cropontology.org/ontology/CO_326/Coconut/owl", + "example": "0000254", + "homepage": "https://cropontology.org/ontology/CO_326/Coconut", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "cropoct": "CO_326", + "ols": "co_326" + }, + "name": "Coconut ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_326", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_326:$1" + }, + "co_327": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016", + "download_owl": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet/owl", + "example": "0000095", + "homepage": "http://www.cropontology.org/ontology/CO_327/Pearl%20millet", + "keywords": [ + "agriculture", + "botany", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_327", + "cropoct": "CO_327", + "fairsharing": "FAIRsharing.4e3qh9", + "ols": "co_327" + }, + "name": "Pearl millet ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_327", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_327:$1" + }, + "co_330": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "CIP - potato ontology - december 2018", + "download_owl": "https://cropontology.org/ontology/CO_330/Potato/owl", + "example": "0000106", + "homepage": "https://cropontology.org/ontology/CO_330/Potato", + "keywords": [ + "agriculture", + "botany", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_330", + "cropoct": "CO_330", + "fairsharing": "FAIRsharing.4fa657", + "ols": "co_330" + }, + "name": "Potato ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_330", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_330:$1", + "version": "2019-10-09" + }, + "co_331": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Vilma Hualla Mamani", + "orcid": "0000-0003-0595-5271" + }, + "description": "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019", + "download_owl": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato/owl", + "example": "0000088", + "homepage": "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato", + "keywords": [ + "agriculture", + "botany", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_331", + "cropoct": "CO_331", + "fairsharing": "FAIRsharing.4g5qcw", + "ols": "co_331" + }, + "name": "Sweet Potato ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_331", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_331:$1" + }, + "co_333": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "This ontology was built as part of the AKER project. 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Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE.", + "download_owl": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology/owl", + "example": "1000290", + "homepage": "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology", + "keywords": [ + "botany", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_357", + "cropoct": "CO_357", + "fairsharing": "FAIRsharing.2b04ae", + "ols": "co_357" + }, + "name": "Woody Plant Ontology ontology", + "pattern": "^\\d+$", + "preferred_prefix": "CO_357", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_357:$1" + }, + "co_358": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "Cotton ontology from CottonGen database - June 2019", + "download_owl": "https://cropontology.org/ontology/CO_358/Cotton/owl", + "example": "0000139", + "homepage": "https://cropontology.org/ontology/CO_358/Cotton", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_358", + "cropoct": "CO_358", + "ols": "co_358" + }, + "name": "Cotton ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_358", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_358:$1", + "version": "2020-01-03" + }, + "co_359": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "December 2019", + "download_owl": "https://cropontology.org/ontology/CO_359/Sunflower/owl", + "example": "0000947", + "homepage": "https://cropontology.org/ontology/CO_359/Sunflower", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_359", + "cropoct": "CO_359", + "ols": "co_359" + }, + "name": "Sunflower ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_359", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_359:$1" + }, + "co_360": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "Sugar Kelp trait ontology", + "download_owl": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait/owl", + "example": "0000071", + "homepage": "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait", + "keywords": [ + "botany", + "life science", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_360", + "cropoct": "CO_360", + "fairsharing": "FAIRsharing.1c1738", + "ols": "co_360" + }, + "name": "Sugar Kelp trait ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_360", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_360:$1" + }, + "co_365": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "ICARDA Ethiopia", + "orcid": null + }, + "description": "developed by ICARDA - Dec 2018", + "download_owl": "https://cropontology.org/ontology/CO_365/Fababean/owl", + "example": "0000205", + "homepage": "https://cropontology.org/ontology/CO_365/Fababean", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_365", + "cropoct": "CO_365", + "ols": "co_365" + }, + "name": "Fababean ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_365", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_365:$1", + "version": "2019-10-15" + }, + "co_366": { + "contact": { + "email": "helpdesk@cropontology-curationtool.org", + "github": null, + "name": "Crop Ontology Helpdesk", + "orcid": null + }, + "description": "version Dec 2019", + "download_owl": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut/owl", + "example": "0000072", + "homepage": "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_366", + "cropoct": "CO_366", + "ols": "co_366" + }, + "name": "Bambara groundnut ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_366", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_366:$1" + }, + "co_367": { + "description": "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021", + "example": "0000004", + "homepage": "https://cropontology.org/term/CO_367:ROOT", + "license": "CC-BY-4.0", + "mappings": { + "cropoct": "CO_367" + }, + "name": "Quinoa Ontology ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_367", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_367:$1" + }, + "co_370": { + "contact": { + "email": "ekaterina.chuprikova@eurac.edu", + "github": null, + "name": "Ekaterina Chuprikova", + "orcid": "0000-0002-8981-0442" + }, + "description": "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales.", + "example": "0000890", + "homepage": "https://cropontology.org/term/CO_370:ROOT", + "license": "CC-BY-4.0", + "mappings": { + "agroportal": "CO_370", + "cropoct": "CO_370" + }, + "name": "Apple Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CO_370", + "repository": "https://github.com/bioversity/Crop-Ontology", + "uri_format": "https://cropontology.org/rdf/CO_370:$1" + }, + "cob": { + "contact": { + "email": "bpeters@lji.org", + "github": "bpeters42", + "name": "Bjoern Peters", + "orcid": "0000-0002-8457-6693" + }, + "description": "COB brings together key terms from a wide range of OBO projects to improve interoperability.", + "download_owl": "http://purl.obolibrary.org/obo/cob.owl", + "example": "0000080", + "homepage": "https://obofoundry.org/COB/", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "COB", + "bioportal": "COB", + "obofoundry": "cob", + "ols": "cob", + "ontobee": "COB" + }, + "name": "Core Ontology for Biology and Biomedicine", + "pattern": "^\\d{7}$", + "preferred_prefix": "COB", + "repository": "https://github.com/OBOFoundry/COB", + "uri_format": "http://purl.obolibrary.org/obo/COB_$1", + "version": "2022-05-02" + }, + "coconut": { + "comment": "@mSorok is the dev of the resource, hope I got it right!", + "contributor": { + "email": "adriano.rutz@ik.me", + "github": "adafede", + "name": "Adriano Rutz", + "orcid": "0000-0003-0443-9902" + }, + "description": "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties.", + "example": "CNP0171505", + "github_request_issue": 221, + "homepage": "https://coconut.naturalproducts.net", + "keywords": [ + "chemistry", + "natural producs", + "organic chemistry" + ], + "name": "COlleCtion of Open Natural ProdUcTs", + "pattern": "^CNP\\d{7}$", + "preferred_prefix": "coconut", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://coconut.naturalproducts.net/compound/coconut_id/$1" + }, + "codelink": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release).", + "example": "GE86325", + "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt", + "keywords": [ + "microarray", + "transcriptomics" + ], + "name": "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray", + "pattern": "^GE\\d+$", + "preferred_prefix": "codelink", + "references": [ + "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-8060/A-GEOD-8060.adf.txt", + "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt" + ] + }, + "cog": { + "contact": { + "email": "cogs@ncbi.nlm.nih.gov", + "github": null, + "name": "Michael Y Galperin", + "orcid": "0000-0002-2265-5572" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems.", + "example": "COG0001", + "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", + "keywords": [ + "genome", + "life science", + "protein" + ], + "mappings": { + "biolink": "COG", + "fairsharing": "FAIRsharing.djsbw2", + "go": "COG_Cluster", + "prefixcommons": "cog" + }, + "name": "Cluster of orthologous genes", + "pattern": "^COG\\d+$", + "preferred_prefix": "cog", + "publications": [ + { + "doi": "10.1126/science.278.5338.631", + "pmc": null, + "pubmed": "9381173", + "title": "A genomic perspective on protein families.", + "year": 1997 + }, + { + "doi": "10.1093/nar/gku1223", + "pmc": "PMC4383993", + "pubmed": "25428365", + "title": "Expanded microbial genome coverage and improved protein family annotation in the COG database.", + "year": 2014 + } + ], + "synonyms": [ + "COG_Cluster" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1" + }, + "cog.category": { + "contact": { + "email": "cogs@ncbi.nlm.nih.gov", + "github": null, + "name": "Michael Y Galperin", + "orcid": "0000-0002-2265-5572" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Higher-level classifications of COG Pathways", + "example": "K", + "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/", + "keywords": [ + "pathways" + ], + "name": "COG Categories", + "part_of": "cog", + "preferred_prefix": "cog.category", + "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1" + }, + "cog.pathway": { + "contact": { + "email": "cogs@ncbi.nlm.nih.gov", + "github": null, + "name": "Michael Y Galperin", + "orcid": "0000-0002-2265-5572" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera.", + "example": "NAD%20biosynthesis", + "homepage": "https://www.ncbi.nlm.nih.gov/research/cog/pathways", + "mappings": { + "go": "COG_Pathway" + }, + "name": "COG Pathways", + "part_of": "cog", + "preferred_prefix": "cog.pathway", + "uri_format": "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1" + }, + "cohd": { + "comment": "not really sure where the source is. this also links to a system called athena. I was not able to figure out what COHD stands for.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012", + "homepage": "https://github.com/MIT-LCP/mimic-omop", + "keywords": [ + "clinical data", + "clinical trials", + "health", + "health sciences" + ], + "name": "MIMIC III Database", + "no_own_terms": true, + "preferred_prefix": "cohd", + "repository": "https://github.com/MIT-LCP/mimic-omop" + }, + "col": { + "description": "Identifier of a taxon or synonym in the Catalogue of Life", + "example": "4QHKG", + "homepage": "https://www.checklistbank.org", + "mappings": { + "bartoc": "1915", + "miriam": "col" + }, + "name": "Catalogue of Life", + "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", + "preferred_prefix": "col", + "providers": [ + { + "code": "col", + "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", + "homepage": "https://www.catalogueoflife.org", + "name": "Catalogue of Life (COL)", + "uri_format": "https://www.catalogueoflife.org/data/taxon/$1" + } + ], + "uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1" + }, + "col.taiwan": { + "contributor": { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + }, + "description": "Identifier (name code) for a taxon in the catalogue of life in taiwan", + "example": "431472", + "github_request_issue": 466, + "homepage": "http://taibnet.sinica.edu.tw/home.php", + "mappings": { + "wikidata": "P3088" + }, + "name": "Catalogue of Life in Taiwan", + "pattern": "^[1-9]\\d{5}$", + "preferred_prefix": "col.taiwan", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1" + }, + "colao": { + "contact": { + "email": "entiminae@gmail.com", + "github": "JCGiron", + "name": "Jennifer C. Giron", + "orcid": "0000-0002-0851-6883" + }, + "depends_on": [ + "aism", + "bfo", + "bspo", + "caro", + "pato", + "ro", + "uberon" + ], + "description": "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research.", + "download_obo": "http://purl.obolibrary.org/obo/colao.obo", + "download_owl": "http://purl.obolibrary.org/obo/colao.owl", + "example": "0000000", + "homepage": "https://github.com/insect-morphology/colao", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "COLAO", + "bioportal": "COLAO", + "obofoundry": "colao", + "ols": "colao", + "ontobee": "COLAO" + }, + "name": "Coleoptera Anatomy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "COLAO", + "repository": "https://github.com/insect-morphology/colao", + "uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", + "version": "2022-06-18" + }, + "collagenmutdb": { + "description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.", + "example": "COL3A1", + "homepage": "http://www.le.ac.uk/genetics/collagen/", + "keywords": [ + "gene" + ], + "mappings": { + "prefixcommons": "cmd" + }, + "name": "Collagen Mutation Database", + "preferred_prefix": "collagenmutdb", + "provides": "hgnc.symbol", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://eds.gene.le.ac.uk/home.php?select_db=$1" + }, + "colonatlas": { + "description": "Cell line databases/resources", + "example": "ALA", + "homepage": "http://www.coloncanceratlas.org", + "mappings": { + "cellosaurus": "ColonAtlas" + }, + "name": "Colorectal Cancer Atlas", + "preferred_prefix": "colonatlas", + "uri_format": "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1" + }, + "combine.specifications": { + "description": "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network.", + "example": "sed-ml.level-1.version-1", + "homepage": "https://co.mbine.org/standards/", + "mappings": { + "biocontext": "COMBINE.SPECIFICATIONS", + "miriam": "combine.specifications", + "n2t": "combine.specifications" + }, + "name": "COMBINE specifications", + "pattern": "^\\w+(\\-|\\.|\\w)*$", + "preferred_prefix": "combine.specifications", + "uri_format": "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md" + }, + "come": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif.", + "example": "MOL000160", + "homepage": "https://www.flymine.org/come", + "keywords": [ + "protein" + ], + "mappings": { + "prefixcommons": "come" + }, + "name": "The Bioinorganic Motif Database", + "preferred_prefix": "come", + "uri_format": "https://www.flymine.org/come/entry?gn=$1" + }, + "commoncoreontology": { + "contact": { + "email": "mpjensen@buffalo.edu", + "github": "mark-jensen", + "name": "Mark Jensen", + "orcid": "0000-0001-9228-8838" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships.", + "example": "DirectiveInformationContentEntity", + "homepage": "http://www.ontologyrepository.com", + "keywords": [ + "ontology", + "upper-level ontology" + ], + "license": "CC-BY-4.0", + "name": "Common Core Ontologies", + "preferred_prefix": "commoncoreontology", + "repository": "https://github.com/CommonCoreOntology/CommonCoreOntologies", + "uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1" + }, + "complexportal": { + "description": "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases.", + "example": "CPX-263", + "homepage": "https://www.ebi.ac.uk/complexportal", + "mappings": { + "biocontext": "COMPLEXPORTAL", + "biolink": "ComplexPortal", + "go": "ComplexPortal", + "miriam": "complexportal", + "n2t": "complexportal", + "re3data": "r3d100013295", + "uniprot": "DB-0228", + "wikidata": "P7718" + }, + "name": "Complex Portal", + "pattern": "^CPX-[0-9]+$", + "preferred_prefix": "complexportal", + "publications": [ + { + "doi": "10.1093/nar/gku975", + "pmc": "PMC4384031", + "pubmed": "25313161", + "title": "The complex portal--an encyclopaedia of macromolecular complexes.", + "year": 2014 + } + ], + "synonyms": [ + "ComplexPortal" + ], + "uri_format": "https://www.ebi.ac.uk/complexportal/complex/$1" + }, + "comptox": { + "description": "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.", + "example": "DTXSID2021028", + "homepage": "https://comptox.epa.gov/dashboard", + "mappings": { + "biocontext": "COMPTOX", + "miriam": "comptox", + "n2t": "comptox", + "wikidata": "P3117" + }, + "name": "DSSTox substance", + "pattern": "^DTXSID\\d+$", + "preferred_prefix": "comptox", + "uri_format": "https://comptox.epa.gov/dashboard/$1" + }, + "compulyeast": { + "description": "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record.", + "example": "O08709", + "homepage": "http://compluyeast2dpage.dacya.ucm.es/", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "COMPULYEAST", + "fairsharing": "FAIRsharing.rbjs3e", + "miriam": "compulyeast", + "n2t": "compulyeast", + "prefixcommons": "compluyeast2dpage" + }, + "name": "Compluyeast-2D-DB", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", + "preferred_prefix": "compulyeast", + "provides": "uniprot", + "uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1" + }, + "confident.event": { + "contact": { + "email": "Philip.Stroemert@tib.eu", + "github": "StroemPhi", + "name": "Philip Strömert", + "orcid": "0000-0002-1595-3213" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", + "example": "37af84f2-bfd7-4653-b608-eaff44febba6", + "github_request_issue": 519, + "homepage": "https://www.confident-conference.org/index.php/Category:Event", + "keywords": [ + "conferences", + "meetings", + "metascience" + ], + "name": "ConfIDent Event", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", + "preferred_prefix": "confident.event", + "uri_format": "https://www.confident-conference.org/index.php/Event:$1" + }, + "confident.series": { + "contact": { + "email": "Philip.Stroemert@tib.eu", + "github": "StroemPhi", + "name": "Philip Strömert", + "orcid": "0000-0002-1595-3213" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating.", + "example": "AAC", + "github_request_issue": 519, + "homepage": "https://www.confident-conference.org/index.php/Category:Event_Series", + "keywords": [ + "conferences", + "grouping", + "meetings", + "metascience" + ], + "name": "ConfIDent Event Series", + "preferred_prefix": "confident.series", + "uri_format": "https://www.confident-conference.org/index.php/Event_Series:$1" + }, + "conoserver": { + "contact": { + "email": "d.craik@imb.uq.edu.au", + "github": null, + "name": "David Craik", + "orcid": "0000-0003-0007-6796" + }, + "description": "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails.", + "example": "2639", + "homepage": "http://www.conoserver.org/", + "keywords": [ + "life science", + "neurophysiology", + "statistics", + "synthetic biology" + ], + "mappings": { + "biocontext": "CONOSERVER", + "fairsharing": "FAIRsharing.y00hz4", + "miriam": "conoserver", + "n2t": "conoserver", + "uniprot": "DB-0156" + }, + "name": "ConoServer", + "pattern": "^\\d+$", + "preferred_prefix": "conoserver", + "publications": [ + { + "doi": "10.1093/nar/gkr886", + "pmc": "PMC3245185", + "pubmed": "22058133", + "title": "ConoServer: updated content, knowledge, and discovery tools in the conopeptide database.", + "year": 2011 + }, + { + "doi": "10.1016/j.toxicon.2010.03.002", + "pmc": null, + "pubmed": "20211197", + "title": "Conopeptide characterization and classifications: an analysis using ConoServer.", + "year": 2010 + }, + { + "doi": "10.1093/bioinformatics/btm596", + "pmc": null, + "pubmed": "18065428", + "title": "ConoServer, a database for conopeptide sequences and structures.", + "year": 2007 + }, + { + "doi": "10.1021/cb700091j", + "pmc": null, + "pubmed": "17649970", + "title": "Chemical modification of conotoxins to improve stability and activity.", + "year": 2007 + }, + { + "doi": "10.1152/physrev.00020.2003", + "pmc": null, + "pubmed": "14715910", + "title": "Conus venoms: a rich source of novel ion channel-targeted peptides.", + "year": 2004 + } + ], + "uri_format": "http://www.conoserver.org/?page=card&table=protein&id=$1" + }, + "conso": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases.", + "example": "CONSO00010", + "homepage": "https://pharmacome.github.io/conso/", + "keywords": [ + "biology", + "life science", + "neurodegeneration", + "neuroscience", + "ontology" + ], + "name": "Curation of Neurodegeneration Supporting Ontology", + "pattern": "^CONSO\\d{5}$", + "preferred_prefix": "conso", + "uri_format": "https://pharmacome.github.io/conso/$1" + }, + "cordis.article": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", + "example": "436605", + "homepage": "https://cordis.europa.eu/", + "name": "CORDIS Article", + "pattern": "^\\d+$", + "preferred_prefix": "cordis.article", + "uri_format": "https://cordis.europa.eu/article/id/$1" + }, + "cordis.project": { + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", + "example": "817732", + "github_request_issue": 450, + "homepage": "https://cordis.europa.eu/", + "name": "CORDIS Project", + "pattern": "^\\d+$", + "preferred_prefix": "cordis.project", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://cordis.europa.eu/project/id/$1" + }, + "coriell": { + "description": "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world.", + "example": "GM17027", + "homepage": "http://ccr.coriell.org/", + "mappings": { + "biocontext": "Coriell", + "cellosaurus": "Coriell", + "go": "CORIELL", + "miriam": "coriell", + "n2t": "coriell" + }, + "name": "Coriell Institute for Medical Research", + "pattern": "^[A-Z]{2}\\d+$", + "preferred_prefix": "coriell", + "uri_format": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1" + }, + "corrdb": { + "contact": { + "email": "zhu@iastate.edu", + "github": null, + "name": "Zhiliang Hu", + "orcid": "0000-0002-6704-7538" + }, + "description": "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.", + "example": "37232", + "homepage": "https://www.animalgenome.org", + "keywords": [ + "animal genetics", + "genetics", + "life science", + "systems biology" + ], + "mappings": { + "fairsharing": "FAIRsharing.IziuCK", + "miriam": "corrdb", + "re3data": "r3d100011496" + }, + "name": "CorrDB", + "pattern": "^[0-9]+$", + "preferred_prefix": "corrdb", + "uri_format": "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1" + }, + "corum": { + "contact": { + "email": "andreas.ruepp@helmholtz-muenchen.de", + "github": null, + "name": "Andreas Ruepp", + "orcid": "0000-0003-1705-3515" + }, + "description": "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.", + "example": "100", + "homepage": "https://mips.helmholtz-muenchen.de/genre/proj/corum/", + "keywords": [ + "bioinformatics", + "biology", + "protein" + ], + "mappings": { + "biocontext": "CORUM", + "fairsharing": "FAIRsharing.ohbpNw", + "go": "CORUM", + "miriam": "corum", + "n2t": "corum", + "prefixcommons": "corum", + "uniprot": "DB-0224" + }, + "name": "Comprehensive Resource of Mammalian protein complexes", + "pattern": "^\\d+$", + "preferred_prefix": "corum", + "publications": [ + { + "doi": "10.1093/nar/gky973", + "pmc": "PMC6323970", + "pubmed": "30357367", + "title": "CORUM: the comprehensive resource of mammalian protein complexes-2019.", + "year": 2019 + } + ], + "uri_format": "https://mips.helmholtz-muenchen.de/corum/?id=$1" + }, + "cosmic": { + "description": "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.", + "example": "BRAF", + "homepage": "http://cancer.sanger.ac.uk/cosmic/", + "keywords": [ + "biomedical science", + "genetics" + ], + "mappings": { + "biocontext": "COSMIC", + "cellosaurus": "Cosmic", + "edam": "3264", + "fairsharing": "FAIRsharing.s5zmbp", + "miriam": "cosmic", + "n2t": "cosmic" + }, + "name": "COSMIC Gene", + "pattern": "^[A-Z0-9]+$", + "preferred_prefix": "cosmic", + "publications": [ + { + "doi": "10.1093/nar/gky1015", + "pmc": "PMC6323903", + "pubmed": "30371878", + "title": "COSMIC: the Catalogue Of Somatic Mutations In Cancer.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gku1075", + "pmc": "PMC4383913", + "pubmed": "25355519", + "title": "COSMIC: exploring the world's knowledge of somatic mutations in human cancer.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkq929", + "pmc": "PMC3013785", + "pubmed": "20952405", + "title": "COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.", + "year": 2010 + }, + { + "doi": "10.1038/sj.bjc.6601894", + "pmc": "PMC2409828", + "pubmed": "15188009", + "title": "The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.", + "year": 2004 + } + ], + "uri_format": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1" + }, + "cosmic.cell": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer", + "example": "906801", + "homepage": "https://cancer.sanger.ac.uk/cell_lines/", + "mappings": { + "cellosaurus": "Cosmic-CLP" + }, + "name": "COSMIC Cell Lines", + "pattern": "^\\d+$", + "preferred_prefix": "cosmic.cell", + "uri_format": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1" + }, + "covid19": { + "contact": { + "email": "dylan.mcgagh@magd.ox.ac.uk", + "github": null, + "name": "Dylan McGagh", + "orcid": "0000-0002-6772-2775" + }, + "description": "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.", + "download_owl": "http://aber-owl.net/media/ontologies/COVID19/3/covid19.owl", + "example": "SFB_COVID19_MW286762", + "homepage": "https://covid19.sfb.uit.no", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "COVID19", + "bioportal": "COVID19", + "miriam": "covid19" + }, + "name": "COVID-19 Surveillance Ontology", + "pattern": "^\\w+_COVID19_[-\\w]+$", + "preferred_prefix": "covid19", + "uri_format": "https://covid19.sfb.uit.no/api/records/$1" + }, + "covoc": { + "contact": { + "email": "zmp@ebi.ac.uk", + "github": "zoependlington", + "name": "Zoë May Pendlington", + "orcid": "0000-0002-4071-8397" + }, + "description": "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.", + "download_json": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.json", + "download_obo": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.obo", + "download_owl": "https://github.com/EBISPOT/covoc/releases/download/current/covoc.owl", + "example": "0010034", + "homepage": "https://github.com/EBISPOT/covoc", + "keywords": [ + "ontology" + ], + "mappings": { + "ols": "covoc" + }, + "name": "CoVoc Coronavirus Vocabulary", + "pattern": "^\\d{7}$", + "preferred_prefix": "covoc", + "repository": "https://github.com/EBISPOT/covoc", + "uri_format": "http://purl.obolibrary.org/obo/COVOC_$1", + "version": "2020-08-28" + }, + "cp": { + "appears_in": [ + "cl" + ], + "comment": "Part of cell ontology but deprecated, see https://github.com/obophenotype/cell-ontology/issues/572", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "name": "Cellular Phenotypes", + "preferred_prefix": "cp" + }, + "cpc": { + "description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.", + "example": "A01M1/026", + "homepage": "https://worldwide.espacenet.com/classification", + "keywords": [ + "atmospheric science", + "earth science", + "geodesy", + "geography", + "hydrogeology", + "meteorology" + ], + "mappings": { + "biocontext": "CPC", + "fairsharing": "FAIRsharing.e08886", + "miriam": "cpc", + "n2t": "cpc" + }, + "name": "Cooperative Patent Classification", + "pattern": "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$", + "preferred_prefix": "cpc", + "uri_format": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1" + }, + "cpt": { + "contact": { + "email": "Intellectual.PropertyServices@ama-assn.org", + "github": null, + "name": "American Medical Association", + "orcid": null + }, + "contributor": { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + }, + "contributor_extras": [ + { + "email": null, + "github": "colleenXu", + "name": "Colleen Xu", + "orcid": "0000-0003-2975-882X" + } + ], + "description": "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]", + "example": "00103", + "github_request_issue": 357, + "homepage": "https://www.aapc.com", + "keywords": [ + "biomedical science", + "health science", + "medicine", + "ontology" + ], + "mappings": { + "aberowl": "CPT", + "biolink": "CPT", + "bioportal": "CPT", + "fairsharing": "FAIRsharing.wpxab1" + }, + "name": "Current Procedural Terminology", + "pattern": "^\\d+$", + "preferred_prefix": "cpt", + "publications": [ + { + "doi": "10.1136/neurintsurg-2014-011156", + "pmc": null, + "pubmed": "24589819", + "title": "Current procedural terminology; a primer.", + "year": 2014 + }, + { + "doi": "10.1016/j.jacr.2007.10.004", + "pmc": null, + "pubmed": "18359442", + "title": "CPT: an open system that describes all that you do.", + "year": 2008 + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/pull/358", + "https://github.com/biolink/biolink-model/pull/993" + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "ama-cpt" + ], + "uri_format": "https://www.aapc.com/codes/cpt-codes/$1" + }, + "credit": { + "contact": { + "email": "info@casrai.org", + "github": null, + "name": "Liz Allen", + "orcid": "0000-0002-9298-3168" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.", + "example": "Software", + "homepage": "https://casrai.org/credit/", + "keywords": [ + "data quality", + "ontology and terminology", + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.fe4816" + }, + "name": "CASRAI Contributor Roles Taxonomy", + "preferred_prefix": "credit", + "publications": [ + { + "doi": "10.1038/d41586-019-01715-4", + "pmc": null, + "pubmed": "31164773", + "title": "Credit data generators for data reuse.", + "year": 2019 + }, + { + "doi": "10.1038/508312a", + "pmc": null, + "pubmed": "24745070", + "title": "Publishing: Credit where credit is due.", + "year": 2014 + }, + { + "doi": "10.3789/ansi.niso.z39.104-2022", + "pmc": null, + "pubmed": null, + "title": "ANSI/NISO Z39.104-2022, CRediT, Contributor Roles Taxonomy", + "year": null + }, + { + "doi": "10.1087/20150211", + "pmc": null, + "pubmed": null, + "title": "Beyond authorship: attribution, contribution, collaboration, and credit", + "year": 2015 + }, + { + "doi": "10.1002/leap.1210", + "pmc": null, + "pubmed": null, + "title": "How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship", + "year": 2019 + } + ], + "twitter": "contrib_roles" + }, + "crisprdb": { + "contact": { + "email": "Christine.Pourcel@u-psud.fr", + "github": null, + "name": "Christine Pourcel", + "orcid": "0000-0002-8951-466X" + }, + "description": "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data.", + "example": "551115", + "homepage": "http://crispr.i2bc.paris-saclay.fr/", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "CRISPRDB", + "fairsharing": "FAIRsharing.7sfedh", + "miriam": "crisprdb", + "n2t": "crisprdb" + }, + "name": "CRISPRdb", + "pattern": "^[0-9]+$", + "preferred_prefix": "crisprdb", + "publications": [ + { + "doi": "10.1093/nar/gkn228", + "pmc": "PMC2447796", + "pubmed": "18442988", + "title": "CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkm360", + "pmc": "PMC1933234", + "pubmed": "17537822", + "title": "CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.", + "year": 2007 + }, + { + "doi": "10.1186/1471-2105-8-172", + "pmc": "PMC1892036", + "pubmed": "17521438", + "title": "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.", + "year": 2007 + } + ], + "uri_format": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1" + }, + "cro": { + "contact": { + "email": "whimar@ohsu.edu", + "github": "marijane", + "name": "Marijane White", + "orcid": "0000-0001-5059-4132" + }, + "description": "A classification of the diverse roles performed in the work leading to a published research output in the sciences. 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While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "cgd7_230", + "homepage": "https://cryptodb.org/cryptodb/", + "keywords": [ + "functional genomics", + "genome", + "genomics", + "parasitology" + ], + "mappings": { + "biocontext": "CRYPTODB", + "fairsharing": "FAIRsharing.t3nprm", + "miriam": "cryptodb", + "n2t": "cryptodb", + "prefixcommons": "cryptodb", + "re3data": "r3d100012265" + }, + "name": "CryptoDB", + "pattern": "^\\w+$", + "preferred_prefix": "cryptodb", + "publications": [ + { + "doi": "10.1007/978-1-4939-9748-0_10", + "pmc": null, + "pubmed": "31452162", + "title": "Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gkj078", + "pmc": "PMC1347441", + "pubmed": "16381902", + "title": "CryptoDB: a Cryptosporidium bioinformatics resource update.", + "year": 2006 + } + ], + "twitter": "VEuPathDB", + "uri_format": "https://cryptodb.org/cryptodb/app/record/gene/$1" + }, + "csa": { + "contact": { + "email": "nickf@ebi.ac.uk", + "github": null, + "name": "Nicholas Furnham", + "orcid": "0000-0002-7532-1269" + }, + "description": "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. 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Entries curated into the CSD are identified by a CSD Refcode.", + "example": "PELNAW", + "homepage": "https://www.ccdc.cam.ac.uk/", + "keywords": [ + "biochemistry", + "chemistry", + "organic chemistry", + "organic molecular chemistry" + ], + "mappings": { + "fairsharing": "FAIRsharing.vs7865", + "miriam": "csd", + "re3data": "r3d100010197" + }, + "name": "Cambridge Structural Database", + "pattern": "^[A-Z]{6}(\\d{2})?$", + "preferred_prefix": "csd", + "publications": [ + { + "doi": "10.1107/s2052520616003954", + "pmc": "PMC4822653", + "pubmed": "27048719", + "title": "The Cambridge Structural Database.", + "year": 2016 + }, + { + "doi": "10.1107/s0108768102003890", + "pmc": null, + "pubmed": "12037359", + "title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising.", + "year": 2002 + } + ], + "twitter": "ccdc_cambridge", + "uri_format": "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG" + }, + "csp": { + "contact": { + "email": "af8d@nih.gov", + "github": null, + "name": "Anita Ghebeles", + "orcid": null + }, + "deprecated": true, + "description": "CRISP is a terminology used for indexing biomedical information. 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The CTCAE system is a product of the US National Cancer Institute (NCI).", + "download_owl": "http://aber-owl.net/media/ontologies/CTCAE/2/ctcae.owl", + "example": "E12768", + "homepage": "https://evs.nci.nih.gov/ftp1/CTCAE/About.html", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "CTCAE", + "bioportal": "CTCAE" + }, + "name": "Common Terminology Criteria for Adverse Events", + "pattern": "^E\\d+$", + "preferred_prefix": "ctcae", + "publications": [ + { + "doi": null, + "pmc": "PMC5977606", + "pubmed": "29854250", + "title": "Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.", + "year": 2018 + } + ], + "references": [ + "https://github.com/OAE-ontology/OAE/issues/8", + "https://en.wikipedia.org/wiki/Common_Terminology_Criteria_for_Adverse_Events" + ], + "synonyms": [ + "CTCAE" + ] + }, + "ctd.chemical": { + "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", + "example": "D001151", + "homepage": "http://ctdbase.org/", + "mappings": { + "biocontext": "CTD.CHEMICAL", + "biolink": "CTD.CHEMICAL", + "miriam": "ctd.chemical", + "n2t": "ctd.chemical" + }, + "name": "CTD Chemical", + "part_of": "ctd", + "pattern": "^[CD]\\d+$", + "preferred_prefix": "ctd.chemical", + "provides": "mesh", + "uri_format": "http://ctdbase.org/detail.go?type=chem&acc=$1" + }, + "ctd.disease": { + "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", + "example": "D053716", + "homepage": "http://ctdbase.org/", + "mappings": { + "biocontext": "CTD.DISEASE", + "biolink": "CTD.DISEASE", + "miriam": "ctd.disease", + "n2t": "ctd.disease" + }, + "name": "CTD Disease", + "part_of": "ctd", + "pattern": "^D\\d+$", + "preferred_prefix": "ctd.disease", + "provides": "mesh", + "uri_format": "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1" + }, + "ctd.gene": { + "description": "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences.", + "example": "101", + "homepage": "http://ctdbase.org/", + "mappings": { + "biocontext": "CTD.GENE", + "biolink": "CTD.GENE", + "miriam": "ctd.gene", + "n2t": "ctd.gene", + "uniprot": "DB-0140" + }, + "name": "CTD Gene", + "part_of": "ctd", + "pattern": "^\\d+$", + "preferred_prefix": "ctd.gene", + "provides": "ncbigene", + "publications": [ + { + "doi": "10.1093/nar/gkaa891", + "pmc": "PMC7779006", + "pubmed": "33068428", + "title": "Comparative Toxicogenomics Database (CTD): update 2021.", + "year": 2021 + } + ], + "uri_format": "http://ctdbase.org/detail.go?type=gene&acc=$1" + }, + "cteno": { + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "depends_on": [ + "ro", + "uberon" + ], + "description": "An anatomical and developmental ontology for ctenophores (Comb Jellies)", + "download_obo": "https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo", + "download_owl": "http://purl.obolibrary.org/obo/cteno.owl", + "example": "0000047", + "homepage": "https://github.com/obophenotype/ctenophore-ontology", + "keywords": [ + "anatomy", + "developmental biology", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "CTENO", + "biocontext": "CTENO", + "bioportal": "CTENO", + "fairsharing": "FAIRsharing.mgxgza", + "obofoundry": "cteno", + "ols": "cteno", + "ontobee": "CTENO" + }, + "name": "Ctenophore Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CTENO", + "repository": "https://github.com/obophenotype/ctenophore-ontology", + "uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", + "version": "2016-10-19" + }, + "cto": { + "contact": { + "email": "alpha.tom.kodamullil@scai.fraunhofer.de", + "github": "akodamullil", + "name": "Dr. Alpha Tom Kodamullil", + "orcid": "0000-0001-9896-3531" + }, + "description": "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.", + "download_owl": "http://purl.obolibrary.org/obo/cto.owl", + "example": "0000022", + "homepage": "https://github.com/ClinicalTrialOntology/CTO/", + "keywords": [ + "biomedical science", + "neurobiology", + "obo", + "ontology", + "preclinical studies" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CTO", + "bioportal": "CTO", + "fairsharing": "FAIRsharing.qp211a", + "obofoundry": "cto", + "ols": "cto", + "ontobee": "CTO" + }, + "name": "Clinical Trials Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CTO", + "repository": "https://github.com/ClinicalTrialOntology/CTO", + "uri_format": "http://purl.obolibrary.org/obo/CTO_$1", + "version": "1.0.0" + }, + "cubedb": { + "comment": "website down as of 2021-10-04", + "deprecated": true, + "description": "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available.", + "example": "AKR", + "homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html", + "mappings": { + "biocontext": "CUBEDB", + "miriam": "cubedb", + "n2t": "cubedb" + }, + "name": "Cube db", + "pattern": "^[A-Za-z_0-9]+$", + "preferred_prefix": "cubedb", + "uri_format": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/" + }, + "cutg": { + "description": "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.", + "example": "9606", + "homepage": "http://www.kazusa.or.jp/codon/", + "keywords": [ + "dna", + "gene" + ], + "mappings": { + "prefixcommons": "cutg" + }, + "name": "Codon Usage Tabulated from GenBank", + "preferred_prefix": "cutg", + "provides": "ncbitaxon", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1" + }, + "cvdo": { + "contact": { + "email": "paul.fabry@usherbrooke.ca", + "github": "pfabry", + "name": "Paul Fabry", + "orcid": "0000-0002-3336-2476" + }, + "description": "An ontology to describe entities related to cardiovascular diseases", + "download_owl": "http://purl.obolibrary.org/obo/cvdo.owl", + "example": "0000546", + "homepage": "https://github.com/OpenLHS/CVDO", + "keywords": [ + "cardiology", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CVDO", + "biocontext": "CVDO", + "bioportal": "CVDO", + "fairsharing": "FAIRsharing.2basyz", + "obofoundry": "cvdo", + "ols": "cvdo", + "ontobee": "CVDO" + }, + "name": "Cardiovascular Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "CVDO", + "repository": "https://github.com/OpenLHS/CVDO", + "uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", + "version": "2020-03-05" + }, + "cvx": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records.", + "example": "54", + "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx", + "mappings": { + "hl7": "2.16.840.1.113883.6.59" + }, + "name": "Vaccine administered code set", + "pattern": "^\\d+$", + "preferred_prefix": "cvx" + }, + "d1id": { + "description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.", + "example": "00030692-0FE1-4A1B-955E-A2E55D659267", + "homepage": "https://www.dataone.org", + "mappings": { + "biocontext": "D1ID", + "miriam": "d1id", + "n2t": "d1id" + }, + "name": "DataONE", + "pattern": "^\\S+$", + "preferred_prefix": "d1id", + "uri_format": "https://cn.dataone.org/cn/v2/resolve/{$1}" + }, + "dailymed": { + "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", + "example": "973a9333-fec7-46dd-8eb5-25738f06ee54", + "homepage": "https://dailymed.nlm.nih.gov/dailymed/", + "mappings": { + "biocontext": "DAILYMED", + "miriam": "dailymed", + "n2t": "dailymed", + "prefixcommons": "dailymed" + }, + "name": "DailyMed", + "pattern": "^[A-Za-z0-9-]+$", + "preferred_prefix": "dailymed", + "uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1" + }, + "dandi": { + "contact": { + "email": "yoh@dartmouth.edu", + "github": null, + "name": "Yaroslav Halchenko", + "orcid": "0000-0003-3456-2493" + }, + "description": "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders.", + "example": "000017", + "homepage": "https://dandiarchive.org/", + "keywords": [ + "neurophysiology" + ], + "mappings": { + "fairsharing": "FAIRsharing.f2c119", + "miriam": "dandi", + "re3data": "r3d100013638" + }, + "name": "Distributed Archives for Neurophysiology Data Integration", + "pattern": "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$", + "preferred_prefix": "dandi", + "repository": "https://github.com/dandi/dandiarchive", + "twitter": "dandiarchive", + "uri_format": "https://dandiarchive.org/dandiset/$1" + }, + "darc": { + "description": "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.", + "example": "1250", + "homepage": "http://darcsite.genzentrum.lmu.de/darc/index.php", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "DARC", + "fairsharing": "FAIRsharing.evfe2s", + "miriam": "darc", + "n2t": "darc" + }, + "name": "Database of Aligned Ribosomal Complexes", + "pattern": "^\\d+$", + "preferred_prefix": "darc", + "publications": [ + { + "doi": "10.1093/nar/gkr824", + "pmc": "PMC3245104", + "pubmed": "22009674", + "title": "The DARC site: a database of aligned ribosomal complexes.", + "year": 2011 + } + ], + "uri_format": "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1" + }, + "dashr": { + "contact": { + "email": "dashr@lisanwanglab.org", + "github": null, + "name": "Li-San Wang", + "orcid": "0000-0002-3684-0031" + }, + "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.", + "example": "hsa-mir-200a", + "homepage": "http://lisanwanglab.org/DASHR/", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "DASHR", + "fairsharing": "FAIRsharing.ztvs34", + "miriam": "dashr", + "n2t": "dashr" + }, + "name": "Database of small human noncoding RNAs", + "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", + "preferred_prefix": "dashr", + "publications": [ + { + "doi": "10.1093/nar/gkv1188", + "pmc": "PMC4702848", + "pubmed": "26553799", + "title": "DASHR: database of small human noncoding RNAs.", + "year": 2015 + } + ], + "uri_format": "http://lisanwanglab.org/DASHR/entry/$1" + }, + "dashr.expression": { + "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.", + "example": "hsa-mir-200a", + "homepage": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0", + "mappings": { + "biocontext": "DASHR.EXPRESSION", + "miriam": "dashr.expression", + "n2t": "dashr.expression" + }, + "name": "DASHR expression", + "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", + "preferred_prefix": "dashr.expression", + "uri_format": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable" + }, + "datacite": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF.", + "download_owl": "http://aber-owl.net/media/ontologies/DATACITE/2/datacite.owl", + "example": "AgentIdentifierScheme", + "homepage": "http://www.sparontologies.net/ontologies/datacite", + "keywords": [ + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "DATACITE", + "bioportal": "DATACITE", + "fairsharing": "FAIRsharing.c06f1e" + }, + "name": "DataCite Ontology", + "preferred_prefix": "DataCite", + "repository": "https://github.com/sparontologies/datacite", + "twitter": "datacite", + "uri_format": "http://purl.org/spar/datacite/$1" + }, + "datacommons": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.", + "example": "Gene", + "homepage": "https://datacommons.org", + "mappings": { + "biolink": "dcid" + }, + "name": "Data Commons", + "preferred_prefix": "datacommons", + "repository": "https://github.com/datacommonsorg/website", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://datacommons.org/browser/$1" + }, + "datanator.gene": { + "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", + "example": "K00973", + "homepage": "https://datanator.info/", + "mappings": { + "miriam": "datanator.gene" + }, + "name": "Datanator Gene", + "part_of": "datanator", + "pattern": "^K[0-9]+$", + "preferred_prefix": "datanator.gene", + "uri_format": "https://www.datanator.info/gene/$1" + }, + "datanator.metabolite": { + "description": "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", + "example": "OUYCCCASQSFEME-MRVPVSSYSA-N", + "homepage": "https://datanator.info/", + "mappings": { + "miriam": "datanator.metabolite" + }, + "name": "Datanator Metabolite", + "part_of": "datanator", + "pattern": "^[A-Z\\-]+$", + "preferred_prefix": "datanator.metabolite", + "uri_format": "https://www.datanator.info/metabolite/$1" + }, + "datanator.reaction": { + "description": "\tDatanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.", + "example": "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N", + "homepage": "https://icahn.mssm.edu/", + "mappings": { + "miriam": "datanator.reaction" + }, + "name": "Datanator Reaction", + "pattern": "^.*?--%3E.*?$", + "preferred_prefix": "datanator.reaction", + "uri_format": "https://datanator.info/reaction/$1" + }, + "datf": { + "deprecated": true, + "description": "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals.", + "example": "AT1G01030.1", + "homepage": "http://datf.cbi.pku.edu.cn/", + "keywords": [ + "regulation" + ], + "mappings": { + "biocontext": "DATF", + "miriam": "datf", + "n2t": "datf", + "prefixcommons": "datf" + }, + "name": "Database of Arabidopsis Transcription Factors", + "pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$", + "preferred_prefix": "datf", + "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1" + }, + "dbd": { + "description": "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins.", + "example": "0045310", + "homepage": "http://www.transcriptionfactor.org/", + "keywords": [ + "genome", + "regulation" + ], + "mappings": { + "biocontext": "DBD", + "edam": "2716", + "miriam": "dbd", + "n2t": "dbd", + "prefixcommons": "dbd" + }, + "name": "Transcription Factor Database", + "pattern": "^\\d+$", + "preferred_prefix": "dbd", + "uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD" + }, + "dbest": { + "description": "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms.", + "example": "BP100000", + "homepage": "https://www.ncbi.nlm.nih.gov/nucest", + "keywords": [ + "bioinformatics", + "dna", + "life science" + ], + "mappings": { + "biocontext": "DBEST", + "edam": "1105", + "fairsharing": "FAIRsharing.v9fya8", + "miriam": "dbest", + "n2t": "dbest", + "ncbi": "dbEST", + "prefixcommons": "dbest", + "re3data": "r3d100010648" + }, + "name": "EST database maintained at the NCBI.", + "pattern": "^([A-Z]+)?\\d+(\\.\\d+)?$", + "preferred_prefix": "dbest", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "dbEST through DNA Data Bank of Japan (DDBJ)", + "homepage": "http://www.ddbj.nig.ac.jp/", + "name": "dbEST through DNA Data Bank of Japan (DDBJ)", + "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/na/$1" + }, + { + "code": "ebi", + "description": "dbEST through European Nucleotide Archive (ENA)", + "homepage": "https://www.ebi.ac.uk/ena", + "name": "dbEST through European Nucleotide Archive (ENA)", + "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" + } + ], + "publications": [ + { + "doi": "10.1038/ng0893-332", + "pmc": null, + "pubmed": "8401577", + "title": "dbEST--database for \"expressed sequence tags\".", + "year": 1993 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" + }, + "dbg2introns": { + "description": "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank.", + "example": "Cu.me.I1", + "homepage": "http://webapps2.ucalgary.ca/~groupii/", + "keywords": [ + "dna" + ], + "mappings": { + "biocontext": "DBG2INTRONS", + "miriam": "dbg2introns", + "n2t": "dbg2introns", + "prefixcommons": "mgiid" + }, + "name": "DBG2 Introns", + "pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$", + "preferred_prefix": "dbg2introns", + "publications": [ + { + "doi": "10.1093/nar/gkr1043", + "pmc": "PMC3245105", + "pubmed": "22080509", + "title": "Database for bacterial group II introns.", + "year": 2011 + } + ], + "uri_format": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1" + }, + "dbgap": { + "description": "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.", + "example": "phs000768.v2.p1", + "homepage": "https://www.ncbi.nlm.nih.gov/projects/gap", + "keywords": [ + "biomedical science", + "epigenetics", + "genetics" + ], + "mappings": { + "biocontext": "DBGAP", + "cellosaurus": "dbGAP", + "fairsharing": "FAIRsharing.88v2k0", + "miriam": "dbgap", + "n2t": "dbgap" + }, + "name": "Database of Genotypes and Phenotypes", + "pattern": "^phs[0-9]{6}(.v\\d+.p\\d+)?$", + "preferred_prefix": "dbgap", + "publications": [ + { + "doi": "10.1093/nar/gkt1211", + "pmc": "PMC3965052", + "pubmed": "24297256", + "title": "NCBI's Database of Genotypes and Phenotypes: dbGaP.", + "year": 2013 + }, + { + "doi": "10.1038/ng1007-1181", + "pmc": "PMC2031016", + "pubmed": "17898773", + "title": "The NCBI dbGaP database of genotypes and phenotypes.", + "year": 2007 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1" + }, + "dbmhc": { + "appears_in": [ + "cellosaurus" + ], + "deprecated": true, + "description": "Cell line databases/resources", + "example": "48439", + "homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/", + "mappings": { + "cellosaurus": "dbMHC" + }, + "name": "Database of human Major Histocompatibility Complex", + "pattern": "^\\d+$", + "preferred_prefix": "dbmhc" + }, + "dbo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.", + "example": "careerPrizeMoney", + "github_request_issue": 515, + "homepage": "https://dbpedia.org/ontology", + "keywords": [ + "dbpedia", + "ontology" + ], + "name": "DBPedia Ontology", + "preferred_prefix": "dbo", + "uri_format": "https://dbpedia.org/ontology/$1" + }, + "dbprobe": { + "description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", + "example": "1000000", + "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe", + "keywords": [ + "nucleotide" + ], + "mappings": { + "biocontext": "DBPROBE", + "edam": "2719", + "miriam": "dbprobe", + "n2t": "dbprobe", + "ncbi": "dbProbe", + "prefixcommons": "dbprobe" + }, + "name": "NCBI Probe database Public registry of nucleic acid reagents", + "pattern": "^\\d+$", + "preferred_prefix": "dbprobe", + "uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1" + }, + "dbsnp": { + "description": "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.", + "example": "rs121909098", + "homepage": "https://www.ncbi.nlm.nih.gov/snp/", + "keywords": [ + "genome", + "life science" + ], + "mappings": { + "biocontext": "dbSNP", + "cellosaurus": "dbSNP", + "edam": "1106", + "fairsharing": "FAIRsharing.edxb58", + "go": "dbSNP", + "hl7": "2.16.840.1.113883.6.284", + "miriam": "dbsnp", + "n2t": "dbsnp", + "ncbi": "dbSNP", + "prefixcommons": "dbsnp", + "re3data": "r3d100010652", + "uniprot": "DB-0013", + "wikidata": "P6861" + }, + "name": "dbSNP Reference SNP number", + "pattern": "^rs\\d+$", + "preferred_prefix": "dbsnp", + "providers": [ + { + "code": "sib", + "description": "SNP2TFBS", + "homepage": "https://ccg.epfl.ch/snp2tfbs/", + "name": "SNP2TFBS", + "uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkl1031", + "pmc": "PMC1781113", + "pubmed": "17170002", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2006 + }, + { + "doi": "10.1093/nar/29.1.308", + "pmc": "PMC29783", + "pubmed": "11125122", + "title": "dbSNP: the NCBI database of genetic variation.", + "year": 2001 + } + ], + "repository": "https://github.com/ncbi/dbsnp/tree/master/tutorials", + "uri_format": "https://www.ncbi.nlm.nih.gov/snp/$1" + }, + "dbvar.study": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Studies in dbVar.", + "example": "nstd102", + "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", + "name": "Database of Genomic Structural Variation - Study", + "preferred_prefix": "dbvar.study", + "synonyms": [ + "dbvar.studies" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1" + }, + "dbvar.variant": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Variants in dbVar.", + "example": "nsv3875336", + "homepage": "https://www.ncbi.nlm.nih.gov/dbvar", + "name": "Database of Genomic Structural Variation - Variant", + "preferred_prefix": "dbvar.variant", + "synonyms": [ + "dbvar.variants" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1" + }, + "dc": { + "contact": { + "email": "kdurante@stanford.edu", + "github": null, + "name": "Kim Durante", + "orcid": "0000-0001-9052-2854" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).", + "download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl", + "example": "contributor", + "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", + "keywords": [ + "biomedical science", + "life science", + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "dcelements", + "biocontext": "dc", + "bioportal": "DC", + "fairsharing": "FAIRsharing.3nx7t" + }, + "name": "Dublin Core Elements (1.1)", + "preferred_prefix": "dc", + "synonyms": [ + "dc.elements", + "dc11", + "dce" + ], + "uri_format": "http://purl.org/dc/elements/1.1/$1" + }, + "dc_cl": { + "contact": { + "email": "Lindsay.Cowell@utsouthwestern.edu", + "github": null, + "name": "Lindsay Cowell", + "orcid": "0000-0003-1617-8244" + }, + "deprecated": true, + "example": "0000003", + "homepage": "http://www.dukeontologygroup.org/Projects.html", + "keywords": [ + "obo", + 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It includes operons for RNA genes.", + "example": "1398574", + "homepage": "http://csbl.bmb.uga.edu/DOOR/operon.php", + "keywords": [ + "dna" + ], + "mappings": { + "biocontext": "DOOR", + "miriam": "door", + "n2t": "door", + "prefixcommons": "door", + "re3data": "r3d100014113" + }, + "name": "Database for Prokaryotic Operons", + "pattern": "^\\d+$", + "preferred_prefix": "door", + "uri_format": "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1" + }, + "doqcs.model": { + "description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models.", + "example": "57", + "homepage": "http://doqcs.ncbs.res.in/", + "keywords": [ + "model" + ], + "mappings": { + "biocontext": "DOQCS.MODEL", + "miriam": "doqcs.model", + "n2t": "doqcs.model", + "prefixcommons": "doqcs.model" + }, + "name": "Database of Quantitative Cellular Signaling: Model", + "part_of": "doqcs", + "pattern": "^\\d+$", + "preferred_prefix": "doqcs.model", + "publications": [ + { + "doi": "10.1093/bioinformatics/btf860", + "pmc": null, + "pubmed": "12584128", + "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.", + "year": 2003 + } + ], + "uri_format": "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1" + }, + "doqcs.pathway": { + "description": "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. 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This datatype provides access to pathways.", + "example": "131", + "homepage": "http://doqcs.ncbs.res.in/", + "keywords": [ + "pathway" + ], + "mappings": { + "biocontext": "DOQCS.PATHWAY", + "miriam": "doqcs.pathway", + "n2t": "doqcs.pathway", + "prefixcommons": "doqcs.pathway" + }, + "name": "Database of Quantitative Cellular Signaling: Pathway", + "part_of": "doqcs", + "pattern": "^\\d+$", + "preferred_prefix": "doqcs.pathway", + "publications": [ + { + "doi": "10.1093/bioinformatics/btf860", + "pmc": null, + "pubmed": "12584128", + "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.", + "year": 2003 + } + ], + "uri_format": "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1" + }, + "dpo": { + "comment": "DPO is a subset of terms from FBcv", + "contact": { + "email": "cp390@cam.ac.uk", + "github": "Clare72", + "name": "Clare Pilgrim", + "orcid": "0000-0002-1373-1705" + }, + "description": "An ontology for the description of Drosophila melanogaster phenotypes.", + "download_json": "http://purl.obolibrary.org/obo/dpo.json", + "download_obo": "http://purl.obolibrary.org/obo/dpo.obo", + "download_owl": "http://purl.obolibrary.org/obo/dpo.owl", + "homepage": "http://purl.obolibrary.org/obo/fbcv", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "DPO", + "bioportal": "DPO", + "obofoundry": "dpo", + "ols": "dpo", + "ontobee": "DPO" + }, + "name": "Drosophila Phenotype Ontology", + "no_own_terms": true, + "part_of": "fbcv", + "preferred_prefix": "DPO", + "publications": [ + { + "doi": "10.1186/2041-1480-4-30", + "pmc": "PMC3816596", + "pubmed": "24138933", + "title": "The Drosophila phenotype ontology.", + "year": 2013 + } + ], + "repository": "https://github.com/FlyBase/drosophila-phenotype-ontology", + "uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", + "version": "2022-08-11" + }, + "dpv": { + "description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.", + "example": "100", + "homepage": "http://www.dpvweb.net/", + "keywords": [ + "classification", + "gene" + ], + "mappings": { + "biocontext": "DPV", + "miriam": "dpv", + "n2t": "dpv", + "prefixcommons": "dpvweb" + }, + "name": "Description of Plant Viruses", + "pattern": "^\\d+$", + "preferred_prefix": "dpv", + "publications": [ + { + "doi": "10.1093/nar/gkj023", + "pmc": "PMC1347386", + "pubmed": "16381892", + "title": "DPVweb: a comprehensive database of plant and fungal virus genes and genomes.", + "year": 2006 + } + ], + "uri_format": "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1" + }, + "dragondb.allele": { + "comment": "Deprecated because the website is dead", + "deprecated": true, + "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). 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This collection refers to DNA sequence information.", + "example": "3hB06", + "homepage": "http://www.antirrhinum.net/", + "mappings": { + "biocontext": "DRAGONDB.DNA", + "miriam": "dragondb.dna", + "n2t": "dragondb.dna" + }, + "name": "DragonDB DNA", + "part_of": "dragondb", + "pattern": "^\\d\\w+$", + "preferred_prefix": "dragondb.dna", + "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA" + }, + "dragondb.locus": { + "comment": "Deprecated because the website is dead", + "deprecated": true, + "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information.", + "example": "DEF", + "homepage": "http://www.antirrhinum.net/", + "mappings": { + "biocontext": "DRAGONDB.LOCUS", + "miriam": "dragondb.locus", + "n2t": "dragondb.locus" + }, + "name": "DragonDB Locus", + "part_of": "dragondb", + "pattern": "^\\w+$", + "preferred_prefix": "dragondb.locus", + "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus" + }, + "dragondb.protein": { + "comment": "Deprecated because the website is dead", + "deprecated": true, + "description": "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information.", + "example": "AMDEFA", + "homepage": "http://www.antirrhinum.net/", + "mappings": { + "biocontext": "DRAGONDB.PROTEIN", + "miriam": "dragondb.protein", + "n2t": "dragondb.protein" + }, + "name": "DragonDB Protein", + "part_of": "dragondb", + "pattern": "^\\w+$", + "preferred_prefix": "dragondb.protein", + "uri_format": "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide" + }, + "drduke": { + "description": "identifier for chemicals linked to information on occurrence in plants", + "example": "19", + "homepage": "https://phytochem.nal.usda.gov/phytochem/search/list", + "mappings": { + "wikidata": "P10074" + }, + "name": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical", + "preferred_prefix": "drduke", + "uri_format": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1" + }, + "dron": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "hoganwr@gmail.com", + "github": "hoganwr", + "name": "William Hogan", + "orcid": "0000-0002-9881-1017" + }, + "description": "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive).", + "download_json": "http://purl.obolibrary.org/obo/dron.json", + "download_obo": "http://purl.obolibrary.org/obo/dron.obo", + "download_owl": "http://purl.obolibrary.org/obo/dron.owl", + "example": "00023232", + "homepage": "https://github.com/ufbmi/dron", + "keywords": [ + "biomedical science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "DRON", + "biocontext": "DRON", + "bioportal": "DRON", + "fairsharing": "FAIRsharing.w5ntfd", + "obofoundry": "dron", + "ols": "dron", + "ontobee": "DRON" + }, + "name": "The Drug Ontology", + "pattern": "^\\d{8}$", + "preferred_prefix": "DRON", + "publications": [ + { + "doi": "10.1186/s13326-017-0121-5", + "pmc": "PMC5335794", + "pubmed": "28253937", + "title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.", + "year": 2017 + }, + { + "doi": "10.1186/s13326-016-0048-2", + "pmc": "PMC4836073", + "pubmed": "27096073", + "title": "An accurate and precise representation of drug ingredients.", + "year": 2016 + }, + { + "doi": "10.1186/2041-1480-4-44", + "pmc": "PMC3931349", + "pubmed": "24345026", + "title": "Building a drug ontology based on RxNorm and other sources.", + "year": 2013 + } + ], + "repository": "https://github.com/ufbmi/dron", + "uri_format": "http://purl.obolibrary.org/obo/DRON_$1", + "version": "2022-04-22" + }, + "drsc": { + "description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.", + "example": "DRSC05221", + "homepage": "http://flyrnai.org/", + "mappings": { + "biocontext": "DRSC", + "miriam": "drsc", + "n2t": "drsc" + }, + "name": "Drosophila RNAi Screening Center", + "pattern": "^DRSC\\d+$", + "preferred_prefix": "drsc", + "uri_format": "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1" + }, + "drugbank": { + "contact": { + "email": "david.wishart@ualberta.ca", + "github": null, + "name": "David Wishart", + "orcid": "0000-0002-3207-2434" + }, + "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information.", + "example": "DB14938", + "homepage": "http://www.drugbank.ca", + "keywords": [ + "biomedical science", + "drug", + "life science", + "protein" + ], + "mappings": { + "bartoc": "18377", + "biocontext": "DrugBank", + "cellosaurus": "DrugBank", + "cheminf": "000406", + "edam": "2326", + "fairsharing": "FAIRsharing.353yat", + "miriam": "drugbank", + "n2t": "drugbank", + "prefixcommons": "drugbank", + "re3data": "r3d100010544", + "uniprot": "DB-0019", + "wikidata": "P715" + }, + "name": "DrugBank", + "pattern": "^DB\\d{5}$", + "preferred_prefix": "drugbank", + "publications": [ + { + "doi": "10.1093/nar/gkt1068", + "pmc": "PMC3965102", + "pubmed": "24203711", + "title": "DrugBank 4.0: shedding new light on drug metabolism.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkq1126", + "pmc": "PMC3013709", + "pubmed": "21059682", + "title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkm958", + "pmc": "PMC2238889", + "pubmed": "18048412", + "title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkj067", + "pmc": "PMC1347430", + "pubmed": "16381955", + "title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration.", + "year": 2006 + } + ], + "synonyms": [ + "DRUGBANK_ID", + "DrugBank" + ], + "twitter": "DrugBankDB", + "uri_format": "http://www.drugbank.ca/drugs/$1" + }, + "drugbank.category": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Close to 5K Categorizations for drugs, similar to ATCC.", + "example": "DBCAT000600", + "homepage": "https://go.drugbank.com/categories", + "keywords": [ + "chemistry", + "drugs", + "metascience", + "topics" + ], + "name": "DrugBank Drug Category", + "part_of": "drugbank", + "pattern": "^DBCAT\\d+$", + "preferred_prefix": "drugbank.category", + "uri_format": "https://www.drugbank.ca/categories/$1" + }, + "drugbank.salt": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.", + "example": "DBSALT001211", + "homepage": "http://www.drugbank.ca", + "mappings": { + "biocontext": "DRUGBANK.TARGET" + }, + "name": "DrugBank Salts", + "part_of": "drugbank", + "pattern": "^DBSALT\\d{6}$", + "preferred_prefix": "drugbank.salt", + "synonyms": [ + "drugbank.target" + ], + "uri_format": "https://go.drugbank.com/salts/$1" + }, + "drugbankv4.target": { + "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.", + "example": "BE0000048", + "homepage": "http://www.drugbank.ca/targets", + "mappings": { + "biocontext": "DRUGBANKV4.TARGET", + "miriam": "drugbankv4.target", + "n2t": "drugbankv4.target" + }, + "name": "DrugBank Target v4", + "part_of": "drugbank", + "pattern": "^BE\\d{7}$", + "preferred_prefix": "drugbankv4.target", + "uri_format": "http://www.drugbank.ca/biodb/bio_entities/$1" + }, + "drugcentral": { + "contact": { + "email": "toprea@salud.unm.edu", + "github": null, + "name": "Tudor Oprea", + "orcid": "0000-0002-6195-6976" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.", + "example": "307", + "homepage": "http://drugcentral.org", + "keywords": [ + "biomedical science", + "drug development", + "drug discovery", + "drug repositioning", + "pharmacology", + "pharmacy" + ], + "mappings": { + "biolink": "DrugCentral", + "fairsharing": "FAIRsharing.3me82d", + "miriam": "drugcentral", + "uniprot": "DB-0239", + "wikidata": "P11198" + }, + "name": "Drug Central", + "pattern": "^\\d+$", + "preferred_prefix": "drugcentral", + "publications": [ + { + "doi": "10.1093/nar/gky963", + "pmc": "PMC6323925", + "pubmed": "30371892", + "title": "DrugCentral 2018: an update.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw993", + "pmc": "PMC5210665", + "pubmed": "27789690", + "title": "DrugCentral: online drug compendium.", + "year": 2016 + } + ], + "synonyms": [ + "Drug_Central" + ], + "uri_format": "http://drugcentral.org/drugcard/$1" + }, + "dsm4": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]", + "example": "315.1", + "example_extras": [ + "291.89" + ], + "homepage": "https://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders#DSM-IV-TR_(2000)", + "mappings": { + "hl7": "2.16.840.1.113883.6.126", + "wikidata": "P663" + }, + "name": "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)", + "pattern": "^\\d+\\.\\d+$", + "preferred_prefix": "dsm4", + "synonyms": [ + "dsm-iv" + ] + }, + "dsm5": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. 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Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science.", + "example": "classification-model", + "homepage": "https://www.datascienceontology.org/", + "keywords": [ + "data science", + "ontology" + ], + "name": "Data Science Ontology", + "preferred_prefix": "dso", + "repository": "https://github.com/IBM/datascienceontology", + "uri_format": "https://www.datascienceontology.org/concept/$1" + }, + "dto": { + "appears_in": [ + "pr" + ], + "contact": { + "email": "sschurer@med.miami.edu", + "github": null, + "name": "Stephan Schurer", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors.", + "download_owl": "http://aber-owl.net/media/ontologies/DTO/4/dto.owl", + "example": "90000018", + "homepage": "https://github.com/DrugTargetOntology/DTO", + "keywords": [ + "biomedical science", + "drug discovery", + "ontology" + ], + "mappings": { + "aberowl": "DTO", + "bioportal": "DTO", + "fairsharing": "FAIRsharing.tke3y2" + }, + "name": "Drug Target Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "dto", + "publications": [ + { + "doi": "10.1186/s13326-017-0161-x", + "pmc": "PMC5679337", + "pubmed": "29122012", + "title": "Drug target ontology to classify and integrate drug discovery data.", + "year": 2017 + } + ], + "repository": "https://github.com/DrugTargetOntology/DTO", + "uri_format": "http://www.drugtargetontology.org/dto/DTO_$1" + }, + "duo": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "mcourtot@gmail.com", + "github": "mcourtot", + "name": "Melanie Courtot", + "orcid": "0000-0002-9551-6370" + }, + "depends_on": [ + "bfo", + "iao" + ], + "description": "DUO is an ontology which represent data use conditions.", + "download_owl": "http://purl.obolibrary.org/obo/duo.owl", + "example": "0000046", + "homepage": "https://github.com/EBISPOT/DUO", + "keywords": [ + "biomedical science", + "obo", + "ontology", + "subject agnostic" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "DUO", + "biocontext": "DUO", + "bioportal": "DUO", + "fairsharing": "FAIRsharing.5dnjs2", + "obofoundry": "duo", + "ols": "duo", + "ontobee": "DUO" + }, + "name": "Data Use Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "DUO", + "publications": [ + { + "doi": "10.1016/j.xgen.2021.100028", + "pmc": "PMC8591903", + "pubmed": "34820659", + "title": "The Data Use Ontology to streamline responsible access to human biomedical datasets.", + "year": 2021 + } + ], + "repository": "https://github.com/EBISPOT/DUO", + "uri_format": "http://purl.obolibrary.org/obo/DUO_$1", + "version": "2021-02-23" + }, + "eaglei": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Discovery tool for biomedical research resources available at institutions throughout the U.S.", + "example": "0000012b-5661-2f63-2f73-b43980000000", + "homepage": "https://hawaii.eagle-i.net", + "mappings": { + "cellosaurus": "eagle-i", + "re3data": "r3d100011564" + }, + "name": "eagle-i", + "preferred_prefix": "eaglei", + "uri_format": "http://hawaii.eagle-i.net/i/$1" + }, + "easychair.cfp": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Conferences in EasyChair", + "example": "SysBioCancer2022", + "homepage": "https://easychair.org/cfp/", + "keywords": [ + "conferences", + "metascience" + ], + "name": "EasyChair Call for Paper", + "preferred_prefix": "easychair.cfp", + "uri_format": "https://easychair.org/cfp/$1" + }, + "easychair.topic": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Call for paper topics in EasyChair", + "example": "27106865", + "homepage": "https://easychair.org/cfp/", + "keywords": [ + "metascience", + "topics" + ], + "name": "EasyChair Topic", + "pattern": "^\\d+$", + "preferred_prefix": "easychair.topic", + "uri_format": "https://easychair.org/cfp/topic.cgi?tid=$1" + }, + "ebisc": { + "description": "Cell line collections", + "example": "ESi007-A", + "homepage": "https://www.ebisc.org", + "mappings": { + "cellosaurus": "EBiSC" + }, + "name": "European Bank for induced pluripotent Stem Cells", + "preferred_prefix": "ebisc", + "uri_format": "https://cells.ebisc.org/$1" + }, + "ecacc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).", + "example": "90062901", + "homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx", + "mappings": { + "cellosaurus": "ECACC" + }, + "name": "European Collection of Authenticated Cell Culture", + "pattern": "^\\d+$", + "preferred_prefix": "ecacc", + "uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1" + }, + "ecao": { + "contact": { + "email": "ettensohn@cmu.edu", + "github": "ettensohn", + "name": "Charles Ettensohn", + "orcid": "0000-0002-3625-0955" + }, + "depends_on": [ + "cl", + "ro", + "uberon" + ], + "description": "None", + "download_obo": "http://purl.obolibrary.org/obo/ecao.obo", + "download_owl": "http://purl.obolibrary.org/obo/ecao.owl", + "example": "0107180", + "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "ECAO", + "bioportal": "ECAO", + "obofoundry": "ecao", + "ols": "ecao", + "ontobee": "ECAO" + }, + "name": "The Echinoderm Anatomy and Development Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ECAO", + "repository": "https://github.com/echinoderm-ontology/ecao_ontology", + "uri_format": "http://purl.obolibrary.org/obo/ECAO_$1", + "version": "2020-05-22" + }, + "eccode": { + "contact": { + "email": "kristian.axelsen@sib.swiss", + "github": "kaxelsen", + "name": "Kristian Axelsen", + "orcid": "0000-0003-3889-2879" + }, + "description": "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions.", + "example": "1.1.1.1", + "example_decoys": [ + "100", + "2.", + "2.n1", + "2.3.", + "2.3.n1", + "2.3.1.", + "2.3.1.n", + "2.3.4.1." + ], + "example_extras": [ + "2", + "2.3", + "2.3.1", + "2.3.1.n12", + "3.1.26.n2" + ], + "homepage": "https://www.enzyme-database.org/", + "keywords": [ + "biochemistry", + "classification", + "enzyme", + "enzymology" + ], + "mappings": { + "bartoc": "671", + "biocontext": "EC-CODE", + "edam": "1011", + "fairsharing": "FAIRsharing.rfLD2u", + "go": "EC", + "miriam": "ec-code", + "n2t": "ec-code", + "prefixcommons": "intenz", + "re3data": "r3d100010803", + "uniprot": "DB-0024", + "wikidata": "P591" + }, + "name": "Enzyme Commission Code", + "pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$", + "preferred_prefix": "eccode", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "KEGG Ligand Database for Enzyme Nomenclature", + "homepage": "https://www.genome.jp/dbget-bin/www_bfind?enzyme", + "name": "KEGG Ligand Database for Enzyme Nomenclature", + "uri_format": "https://www.genome.jp/dbget-bin/www_bget?ec:$1" + }, + { + "code": "enzymeportal", + "description": "Enzyme Portal through EMBL-EBI", + "homepage": "https://www.ebi.ac.uk/enzymeportal", + "name": "Enzyme Portal through EMBL-EBI", + "uri_format": "https://www.ebi.ac.uk/enzymeportal/ec/$1" + }, + { + "code": "expasy", + "description": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)", + "homepage": "https://enzyme.expasy.org/", + "name": "Enzyme nomenclature database, ExPASy (Expert Protein Analysis System)", + "uri_format": "https://enzyme.expasy.org/EC/$1" + }, + { + "code": "expenz", + "description": "ExploreEnz at Trinity College", + "homepage": "http://www.enzyme-database.org/", + "name": "ExploreEnz at Trinity College", + "uri_format": "http://www.enzyme-database.org/query.php?ec=$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/28.1.304", + "pmc": "PMC102465", + "pubmed": "10592255", + "title": "The ENZYME database in 2000.", + "year": 2000 + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/681" + ], + "synonyms": [ + "EC", + "EC number", + "EC-CODE", + "ECCODE", + "EC_CODE", + "ec-code", + "intenz" + ], + "uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1" + }, + "ecg": { + "contact": { + "email": "rwinslow@jhu.edu", + "github": null, + "name": "Raimond Winslow", + "orcid": "0000-0003-1719-1651" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.", + "download_owl": "http://aber-owl.net/media/ontologies/ECG/12/ecg.owl", + "example": "000000159", + "homepage": "https://bioportal.bioontology.org/ontologies/ECG", + "keywords": [ + "biomedical science", + "ontology" + ], + "mappings": { + "aberowl": "ECG", + "bioportal": "ECG", + "fairsharing": "FAIRsharing.azr389" + }, + "name": "Electrocardiogram Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "ecg", + "publications": [ + { + "doi": "10.1016/j.jbi.2010.08.007", + "pmc": null, + "pubmed": "20800107", + "title": "Using an ECG reference ontology for semantic interoperability of ECG data.", + "year": 2010 + } + ], + "synonyms": [ + "ECGOntology" + ], + "uri_format": "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1" + }, + "echobase": { + "description": "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.", + "example": "EB0170", + "homepage": "http://www.york.ac.uk/", + "keywords": [ + "gene", + "gene expression" + ], + "mappings": { + "biocontext": "ECHOBASE", + "go": "EchoBASE", + "miriam": "echobase", + "n2t": "echobase", + "prefixcommons": "echobase", + "re3data": "r3d100011646", + "uniprot": "DB-0020" + }, + "name": "EchoBASE post-genomic database for Escherichia coli", + "pattern": "^EB\\d+$", + "preferred_prefix": "echobase", + "publications": [ + { + "doi": "10.1093/nar/gki028", + "pmc": "PMC539982", + "pubmed": "15608209", + "title": "EchoBASE: an integrated post-genomic database for Escherichia coli.", + "year": 2005 + } + ], + "uri_format": "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1" + }, + "ecmdb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes.", + "example": "ECMDB00005", + "homepage": "https://ecmdb.ca", + "name": "E. coli Metabolite Database", + "pattern": "^ECMDB\\d+$", + "preferred_prefix": "ecmdb", + "synonyms": [ + "ECMDB" + ], + "uri_format": "http://ecmdb.ca/compounds/$1" + }, + "ecn": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "identifier for a chemical compound per EINECS or ELINCS", + "example": "200-003-9", + "homepage": "https://echa.europa.eu/information-on-chemicals", + "mappings": { + "cheminf": "000447", + "wikidata": "P232" + }, + "name": "EC number", + "pattern": "^\\d{3}-\\d{3}-\\d$", + "preferred_prefix": "ecn", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/257", + "https://en.wikipedia.org/wiki/European_Community_number" + ] + }, + "eco": { + "banana": "ECO", + "contact": { + "email": "mgiglio@som.umaryland.edu", + "github": "mgiglio99", + "name": "Michelle Giglio", + "orcid": "0000-0001-7628-5565" + }, + "description": "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity.", + "download_obo": "http://purl.obolibrary.org/obo/eco.obo", + "download_owl": "http://purl.obolibrary.org/obo/eco.owl", + "example": "0007807", + "homepage": "https://www.evidenceontology.org", + "keywords": [ + "computational biology", + "life science", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "ECO", + "bartoc": "1028", + "biocontext": "ECO", + "bioportal": "ECO", + "fairsharing": "FAIRsharing.wvpgwn", + "go": "ECO", + "miriam": "eco", + "n2t": "eco", + "obofoundry": "eco", + "ols": "eco", + "ontobee": "ECO", + "prefixcommons": "eco", + "wikidata": "P3811" + }, + "name": "Evidence ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "ECO", + "publications": [ + { + "doi": "10.1093/nar/gkab1025", + "pmc": "PMC8728134", + "pubmed": "34986598", + "title": "ECO: the Evidence and Conclusion Ontology, an update for 2022.", + "year": 2022 + }, + { + "doi": "10.1093/nar/gky1036", + "pmc": "PMC6323956", + "pubmed": "30407590", + "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information.", + "year": 2019 + }, + { + "doi": "10.1007/978-1-4939-3743-1_18", + "pmc": "PMC6377151", + "pubmed": "27812948", + "title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.", + "year": 2017 + }, + { + "doi": "10.1093/database/bau075", + "pmc": "PMC4105709", + "pubmed": "25052702", + "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO).", + "year": 2014 + }, + { + "doi": "10.1142/9789812704856_0019", + "pmc": null, + "pubmed": "14992503", + "title": "An evidence ontology for use in pathway/genome databases.", + "year": 2004 + } + ], + "repository": "https://github.com/evidenceontology/evidenceontology", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1", + "version": "2022-08-05" + }, + "ecocore": { + "contact": { + "email": "p.buttigieg@gmail.com", + "github": "pbuttigieg", + "name": "Pier Luigi Buttigieg", + "orcid": "0000-0002-4366-3088" + }, + "depends_on": [ + "bfo", + "chebi", + "envo", + "go", + "iao", + "pato", + "pco", + "po", + "ro", + "uberon" + ], + "description": "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms.", + "download_obo": "http://purl.obolibrary.org/obo/ecocore.obo", + "download_owl": "http://purl.obolibrary.org/obo/ecocore.owl", + "example": "00000001", + "homepage": "https://github.com/EcologicalSemantics/ecocore", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "ECOCORE", + "biocontext": "ECOCORE", + "bioportal": "ECOCORE", + "obofoundry": "ecocore", + "ols": "ecocore", + "ontobee": "ECOCORE" + }, + "name": "An ontology of core ecological entities", + "pattern": "^\\d+$", + "preferred_prefix": "ECOCORE", + "repository": "https://github.com/EcologicalSemantics/ecocore", + "uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1", + "version": "2022-03-09" + }, + "ecocyc": { + "contributor_extras": [ + { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + } + ], + "description": "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways.", + "example": "AICARTRANSIMPCYCLO-CPLX", + "homepage": "https://ecocyc.org/", + "keywords": [ + "biology" + ], + "mappings": { + "fairsharing": "FAIRsharing.65dmtr", + "go": "EcoCyc", + "ncbi": "ECOCYC", + "re3data": "r3d100011277" + }, + "name": "EcoCyc", + "preferred_prefix": "ecocyc", + "publications": [ + { + "doi": "10.3389/fmicb.2021.711077", + "pmc": "PMC8357350", + "pubmed": "34394059", + "title": "The EcoCyc Database in 2021.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gkw1003", + "pmc": "PMC5210515", + "pubmed": "27899573", + "title": "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.", + "year": 2016 + }, + { + "doi": "10.1128/ecosalplus.esp-0009-2013", + "pmc": "PMC4243172", + "pubmed": "26442933", + "title": "The EcoCyc Database.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks1027", + "pmc": "PMC3531154", + "pubmed": "23143106", + "title": "EcoCyc: fusing model organism databases with systems biology.", + "year": 2012 + } + ], + "uri_format": "https://ecocyc.org/gene?id=$1" + }, + "ecogene": { + "description": "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.", + "example": "EG10173", + "homepage": "http://ecogene.org/", + "keywords": [ + "genome", + "protein" + ], + "mappings": { + "biocontext": "EcoGene", + "fairsharing": "FAIRsharing.3q3kvn", + "miriam": "ecogene", + "n2t": "ecogene", + "ncbi": "EcoGene", + "prefixcommons": "ecogene", + "re3data": "r3d100010546" + }, + "name": "Database of Escherichia coli Sequence and Function", + "pattern": "^EG\\d+$", + "preferred_prefix": "ecogene", + "publications": [ + { + "doi": "10.1093/nar/28.1.60", + "pmc": "PMC102481", + "pubmed": "10592181", + "title": "EcoGene: a genome sequence database for Escherichia coli K-12.", + "year": 2000 + } + ], + "uri_format": "http://www.ecogene.org/gene/$1" + }, + "ecolexicon": { + "comment": "No resolution - everything is in a single page app", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology.", + "example": "canal", + "homepage": "http://ecolexicon.ugr.es/en/index.htm", + "keywords": [ + "ecology", + "environmental science" + ], + "name": "EcoLexicon", + "preferred_prefix": "ecolexicon" + }, + "ecoliwiki": { + "description": "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes.", + "example": "aaeA", + "homepage": "http://ecoliwiki.net/colipedia/", + "keywords": [ + "bioinformatics", + "genomics", + "life science", + "ontology and terminology" + ], + "mappings": { + "biocontext": "ECOLIWIKI", + "fairsharing": "FAIRsharing.tx95wa", + "go": "EcoliWiki", + "miriam": "ecoliwiki", + "n2t": "ecoliwiki" + }, + "name": "EcoliWiki from EcoliHub", + "pattern": "^[A-Za-z0-9-]+$", + "preferred_prefix": "ecoliwiki", + "publications": [ + { + "doi": "10.1016/j.tim.2009.04.004", + "pmc": "PMC3575750", + "pubmed": "19576778", + "title": "What we can learn about Escherichia coli through application of Gene Ontology.", + "year": 2009 + } + ], + "uri_format": "http://ecoliwiki.net/colipedia/index.php/$1:Gene" + }, + "ecto": { + "contact": { + "email": "annethessen@gmail.com", + "github": "diatomsRcool", + "name": "Anne Thessen", + "orcid": "0000-0002-2908-3327" + }, + "depends_on": [ + "chebi", + "envo", + "exo", + "go", + "iao", + "maxo", + "nbo", + "ncbitaxon", + "ncit", + "pato", + "ro", + "uberon", + "xco" + ], + "description": "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology).", + "download_json": "http://purl.obolibrary.org/obo/ecto.json", + "download_obo": "http://purl.obolibrary.org/obo/ecto.obo", + "download_owl": "http://purl.obolibrary.org/obo/ecto.owl", + "example": "0000001", + "homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "ECTO", + "biolink": "ECTO", + "bioportal": "ECTO", + "obofoundry": "ecto", + "ols": "ecto", + "ontobee": "ECTO" + }, + "name": "Environmental conditions, treatments and exposures ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ECTO", + "repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", + "uri_format": "http://purl.obolibrary.org/obo/ECTO_$1", + "version": "2022-12-12" + }, + "ecyano.entity": { + "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.", + "example": "23", + "homepage": "http://www.e-cyanobacterium.org/bcs/entity/", + "mappings": { + "biocontext": "ECYANO.ENTITY", + "miriam": "ecyano.entity", + "n2t": "ecyano.entity" + }, + "name": "E-cyanobacterium entity", + "part_of": "ecyano", + "pattern": "^\\d+$", + "preferred_prefix": "ecyano.entity", + "uri_format": "https://www.e-cyanobacterium.org/bcs/entity/$1" + }, + "ecyano.experiment": { + "description": "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments.", + "example": "18", + "homepage": "https://www.e-cyanobacterium.org/experiments-repository/", + "mappings": { + "miriam": "ecyano.experiment" + }, + "name": "E-cyanobacterium Experimental Data", + "part_of": "ecyano", + "pattern": "^\\d+$", + "preferred_prefix": "ecyano.experiment", + "uri_format": "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1" + }, + "ecyano.model": { + "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models.", + "example": "26", + "homepage": "http://e-cyanobacterium.org/models/", + "mappings": { + "biocontext": "ECYANO.MODEL", + "miriam": "ecyano.model", + "n2t": "ecyano.model" + }, + "name": "E-cyanobacterium model", + "pattern": "^\\d+$", + "preferred_prefix": "ecyano.model", + "uri_format": "https://e-cyanobacterium.org/models/model/$1" + }, + "ecyano.rule": { + "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules.", + "example": "56", + "homepage": "http://www.e-cyanobacterium.org/bcs/rule/", + "mappings": { + "biocontext": "ECYANO.RULE", + "miriam": "ecyano.rule", + "n2t": "ecyano.rule" + }, + "name": "E-cyanobacterium rule", + "part_of": "ecyano", + "pattern": "^\\d+$", + "preferred_prefix": "ecyano.rule", + "uri_format": "https://e-cyanobacterium.org/bcs/rule/$1" + }, + "edam": { + "contact": { + "email": "matus.kalas@uib.no", + "github": "matuskalas", + "name": "Matúš Kalaš", + "orcid": "0000-0002-1509-4981" + }, + "description": "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).", + "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", + "download_owl": "https://raw.githubusercontent.com/edamontology/edamontology/master/releases/EDAM.owl", + "example": "data_1664", + "homepage": "http://edamontology.org", + "keywords": [ + "bioinformatics", + "life science", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "EDAM", + "agroportal": "EDAM", + "biocontext": "EDAM", + "bioportal": "EDAM", + "fairsharing": "FAIRsharing.a6r7zs", + "miriam": "edam", + "n2t": "edam", + "ols": "edam", + "ontobee": "EDAM", + "prefixcommons": "edam" + }, + "name": "Bioinformatics operations, data types, formats, identifiers and topics", + "pattern": "^(data|topic|operation|format)\\_\\d{4}$", + "preferred_prefix": "edam", + "publications": [ + { + "doi": "10.1093/bioinformatics/btt113", + "pmc": "PMC3654706", + "pubmed": "23479348", + "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.", + "year": 2013 + } + ], + "repository": "https://github.com/edamontology/edamontology", + "twitter": "edamontology", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1", + "version": "2019-07-17" + }, + "edam.data": { + "contact": { + "email": "matus.kalas@uib.no", + "github": "matuskalas", + "name": "Matúš Kalaš", + "orcid": "0000-0002-1509-4981" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.", + "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", + "example": "1664", + "homepage": "http://edamontology.org", + "keywords": [ + "ontology" + ], + "mappings": { + "biolink": "EDAM-DATA" + }, + "name": "EDAM Data", + "part_of": "edam", + "pattern": "^\\d+$", + "preferred_prefix": "edam.data", + "repository": "https://github.com/edamontology/edamontology", + "twitter": "edamontology", + "uri_format": "http://edamontology.org/data_$1" + }, + "edam.format": { + "contact": { + "email": "matus.kalas@uib.no", + "github": "matuskalas", + "name": "Matúš Kalaš", + "orcid": "0000-0002-1509-4981" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.", + "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", + "example": "1915", + "homepage": "http://edamontology.org", + "keywords": [ + "ontology" + ], + "mappings": { + "biolink": "EDAM-FORMAT" + }, + "name": "EDAM Format", + "part_of": "edam", + "pattern": "^\\d+$", + "preferred_prefix": "edam.format", + "repository": "https://github.com/edamontology/edamontology", + "twitter": "edamontology", + "uri_format": "http://edamontology.org/format_$1" + }, + "edam.operation": { + "contact": { + "email": "matus.kalas@uib.no", + "github": "matuskalas", + "name": "Matúš Kalaš", + "orcid": "0000-0002-1509-4981" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.", + "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", + "example": "0004", + "homepage": "http://edamontology.org", + "keywords": [ + "ontology" + ], + "mappings": { + "biolink": "EDAM-OPERATION" + }, + "name": "EDAM Operation", + "part_of": "edam", + "pattern": "^\\d+$", + "preferred_prefix": "edam.operation", + "repository": "https://github.com/edamontology/edamontology", + "twitter": "edamontology", + "uri_format": "http://edamontology.org/operation_$1" + }, + "edam.topic": { + "contact": { + "email": "matus.kalas@uib.no", + "github": "matuskalas", + "name": "Matúš Kalaš", + "orcid": "0000-0002-1509-4981" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.", + "download_obo": "https://github.com/edamontology/edamontology/raw/main/releases/EDAM.obo", + "example": "0003", + "homepage": "http://edamontology.org", + "keywords": [ + "ontology" + ], + "mappings": { + "biolink": "EDAM-TOPIC" + }, + "name": "EDAM Topic", + "part_of": "edam", + "pattern": "^\\d+$", + "preferred_prefix": "edam.topic", + "repository": "https://github.com/edamontology/edamontology", + "twitter": "edamontology", + "uri_format": "http://edamontology.org/topic_$1" + }, + "edda": { + "contact": { + "email": "tanja.bekhuis@tcbinfosci.com", + "github": null, + "name": "Tanja Bekhuis", + "orcid": "0000-0002-8537-9077" + }, + "description": "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries.", + "download_owl": "http://aber-owl.net/media/ontologies/EDDA/11/edda.owl", + "example": "health_care_quality_assessment", + "homepage": "https://bioportal.bioontology.org/ontologies/EDDA", + "keywords": [ + "medicine", + "ontology" + ], + "mappings": { + "aberowl": "EDDA", + "bioportal": "EDDA", + "fairsharing": "FAIRsharing.2ffmsb" + }, + "name": "EDDA Study Designs Taxonomy", + "preferred_prefix": "edda", + "uri_format": "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1" + }, + "efo": { + "contact": { + "email": "plwhetzel@gmail.com", + "github": "twhetzel", + "name": "Trish Whetzel", + "orcid": "0000-0002-3458-4839" + }, + "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team.", + "download_obo": "http://www.ebi.ac.uk/efo/efo.obo", + "download_owl": "http://www.ebi.ac.uk/efo/efo.owl", + "example": "0005147", + "homepage": "http://www.ebi.ac.uk/efo", + "keywords": [ + "functional genomics", + "ontology" + ], + "mappings": { + "aberowl": "EFO", + "agroportal": "EFO", + "biocontext": "EFO", + "biolink": "EFO", + "bioportal": "EFO", + "cellosaurus": "EFO", + "fairsharing": "FAIRsharing.1gr4tz", + "miriam": "efo", + "n2t": "efo", + "ols": "efo", + "ontobee": "EFO" + }, + "name": "Experimental Factor Ontology", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^\\d{7}$", + "preferred_prefix": "EFO", + "providers": [ + { + "code": "ebi", + "description": "EFO through Functional Genomics Group (EBI)", + "homepage": "https://www.ebi.ac.uk/efo/", + "name": "EFO through Functional Genomics Group (EBI)", + "uri_format": "https://www.ebi.ac.uk/efo/EFO_$1" + } + ], + "publications": [ + { + "doi": "10.1093/bioinformatics/btq099", + "pmc": "PMC2853691", + "pubmed": "20200009", + "title": "Modeling sample variables with an Experimental Factor Ontology.", + "year": 2010 + } + ], + "repository": "https://github.com/EBISPOT/efo/", + "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1", + "version": "3.49.0" + }, + "ega.dataset": { + "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", + "example": "EGAD00000000001", + "homepage": "https://ega-archive.org/", + "keywords": [ + "biology", + "biomedical science", + "clinical studies", + "genomics", + "phenomics" + ], + "mappings": { + "biocontext": "EGA.DATASET", + "fairsharing": "FAIRsharing.mya1ff", + "miriam": "ega.dataset", + "n2t": "ega.dataset", + "re3data": "r3d100011242" + }, + "name": "European Genome-phenome Archive Dataset", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^EGAD\\d{11}$", + "preferred_prefix": "ega.dataset", + "providers": [ + { + "code": "omicsdi", + "description": "EGA Dataset through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "EGA Dataset through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/ega/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkab1059", + "pmc": "PMC8728218", + "pubmed": "34791407", + "title": "The European Genome-phenome Archive in 2021.", + "year": 2022 + }, + { + "doi": "10.1038/ng.3312", + "pmc": "PMC5426533", + "pubmed": "26111507", + "title": "The European Genome-phenome Archive of human data consented for biomedical research.", + "year": 2015 + } + ], + "twitter": "EGAarchive", + "uri_format": "https://www.ebi.ac.uk/ega/datasets/$1" + }, + "ega.study": { + "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", + "example": "EGAS00000000001", + "homepage": "https://www.ebi.ac.uk/ega/studies", + "mappings": { + "biocontext": "EGA.STUDY", + "miriam": "ega.study", + "n2t": "ega.study" + }, + "name": "European Genome-phenome Archive Study", + "pattern": "^EGAS\\d{11}$", + "preferred_prefix": "ega.study", + "uri_format": "https://www.ebi.ac.uk/ega/studies/$1" + }, + "eggnog": { + "description": "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories).", + "example": "veNOG12876", + "homepage": "http://eggnog.embl.de/version_3.0/", + "keywords": [ + "gene", + "life science" + ], + "mappings": { + "biocontext": "EGGNOG", + "fairsharing": "FAIRsharing.j1wj7d", + "miriam": "eggnog", + "n2t": "eggnog", + "prefixcommons": "eggnog", + "uniprot": "DB-0152" + }, + "name": "eggNOG", + "pattern": "^\\w+$", + "preferred_prefix": "eggnog", + "publications": [ + { + "doi": "10.1093/nar/gkp951", + "pmc": "PMC2808932", + "pubmed": "19900971", + "title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkm796", + "pmc": "PMC2238944", + "pubmed": "17942413", + "title": "eggNOG: automated construction and annotation of orthologous groups of genes.", + "year": 2007 + } + ], + "uri_format": "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1" + }, + "ehda": { + "contact": { + "email": "J.Bard@ed.ac.uk", + "github": null, + "name": "Jonathan Bard", + "orcid": null + }, + "deprecated": true, + "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once.", + "download_obo": "http://aber-owl.net/media/ontologies/EHDA/6/ehda.obo", + "example": "1", + "homepage": "http://genex.hgu.mrc.ac.uk/", + "keywords": [ + "anatomy", + "development", + "human", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "EHDA", + "biocontext": "EHDA", + "bioportal": "EHDA", + "obofoundry": "ehda", + "prefixcommons": "ehda" + }, + "name": "Human developmental anatomy, timed version", + "pattern": "^\\d+$", + "preferred_prefix": "EHDA", + "uri_format": "http://purl.obolibrary.org/obo/EHDA_$1" + }, + "ehdaa": { + "contact": { + "email": "J.Bard@ed.ac.uk", + "github": null, + "name": "Jonathan Bard", + "orcid": null + }, + "deprecated": true, + "description": "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.", + "download_obo": "http://aber-owl.net/media/ontologies/EHDAA/6/ehdaa.obo", + "example": "1", + "homepage": "http://genex.hgu.mrc.ac.uk/", + "keywords": [ + "anatomy", + "development", + "human", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "EHDAA", + "biocontext": "EHDAA", + "bioportal": "EHDAA", + "obofoundry": "ehdaa", + "prefixcommons": "ehdaa" + }, + "name": "Human developmental anatomy, abstract version", + "pattern": "^\\d+$", + "preferred_prefix": "EHDAA", + "uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1" + }, + "ehdaa2": { + "contact": { + "email": "J.Bard@ed.ac.uk", + "github": null, + "name": "Jonathan Bard", + "orcid": null + }, + "depends_on": [ + "aeo", + "caro", + "cl" + ], + "deprecated": true, + "description": "A structured controlled vocabulary of stage-specific anatomical structures of the developing human.", + "download_obo": "http://purl.obolibrary.org/obo/ehdaa2.obo", + "download_owl": "http://purl.obolibrary.org/obo/ehdaa2.owl", + "example": "0000000", + "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology", + "keywords": [ + "anatomy", + "biomedical science", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "EHDAA2", + "biocontext": "EHDAA2", + "bioportal": "EHDAA2", + "fairsharing": "FAIRsharing.7zxrs6", + "obofoundry": "ehdaa2", + "ols": "ehdaa2", + "ontobee": "EHDAA2" + }, + "name": "Human developmental anatomy, abstract", + "pattern": "^\\d{7}$", + "preferred_prefix": "EHDAA2", + "publications": [ + { + "doi": "10.1111/j.1469-7580.2012.01566.x", + "pmc": "PMC3482348", + "pubmed": "22973865", + "title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).", + "year": 2012 + } + ], + "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", + "synonyms": [ + "EHDAA2_RETIRED", + "HDAA2", + "RETIRED_EHDAA2" + ], + "uri_format": "http://purl.obolibrary.org/obo/EHDAA2_$1", + "version": "2013-07-04" + }, + "elm": { + "description": "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances.", + "example": "CLV_MEL_PAP_1", + "homepage": "http://elm.eu.org/", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "ELM", + "fairsharing": "FAIRsharing.rj3kj5", + "miriam": "elm", + "n2t": "elm", + "uniprot": "DB-0223" + }, + "name": "Eukaryotic Linear Motif Resource", + "pattern": "^[A-Za-z_0-9]+$", + "preferred_prefix": "elm", + "publications": [ + { + "doi": "10.1093/nar/gkz1030", + "pmc": "PMC7145657", + "pubmed": "31680160", + "title": "ELM-the eukaryotic linear motif resource in 2020.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gkv1291", + "pmc": "PMC4702912", + "pubmed": "26615199", + "title": "ELM 2016--data update and new functionality of the eukaryotic linear motif resource.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkr1064", + "pmc": "PMC3245074", + "pubmed": "22110040", + "title": "ELM--the database of eukaryotic linear motifs.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkg545", + "pmc": "PMC168952", + "pubmed": "12824381", + "title": "ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.", + "year": 2003 + } + ], + "uri_format": "http://elm.eu.org/elms/elmPages/$1.html" + }, + "emap": { + "contact": { + "email": "Terry.Hayamizu@jax.org", + "github": "tfhayamizu", + "name": "Terry Hayamizu", + "orcid": "0000-0002-0956-8634" + }, + "deprecated": true, + "description": "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).", + "download_owl": "http://purl.obolibrary.org/obo/emap.owl", + "example": "1", + "homepage": "http://emouseatlas.org", + "keywords": [ + "anatomy", + "development", + "mouse", + "obo", + "ontology" + ], + "mappings": { + "biocontext": "EMAP", + "bioportal": "EMAP", + "obofoundry": "emap", + "prefixcommons": "emap.ontology" + }, + "name": "Mouse gross anatomy and development, timed", + "pattern": "^\\d+$", + "preferred_prefix": "EMAP", + "uri_format": "http://purl.obolibrary.org/obo/EMAP_$1" + }, + "emapa": { + "contact": { + "email": "Terry.Hayamizu@jax.org", + "github": "tfhayamizu", + "name": "Terry Hayamizu", + "orcid": "0000-0002-0956-8634" + }, + "description": "An ontology for mouse anatomy covering embryonic development and postnatal stages.", + "download_obo": "http://purl.obolibrary.org/obo/emapa.obo", + "download_owl": "http://purl.obolibrary.org/obo/emapa.owl", + "example": "26753", + "homepage": "http://www.informatics.jax.org/expression.shtml", + "keywords": [ + "anatomy", + "developmental biology", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "EMAPA", + "bartoc": "549", + "biocontext": "EMAPA", + "bioportal": "EMAPA", + "fairsharing": "FAIRsharing.j0fa1d", + "go": "EMAPA", + "obofoundry": "emapa", + "ols": "emapa", + "ontobee": "EMAPA" + }, + "name": "Mouse Developmental Anatomy Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "EMAPA", + "publications": [ + { + "doi": "10.1016/s0925-4773(98)00069-0", + "pmc": null, + "pubmed": "9651497", + "title": "An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature.", + "year": 1998 + }, + { + "doi": "10.1007/s00335-015-9584-9", + "pmc": "PMC4602063", + "pubmed": "26208972", + "title": "Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.", + "year": 2015 + }, + { + "doi": "10.1186/2041-1480-4-15", + "pmc": "PMC3851555", + "pubmed": "23972281", + "title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.", + "year": 2013 + }, + { + "doi": "10.1016/b978-0-12-800043-4.00023-3", + "pmc": null, + "pubmed": null, + "title": "Textual Anatomics", + "year": 2016 + } + ], + "repository": "https://github.com/obophenotype/mouse-anatomy-ontology", + "synonyms": [ + "EMAPA_RETIRED" + ], + "uri_format": "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1", + "version": "2022-07-14" + }, + "emaps": { + "contact": { + "email": "Terry.Hayamizu@jax.org", + "github": "tfhayamizu", + "name": "Terry Hayamizu", + "orcid": "0000-0002-0956-8634" + }, + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "depends_on": [ + "emapa" + ], + "description": "EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823", + "example": "3517823", + "github_request_issue": 747, + "homepage": "https://www.informatics.jax.org/vocab/gxd/anatomy/", + "name": "Mouse Developmental Anatomy Ontology with Theiler Stage", + "pattern": "^\\d+$", + "preferred_prefix": "EMAPS", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1" + }, + "emdb": { + "contact": { + "email": "help@emdatabank.org", + "github": null, + "name": "Ardan Patwardhan", + "orcid": "0000-0001-7663-9028" + }, + "description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.", + "example": "EMD-1001", + "homepage": "https://www.ebi.ac.uk/pdbe/emdb/", + "keywords": [ + "epidemiology", + "structural biology", + "virology" + ], + "mappings": { + "biocontext": "EMDB", + "edam": "1146", + "fairsharing": "FAIRsharing.651n9j", + "miriam": "emdb", + "n2t": "emdb", + "re3data": "r3d100010562" + }, + "name": "Electron Microscopy Data Bank", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^EMD-\\d{4,5}$", + "preferred_prefix": "emdb", + "publications": [ + { + "doi": "10.1093/nar/gkv1126", + "pmc": "PMC4702818", + "pubmed": "26578576", + "title": "EMDataBank unified data resource for 3DEM.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkq880", + "pmc": "PMC3013769", + "pubmed": "20935055", + "title": "EMDataBank.org: unified data resource for CryoEM.", + "year": 2010 + }, + { + "doi": "10.1016/s0968-0004(02)02176-x", + "pmc": null, + "pubmed": "12417136", + "title": "New electron microscopy database and deposition system.", + "year": 2002 + } + ], + "uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1" + }, + "emolecules": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Catalog of purchasable reagents and building blocks", + "example": "491187", + "homepage": "https://reaxys.emolecules.com", + "keywords": [ + "chemistry", + "reagents", + "vendor" + ], + "name": "Reaxys eMolecules", + "pattern": "^\\d+$", + "preferred_prefix": "emolecules", + "uri_format": "https://reaxys.emolecules.com/cgi-bin/more?vid=$1" + }, + "empiar": { + "banana": "EMPIAR", + "banana_peel": "-", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure", + "example": "10595", + "homepage": "https://www.ebi.ac.uk/pdbe/emdb", + "keywords": [ + "bioinformatics", + "biology" + ], + "mappings": { + "fairsharing": "FAIRsharing.dff3ef", + "miriam": "empiar" + }, + "name": "Electron Microscopy Public Image Archive", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^\\d+$", + "preferred_prefix": "empiar", + "publications": [ + { + "doi": "10.1038/nmeth.3806", + "pmc": null, + "pubmed": "27067018", + "title": "EMPIAR: a public archive for raw electron microscopy image data.", + "year": 2016 + } + ], + "uri_format": "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1" + }, + "ena.embl": { + "contact": { + "email": "datasubs@ebi.ac.uk", + "github": null, + "name": "Guy Cochrane", + "orcid": "0000-0001-7954-7057" + }, + "description": "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers.", + "example": "BN000065", + "homepage": "https://www.ebi.ac.uk/ena/", + "keywords": [ + "biodiversity", + "bioinformatics", + "data management", + "dna", + "functional genomics", + "genomics", + "metagenomics", + "transcriptomics" + ], + "mappings": { + "biocontext": "ENA.EMBL", + "fairsharing": "FAIRsharing.dj8nt8", + "go": "ENA", + "miriam": "ena.embl", + "n2t": "ena.embl", + "prefixcommons": "ena", + "re3data": "r3d100010527", + "uniprot": "DB-0022" + }, + "name": "European Nucleotide Archive", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^[A-Z]+[0-9]+(\\.\\d+)?$", + "preferred_prefix": "ena.embl", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "ENA through GenBank", + "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", + "name": "ENA through GenBank", + "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkaa1028", + "pmc": "PMC7778925", + "pubmed": "33175160", + "title": "The European Nucleotide Archive in 2020.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gkw1106", + "pmc": "PMC5210577", + "pubmed": "27899630", + "title": "European Nucleotide Archive in 2016.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkv1323", + "pmc": "PMC4702924", + "pubmed": "26657633", + "title": "The International Nucleotide Sequence Database Collaboration.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkv1311", + "pmc": "PMC4702917", + "pubmed": "26615190", + "title": "Biocuration of functional annotation at the European nucleotide archive.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gku1129", + "pmc": "PMC4383942", + "pubmed": "25404130", + "title": "Content discovery and retrieval services at the European Nucleotide Archive.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks1175", + "pmc": "PMC3531187", + "pubmed": "23203883", + "title": 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Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", + "download_obo": "http://purl.obolibrary.org/obo/eo.obo", + "download_owl": "http://purl.obolibrary.org/obo/eo.owl", + "example": "0007404", + "homepage": "http://planteome.org/", + "keywords": [ + "obo", + "ontology", + "plant" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "EO", + "agroportal": "EO", + "biocontext": "EO", + "miriam": "eo", + "n2t": "eo", + "obofoundry": "eo", + "prefixcommons": "eo" + }, + "name": "Plant Environment Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "EO", + "publications": [ + { + "doi": "10.3732/ajb.1200222", + "pmc": "PMC3492881", + "pubmed": "22847540", + "title": "Ontologies as integrative tools for plant science.", + "year": 2012 + } + ], + "repository": "https://github.com/Planteome/plant-environment-ontology", + "uri_format": "http://archive.gramene.org/db/ontology/search?query=EO:$1" + }, + "eol": { + "contact": { + "email": "pylebail@rennes.inra.fr", + "github": null, + "name": "Pierre-Yves LeBail", + "orcid": "0000-0002-8310-5195" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The EOL ontology describes environmental conditions of livestock farms. 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EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.", + "example": "TA_H3", + "homepage": "http://epd.vital-it.ch/", + "keywords": [ + "bioinformatics", + "biology" + ], + "mappings": { + "biocontext": "EPD", + "edam": "2386", + "fairsharing": "FAIRsharing.yk1krv", + "miriam": "epd", + "n2t": "epd", + "ncbi": "EPD", + "uniprot": "DB-0205" + }, + "name": "Eukaryotic Promoter Database", + "pattern": "^[A-Z-_0-9]+$", + "preferred_prefix": "epd", + "publications": [ + { + "doi": "10.1093/nar/27.1.307", + "pmc": "PMC148166", + "pubmed": "9847211", + "title": "The Eukaryotic Promoter Database (EPD): recent developments.", + "year": 1999 + }, + { + "doi": "10.1093/nar/26.1.353", + "pmc": "PMC147208", + "pubmed": "9399872", + "title": "The Eukaryotic Promoter Database EPD.", + "year": 1998 + }, + { + "doi": "10.1093/nar/14.24.10009", + "pmc": "PMC341352", + "pubmed": "3808945", + "title": "Compilation and analysis of eukaryotic POL II promoter sequences.", + "year": 1986 + }, + { + "doi": "10.1093/nar/gkx807", + "pmc": "PMC5753345", + "pubmed": "28981707", + "title": "The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gkw1069", + "pmc": "PMC5210552", + "pubmed": "27899657", + "title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gku1111", + "pmc": "PMC4383928", + "pubmed": "25378343", + "title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks1233", + "pmc": "PMC3531148", + "pubmed": "23193273", + "title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkj146", + "pmc": "PMC1347508", + "pubmed": "16381980", + "title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms.", + "year": 2006 + }, + { + "doi": "10.1093/nar/gkh122", + "pmc": "PMC308856", + "pubmed": "14681364", + "title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.", + "year": 2004 + }, + { + "doi": "10.1093/nar/30.1.322", + "pmc": "PMC99099", + "pubmed": "11752326", + "title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.", + "year": 2002 + }, + { + "doi": "10.1093/nar/28.1.302", + "pmc": "PMC102462", + "pubmed": "10592254", + "title": "The eukaryotic promoter database (EPD).", + "year": 2000 + } + ], + "uri_format": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1" + }, + "epio": { + "contact": { + "email": "alpha.tom.kodamullil@scai.fraunhofer.de", + "github": "akodamullil", + "name": "Alpha Tom Kodamullil", + "orcid": "0000-0001-9896-3531" + }, + "depends_on": [ + "bfo" + ], + "description": "A application driven Epilepsy Ontology with official terms from the ILAE.", + "download_owl": "http://purl.obolibrary.org/obo/epio.owl", + "example": "0000011", + "homepage": "https://github.com/SCAI-BIO/EpilepsyOntology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "EPIO", + "bioportal": "EPIO", + "obofoundry": "epio", + "ontobee": "EPIO" + }, + "name": "Epilepsy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "EPIO", + "repository": "https://github.com/SCAI-BIO/EpilepsyOntology", + "uri_format": "http://purl.obolibrary.org/obo/EPIO_$1" + }, + "epo": { + "contributor_extras": [ + { + "email": null, + "github": "djinnome", + "name": "Jeremy Zucker", + "orcid": "0000-0002-7276-9009" + } + ], + "deprecated": true, + "description": "An ontology designed to support the semantic annotation of epidemiology resources", + "download_owl": "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl", + "homepage": "https://code.google.com/p/epidemiology-ontology/", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "EPO", + "obofoundry": "epo", + "ontobee": "EPO" + }, + "name": "Epidemiology Ontology", + "preferred_prefix": "EPO", + "uri_format": "http://purl.obolibrary.org/obo/EPO_$1" + }, + "epso": { + "contact": { + "email": "satyasahoo@ieee.org", + "github": null, + "name": "Satya S. 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", + "download_owl": "http://aber-owl.net/media/ontologies/EPSO/3/epso.owl", + "example": "0000400", + "homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology", + "keywords": [ + "neurology", + "ontology" + ], + "mappings": { + "aberowl": "EPSO", + "bioportal": "EPSO", + "fairsharing": "FAIRsharing.ttprgy", + "ontobee": "EPSO" + }, + "name": "Epilepsy and Seizure Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "epso", + "publications": [ + { + "doi": "10.1136/amiajnl-2013-001696", + "pmc": "PMC3912711", + "pubmed": "23686934", + "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care.", + "year": 2013 + } + ], + "uri_format": "http://www.case.edu/EpilepsyOntology.owl#$1" + }, + "erm": { + "contact": { + "email": "egon.willighagen@gmail.com", + "github": "egonw", + "name": "Egon Willighagen", + "orcid": "0000-0001-7542-0286" + }, + "description": "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project.", + "download_rdf": "https://nanocommons.github.io/identifiers/registry", + "example": "ERM00000044", + "homepage": "https://nanocommons.github.io/identifiers/", + "keywords": [ + "materials informatics", + "nanotechnology" + ], + "mappings": { + "cheminf": "000569", + "fairsharing": "FAIRsharing.c26a4e", + "miriam": "erm", + "n2t": "erm" + }, + "name": "European Registry of Materials", + "pattern": "^ERM[0-9]{8}$", + "preferred_prefix": "erm", + "publications": [ + { + "doi": "10.1186/s13321-022-00614-7", + "pmc": "PMC9400299", + "pubmed": "36002868", + "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials.", + "year": 2022 + } + ], + "twitter": "nanocommons", + "uri_format": "https://nanocommons.github.io/identifiers/registry#$1" + }, + "ero": { + "contact": { + "email": "Marc_Ciriello@hms.harvard.edu", + "github": null, + "name": "Marc Ciriello", + "orcid": "0000-0002-3734-1859" + }, + "deprecated": true, + "description": "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens.", + "download_owl": "http://purl.obolibrary.org/obo/ero.owl", + "example": "0001655", + "homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology", + "keywords": [ + "biomedical science", + "life science", + "obo", + "ontology" + ], + "license": "CC BY 2.0", + "mappings": { + "aberowl": "ERO", + "biocontext": "ERO", + "bioportal": "ERO", + "fairsharing": "FAIRsharing.nwgynk", + "obofoundry": "ero", + "ols": "ero", + "ontobee": "ERO" + }, + "name": "eagle-i resource ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ERO", + "publications": [ + { + "doi": "10.1109/jcdl.2017.7991571", + "pmc": "PMC5868434", + "pubmed": "29599662", + "title": "Automating data citation: the eagle-i experience.", + "year": 2017 + }, + { + "doi": "10.1093/database/bar067", + "pmc": "PMC3308157", + "pubmed": "22434835", + "title": "Research resources: curating the new eagle-i discovery system.", + "year": 2012 + } + ], + "uri_format": "http://purl.obolibrary.org/obo/ERO_$1", + "version": "2016-07-27" + }, + "eropmoscow": { + "description": "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.).", + "example": "E00002", + "homepage": "http://erop.inbi.ras.ru", + "keywords": [ + "protein" + ], + "mappings": { + "prefixcommons": "eropmoscow" + }, + "name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow", + "preferred_prefix": "eropmoscow", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://erop.inbi.ras.ru/result2.php?PepName=$1" + }, + "erv": { + "description": "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. 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It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.", + "example": "HS000015122", + "homepage": "http://gpcr.biocomp.unibo.it/esldb", + "keywords": [ + "protein" + ], + "mappings": { + "prefixcommons": "esldb" + }, + "name": "eukaryotic Subcellular Localization database", + "preferred_prefix": "esldb", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1" + }, + "estdab": { + "comment": "Website is dead", + "deprecated": true, + "description": "Cell line databases/resources", + "example": "046", + "homepage": "https://www.ebi.ac.uk/ipd/estdab/", + "mappings": { + "cellosaurus": "ESTDAB" + }, + "name": "European Searchable Tumour Line Database", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^\\d{3}$", + "preferred_prefix": "estdab", + "uri_format": "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1" + }, + "eu89h": { + "description": "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union.", + "example": "jrc-eurl-ecvam-chemagora", + "homepage": "http://data.jrc.ec.europa.eu/", + "mappings": { + "biocontext": "EU89H", + "miriam": "eu89h", + "n2t": "eu89h" + }, + "name": "JRC Data Catalogue", + "pattern": "^[a-z0-9\\-_]+$", + "preferred_prefix": "eu89h", + "uri_format": "http://data.europa.eu/89h/$1" + }, + "euclinicaltrials": { + "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", + "example": "2008-005144-16", + "homepage": "https://www.clinicaltrialsregister.eu/", + "mappings": { + "biocontext": "EUCLINICALTRIALS", + "miriam": "euclinicaltrials", + "n2t": "euclinicaltrials" + }, + "name": "EU Clinical Trials", + "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", + "preferred_prefix": "euclinicaltrials", + "uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1" + }, + "eugenes": { + "contact": { + "email": "eugenes@iubio.bio.indiana.edu", + "github": null, + "name": "Don Gilbert", + "orcid": "0000-0002-6646-7274" + }, + "description": "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information.", + "example": "MGgn0008978", + "homepage": "http://eugenes.org/", + "keywords": [ + "genome", + "life science", + "ontology" + ], + "mappings": { + "fairsharing": "FAIRsharing.7fc5y6", + "prefixcommons": "eugenes" + }, + "name": "Eukaryotic Genes", + "preferred_prefix": "eugenes", + "publications": [ + { + "doi": "10.1093/nar/30.1.145", + "pmc": "PMC99146", + "pubmed": "11752277", + "title": "euGenes: a eukaryote genome information system.", + "year": 2002 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://eugenes.org:7072/.bin/fbidq.html?$1" + }, + "eupath": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "jiezheng@pennmedicine.upenn.edu", + "github": "zhengj2007", + "name": "Jie Zheng", + "orcid": "0000-0002-2999-0103" + }, + "description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.", + "download_owl": "http://purl.obolibrary.org/obo/eupath.owl", + "example": "0010316", + "homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", + "keywords": [ + "biomedical science", + "epidemiology", + "functional genomics", + "obo", + "ontology", + "population genetics" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "EUPATH", + "biocontext": "EUPATH", + "bioportal": "EUPATH", + "fairsharing": "FAIRsharing.9rhr9j", + "obofoundry": "eupath", + "ols": "eupath", + "ontobee": "EUPATH" + }, + "name": "VEuPathDB ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "EUPATH", + "publications": [ + { + "doi": "10.5281/zenodo.6685957", + "pmc": null, + "pubmed": null, + "title": "Malaria study data integration and information retrieval based on OBO Foundry ontologies", + "year": 2016 + } + ], + "repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", + "uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", + "version": "2022-06-08" + }, + "eurofir": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries.", + "homepage": "https://www.eurofir.org", + "name": "European Food Information Resource Network", + "preferred_prefix": "eurofir", + "proprietary": true + }, + "ev": { + "appears_in": [ + "cl" + ], + "contact": { + "email": "evoc@sanbi.ac.za", + "github": null, + "name": "eVOC mailing list", + "orcid": null + }, + "deprecated": true, + "description": "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment.", + "example": "EV_0100011", + "homepage": "http://www.evocontology.org/", + "keywords": [ + "anatomy", + "cell", + "development", + "experiment", + "obo", + "ontology" + ], + "mappings": { + "biocontext": "EV", + "obofoundry": "ev", + "prefixcommons": "evoc" + }, + "name": "eVOC (Expressed Sequence Annotation for Humans)", + "preferred_prefix": "EV", + "references": [ + "https://twitter.com/Bgeedb/status/1350124337815281664" + ], + "uri_format": "http://purl.obolibrary.org/obo/EV_$1" + }, + "evm": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "name": "eVOC mouse development stage", + "preferred_prefix": "evm", + "references": [ + "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r229" + ] + }, + "exac.gene": { + "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information.", + "example": "ENSG00000169174", + "homepage": "http://exac.broadinstitute.org/", + "mappings": { + "biocontext": "EXAC.GENE", + "miriam": "exac.gene", + "n2t": "exac.gene" + }, + "name": "ExAC Gene", + "pattern": "^ENSG\\d{11}$", + "preferred_prefix": "exac.gene", + "uri_format": "http://exac.broadinstitute.org/gene/$1" + }, + "exac.transcript": { + "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information.", + "example": "ENST00000407236", + "homepage": "http://exac.broadinstitute.org/", + "mappings": { + "biocontext": "EXAC.TRANSCRIPT", + "miriam": "exac.transcript", + "n2t": "exac.transcript" + }, + "name": "ExAC Transcript", + "pattern": "^ENST\\d{11}$", + "preferred_prefix": "exac.transcript", + "uri_format": "http://exac.broadinstitute.org/transcript/$1" + }, + "exac.variant": { + "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.", + "example": "22-46615880-T-C", + "homepage": "http://exac.broadinstitute.org/", + "mappings": { + "biocontext": "EXAC.VARIANT", + "miriam": "exac.variant", + "n2t": "exac.variant" + }, + "name": "ExAC Variant", + "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", + "preferred_prefix": "exac.variant", + "uri_format": "http://exac.broadinstitute.org/variant/$1" + }, + "exo": { + "appears_in": [ + "ecto", + "scdo" + ], + "contact": { + "email": "annethessen@gmail.com", + "github": "diatomsRcool", + "name": "Anne Thessen", + "orcid": "0000-0002-2908-3327" + }, + "description": "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.", + "download_obo": "http://purl.obolibrary.org/obo/exo.obo", + "download_owl": "http://purl.obolibrary.org/obo/exo.owl", + "example": "0000078", + "homepage": "https://github.com/CTDbase/exposure-ontology", + "keywords": [ + "environmental science", + "epigenetics", + "obo", + "ontology", + "toxicology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "EXO", + "biocontext": "EXO", + "biolink": "ExO", + "bioportal": "EXO", + "fairsharing": "FAIRsharing.6hna78", + "obofoundry": "exo", + "ols": "exo", + "ontobee": "ExO" + }, + "name": "Exposure ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ExO", + "publications": [ + { + "doi": "10.1021/es2033857", + "pmc": "PMC3314380", + "pubmed": "22324457", + "title": "Providing the missing link: the exposure science ontology ExO.", + "year": 2012 + } + ], + "repository": "https://github.com/CTDbase/exposure-ontology", + "synonyms": [ + "ExO" + ], + "uri_format": "http://purl.obolibrary.org/obo/EXO_$1", + "version": "2022-06-29" + }, + "fabio": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references.", + "download_owl": "http://aber-owl.net/media/ontologies/FaBiO/1/fabio.owl", + "example": "d4e2515", + "homepage": "https://github.com/sparontologies/fabio", + "keywords": [ + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "FaBiO", + "biolink": "fabio", + "fairsharing": "FAIRsharing.2f3180" + }, + "name": "FaBiO, the FRBR-aligned Bibliographic Ontology", + "preferred_prefix": "fabio", + "providers": [ + { + "code": "rdf", + "description": "A persistent URL for FaBiO", + "homepage": "https://github.com/sparontologies/fabio", + "name": "FABIO PURL", + "uri_format": "http://purl.org/spar/fabio/$1" + } + ], + "publications": [ + { + "doi": "10.1016/j.websem.2012.08.001", + "pmc": null, + "pubmed": null, + "title": "FaBiO and CiTO: Ontologies for describing bibliographic resources and citations", + "year": 2012 + } + ], + "repository": "https://github.com/sparontologies/fabio", + "twitter": "sparontologies", + "uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1" + }, + "facebase": { + "description": "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects.", + "example": "FB00000917", + "homepage": "https://www.facebase.org", + "keywords": [ + "anatomy", + "developmental biology", + "epigenetics", + "genetics", + "medicine" + ], + "mappings": { + "biocontext": "FACEBASE", + "fairsharing": "FAIRsharing.mqvqde", + "miriam": "facebase", + "n2t": "facebase", + "re3data": "r3d100013263" + }, + "name": "FaceBase Data Repository", + "pattern": "^FB\\d{8}$", + "preferred_prefix": "facebase", + "publications": [ + { + "doi": "10.1242/dev.191213", + "pmc": "PMC7522026", + "pubmed": "32958507", + "title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research.", + "year": 2020 + } + ], + "uri_format": "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1" + }, + "fairsharing": { + "contact": { + "email": "allyson.lister@oerc.ox.ac.uk", + "github": null, + "name": "Allyson Lister", + "orcid": "0000-0002-7702-4495" + }, + "description": "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies.", + "example": "bsg-000052", + "example_extras": [ + "FAIRsharing.CugtbQ" + ], + "homepage": "https://fairsharing.org/", + "keywords": [ + "agriculture", + "biomedical science", + "data governance", + "database management", + "earth science", + "environmental science", + "humanities", + "life science", + "natural science", + "ontology and terminology", + "policy" + ], + "mappings": { + "biocontext": "FAIRSHARING", + "fairsharing": "FAIRsharing.2abjs5", + "miriam": "fairsharing", + "n2t": "fairsharing", + "re3data": "r3d100010142" + }, + "name": "FAIRsharing", + "pattern": "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$", + "preferred_prefix": "fairsharing", + "publications": [ + { + "doi": "10.1038/s41587-019-0080-8", + "pmc": "PMC6785156", + "pubmed": "30940948", + "title": "FAIRsharing as a community approach to standards, repositories and policies.", + "year": 2019 + }, + { + "doi": "10.1093/database/baw075", + "pmc": "PMC4869797", + "pubmed": "27189610", + "title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.", + "year": 2016 + }, + { + "doi": "10.5281/zenodo.5106255", + "pmc": null, + "pubmed": null, + "title": "FAIRsharing, a FAIR-enabling service for repositories, standards and policies", + "year": 2021 + } + ], + "repository": "https://github.com/FAIRsharing", + "twitter": "fairsharing_org", + "uri_format": "https://fairsharing.org/$1" + }, + "fairsharing.organization": { + "contact": { + "email": "allyson.lister@oerc.ox.ac.uk", + "github": "allysonlister", + "name": "Allyson Lister", + "orcid": "0000-0002-7702-4495" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An organization in FAIRsharing, including universities, labs, etc.", + "example": "3851", + "homepage": "https://fairsharing.org", + "name": "FAIRsharing Organization", + "part_of": "fairsharing", + "pattern": "^\\d+$", + "preferred_prefix": "fairsharing.organization", + "uri_format": "https://fairsharing.org/organisations/$1" + }, + "fairsharing.user": { + "contact": { + "email": "allyson.lister@oerc.ox.ac.uk", + "github": "allysonlister", + "name": "Allyson Lister", + "orcid": "0000-0002-7702-4495" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A user of FAIRsharing", + "example": "5112", + "homepage": "https://fairsharing.org", + "name": "FAIRsharing User", + "part_of": "fairsharing", + "pattern": "^\\d+$", + "preferred_prefix": "fairsharing.user", + "uri_format": "https://fairsharing.org/users/$1" + }, + "faldo": { + "contact": { + "email": "faldo@googlegroups.com", + "github": null, + "name": "FALDO group", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources", + "download_owl": "http://aber-owl.net/media/ontologies/FALDO/1/faldo.owl", + "example": "ForwardStrandPosition", + "homepage": "http://biohackathon.org/resource/faldo", + "keywords": [ + "genetics", + "ontology" + ], + "mappings": { + "aberowl": "FALDO", + "agroportal": "FALDO", + "biocontext": "faldo", + "bioportal": "FALDO", + "fairsharing": "FAIRsharing.haxp7g" + }, + "name": "Feature Annotation Location Description Ontology ", + "preferred_prefix": "faldo", + "publications": [ + { + "doi": "10.1186/s13326-016-0067-z", + "pmc": "PMC4907002", + "pubmed": "27296299", + "title": "FALDO: a semantic standard for describing the location of nucleotide and protein 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The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there.", + "download_owl": "http://purl.obolibrary.org/obo/fideo.owl", + "example": "00000021", + "homepage": "https://gitub.u-bordeaux.fr/erias/fideo", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "FIDEO", + "bioportal": "FIDEO", + "obofoundry": "fideo", + "ols": "fideo", + "ontobee": "FIDEO" + }, + "name": "Food Interactions with Drugs Evidence Ontology", + "pattern": "^\\d{8}$", + "preferred_prefix": "FIDEO", + "repository": "https://gitub.u-bordeaux.fr/erias/fideo", + "uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1" + }, + "fishbase.species": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Global biodiversity database on finfishes. 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This collection references compounds.", + "example": "FDB002100", + "homepage": "https://foodb.ca/", + "mappings": { + "biocontext": "FOODB.COMPOUND", + "biolink": "foodb.compound", + "miriam": "foodb.compound", + "n2t": "foodb.compound", + "re3data": "r3d100012152", + "wikidata": "P8117" + }, + "name": "FooDB compound", + "pattern": "^FDB\\d+$", + "preferred_prefix": "foodb.compound", + "synonyms": [ + "foodb" + ], + "uri_format": "http://foodb.ca/compounds/$1" + }, + "foodb.food": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Foods in FooDB", + "example": "FOOD00020", + "homepage": "https://foodb.ca/foods", + "mappings": { + "biolink": "foodb.food" + }, + "name": "FooDB Food", + "pattern": "^FOOD\\d+$", + "preferred_prefix": "foodb.food", + "uri_format": "https://foodb.ca/foods/$1" + }, + "foodex2": { + "contact": { + "email": "datex@efsa.europa.eu", + "github": null, + "name": "European Food Safety Authority", + "orcid": null + }, + "description": "FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains.", + "example": "A0TMC", + "homepage": "http://www.efsa.europa.eu/", + "mappings": { + "agroportal": "FOODEX2" + }, + "name": "Food classification and description system", + "preferred_prefix": "foodex2", + "uri_format": "http://data.food.gov.uk/codes/foodtype/id/$1" + }, + "foodon": { + "appears_in": [ + "agro", + "envo", + "fobi", + "maxo", + "one", + "ons" + ], + "banana": "FOODON", + "contact": { + "email": "damion_dooley@sfu.ca", + "github": "ddooley", + "name": "Damion Dooley", + "orcid": "0000-0002-8844-9165" + }, + "depends_on": [ + "bfo", + "chebi", + "envo", + "eo", + "ncbitaxon", + "obi", + "ro", + "uberon" + ], + "description": "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies.", + "download_obo": "http://purl.obolibrary.org/obo/foodon.obo", + "download_owl": "http://purl.obolibrary.org/obo/foodon.owl", + "example": "03307879", + "homepage": "https://foodon.org/", + "keywords": [ + "agriculture", + "botany", + "environmental science", + "medicine", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "FOODON", + "agroportal": "FOODON", + "biocontext": "FOODON", + "bioportal": "FOODON", + "fairsharing": "FAIRsharing.dzxae", + "miriam": "foodon", + "n2t": "foodon", + "obofoundry": "foodon", + "ols": "foodon", + "ontobee": "FOODON" + }, + "name": "The Food Ontology", + "namespace_in_lui": true, + "pattern": "^[0-9]{8}$", + "preferred_prefix": "FOODON", + "publications": [ + { + "doi": "10.1038/s41538-018-0032-6", + "pmc": "PMC6550238", + "pubmed": "31304272", + "title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.", + "year": 2018 + }, + { + "doi": "10.3389/fmicb.2017.01068", + "pmc": "PMC5483436", + "pubmed": "28694792", + "title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.", + "year": 2017 + } + ], + "repository": "https://github.com/FoodOntology/foodon", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1", + "version": "2022-02-01" + }, + "fossilworks.journal": { + "contributor": { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + }, + "description": "Identifier for a journal article in the fossilworks website", + "example": "61467", + "github_request_issue": 468, + "homepage": "http://fossilworks.org", + "mappings": { + "wikidata": "P7720" + }, + "name": "Fossilworks Journal", + "part_of": "fossilworks", + "pattern": "^\\d+$", + "preferred_prefix": "fossilworks.journal", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://fossilworks.org/?a=referenceInfo&reference_no=$1" + }, + "fossilworks.taxon": { + "contributor": { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + }, + "description": "Identifier for an animal, plant, or microorganism from the fossilworks website", + "example": "40565", + "github_request_issue": 469, + "homepage": "http://www.fossilworks.org", + "mappings": { + "wikidata": "P842" + }, + "name": "Fossilworks Taxon", + "part_of": "fossilworks", + "pattern": "^[1-9]\\d{0,5}$", + "preferred_prefix": "fossilworks.taxon", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1" + }, + "fovt": { + "contact": { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + }, + "depends_on": [ + "bco", + "bfo", + "bspo", + "iao", + "oba", + "pato", + "ro", + "uberon" + ], + "description": "None", + "download_obo": "http://purl.obolibrary.org/obo/fovt.obo", + "download_owl": "http://purl.obolibrary.org/obo/fovt.owl", + "example": "0000009", + "homepage": "https://github.com/futres/fovt", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "FOVT", + "bioportal": "FOVT", + "obofoundry": "fovt", + "ols": "fovt", + "ontobee": "FOVT" + }, + "name": "FuTRES Ontology of Vertebrate Traits", + "pattern": "^\\d{7}$", + "preferred_prefix": "FOVT", + "repository": "https://github.com/futres/fovt", + "uri_format": "http://purl.obolibrary.org/obo/FOVT_$1", + "version": "2021-11-10" + }, + "fplx": { + "contact": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships.", + "example": "GPIb_IX_V", + "homepage": "https://sorgerlab.github.io/famplex/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "FPLX", + "biocontext": "FPLX", + "bioportal": "FPLX", + "miriam": "fplx", + "n2t": "fplx" + }, + "name": "FamPlex", + "pattern": "^[a-zA-Z0-9][A-Za-z0-9_]+$", + "preferred_prefix": "fplx", + "publications": [ + { + "doi": "10.1186/s12859-018-2211-5", + "pmc": "PMC6022344", + "pubmed": "29954318", + "title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.", + "year": 2018 + } + ], + "synonyms": [ + "famplex" + ], + "uri_format": "https://sorgerlab.github.io/famplex/$1" + }, + "fr": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology that enables the description of reviews of scientific articles and other scholarly resources.", + "example": "ReviewVersion", + "homepage": "http://www.sparontologies.net/ontologies/fr", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.e7e609" + }, + "name": "FAIR* Reviews Ontology", + "preferred_prefix": "FR", + "repository": "https://github.com/sparontologies/fr", + "twitter": "sparontologies" + }, + "frapo": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc.", + "example": "Grant", + "homepage": "http://www.sparontologies.net/ontologies/frapo", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "aberowl": "FRAPO", + "fairsharing": "FAIRsharing.0a2576" + }, + "name": "Funding, Research Administration and Projects Ontology", + "preferred_prefix": "FRAPO", + "repository": "https://github.com/sparontologies/frapo", + "twitter": "sparontologies", + "uri_format": "http://purl.org/cerif/frapo/$1" + }, + "frbr": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO.", + "example": "Expression", + "homepage": "http://www.sparontologies.net/ontologies/frbr", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.b34b43" + }, + "name": "Functional Requirements for Bibliographic Records", + "preferred_prefix": "FRBR", + "repository": "https://github.com/sparontologies/frbr", + "twitter": "sparontologies", + "uri_format": "http://purl.org/vocab/frbr/core#$1" + }, + "fsnp": { + "description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", + "example": "rs17852708", + "homepage": "http://compbio.cs.queensu.ca/F-SNP/", + "keywords": [ + "dna", + "protein" + ], + "mappings": { + "biocontext": "FSNP", + "miriam": "fsnp", + "n2t": "fsnp", + "prefixcommons": "fsnp" + }, + "name": "F-SNP", + "pattern": "^rs\\d+$", + "preferred_prefix": "fsnp", + "uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1" + }, + "ftt": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific.", + "example": "273", + "homepage": "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3", + "name": "Feature Type Thesaurus", + "pattern": "^\\d+$", + "preferred_prefix": "ftt", + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200", + "https://github.com/EnvironmentOntology/envo/issues/1130" + ], + "uri_format": "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1" + }, + "funcbase.fly": { + "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", + "example": "10194", + "homepage": "http://func.mshri.on.ca/fly", + "mappings": { + "biocontext": "FUNCBASE.FLY", + "miriam": "funcbase.fly", + "n2t": "funcbase.fly" + }, + "name": "FuncBase Fly", + "pattern": "^\\d+$", + "preferred_prefix": "funcbase.fly", + "uri_format": "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1" + }, + "funcbase.human": { + "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data.", + "example": "119514", + "homepage": "http://func.mshri.on.ca/human/", + "mappings": { + "biocontext": "FUNCBASE.HUMAN", + "miriam": "funcbase.human", + "n2t": "funcbase.human" + }, + "name": "FuncBase Human", + "pattern": "^\\d+$", + "preferred_prefix": "funcbase.human", + "uri_format": "http://func.mshri.on.ca/human/genes/list_functional_scores/$1" + }, + "funcbase.mouse": { + "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse.", + "example": "1351341", + "homepage": "http://func.mshri.on.ca/mouse/", + "mappings": { + "biocontext": "FUNCBASE.MOUSE", + "miriam": "funcbase.mouse", + "n2t": "funcbase.mouse" + }, + "name": "FuncBase Mouse", + "pattern": "^\\d+$", + "preferred_prefix": "funcbase.mouse", + "uri_format": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1" + }, + "funcbase.yeast": { + "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast.", + "example": "2701", + "homepage": "http://func.mshri.on.ca/yeast", + "mappings": { + "biocontext": "FUNCBASE.YEAST", + "miriam": "funcbase.yeast", + "n2t": "funcbase.yeast" + }, + "name": "FuncBase Yeast", + "pattern": "^\\d+$", + "preferred_prefix": "funcbase.yeast", + "uri_format": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1" + }, + "funderregistry": { + "description": "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world.", + "example": "100000001", + "homepage": "https://www.crossref.org/", + "mappings": { + "miriam": "funderregistry" + }, + "name": "FunderRegistry", + "pattern": "^\\d{9,9}$", + "preferred_prefix": "funderregistry", + "providers": [ + { + "code": "crossref.api", + "description": "Access funder data through the Crossref API", + "homepage": "https://api.crossref.org", + "name": "Crossref API", + "uri_format": "https://api.crossref.org/funders/$1" + }, + { + "code": "doi", + "description": "Access funder data through a DOI for crossref funders.", + "homepage": "https://doi.org", + "name": "DOI", + "uri_format": "https://dx.doi.org/10.13039/501100000995" + } + ], + "synonyms": [ + "FundRef", + "crossref.funder" + ], + "uri_format": "http://data.crossref.org/fundingdata/funder/10.13039/$1" + }, + "fungidb": { + "contact": { + "email": "jason.stajich@ucr.edu", + "github": null, + "name": "Jason E. Stajich", + "orcid": "0000-0002-7591-0020" + }, + "description": "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina.", + "example": "CNBG_0001", + "homepage": "https://fungidb.org/fungidb", + "keywords": [ + "genomics" + ], + "mappings": { + "biocontext": "FUNGIDB", + "fairsharing": "FAIRsharing.xf30yc", + "miriam": "fungidb", + "n2t": "fungidb", + "re3data": "r3d100011906" + }, + "name": "FungiDB", + "pattern": "^[A-Za-z_0-9]+$", + "preferred_prefix": "fungidb", + "publications": [ + { + "doi": "10.1016/j.fgb.2016.04.002", + "pmc": null, + "pubmed": "27259951", + "title": "Database whiplash, crowdsourcing, and FungiDB.", + "year": 2016 + }, + { + "doi": "10.1128/ec.00083-14", + "pmc": "PMC4135733", + "pubmed": "24813190", + "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkr918", + "pmc": "PMC3245123", + "pubmed": "22064857", + "title": "FungiDB: an integrated functional genomics database for fungi.", + "year": 2011 + } + ], + "twitter": "fungidb", + "uri_format": "https://fungidb.org/fungidb/app/record/gene/$1" + }, + "fungorum": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "identifier for a fungus taxon in Index Fungorum", + "example": "154022", + "homepage": "http://www.indexfungorum.org", + "mappings": { + "ncbi": "Fungorum", + "wikidata": "P1391" + }, + "name": "Index Fungorum", + "pattern": "^[1-9]\\d{0,5}$", + "preferred_prefix": "fungorum", + "uri_format": "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1" + }, + "fyeco": { + "comment": "Rather than admitting FYECO to the OBO foundry, we secure the prefix here at bioregistry. The FYECO namespace shows up in a lot of ingests (basically anywhere you ingest PomBase gene-phenotype data). Future work includes mapping FYECO to other OBO ontologies, but this is way ahead in the future.", + "contact": { + "email": "vw253@cam.ac.uk", + "github": "ValWood", + "name": "Val Wood", + "orcid": "0000-0001-6330-7526" + }, + "contributor": { + "email": "vw253@cam.ac.uk", + "github": "ValWood", + "name": "Val Wood", + "orcid": "0000-0001-6330-7526" + }, + "description": "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase.", + "example": "0000003", + "github_request_issue": 268, + "homepage": "https://github.com/pombase/fypo", + "mappings": { + "biolink": "FYECO" + }, + "name": "Fission Yeast Experimental Conditions Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "FYECO", + "repository": "https://github.com/pombase/fypo", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + }, + "fyler": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A hierarchical classification of congenital heart disease ", + "example": "4447", + "homepage": "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906", + "name": "Fyler", + "pattern": "^\\d+$", + "preferred_prefix": "fyler", + "references": [ + "https://github.com/obophenotype/human-phenotype-ontology/issues/2568", + "https://github.com/obophenotype/human-phenotype-ontology/issues/2511" + ] + }, + "fypo": { + "contact": { + "email": "vw253@cam.ac.uk", + "github": "ValWood", + "name": "Val Wood", + "orcid": "0000-0001-6330-7526" + }, + "description": "A formal ontology of phenotypes observed in fission yeast.", + "download_json": "http://purl.obolibrary.org/obo/fypo.json", + "download_obo": "http://purl.obolibrary.org/obo/fypo.obo", + "download_owl": "http://purl.obolibrary.org/obo/fypo.owl", + "example": "0001707", + "homepage": "https://github.com/pombase/fypo", + "keywords": [ + "genetics", + "life science", + "obo", + "ontology", + "phylogenetics" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "FYPO", + "biocontext": "FYPO", + "biolink": "FYPO", + "bioportal": "FYPO", + "fairsharing": "FAIRsharing.4vr0ys", + "go": "FYPO", + "obofoundry": "fypo", + "ols": "fypo", + "ontobee": "FYPO" + }, + "name": "Fission Yeast Phenotype Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "FYPO", + "publications": [ + { + "doi": "10.1093/bioinformatics/btt266", + "pmc": "PMC3694669", + "pubmed": "23658422", + "title": "FYPO: the fission yeast phenotype ontology.", + "year": 2013 + } + ], + "repository": "https://github.com/pombase/fypo", + "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", + "version": "2022-07-14" + }, + "ga4ghdos": { + "description": "Assists in resolving data across cloud resources.", + "example": "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d", + "homepage": "http://github.com/ga4gh/data-object-service-schemas", + "mappings": { + "biocontext": "GA4GHDOS", + "miriam": "ga4ghdos", + "n2t": "ga4ghdos" + }, + "name": "Data Object Service", + "pattern": "^[a-zA-Z0-9\\-:#/\\.]+$", + "preferred_prefix": "ga4ghdos", + "uri_format": "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1" + }, + "gabi": { + "description": "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'.", + "example": "2679240", + "homepage": "http://www.gabipd.org/", + "keywords": [ + "gene", + "genome", + "plant" + ], + "mappings": { + "biocontext": "GABI", + "miriam": "gabi", + "n2t": "gabi", + "ncbi": "GABI", + "prefixcommons": "gabi" + }, + "name": "Network of Different Plant Genomic Research Projects", + "pattern": "^\\w+$", + "preferred_prefix": "gabi", + "publications": [ + { + "doi": "10.1093/nar/gkn611", + "pmc": "PMC2686513", + "pubmed": "18812395", + "title": "GabiPD: the GABI primary database--a plant integrative 'omics' database.", + "year": 2008 + } + ], + "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" + }, + "galen": { + "comment": "I really tried, but could not figure out what GALEN stands for", + "contact": { + "email": "j@deltaflow.com", + "github": null, + "name": "Julian Seidenberg", + "orcid": null + }, + "deprecated": true, + "description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.", + "download_owl": "http://aber-owl.net/media/ontologies/GALEN/1/galen.owl", + "example": "MagnitudeValueType", + "homepage": "https://www.opengalen.org", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "GALEN", + "bioportal": "GALEN" + }, + "name": "GALEN", + "preferred_prefix": "galen", + "uri_format": "http://www.co-ode.org/ontologies/galen#$1" + }, + "gard": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease.", + "example": "6038", + "homepage": "https://rarediseases.info.nih.gov/diseases", + "mappings": { + "wikidata": "P4317" + }, + "name": "Genetic and Rare Diseases Information Center", + "pattern": "^\\d+$", + "preferred_prefix": "gard", + "synonyms": [ + "GARD", + "Genetic and Rare Diseases Information Center" + ], + "uri_format": "https://rarediseases.info.nih.gov/diseases/$1/index" + }, + "gateway": { + "description": "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access.", + "example": "fd8d0743-344a-4758-bb97-f8ad84a37357", + "homepage": "https://www.hdruk.ac.uk", + "mappings": { + "miriam": "gateway" + }, + "name": "Health Data Research Innovation Gateway", + "pattern": "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", + "preferred_prefix": "gateway", + "uri_format": "https://web.www.healthdatagateway.org/dataset/$1" + }, + "gaz": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "lschriml@som.umaryland.edu", + "github": "lschriml", + "name": "Lynn Schriml", + "orcid": "0000-0001-8910-9851" + }, + "deprecated": true, + "description": "A gazetteer constructed on ontological principles", + "download_obo": "http://purl.obolibrary.org/obo/gaz.obo", + "download_owl": "http://purl.obolibrary.org/obo/gaz.owl", + "example": "00620027", + "homepage": "http://environmentontology.github.io/gaz/", + "keywords": [ + "environmental science", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "GAZ", + "biocontext": "GAZ", + "bioportal": "GAZ", + "fairsharing": "FAIRsharing.wkdjpb", + "obofoundry": "gaz", + "ols": "gaz", + "ontobee": "GAZ", + "wikidata": "P6778" + }, + "name": "Gazetteer", + "pattern": "^\\d{8}$", + "preferred_prefix": "GAZ", + "repository": "https://github.com/EnvironmentOntology/gaz", + "uri_format": "http://purl.obolibrary.org/obo/GAZ_$1" + }, + "gbif": { + "contact": { + "email": "timrobertson100@gmail.com", + "github": "timrobertson100", + "name": "Tim Robertson", + "orcid": "0000-0001-6215-3617" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth.", + "example": "4238", + "homepage": "https://www.gbif.org/species", + "keywords": [ + "biodiversity", + "bioinformatics", + "marine biology", + "metagenomics", + "natural history", + "natural science", + "taxonomy" + ], + "mappings": { + "fairsharing": "FAIRsharing.zv11j3", + "re3data": "r3d100000039", + "wikidata": "P846" + }, + "name": "Global Biodiversity Information Facility", + "pattern": "^\\d+$", + "preferred_prefix": "gbif", + "publications": [ + { + "doi": "10.1371/journal.pone.0102623", + "pmc": "PMC4123864", + "pubmed": "25099149", + "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.", + "year": 2014 + } + ], + "repository": "https://github.com/gbif/", + "twitter": "GBIF", + "uri_format": "https://www.gbif.org/species/$1" + }, + "gc": { + "comment": "see comment here: https://github.com/obophenotype/ncbitaxon/issues/47", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries.", + "example": "11", + "homepage": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html", + "name": "Genetic Code", + "pattern": "^\\d+$", + "preferred_prefix": "gc", + "references": [ + "https://github.com/obophenotype/ncbitaxon/issues/47" + ], + "synonyms": [ + "gc_id" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1" + }, + "gcst": { + "description": "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide.", + "example": "GCST000035", + "homepage": "https://www.ebi.ac.uk", + "mappings": { + "miriam": "gcst", + "n2t": "gcst" + }, + "name": "GWAS Catalog", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^GCST\\d{6}\\d*$", + "preferred_prefix": "gcst", + "uri_format": "https://www.ebi.ac.uk/gwas/studies/$1" + }, + "gdc": { + "description": "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis.", + "example": "ae8c77fe-e6c8-44d5-8265-4a38c637bbef", + "homepage": "https://gdc.cancer.gov", + "mappings": { + "biocontext": "GDC", + "miriam": "gdc", + "n2t": "gdc" + }, + "name": "Genomic Data Commons Data Portal", + "pattern": "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$", + "preferred_prefix": "gdc", + "uri_format": "https://portal.gdc.cancer.gov/cases/$1" + }, + "gdsc": { + "description": "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies.", + "example": "1242", + "homepage": "https://www.cancerrxgene.org", + "mappings": { + "cellosaurus": "GDSC", + "miriam": "gdsc", + "n2t": "gdsc" + }, + "name": "Genomics of Drug Sensitivity in Cancer", + "pattern": "^[0-9]+$", + "preferred_prefix": "gdsc", + "uri_format": "https://www.cancerrxgene.org/translation/Drug/$1" + }, + "gear": { + "contact": { + "email": "jorvis@gmail.com", + "github": "jorvis", + "name": "Joshua Orvis", + "orcid": "0000-0002-5705-5710" + }, + "contributor": { + "email": "jorvis@gmail.com", + "github": "jorvis", + "name": "Joshua Orvis", + "orcid": "0000-0002-5705-5710" + }, + "description": "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains.", + "example": "d.a59037e8", + "example_extras": [ + "p.bfd178f5" + ], + "github_request_issue": 728, + "homepage": "https://umgear.org", + "license": "AGPL-3.0-only", + "name": "Gene Expression Analysis Resource", + "pattern": "^[dp]\\.[a-z0-9]{8}$", + "preferred_prefix": "gear", + "repository": "https://github.com/IGS/gEAR", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://umgear.org/p?id=$1" + }, + "gecko": { + "contact": { + "email": "rbca.jackson@gmail.com", + "github": "beckyjackson", + "name": "Rebecca Jackson", + "orcid": "0000-0003-4871-5569" + }, + "description": "An ontology to represent genomics cohort attributes.", + "download_owl": "http://purl.obolibrary.org/obo/gecko.owl", + "example": "0000044", + "homepage": "https://github.com/IHCC-cohorts/GECKO", + "keywords": [ + "genomics", + "life science", + "obo", + "ontology", + "statistics" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "GECKO", + "bioportal": "GECKO", + "fairsharing": "FAIRsharing.3da56b", + "obofoundry": "gecko", + "ols": "gecko", + "ontobee": "GECKO" + }, + "name": "Genomics Cohorts Knowledge Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "GECKO", + "repository": "https://github.com/IHCC-cohorts/GECKO", + "uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", + "version": "2021-01-18" + }, + "gemet": { + "contact": { + "email": "helpdesk@eionet.europa.eu", + "github": null, + "name": "Eionet Helpdesk", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", + "example": "627", + "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", + "mappings": { + "agroportal": "GEMET", + "bartoc": "16" + }, + "name": "General Multilingual Environmental Thesaurus", + "pattern": "^\\d+$", + "preferred_prefix": "gemet", + "uri_format": "https://www.eionet.europa.eu/gemet/en/concept/$1" + }, + "genatlas": { + "description": "GenAtlas is a database containing information on human genes, markers and phenotypes.", + "example": "HBB", + "homepage": "http://genatlas.medecine.univ-paris5.fr/", + "keywords": [ + "disorder", + "gene", + "human", + "life science" + ], + "mappings": { + "biocontext": "GENATLAS", + "fairsharing": "FAIRsharing.pmg2vd", + "miriam": "genatlas", + "n2t": "genatlas", + "prefixcommons": "genatlas", + "uniprot": "DB-0027" + }, + "name": "Genatlas", + "pattern": "^\\w+$", + "preferred_prefix": "genatlas", + "publications": [ + { + "doi": "10.1016/s0764-4469(99)80021-3", + "pmc": null, + "pubmed": "9835018", + "title": "Genatlas database, genes and development defects.", + "year": 1998 + }, + { + "doi": "10.1006/mgme.1999.2867", + "pmc": null, + "pubmed": "10444337", + "title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database.", + "year": 1999 + } + ], + "uri_format": "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1" + }, + "genbank": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42).", + "example": "U49845", + "homepage": "https://www.ncbi.nlm.nih.gov/genbank/", + "keywords": [ + "bioinformatics", + "data management", + "dna", + "epidemiology", + "functional genomics", + "genomics", + "metagenomics", + "transcriptomics", + "virology" + ], + "mappings": { + "biocontext": "GenBank", + "cheminf": "000304", + "edam": "2292", + "fairsharing": "FAIRsharing.9kahy4", + "go": "GenBank", + "prefixcommons": "genbank", + "re3data": "r3d100010528", + "uniprot": "DB-0028" + }, + "name": "GenBank", + "preferred_prefix": "genbank", + "publications": [ + { + "doi": "10.1186/s12859-020-3537-3", + "pmc": "PMC7245624", + "pubmed": "32448124", + "title": "VADR: validation and annotation of virus sequence submissions to GenBank.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gkz956", + "pmc": "PMC7145611", + "pubmed": "31665464", + "title": "GenBank.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gky989", + "pmc": "PMC6323954", + "pubmed": "30365038", + "title": "GenBank.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkx1094", + "pmc": "PMC5753231", + "pubmed": "29140468", + "title": "GenBank.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gkw1070", + "pmc": "PMC5210553", + "pubmed": "27899564", + "title": "GenBank.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkv1276", + "pmc": "PMC4702903", + "pubmed": "26590407", + "title": "GenBank.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gku1216", + "pmc": "PMC4383990", + "pubmed": "25414350", + "title": "GenBank.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkt1030", + "pmc": "PMC3965104", + "pubmed": "24217914", + "title": "GenBank.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gks1195", + "pmc": "PMC3531190", + "pubmed": "23193287", + "title": "GenBank.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkr1202", + "pmc": "PMC3245039", + "pubmed": "22144687", + "title": "GenBank.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkq1079", + "pmc": "PMC3013681", + "pubmed": "21071399", + "title": "GenBank.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkn723", + "pmc": "PMC2686462", + "pubmed": "18940867", + "title": "GenBank.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkm929", + "pmc": "PMC2238942", + "pubmed": "18073190", + "title": "GenBank.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkl1031", + "pmc": "PMC1781113", + "pubmed": "17170002", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2006 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/nucleotide/$1" + }, + "gendis": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases.", + "example": "46946", + "homepage": "http://caps.ncbs.res.in/gendis/home.html", + "keywords": [ + "classification", + "genome" + ], + "mappings": { + "prefixcommons": "gendis" + }, + "name": "Genomic Distribution of structural Superfamilies", + "preferred_prefix": "gendis", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1" + }, + "genecards": { + "contact": { + "email": "marilyn.safran@weizmann.ac.il", + "github": null, + "name": "Marilyn Safran", + "orcid": "0000-0001-5424-1393" + }, + "description": "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene.", + "example": "ABL1", + "homepage": "http://www.genecards.org/", + "keywords": [ + "genetics", + "genome", + "life science", + "transcriptomics" + ], + "mappings": { + "biocontext": "GENECARDS", + "fairsharing": "FAIRsharing.g7jbvn", + "miriam": "genecards", + "n2t": "genecards", + "prefixcommons": "genecards", + "re3data": "r3d100012015", + "uniprot": "DB-0030" + }, + "name": "GeneCards", + "pattern": "^[A-Za-z-0-9_]+(\\@)?$", + "preferred_prefix": "genecards", + "publications": [ + { + "doi": "10.1016/s0168-9525(97)01103-7", + "pmc": null, + "pubmed": "9097728", + "title": "GeneCards: integrating information about genes, proteins and diseases.", + "year": 1997 + }, + { + "doi": "10.1186/s12864-016-2722-2", + "pmc": "PMC4928145", + "pubmed": "27357693", + "title": "VarElect: the phenotype-based variation prioritizer of the GeneCards Suite.", + "year": 2016 + }, + { + "doi": "10.1002/cpbi.5", + "pmc": null, + "pubmed": "27322403", + "title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.", + "year": 2016 + }, + { + "doi": "10.1093/database/baw030", + "pmc": "PMC4820835", + "pubmed": "27048349", + "title": "Genic insights from integrated human proteomics in GeneCards.", + "year": 2016 + }, + { + "doi": "10.1089/omi.2015.0168", + "pmc": "PMC4799705", + "pubmed": "26983021", + "title": "GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.", + "year": 2016 + }, + { + "doi": "10.1093/database/bav006", + "pmc": "PMC4343183", + "pubmed": "25725062", + "title": "PathCards: multi-source consolidation of human biological pathways.", + "year": 2015 + }, + { + "doi": "10.1093/database/baq020", + "pmc": "PMC2938269", + "pubmed": "20689021", + "title": "GeneCards Version 3: the human gene integrator.", + "year": 2010 + }, + { + "doi": "10.1093/bioinformatics/18.11.1542", + "pmc": null, + "pubmed": "12424129", + "title": "GeneCards 2002: towards a complete, object-oriented, human gene compendium.", + "year": 2002 + } + ], + "uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1" + }, + "genecards.geneannot": { + "description": "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match.", + "example": "GSTA1", + "homepage": "http://genecards.weizmann.ac.il/geneannot/", + "keywords": [ + "gene expression" + ], + "mappings": { + "prefixcommons": "geneannot" + }, + "name": "GeneAnnot: Microarray Gene Annotation", + "preferred_prefix": "genecards.geneannot" + }, + "genecards.geneloc": { + "description": "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. 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It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.", + "example": "GC06M052656", + "homepage": "http://genecards.weizmann.ac.il/genenote/", + "keywords": [ + "gene expression" + ], + "mappings": { + "prefixcommons": "genenote" + }, + "name": "Gene Normal Tissue Expression", + "preferred_prefix": "genecards.genenote", + "uri_format": "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes" + }, + "genedb": { + "deprecated": true, + "description": "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed.", + "example": "LinJ.20.0070", + "homepage": "https://www.genedb.org/", + "keywords": [ + "genome", + "life science", + "sequence" + ], + "mappings": { + "biocontext": "GENEDB", + "edam": "1035", + "fairsharing": "FAIRsharing.j7esqq", + "go": "GeneDB", + "miriam": "genedb", + "n2t": "genedb", + "ncbi": "GeneDB", + "prefixcommons": "genedb", + "re3data": "r3d100010626", + "wikidata": "P3382" + }, + "name": "GeneDB", + "pattern": "^[\\w\\d\\.-]*$", + "preferred_prefix": "genedb", + "publications": [ + { + "doi": "10.1093/nar/gkh007", + "pmc": "PMC308742", + "pubmed": "14681429", + "title": "GeneDB: a resource for prokaryotic and eukaryotic organisms.", + "year": 2004 + } + ], + "uri_format": "https://www.genedb.org/gene/$1" + }, + "genefarm": { + "description": "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products.", + "example": "4892", + "homepage": "http://urgi.versailles.inra.fr/Genefarm/", + "keywords": [ + "expression", + "genome", + "life science", + "nucleotide", + "sequence" + ], + "mappings": { + "biocontext": "GENEFARM", + "fairsharing": "FAIRsharing.2mayq0", + "miriam": "genefarm", + "n2t": "genefarm", + "prefixcommons": "genefarm" + }, + "name": "GeneFarm", + "pattern": "^\\d+$", + "preferred_prefix": "genefarm", + "publications": [ + { + "doi": "10.1093/nar/gki115", + "pmc": "PMC540069", + "pubmed": "15608279", + "title": "GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.", + "year": 2005 + } + ], + "uri_format": "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1" + }, + "genepio": { + "contact": { + "email": "damion_dooley@sfu.ca", + "github": "ddooley", + "name": "Damion Dooley", + "orcid": "0000-0002-8844-9165" + }, + "depends_on": [ + "chebi", + "ncbitaxon", + "po", + "ro", + "uberon" + ], + "description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.", + "download_owl": "http://purl.obolibrary.org/obo/genepio.owl", + "example": "0001885", + "homepage": "http://genepio.org/", + "keywords": [ + "epidemiology", + "genomics", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "GENEPIO", + "biocontext": "GENEPIO", + "fairsharing": "FAIRsharing.y1mmbv", + "obofoundry": "genepio", + "ols": "genepio", + "ontobee": "GENEPIO" + }, + "name": "Genomic Epidemiology Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "GENEPIO", + "repository": "https://github.com/GenEpiO/genepio", + "uri_format": "http://purl.obolibrary.org/obo/GENEPIO_$1", + "version": "2022-02-06" + }, + "genetree": { + "description": "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl.", + "example": "ENSGT00550000074763", + "homepage": "http://www.ensembl.org/", + "keywords": [ + "classification", + "gene", + "protein" + ], + "mappings": { + "biocontext": "GENETREE", + "miriam": "genetree", + "n2t": "genetree", + "prefixcommons": "genetree", + "uniprot": "DB-0162" + }, + "name": "GeneTree", + "pattern": "^ENSGT\\d+$", + "preferred_prefix": "genetree", + "publications": [ + { + "doi": "10.1093/database/bav096", + "pmc": "PMC4761110", + "pubmed": "26896847", + "title": "Ensembl comparative genomics resources.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkj133", + "pmc": "PMC1347495", + "pubmed": "16381931", + "title": "Ensembl 2006.", + "year": 2006 + } + ], + "uri_format": "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1" + }, + "genewiki": { + "description": "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI.", + "example": "1017", + "homepage": "http://en.wikipedia.org/wiki/Gene_Wiki", + "keywords": [ + "genetics", + "life science" + ], + "mappings": { + "biocontext": "GENEWIKI", + "fairsharing": "FAIRsharing.t3snf", + "miriam": "genewiki", + "n2t": "genewiki", + "uniprot": "DB-0180" + }, + "name": "Gene Wiki", + "pattern": "^\\d+$", + "preferred_prefix": "genewiki", + "provides": "ncbigene", + "publications": [ + { + "doi": "10.1093/database/baw015", + "pmc": "PMC4795929", + "pubmed": "26989148", + "title": "Wikidata as a semantic framework for the Gene Wiki initiative.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkr925", + "pmc": "PMC3245148", + "pubmed": "22075991", + "title": "The Gene Wiki in 2011: community intelligence applied to human gene annotation.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkp760", + "pmc": "PMC2808918", + "pubmed": "19755503", + "title": "The Gene Wiki: community intelligence applied to human gene annotation.", + "year": 2009 + }, + { + "doi": "10.1371/journal.pbio.0060175", + "pmc": "PMC2443188", + "pubmed": "18613750", + "title": "A gene wiki for community annotation of gene function.", + "year": 2008 + } + ], + "twitter": "GeneWikiPulse", + "uri_format": "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1" + }, + "geno": { + "contact": { + "email": "mhb120@gmail.com", + "github": "mbrush", + "name": "Matthew Brush", + "orcid": "0000-0002-1048-5019" + }, + "description": "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. 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We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\".", + "download_owl": "http://purl.obolibrary.org/obo/geo.owl", + "example": "000000021", + "homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki", + "keywords": [ + "human geography", + "obo", + "ontology", + "physical geography" + ], + "license": "CC-BY-4.0", + "mappings": { + "biocontext": "GEO", + "bioportal": "GEO", + "fairsharing": "FAIRsharing.27rndz", + "miriam": "geogeo", + "obofoundry": "geo", + "ols": "geo", + "ontobee": "GEO" + }, + "name": "Geographical Entity Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{9}$", + "preferred_prefix": "GEOGEO", + "repository": "https://github.com/ufbmi/geographical-entity-ontology", + "uri_format": "http://purl.obolibrary.org/obo/GEO_$1", + "version": "2016-03-26" + }, + "geonames": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.", + "example": "3532759", + "homepage": "https://www.geonames.org", + "keywords": [ + "geography", + "geoinformatics" + ], + "mappings": { + "fairsharing": "FAIRsharing.6dba71", + "re3data": "r3d100010245" + }, + "name": "GeoNames", + "pattern": "^\\d+$", + "preferred_prefix": "geonames", + "synonyms": [ + "Geomames", + "Geonamaes" + ], + "uri_format": "https://www.geonames.org/$1" + }, + "geonames.feature": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes.", + "example": "ADM1", + "homepage": "https://www.geonames.org/export/codes.html", + "name": "GeoNames Feature Code", + "preferred_prefix": "geonames.feature", + "uri_format": "https://www.geonames.org/recent-changes/featurecode/$1/" + }, + "gexo": { + "contact": { + "email": "kuiper@bio.ntnu.no", + "github": "makuintnu", + "name": "Martin Kuiper", + "orcid": "0000-0002-1171-9876" + }, + "description": "Gene Expression Ontology", + "download_obo": "https://www.bio.ntnu.no/ontology/GeXO/gexo.obo", + "download_owl": "https://www.bio.ntnu.no/ontology/GeXO/gexo.owl", + "homepage": "http://www.semantic-systems-biology.org/apo", + "keywords": [ + "life science", + "ontology" + ], + "mappings": { + "aberowl": "GEXO", + "bioportal": "GEXO", + "fairsharing": "FAIRsharing.3e0sn4", + "ols": "gexo" + }, + "name": "Gene Expression Ontology", + "no_own_terms": true, + "preferred_prefix": "gexo", + "publications": [ + { + "doi": "10.1186/s12859-014-0386-y", + "pmc": "PMC4279962", + "pubmed": "25490885", + "title": "Finding gene regulatory network candidates using the gene expression knowledge base.", + "year": 2014 + } + ], + "version": "2019-09-18" + }, + "gfo": { + "contact": { + "email": "heinrich.herre@imise.uni-leipzig.de", + "github": null, + "name": "Heinrich Herre", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas.", + "download_owl": "http://www.onto-med.de/ontologies/gfo.owl", + "example": "projects_to", + "homepage": "https://www.onto-med.de/ontologies/gfo", + "keywords": [ + "biomedical science", + "life science", + "ontology" + ], + "mappings": { + "aberowl": "GFO", + "bioportal": "GFO", + "fairsharing": "FAIRsharing.175hsz" + }, + "name": "General Formal Ontology", + "preferred_prefix": "gfo", + "uri_format": "http://www.onto-med.de/ontologies/gfo.owl#$1" + }, + "ghr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA).", + "example": "saddan", + "homepage": "https://medlineplus.gov/genetics/condition", + "name": "Genetics Home Reference", + "preferred_prefix": "ghr", + "uri_format": "https://medlineplus.gov/genetics/condition/$1" + }, + "giardiadb": { + "description": "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "GL50803_102438", + "homepage": "https://giardiadb.org/giardiadb/", + "keywords": [ + "eukaryotic", + "genome", + "genomics" + ], + "mappings": { + "biocontext": "GIARDIADB", + "fairsharing": "FAIRsharing.e7skwg", + "miriam": "giardiadb", + "n2t": "giardiadb", + "prefixcommons": "giardiadb", + "re3data": "r3d100012458" + }, + "name": "GiardiaDB", + "pattern": "^\\w+$", + "preferred_prefix": "giardiadb", + "publications": [ + { + "doi": "10.1093/nar/gkn631", + "pmc": "PMC2686445", + "pubmed": "18824479", + "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.", + "year": 2008 + } + ], + "twitter": "EuPathDB", + "uri_format": "https://giardiadb.org/giardiadb/app/record/gene/$1" + }, + "github": { + "description": "GitHub is an online host of Git source code repositories.", + "example": "biopragmatics/bioregistry", + "example_extras": [ + "biopragmatics", + "cthoyt" + ], + "homepage": "https://github.com/", + "keywords": [ + "knowledge and information systems", + "software engineering", + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.c55d5e", + "miriam": "github", + "re3data": "r3d100010375" + }, + "name": "github", + "pattern": "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$", + "preferred_prefix": "github", + "repository": "https://services.github.com/", + "uri_format": "https://github.com/$1" + }, + "github.issue": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An issue in any public repository on GitHub.", + "example": "biopragmatics/bioregistry/424", + "homepage": "https://github.com/", + "keywords": [ + "knowledge and information systems", + "project management", + "software engineering", + "version control" + ], + "name": "GitHub Issue", + "preferred_prefix": "github.issue", + "uri_format": "https://bioregistry.io/resolve/github/issue/$1" + }, + "github.pull": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A pull request in any public repository on GitHub.", + "example": "biopragmatics/bioregistry/416", + "homepage": "https://github.com/", + "keywords": [ + "knowledge and information systems", + "project management", + "software engineering", + "version control" + ], + "name": "GitHub Pull Request", + "preferred_prefix": "github.pull", + "uri_format": "https://bioregistry.io/resolve/github/pull/$1" + }, + "gitlab": { + "description": "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability.", + "example": "morpheus.lab/morpheus", + "homepage": "https://gitlab.com/", + "keywords": [ + "knowledge and information systems", + "software engineering", + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.530e61", + "miriam": "gitlab" + }, + "name": "GitLab", + "pattern": "^.*/.*$", + "preferred_prefix": "gitlab", + "twitter": "gitlab", + "uri_format": "https://gitlab.com/$1" + }, + "glida.gpcr": { + "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors.", + "example": "ACM1_HUMAN", + "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", + "mappings": { + "biocontext": "GLIDA.GPCR", + "miriam": "glida.gpcr", + "n2t": "glida.gpcr" + }, + "name": "GLIDA GPCR", + "pattern": "^[A-Z-_0-9]+$", + "preferred_prefix": "glida.gpcr", + "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1" + }, + "glida.ligand": { + "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands.", + "example": "L000001", + "homepage": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", + "mappings": { + "biocontext": "GLIDA.LIGAND", + "miriam": "glida.ligand", + "n2t": "glida.ligand" + }, + "name": "GLIDA Ligand", + "pattern": "^L\\d+$", + "preferred_prefix": "glida.ligand", + "uri_format": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1" + }, + "glycoepitope": { + "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", + "example": "EP0311", + "homepage": "https://www.glycoepitope.jp/epitopes/", + "mappings": { + "biocontext": "GLYCOEPITOPE", + "miriam": "glycoepitope", + "n2t": "glycoepitope" + }, + "name": "GlycoEpitope", + "pattern": "^EP\\d{4}$", + "preferred_prefix": "glycoepitope", + "uri_format": "https://www.glycoepitope.jp/epitopes/$1" + }, + "glycomapsdb": { + "description": "A database of GlycoMaps containing 2585 conformational maps.", + "example": "6819", + "homepage": "http://www.glycosciences.de/modeling/glycomapsdb/", + "keywords": [ + "small molecule" + ], + "mappings": { + "prefixcommons": "glycomapsdb" + }, + "name": "GlycoMapsDB", + "preferred_prefix": "glycomapsdb", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1" + }, + "glycomedb": { + "description": "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.", + "example": "G77500AY", + "has_canonical": "glytoucan", + "homepage": "https://glytoucan.org/", + "keywords": [ + "life science", + "molecules", + "small molecules", + "structure" + ], + "mappings": { + "biocontext": "GLYCOMEDB", + "edam": "2664", + "fairsharing": "FAIRsharing.k5k0yh", + "miriam": "glycomedb", + "n2t": "glycomedb", + "prefixcommons": "glycomedb", + "re3data": "r3d100011527" + }, + "name": "GlycomeDB", + "pattern": "^\\w+$", + "preferred_prefix": "glycomedb", + "publications": [ + { + "doi": "10.1093/nar/gkq1014", + "pmc": "PMC3013643", + "pubmed": "21045056", + "title": "GlycomeDB--a unified database for carbohydrate structures.", + "year": 2010 + }, + { + "doi": "10.1093/glycob/cwp137", + "pmc": null, + "pubmed": "19759275", + "title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.", + "year": 2009 + }, + { + "doi": "10.1186/1471-2105-9-384", + "pmc": "PMC2567997", + "pubmed": "18803830", + "title": "GlycomeDB - integration of open-access carbohydrate structure databases.", + "year": 2008 + } + ], + "uri_format": "https://glytoucan.org/Structures/Glycans/$1" + }, + "glyconavi": { + "contact": { + "email": "issaku@noguchi.or.jp", + "github": null, + "name": "Issaku Yamada", + "orcid": "0000-0001-9504-189X" + }, + "description": "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools.", + "example": "GN_G03681DA", + "example_extras": [ + "GN_GlyTouCan_G03681DA" + ], + "homepage": "https://www.noguchi.or.jp/", + "keywords": [ + "chemistry", + "glycomics", + "life science", + "organic chemistry" + ], + "mappings": { + "fairsharing": "FAIRsharing.wvp1t7", + "miriam": "glyconavi" + }, + "name": "GlycoNAVI", + "pattern": "^GN_[A-Za-z0-9_:]+$", + "preferred_prefix": "glyconavi", + "repository": "https://glyconavi.github.io/doc/", + "uri_format": "https://glyconavi.org/hub/?id=$1" + }, + "glycopost": { + "description": "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines.", + "example": "GPST000024", + "homepage": "https://glycopost.glycosmos.org", + "keywords": [ + "glycomics", + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.2y1KMt", + "miriam": "glycopost" + }, + "name": "GlycoPOST", + "pattern": "^GPST[0-9]{6}$", + "preferred_prefix": "glycopost", + "uri_format": "https://glycopost.glycosmos.org/entry/$1" + }, + "glycosciencesdb": { + "contact": { + "email": "thomas@luetteke-online.de", + "github": "glycosciences", + "name": "Thomas Lütteke", + "orcid": "0000-0002-7140-9933" + }, + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates.", + "example": "1", + "github_request_issue": 537, + "homepage": "http://www.glycosciences.de/database/", + "name": "Glycosciences.DB", + "pattern": "^\\d+$", + "preferred_prefix": "glycosciencesdb", + "publications": [ + { + "doi": "10.1093/nar/gky994", + "pmc": "PMC6323918", + "pubmed": "30357361", + "title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update).", + "year": 2019 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "glycosciences.db" + ], + "uri_format": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1" + }, + "glygen": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. 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This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena.", + "example": "68513255-fc44-4041-bc4b-4fd2fae7541d", + "homepage": "http://gmd.mpimp-golm.mpg.de/", + "keywords": [ + "life science", + "metabolomics" + ], + "mappings": { + "biocontext": "GMD", + "fairsharing": "FAIRsharing.jykmkw", + "miriam": "gmd", + "n2t": "gmd", + "re3data": "r3d100011046" + }, + "name": "Golm Metabolome Database", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "preferred_prefix": "gmd", + "publications": [ + { + "doi": "doi:10.1007/s11306-010-0198-7", + "pmc": "PMC2874469", + "pubmed": "20526350", + "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles", + "year": null + }, + { + "doi": "10.1007/s11306-010-0198-7", + "pmc": "PMC2874469", + "pubmed": "20526350", + "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles.", + "year": 2010 + } + ], + "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" + }, + "gmd.analyte": { + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", + "example": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", + "homepage": "http://gmd.mpimp-golm.mpg.de/", + "mappings": { + "biocontext": "GMD.ANALYTE", + "miriam": "gmd.analyte", + "n2t": "gmd.analyte" + }, + "name": "Golm Metabolome Database Analyte", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "preferred_prefix": "gmd.analyte", + "uri_format": "http://gmd.mpimp-golm.mpg.de/Analytes/$1" + }, + "gmd.gcms": { + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.", + "example": "53d583d8-40c6-40e1-9296-23f821cd77a5", + "homepage": "http://gmd.mpimp-golm.mpg.de/", + "mappings": { + "biocontext": "GMD.GCMS", + "miriam": "gmd.gcms", + "n2t": "gmd.gcms" + }, + "name": "Golm Metabolome Database GC-MS spectra", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "preferred_prefix": "gmd.gcms", + "uri_format": "http://gmd.mpimp-golm.mpg.de/Spectrums/$1" + }, + "gmd.profile": { + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.", + "example": "10b38aaf-b977-4950-85b8-f4775f66658d", + "homepage": "http://gmd.mpimp-golm.mpg.de/", + "mappings": { + "biocontext": "GMD.PROFILE", + "miriam": "gmd.profile", + "n2t": "gmd.profile" + }, + "name": "Golm Metabolome Database Profile", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "preferred_prefix": "gmd.profile", + "uri_format": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1" + }, + "gmd.ref": { + "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.", + "example": "8cf84adb-b4db-4807-ac98-0004247c35df", + "homepage": "http://gmd.mpimp-golm.mpg.de/", + "mappings": { + "biocontext": "GMD.REF", + "miriam": "gmd.ref", + "n2t": "gmd.ref" + }, + "name": "Golm Metabolome Database Reference Substance", + "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", + "preferred_prefix": "gmd.ref", + "uri_format": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1" + }, + "gmelin": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s.", + "example": "1466", + "homepage": "https://link.springer.com/bookseries/562", + "mappings": { + "edam": "1004", + "wikidata": "P1578" + }, + "name": "Gmelins Handbuch der anorganischen Chemie", + "pattern": "^[1-9][0-9]{3,6}$", + "preferred_prefix": "gmelin", + "proprietary": true, + "references": [ + "https://en.wikipedia.org/wiki/Gmelin_database" + ] + }, + "gno": { + "contact": { + "email": "nje5@georgetown.edu", + "github": "edwardsnj", + "name": "Nathan Edwards", + "orcid": "0000-0001-5168-3196" + }, + "description": "An ontology for glycans based on GlyTouCan, but organized by subsumption.", + "download_json": "http://purl.obolibrary.org/obo/gno.json", + "download_obo": "http://purl.obolibrary.org/obo/gno.obo", + "download_owl": "http://purl.obolibrary.org/obo/gno.owl", + "example": "10004892", + "example_extras": [ + "G99373GG" + ], + "homepage": "https://gnome.glyomics.org/", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "GNO", + "bioportal": "GNO", + "obofoundry": "gno", + "ols": "gno", + "ontobee": "GNO" + }, + "name": "Glycan Naming and Subsumption Ontology", + "pattern": "^(\\d{8}|(\\w+\\d+\\w+))$", + "preferred_prefix": "GNO", + "providers": [ + { + "code": "gno.composition", + "description": "GNOme composition browser", + "homepage": "https://gnome.glyomics.org/CompositionBrowser.html", + "name": "GNOme Composition Browser", + "uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1" + }, + { + "code": "gno.structure", + "description": "GNOme structure browser", + "homepage": "https://gnome.glyomics.org/StructureBrowser.html", + "name": "GNOme Structure Viewer", + "uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1" + } + ], + "publications": [ + { + "doi": "10.5281/zenodo.6678278", + "pmc": null, + "pubmed": null, + "title": "GNOme - Glycan Naming and Subsumption Ontology", + "year": 2021 + } + ], + "repository": "https://github.com/glygen-glycan-data/GNOme", + "synonyms": [ + "gnome" + ], + "uri_format": "http://purl.obolibrary.org/obo/GNO_$1", + "version": "1.10.0" + }, + "gnomad": { + "contact": { + "email": "hrehm@mgh.harvard.edu", + "github": "heidirehm", + "name": "Heidi L. 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"http://www.geneontology.org/GO:$1" + }, + { + "code": "jax", + "description": "The JAX endpoint for exploring GO", + "homepage": "http://www.informatics.jax.org", + "name": "Jackson Laboratories", + "uri_format": "http://www.informatics.jax.org/vocab/gene_ontology/GO:$1" + }, + { + "code": "miriam_obo_legacy", + "description": "An old URI style for MIRIAM + GO", + "homepage": "https://identifiers.org/", + "name": "MIRIAM OBO Legacy", + "uri_format": "http://identifiers.org/obo.go/GO:$1" + }, + { + "code": "nextprot", + "description": "The neXtProt endpoint for exploring GO", + "homepage": "https://www.nextprot.org/", + "name": "neXtProt GO Browser", + "uri_format": "https://www.nextprot.org/term/GO:$1" + }, + { + "code": "quickgo", + "description": "QuickGO (Gene Ontology browser)", + "homepage": "https://www.ebi.ac.uk/QuickGO/", + "name": "QuickGO (Gene Ontology browser)", + "uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkaa1113", + "pmc": "PMC7779012", + "pubmed": "33290552", + "title": "The Gene Ontology resource: enriching a GOld mine.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gky1055", + "pmc": "PMC6323945", + "pubmed": "30395331", + "title": "The Gene Ontology Resource: 20 years and still GOing strong.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gku1179", + "pmc": "PMC4383973", + "pubmed": "25428369", + "title": "Gene Ontology Consortium: going forward.", + "year": 2014 + }, + { + "doi": "10.1186/1471-2164-14-513", + "pmc": "PMC3733925", + "pubmed": "23895341", + "title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gks1050", + "pmc": "PMC3531070", + "pubmed": "23161678", + "title": "Gene Ontology annotations and resources.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkr1028", + "pmc": "PMC3245151", + "pubmed": "22102568", + "title": "The Gene Ontology: enhancements for 2011.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkp1018", + "pmc": "PMC2808930", + "pubmed": "19920128", + "title": "The Gene Ontology in 2010: extensions and refinements.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkh036", + "pmc": "PMC308770", + "pubmed": "14681407", + "title": "The Gene Ontology (GO) database and informatics resource.", + "year": 2004 + }, + { + "doi": "10.1038/75556", + "pmc": "PMC3037419", + "pubmed": "10802651", + "title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.", + "year": 2000 + } + ], + "repository": "https://github.com/geneontology/go-ontology", + "synonyms": [ + "gobp", + "gobpid", + "gocc", + "goccid", + "gomf", + "gomfid" + ], + "twitter": "news4go", + "uri_format": "http://amigo.geneontology.org/amigo/term/GO:$1", + "version": "2022-12-04" + }, + "go.gpi": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + } + ], + "description": "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files.", + "example": "db-object-id", + "homepage": "http://geneontology.org/docs/gene-product-information-gpi-format/#db-object-id", + "mappings": { + "biolink": "gpi" + }, + "name": "Gene Product Information Schema", + "preferred_prefix": "go.gpi", + "uri_format": "http://geneontology.org/docs/gene-product-information-gpi-format/#$1" + }, + "go.model": { + "description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform.", + "example": "5fce9b7300001250", + "homepage": "http://www.geneontology.org/gocam", + "mappings": { + "go": "gomodel" + }, + "name": "Gene Ontology Causal Assembly Model", + "preferred_prefix": "go.model", + "uri_format": "http://noctua.geneontology.org/editor/graph/gomodel:$1" + }, + "go.ref": { + "banana": "GO_REF", + "description": "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made.", + "example": "0000041", + "homepage": "http://www.geneontology.org/cgi-bin/references.cgi", + "mappings": { + "biocontext": "GO_REF", + "go": "GO_REF", + "miriam": "go_ref", + "n2t": "go.ref" + }, + "name": "Gene Ontology Database references", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "go.ref", + "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1" + }, + "go.resource": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A database-specific registry supporting curation in the Gene Ontology", + "example": "CHEBI", + "homepage": "http://geneontology.org/", + "name": "Gene Ontology Registry", + "preferred_prefix": "go.resource", + "uri_format": "https://bioregistry.io/metaregistry/go/$1" + }, + "go.rule": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.", + "example": "0000004", + "homepage": "https://github.com/geneontology/go-site/tree/master/metadata/rules", + "name": "Gene Ontology Rules", + "part_of": "go", + "pattern": "^\\d{7}$", + "preferred_prefix": "GORULE", + "uri_format": "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md" + }, + "goa": { + "description": "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups.", + "example": "P12345", + "homepage": "https://www.ebi.ac.uk/GOA/", + "keywords": [ + "biology", + "gene", + "life science", + "ontology", + "protein" + ], + "mappings": { + "biocontext": "GOA", + "fairsharing": "FAIRsharing.7zffgc", + "miriam": "goa", + "n2t": "goa", + "ncbi": "GOA", + "prefixcommons": "goa" + }, + "name": "Gene Ontology Annotation Database", + "pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$", + "preferred_prefix": "goa", + "provides": "uniprot", + "publications": [ + { + "doi": "10.1093/nar/gku1113", + "pmc": "PMC4383930", + "pubmed": "25378336", + "title": "The GOA database: gene Ontology annotation updates for 2015.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkn803", + "pmc": "PMC2686469", + "pubmed": "18957448", + "title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource.", + "year": 2008 + } + ], + "uri_format": "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1" + }, + "goche": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Represent chemical entities having particular CHEBI roles", + "download_owl": "https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/imports/chebi_roles.owl", + "example": "25512", + "homepage": "https://github.com/geneontology/go-ontology", + "keywords": [ + "ontology" + ], + "name": "GO Chemicals", + "pattern": "^\\d+$", + "preferred_prefix": "GOCHE", + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", + "https://github.com/geneontology/go-ontology/issues/19535" + ], + "repository": "https://github.com/geneontology/go-ontology", + "synonyms": [ + "go.chebi", + "go.chemical", + "go.chemicals" + ], + "uri_format": "https://biopragmatics.github.io/providers/goche/$1" + }, + "goeco": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported.", + "example": "IPI", + "homepage": "http://geneontology.org/docs/guide-go-evidence-codes/", + "name": "GO Evidence Code", + "preferred_prefix": "goeco" + }, + "gold": { + "description": "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project.", + "example": "Gs0000008", + "homepage": "https://gold.jgi.doe.gov/", + "keywords": [ + "genome", + "genomics", + "metabolomics", + "metagenomics", + "ontology and terminology", + "phylogenetics" + ], + "mappings": { + "fairsharing": "FAIRsharing.5q1p14", + "miriam": "gold", + "prefixcommons": "gold", + "re3data": "r3d100010808" + }, + "name": "Genomes Online Database", + "pattern": "^[A-Z][a-z][0-9]+$", + "preferred_prefix": "gold", + "publications": [ + { + "doi": "10.1093/nar/gkaa983", + "pmc": "PMC7778979", + "pubmed": "33152092", + "title": "Genomes OnLine Database (GOLD) v.8: overview and updates.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gky977", + "pmc": "PMC6323969", + "pubmed": "30357420", + "title": "Genomes OnLine database (GOLD) v.7: updates and new features.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkp848", + "pmc": "PMC2808860", + "pubmed": "19914934", + "title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkm884", + "pmc": "PMC2238992", + "pubmed": "17981842", + "title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.", + "year": 2007 + }, + { + "doi": "11125068", + "pmc": "PMC29859", + "pubmed": "11125068", + "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.", + "year": null + }, + { + "doi": "10.1093/nar/29.1.126", + "pmc": "PMC29859", + "pubmed": "11125068", + "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.", + "year": 2001 + }, + { + "doi": "10.1093/bioinformatics/15.9.773", + "pmc": null, + "pubmed": "10498782", + "title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide.", + "year": 1999 + } + ], + "uri_format": "https://gold.jgi.doe.gov/resolver?id=$1" + }, + "gold.genome": { + "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes.", + "example": "Gi07796", + "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", + "mappings": { + "biocontext": "GOLD.GENOME", + "miriam": "gold.genome", + "n2t": "gold.genome" + }, + "name": "GOLD genome", + "pattern": "^(Gi|Gc)\\d+$", + "preferred_prefix": "gold.genome", + "uri_format": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1" + }, + "gold.meta": { + "description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.", + "example": "Gm00047", + "has_canonical": "gold", + "homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", + "mappings": { + "biocontext": "GOLD.META", + "miriam": "gold.meta", + "n2t": "gold.meta" + }, + "name": "GOLD metadata", + "pattern": "^Gm\\d+$", + "preferred_prefix": "gold.meta", + "uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1" + }, + "goldbook": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry.", + "example": "G02681", + "homepage": "https://goldbook.iupac.org", + "license": "CC BY 4.0-NC-ND", + "mappings": { + "bartoc": "1884", + "wikidata": "P4732" + }, + "name": "IUPAC Gold Book Compendium of Chemical Terminology", + "pattern": "^[A-Z]{1,2}\\d{5}$", + "preferred_prefix": "goldbook", + "uri_format": "https://goldbook.iupac.org/terms/view/$1" + }, + "google.book": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Search the world's most comprehensive index of full-text books.", + "example": "qafeQTWIWmcC", + "github_request_issue": 511, + "homepage": "https://books.google.com", + "mappings": { + "wikidata": "P675" + }, + "name": "Google Books", + "preferred_prefix": "google.book", + "uri_format": "https://books.google.com/books?id=$1" + }, + "google.patent": { + "contributor_extras": [ + { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + } + ], + "description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.", + "example": "US4145692", + "example_extras": [ + "USRE38117E1" + ], + "homepage": "https://www.google.com/patents/", + "mappings": { + "biocontext": "GOOGLE.PATENT", + "cellosaurus": "Patent", + "miriam": "google.patent", + "n2t": "google.patent" + }, + "name": "Google Patents", + "pattern": "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$", + "preferred_prefix": "google.patent", + "synonyms": [ + "patent" + ], + "uri_format": "https://www.google.com/patents/$1" + }, + "google.scholar": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.", + "example": "PjrpzUIAAAAJ", + "homepage": "https://scholar.google.com/", + "mappings": { + "biolink": "GSID" + }, + "name": "Google Scholar Researcher", + "preferred_prefix": "google.scholar" + }, + "gorel": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", + "download_owl": "ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl", + "example": "0002005", + "homepage": "http://geneontology.org/docs/ontology-relations/", + "keywords": [ + "ontology" + ], + "mappings": { + "biolink": "GOREL", + "go": "GOREL" + }, + "name": "GO Relations", + "pattern": "^\\d{7}$", + "preferred_prefix": "gorel", + "providers": [ + { + "code": "obo.legacy", + "description": "Legacy OBO PURLs", + "homepage": "http://purl.obolibrary.org/obo/gorel.owl", + "name": "Legacy OBO", + "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" + } + ] + }, + "gpcrdb": { + "contact": { + "email": "david.gloriam@sund.ku.dk", + "github": null, + "name": "David Gloriam", + "orcid": "0000-0002-4299-7561" + }, + "description": "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models.", + "example": "RL3R1_HUMAN", + "homepage": "http://www.gpcrdb.org/", + "keywords": [ + "life science", + "molecular biology", + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "GPCRDB", + "fairsharing": "FAIRsharing.e4n3an", + "miriam": "gpcrdb", + "n2t": "gpcrdb", + "prefixcommons": "gpcrdb", + "uniprot": "DB-0038" + }, + "name": "G protein-coupled receptor database", + "pattern": "^\\w+$", + "preferred_prefix": "gpcrdb", + "publications": [ + { + "doi": "10.1093/nar/26.1.275", + "pmc": "PMC147194", + "pubmed": "9399852", + "title": "GPCRDB: an information system for G protein-coupled receptors.", + "year": 1998 + }, + { + "doi": "10.1093/nar/gkaa1080", + "pmc": "PMC7778909", + "pubmed": "33270898", + "title": "GPCRdb in 2021: integrating GPCR sequence, structure and function.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gkx1109", + "pmc": "PMC5753179", + "pubmed": "29155946", + "title": "GPCRdb in 2018: adding GPCR structure models and ligands.", + "year": 2018 + }, + { + "doi": "10.1111/bph.13509", + "pmc": "PMC4919580", + "pubmed": "27155948", + "title": "GPCRdb: the G protein-coupled receptor database - an introduction.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkv1178", + "pmc": "PMC4702843", + "pubmed": "26582914", + "title": "GPCRdb: an information system for G protein-coupled receptors.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkt1255", + "pmc": "PMC3965068", + "pubmed": "24304901", + "title": "GPCRDB: an information system for G protein-coupled receptors.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkq1009", + "pmc": "PMC3013641", + "pubmed": "21045054", + "title": "GPCRDB: information system for G protein-coupled receptors.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkg103", + "pmc": "PMC165550", + "pubmed": "12520006", + "title": "GPCRDB information system for G protein-coupled receptors.", + "year": 2003 + }, + { + "doi": "10.1093/nar/29.1.346", + "pmc": "PMC29816", + "pubmed": "11125133", + "title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.", + "year": 2001 + } + ], + "twitter": "gpcrdb", + "uri_format": "https://gpcrdb.org/protein/$1" + }, + "gpmdb": { + "description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.", + "example": "GPM32310002988", + "homepage": "http://gpmdb.thegpm.org/", + "keywords": [ + "bioinformatics", + "proteomics" + ], + "mappings": { + "biocontext": "GPMDB", + "fairsharing": "FAIRsharing.fhcmwq", + "miriam": "gpmdb", + "n2t": "gpmdb" + }, + "name": "Global Proteome Machine Database", + "pattern": "^GPM\\d+$", + "preferred_prefix": "gpmdb", + "providers": [ + { + "code": "omicsdi", + "description": "GPMDB through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "GPMDB through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/gpmdb/$1" + } + ], + "publications": [ + { + "doi": "10.1021/pr049882h", + "pmc": null, + "pubmed": "15595733", + "title": "Open source system for analyzing, validating, and storing protein identification data.", + "year": 2004 + } + ], + "twitter": "GPMDB", + "uri_format": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1" + }, + "graingenes.reference": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A database for Triticeae and Avena references.", + "example": "WGS-95-1333", + "homepage": "http://wheat.pw.usda.gov", + "name": "GrainGenes", + "preferred_prefix": "graingenes.reference", + "uri_format": "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1" + }, + "graingenes.symbol": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A database for Triticeae and Avena gene symbols.", + "example": "1-FEH+w3", + "homepage": "http://wheat.pw.usda.gov", + "name": "GrainGenes", + "preferred_prefix": "graingenes.symbol", + "uri_format": "http://wheat.pw.usda.gov/report?class=gene;name=$1" + }, + "gramene.gene": { + "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene.", + "example": "GR:0080039", + "homepage": "http://www.gramene.org/", + "mappings": { + "biocontext": "GRAMENE.GENE", + "go": "GR_GENE", + "miriam": "gramene.gene", + "n2t": "gramene.gene" + }, + "name": "Gramene Gene", + "pattern": "^GR\\:\\d+$", + "preferred_prefix": "gramene.gene", + "synonyms": [ + "GR_GENE" + ], + "uri_format": "http://www.gramene.org/db/genes/search_gene?acc=$1" + }, + "gramene.growthstage": { + "banana": "GRO", + "contact": { + "email": "po-discuss@plantontology.org", + "github": null, + "name": "Plant Ontology Administrators", + "orcid": null + }, + "deprecated": true, + "description": "Gramene is a comparative genome mapping database for grasses and crop plants. 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This collection refers to growth stage ontology information in Gramene.", + "example": "0007133", + "homepage": "http://www.gramene.org/plant_ontology/", + "keywords": [ + "anatomy", + "obo", + "ontology" + ], + "mappings": { + "biocontext": "GRAMENE.GROWTHSTAGE", + "bioportal": "GRO-CPGA", + "miriam": "gro", + "n2t": "gramene.growthstage", + "obofoundry": "gro", + "prefixcommons": "gramene.po" + }, + "name": "Gramene Growth Stage Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "GRO", + "synonyms": [ + "cpga", + "gro-cpga" + ], + "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" + }, + "gramene.protein": { + "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene.", + "example": "78073", + "homepage": "http://www.gramene.org/", + "mappings": { + "biocontext": "GRAMENE.PROTEIN", + "go": "GR_PROTEIN", + "miriam": "gramene.protein", + "n2t": "gramene.protein" + }, + "name": "Gramene protein", + "pattern": "^\\d+$", + "preferred_prefix": "gramene.protein", + "synonyms": [ + "GR_PROTEIN" + ], + "uri_format": "http://www.gramene.org/db/protein/protein_search?protein_id=$1" + }, + "gramene.qtl": { + "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene.", + "example": "CQG5", + "homepage": "http://www.gramene.org/", + "mappings": { + "biocontext": "GRAMENE.QTL", + "go": "GR_QTL", + "miriam": "gramene.qtl", + "n2t": "gramene.qtl" + }, + "name": "Gramene QTL", + "pattern": "^\\w+$", + "preferred_prefix": "gramene.qtl", + "synonyms": [ + "GR_QTL" + ], + "uri_format": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1" + }, + "gramene.reference": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Literature references in Gramene", + "example": "6200", + "homepage": "http://www.gramene.org", + "name": "Gramene Reference", + "pattern": "^\\d+$", + "preferred_prefix": "gramene.reference", + "synonyms": [ + "gramene.ref" + ], + "uri_format": "http://www.gramene.org/db/literature/pub_search?ref_id=$1" + }, + "gramene.taxonomy": { + "banana": "GR_tax", + "banana_peel": ":", + "description": "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene.", + "example": "013681", + "homepage": "http://www.gramene.org/", + "mappings": { + "biocontext": "GRAMENE.TAXONOMY", + "miriam": "gramene.taxonomy", + "n2t": "gramene.taxonomy" + }, + "name": "Gramene Taxonomy", + "pattern": "^\\d+$", + "preferred_prefix": "gramene.taxonomy", + "uri_format": "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1" + }, + "grassbase": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species.", + "example": "imp10873", + "github_request_issue": 218, + "homepage": "https://www.kew.org/data/grasses-syn/index.htm", + "mappings": { + "wikidata": "P1832" + }, + "name": "GrassBase", + "pattern": "^(imp|gen)\\d{5}$", + "preferred_prefix": "grassbase", + "uri_format": "https://www.kew.org/data/grasses-db/www/$1" + }, + "greengenes": { + "contact": { + "email": "GLAndersen@lbl.gov", + "github": null, + "name": "Gary L Andersen", + "orcid": "0000-0002-1618-9827" + }, + "description": "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.", + "example": "100000", + "homepage": "http://greengenes.lbl.gov/", + "keywords": [ + "genetics", + "life science", + "rna" + ], + "mappings": { + "biocontext": "GREENGENES", + "fairsharing": "FAIRsharing.bpxgb6", + "miriam": "greengenes", + "n2t": "greengenes", + "ncbi": "Greengenes", + "prefixcommons": "greengenes", + "re3data": "r3d100010549" + }, + "name": "16S rRNA gene database", + "pattern": "^\\d+$", + "preferred_prefix": "greengenes", + "publications": [ + { + "doi": "10.1128/aem.03006-05", + "pmc": "PMC1489311", + "pubmed": "16820507", + "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.", + "year": 2006 + } + ], + "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" + }, + "grid": { + "description": "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally.", + "example": "grid.225360.0", + "homepage": "https://www.grid.ac/", + "keywords": [ + "data management" + ], + "mappings": { + "biocontext": "GRID", + "fairsharing": "FAIRsharing.0pUMYW", + "miriam": "grid", + "n2t": "grid" + }, + "name": "Global Research Identifier Database", + "pattern": "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$", + "preferred_prefix": "grid", + "twitter": "grid_ac", + "uri_format": "https://www.grid.ac/institutes/$1" + }, + "grin": { + "description": "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections.", + "example": "159787", + "homepage": "http://www.ars-grin.gov/", + "keywords": [ + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.3axym7", + "prefixcommons": "grin" + }, + "name": "Germplasm Resources Information Network", + "preferred_prefix": "grin", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1" + }, + "grin.taxonomy": { + "description": "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact.", + "example": "19333", + "homepage": "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en", + "mappings": { + "biocontext": "GRIN.TAXONOMY", + "go": "GRIN", + "miriam": "grin.taxonomy", + "n2t": "grin.taxonomy", + "ncbi": "GRIN", + "wikidata": "P1421" + }, + "name": "GRIN URL", + "pattern": "^\\d+$", + "preferred_prefix": "grin.taxonomy", + "uri_format": "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1" + }, + "gro": { + "contact": { + "email": "vlee@ebi.ac.uk", + "github": null, + "name": "Vivian Lee", + "orcid": null + }, + "deprecated": true, + "description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.", + "download_owl": "http://aber-owl.net/media/ontologies/GRO/5/gro.owl", + "example": "Lipid", + "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "GRO", + "bioportal": "GRO" + }, + "name": "Gene Regulation Ontology", + "preferred_prefix": "gro", + "uri_format": "http://www.bootstrep.eu/ontology/GRO#$1" + }, + "grsdb": { + "description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank.", + "example": "10142", + "homepage": "http://bioinformatics.ramapo.edu/GRSDB2/", + "keywords": [ + "dna", + "rna" + ], + "mappings": { + "biocontext": "GRSDB", + "miriam": "grsdb", + "n2t": "grsdb", + "prefixcommons": "grsdb" + }, + "name": "G-Rich Sequences Database", + "pattern": "^\\d+$", + "preferred_prefix": "grsdb", + "uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1" + }, + "gsfa": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database.", + "example": "174", + "homepage": "http://www.fao.org/gsfaonline", + "name": "General Standard for Food Additives Online Database", + "pattern": "^\\d+$", + "preferred_prefix": "gsfa", + "synonyms": [ + "FAO/WHO_standards" + ], + "uri_format": "http://www.fao.org/gsfaonline/additives/details.html?id=$1" + }, + "gsso": { + "appears_in": [ + "ontoavida", + "scdo" + ], + "banana": "GSSO", + "contact": { + "email": "kronkcj@mail.uc.edu", + "github": "Superraptor", + "name": "Clair Kronk", + "orcid": "0000-0001-8397-8810" + }, + "description": "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology.", + "download_json": "http://purl.obolibrary.org/obo/gsso.json", + "download_obo": "http://purl.obolibrary.org/obo/gsso.obo", + "download_owl": "http://purl.obolibrary.org/obo/gsso.owl", + "example": "002368", + "homepage": "https://gsso.research.cchmc.org/", + "keywords": [ + "obo", + "ontology" + ], + "license": "Apache 2.0 License", + "mappings": { + "aberowl": "GSSO", + "bioportal": "GSSO", + "miriam": "gsso", + "obofoundry": "gsso", + "ols": "gsso", + "ontobee": "GSSO" + }, + "name": "Gender, Sex, and Sexual Orientation Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{6}$", + "preferred_prefix": "GSSO", + "repository": "https://github.com/Superraptor/GSSO", + "uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", + "version": "2.0.5" + }, + "gtex": { + "description": "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.", + "example": "BRIP1", + "homepage": "https://www.gtexportal.org", + "mappings": { + "biocontext": "GTEX", + "biolink": "GTEx", + "miriam": "gtex", + "n2t": "gtex" + }, + "name": "Genotype-Tissue Expression", + "pattern": "^\\w.+$", + "preferred_prefix": "gtex", + "uri_format": "https://www.gtexportal.org/home/gene/$1" + }, + "gtr": { + "appears_in": [ + "mondo" + ], + "comment": "Identifiers appearing in MONDO don't match any of the resources apparent endpoints", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease", + "example": "AN0097748", + "homepage": "https://www.ncbi.nlm.nih.gov/gtr/", + "name": "Genetic Testing Registry", + "preferred_prefix": "gtr", + "synonyms": [ + "medgen.gtr" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1" + }, + "gudmap": { + "description": "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract.", + "example": "Q-2958", + "homepage": "http://www.gudmap.org/", + "keywords": [ + "cell biology", + "developmental biology", + "genomics", + "molecular biology" + ], + "mappings": { + "biocontext": "GUDMAP", + "fairsharing": "FAIRsharing.910c39", + "miriam": "gudmap", + "n2t": "gudmap", + "re3data": "r3d100012193" + }, + "name": "Genitourinary Development Molecular Anatomy Project", + "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", + "preferred_prefix": "gudmap", + "publications": [ + { + "doi": "10.1242/dev.063594", + "pmc": "PMC3188593", + "pubmed": "21652655", + "title": "The GUDMAP database--an online resource for genitourinary research.", + "year": 2011 + }, + { + "doi": "10.1681/asn.2007101078", + "pmc": null, + "pubmed": "18287559", + "title": "GUDMAP: the genitourinary developmental molecular anatomy project.", + "year": 2008 + } + ], + "twitter": "GUDMAP", + "uri_format": "https://gudmap.org/id/$1" + }, + "gwascentral.marker": { + "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.", + "example": "HGVM15354", + "homepage": "https://www.gwascentral.org/markers", + "mappings": { + "biocontext": "GWASCENTRAL.MARKER", + "miriam": "gwascentral.marker", + "n2t": "gwascentral.marker" + }, + "name": "GWAS Central Marker", + "pattern": "^HGVM\\d+$", + "preferred_prefix": "gwascentral.marker", + "uri_format": "https://www.gwascentral.org/marker/$1" + }, + "gwascentral.phenotype": { + "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.", + "example": "HGVPM623", + "homepage": "https://www.gwascentral.org/phenotypes", + "mappings": { + "biocontext": "GWASCENTRAL.PHENOTYPE", + "miriam": "gwascentral.phenotype", + "n2t": "gwascentral.phenotype" + }, + "name": "GWAS Central Phenotype", + "pattern": "^HGVPM\\d+$", + "preferred_prefix": "gwascentral.phenotype", + "uri_format": "https://www.gwascentral.org/phenotype/$1" + }, + "gwascentral.study": { + "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. 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This collection references a GWAS Central Study.", + "example": "HGVST1828", + "homepage": "https://www.gwascentral.org/studies", + "keywords": [ + "gene", + "genome" + ], + "mappings": { + "biocontext": "GWASCENTRAL.STUDY", + "miriam": "gwascentral.study", + "n2t": "gwascentral.study", + "prefixcommons": "hgvbase" + }, + "name": "GWAS Central Study", + "pattern": "^HGVST\\d+$", + "preferred_prefix": "gwascentral.study", + "uri_format": "https://www.gwascentral.org/study/$1" + }, + "gxa.expt": { + "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments.", + "example": "E-MTAB-2037", + "homepage": "https://www.ebi.ac.uk/gxa/", + "mappings": { + "biocontext": "GXA.EXPT", + "miriam": "gxa.expt", + "n2t": "gxa.expt" + }, + "name": "GXA Expt", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^[AEP]-\\w{4}-\\d+$", + "preferred_prefix": "gxa.expt", + "providers": [ + { + "code": "omicsdi", + "description": "GXA Expt through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "GXA Expt through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/atlas-experiments/$1" + } + ], + "uri_format": "https://www.ebi.ac.uk/gxa/experiments/$1" + }, + "gxa.gene": { + "description": "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes.", + "example": "AT4G01080", + "homepage": "https://www.ebi.ac.uk/gxa/", + "mappings": { + "biocontext": "GXA.GENE", + "miriam": "gxa.gene", + "n2t": "gxa.gene" + }, + "name": "GXA Gene", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^\\w+$", + "preferred_prefix": "gxa.gene", + "uri_format": "https://www.ebi.ac.uk/gxa/genes/$1" + }, + "habronattus": { + "contact": { + "email": "peteremidford@yahoo.com", + "github": null, + "name": "Peter Midford", + "orcid": "0000-0001-6512-3296" + }, + "deprecated": true, + "homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "HABRONATTUS", + "obofoundry": "habronattus" + }, + "name": "Habronattus courtship", + "preferred_prefix": "HABRONATTUS", + "uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1" + }, + "hagr.genage": { + "description": "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group.", + "example": "0001", + "homepage": "http://genomics.senescence.info/genes/", + "keywords": [ + "aging", + "genes", + "longevity" + ], + "mappings": { + "prefixcommons": "genage" + }, + "name": "The Ageing Gene Database", + "preferred_prefix": "hagr.genage", + "publications": [ + { + "doi": "10.1093/nar/gks1155", + "pmc": "PMC3531213", + "pubmed": "23193293", + "title": "Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.", + "year": 2012 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://genomics.senescence.info/genes/details.php?id=$1" + }, + "hagr.gendr": { + "description": "GenDR is a database of genes associated with dietary restriction (DR). 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These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries.", + "example": "MF_01400", + "homepage": "https://hamap.expasy.org/", + "keywords": [ + "life science", + "protein" + ], + "mappings": { + "biocontext": "HAMAP", + "edam": "2766", + "fairsharing": "FAIRsharing.63m4ss", + "go": "HAMAP", + "miriam": "hamap", + "n2t": "hamap", + "prefixcommons": "hamap", + "uniprot": "DB-0041" + }, + "name": "High-quality Automated and Manual Annotation of microbial Proteomes", + "pattern": "^MF_\\d+$", + "preferred_prefix": "hamap", + "publications": [ + { + "doi": "10.1093/nar/gku1002", + "pmc": "PMC4383873", + "pubmed": "25348399", + "title": "HAMAP in 2015: updates to the protein family classification and annotation system.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks1157", + "pmc": "PMC3531088", + "pubmed": "23193261", + "title": "HAMAP in 2013, new developments in the protein family classification and 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Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases.", + "example": "CALM1", + "homepage": "http://www.hgmd.cf.ac.uk/ac/index.php", + "mappings": { + "biocontext": "HGMD", + "edam": "3265", + "miriam": "hgmd", + "n2t": "hgmd" + }, + "name": "Human Gene Mutation Database", + "pattern": "^[A-Z_0-9]+$", + "preferred_prefix": "hgmd", + "uri_format": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1" + }, + "hgnc": { + "contact": { + "email": "elspeth@genenames.org", + "github": null, + "name": "Elspeth Bruford", + "orcid": "0000-0002-8380-5247" + }, + "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. 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Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine).", + "homepage": "https://thegencc.org", + "name": "The Gene Curation Coalition", + "uri_format": "https://search.thegencc.org/genes/HGNC:$1" + }, + { + "code": "indra", + "description": "A large scale database of biomedical statements.", + "homepage": "https://db.indra.bio", + "name": "INDRA Database", + "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@HGNC" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkaa980", + "pmc": "PMC7779007", + "pubmed": "33152070", + "title": "Genenames.org: the HGNC and VGNC resources in 2021.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gky930", + "pmc": "PMC6324057", + "pubmed": "30304474", + "title": "Genenames.org: the HGNC and VGNC resources in 2019.", + "year": 2019 + }, + { + "doi": "10.1159/000131404", + "pmc": null, + "pubmed": "295268", + "title": "International system for human gene nomenclature (1979) ISGN (1979).", + "year": 1979 + } + ], + "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1" + }, + "hgnc.genefamily": { + "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", + "example": "2029", + "has_canonical": "hgnc.genegroup", + "homepage": "http://www.genenames.org", + "mappings": { + "biocontext": "HGNC.GENEFAMILY", + "miriam": "hgnc.genefamily", + "n2t": "hgnc.genefamily" + }, + "name": "HGNC gene family", + "pattern": "^\\d+$", + "preferred_prefix": "hgnc.genefamily", + "synonyms": [ + "GFAM", + "HGNC_GROUP", + "hgnc.family" + ], + "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" + }, + "hgnc.genegroup": { + "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families.", + "example": "141", + "homepage": "https://www.genenames.org", + "mappings": { + "miriam": "hgnc.genegroup" + }, + "name": "HGNC Gene Group", + "pattern": "^\\d+$", + "preferred_prefix": "hgnc.genegroup", + "uri_format": "https://www.genenames.org/cgi-bin/genefamilies/set/$1" + }, + "hgnc.symbol": { + "description": "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol.", + "example": "DAPK1", + "homepage": "https://www.genenames.org/", + "mappings": { + "biocontext": "HGNC.SYMBOL", + "miriam": "hgnc.symbol", + "n2t": "hgnc.symbol", + "wikidata": "P353" + }, + "name": "HGNC gene symbol", + "pattern": "^[A-Za-z-0-9_]+(\\@)?$", + "preferred_prefix": "hgnc.symbol", + "providers": [ + { + "code": "depmap", + "description": "DepMap summary of the given gene", + "homepage": "https://depmap.org", + "name": "DepMap Gene Summary", + "uri_format": "https://depmap.org/portal/gene/$1" + }, + { + "code": "oncomx", + "description": "Mutation profiles for a gene", + "homepage": "https://oncomx.org", + "name": "OncoMX", + "uri_format": "https://oncomx.org/searchview/?gene=$1" + }, + { + "code": "pathwaycommons", + "description": "Interactions between a given gene and other molecular entities", + "homepage": "https://www.pathwaycommons.org/", + "name": "Pathway Commons Gene Interations", + "uri_format": "https://apps.pathwaycommons.org/interactions?source=$1" + } + ], + "uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1" + }, + "hinv.locus": { + "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view.", + "example": "HIX0004394", + "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", + "mappings": { + "biocontext": "HINV.LOCUS", + "miriam": "hinv.locus", + "n2t": "hinv.locus" + }, + "name": "H-InvDb Locus", + "pattern": "^HIX\\d{7}(\\.\\d+)?$", + "preferred_prefix": "hinv.locus", + "uri_format": "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1" + }, + "hinv.protein": { + "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view.", + "example": "HIP000030660", + "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", + "mappings": { + "biocontext": "HINV.PROTEIN", + "miriam": "hinv.protein", + "n2t": "hinv.protein" + }, + "name": "H-InvDb Protein", + "pattern": "^HIP\\d{9}(\\.\\d+)?$", + "preferred_prefix": "hinv.protein", + "uri_format": "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1" + }, + "hinv.transcript": { + "description": "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view.", + "example": "HIT000195363", + "homepage": "http://h-invitational.jp/hinv/ahg-db/index.jsp", + "mappings": { + "biocontext": "HINV.TRANSCRIPT", + "miriam": "hinv.transcript", + "n2t": "hinv.transcript" + }, + "name": "H-InvDb Transcript", + "pattern": "^HIT\\d{9}(\\.\\d+)?$", + "preferred_prefix": "hinv.transcript", + "uri_format": "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1" + }, + "hipsci": { + "description": "Cell line databases/resources", + "example": "HPSI0114i-bezi_1", + "homepage": "http://www.hipsci.org", + "mappings": { + "cellosaurus": "HipSci" + }, + "name": "Human Induced Pluripotent Stem Cells Initiative", + "preferred_prefix": "hipsci", + "uri_format": "http://www.hipsci.org/lines/#/lines/$1" + }, + "hivreagentprogram": { + "description": "Cell line collections", + "example": "ARP-1513", + "homepage": "https://www.hivreagentprogram.org/", + "mappings": { + "cellosaurus": "HIVReagentProgram" + }, + "name": "NIH HIV Reagent Program", + "preferred_prefix": "hivreagentprogram", + "uri_format": "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx" + }, + "hl7.v2codesystem": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", + "example": "0778", + "homepage": "https://terminology.hl7.org/codesystems-v2.html", + "name": "HL7 V2 Code Systems", + "pattern": "^\\d+$", + "preferred_prefix": "hl7.v2codesystem", + "uri_format": "http://terminology.hl7.org/CodeSystem/v2-$1" + }, + "hl7.v3codesystem": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR.", + "example": "AcknowledgementCondition", + "homepage": "https://terminology.hl7.org/codesystems-v2.html", + "name": "HL7 V2 Code Systems", + "pattern": "^\\w+$", + "preferred_prefix": "hl7.v3codesystem", + "uri_format": "https://terminology.hl7.org/CodeSystem-v3-$1" + }, + "hmdb": { + "description": "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data.", + "example": "HMDB00001", + "homepage": "http://www.hmdb.ca/", + "keywords": [ + "biochemistry", + "bioinformatics", + "chemical", + "human", + "life science", + "metabolite", + "metabolomics", + "molecular biology", + "omics", + "phenomics", + "proteomics" + ], + "mappings": { + "biocontext": "HMDB", + "cheminf": "000408", + "edam": "2622", + "fairsharing": "FAIRsharing.sye5js", + "miriam": "hmdb", + "n2t": "hmdb", + "prefixcommons": "hmdb", + "re3data": "r3d100011285", + "wikidata": "P2057" + }, + "name": "Human Metabolome Database", + "pattern": "^HMDB\\d+$", + "preferred_prefix": "hmdb", + "publications": [ + { + "doi": "10.1093/nar/gkab1062", + "pmc": "PMC8728138", + "pubmed": "34986597", + "title": "HMDB 5.0: the Human Metabolome Database for 2022.", + "year": 2022 + }, + { + "doi": "10.1093/nar/gkx1089", + "pmc": "PMC5753273", + "pubmed": "29140435", + "title": "HMDB 4.0: the human metabolome database for 2018.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gks1065", + "pmc": "PMC3531200", + "pubmed": "23161693", + "title": "HMDB 3.0--The Human Metabolome Database in 2013.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkn810", + "pmc": "PMC1899095", + "pubmed": "17202168", + "title": "HMDB: a knowledgebase for the human metabolome", + "year": null + }, + { + "doi": "10.1093/nar/gkl923", + "pmc": "PMC1899095", + "pubmed": "17202168", + "title": "HMDB: the Human Metabolome Database.", + "year": 2007 + } + ], + "synonyms": [ + "HMDB" + ], + "twitter": "WishartLab", + "uri_format": "http://www.hmdb.ca/metabolites/$1" + }, + "hms.lincs.antibody": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", + "example": "80001", + "homepage": "https://lincs.hms.harvard.edu/db/antibodies/", + "name": "HMS Library of Integrated Network-based Cellular Signatures Antibodies", + "pattern": "^8\\d{4}$", + "preferred_prefix": "hms.lincs.antibody", + "uri_format": "https://lincs.hms.harvard.edu/db/antibodies/$1" + }, + "hms.lincs.cell": { + "comment": "this is NOT the same as lincs.cell. On https://lincs.hms.harvard.edu/db/cells/?search=MCF-10A&extra_form_shown=&dataset_types=, you can see there's a mapping to the other resource.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", + "example": "50583", + "homepage": "https://lincs.hms.harvard.edu/db/cell/", + "name": "HMS LINCS Cell", + "pattern": "^5\\d{4}$", + "preferred_prefix": "hms.lincs.cell", + "references": [ + "https://github.com/identifiers-org/identifiers-org.github.io/issues/223" + ], + "uri_format": "https://lincs.hms.harvard.edu/db/cells/$1" + }, + "hms.lincs.compound": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.", + "example": "10001-101", + "example_extras": [ + "11996-999" + ], + "homepage": "https://lincs.hms.harvard.edu/db/sm/", + "name": "HMS LINCS Compound", + "pattern": "^1\\d{4}-\\d{3}$", + "preferred_prefix": "hms.lincs.compound", + "synonyms": [ + "HMS-LINCS", + "hmsl_id" + ], + "uri_format": "https://lincs.hms.harvard.edu/db/sm/$1" + }, + "hms.lincs.dataset": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "example": "20003", + "homepage": "https://lincs.hms.harvard.edu/db/datasets/", + "name": "HMS Library of Integrated Network-based Cellular Signatures Datasets", + "pattern": "^2\\d{4}$", + "preferred_prefix": "hms.lincs.dataset", + "uri_format": "https://lincs.hms.harvard.edu/db/datasets/$1" + }, + "hog": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc.", + "download_obo": "ftp://ftp.bgee.org/general/ontologies/HOG.obo", + "example": "0000255", + "homepage": "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships", + "keywords": [ + "ontology" + ], + "name": "Homologous Organ Groups", + "pattern": "^\\d{7}$", + "preferred_prefix": "hog", + "uri_format": "https://biopragmatics.github.io/providers/hog/$1" + }, + "hogenom": { + "description": "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier.", + "example": "HBG284870", + "homepage": "http://pbil.univ-lyon1.fr/databases/hogenom/", + "keywords": [ + "classification", + "life science", + "phylogenetics", + "phylogeny", + "sequence" + ], + "mappings": { + "biocontext": "HOGENOM", + "fairsharing": "FAIRsharing.qe8tz8", + "miriam": "hogenom", + "n2t": "hogenom", + "prefixcommons": "hogenom", + "uniprot": "DB-0044" + }, + "name": "Database of Complete Genome Homologous Genes Families", + "pattern": "^\\w+$", + "preferred_prefix": "hogenom", + "publications": [ + { + "doi": "10.1186/1471-2105-10-s6-s3", + "pmc": "PMC2697650", + "pubmed": "19534752", + "title": "Databases of homologous gene families for comparative genomics.", + "year": 2009 + }, + { + "doi": "10.1101/gr.10.3.379", + "pmc": "PMC311423", + "pubmed": "10720578", + "title": "HOBACGEN: database system for comparative genomics in bacteria.", + "year": 2000 + } + ], + "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" + }, + "hoip": { + "contact": { + "email": "yuki.yamagata@riken.jp", + "github": "yuki-yamagata", + "name": "Yuki Yamagata", + "orcid": "0000-0002-9673-1283" + }, + "contributor": { + "email": "j.harry.caufield@gmail.com", + "github": "caufieldjh", + "name": "Harry Caufield", + "orcid": "0000-0001-5705-7831" + }, + "description": "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes.", + "download_owl": "https://github.com/yuki-yamagata/hoip/raw/master/hoip_0308.owl", + "example": "0040379", + "github_request_issue": 668, + "homepage": "https://knowledge.brc.riken.jp/bioresource/ontology/HOIP", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "HOIP", + "bioportal": "HOIP" + }, + "name": "Homeostasis imbalance process ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "hoip", + "repository": "https://github.com/yuki-yamagata/hoip", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://purl.bioontology.org/ontology/HOIP/HOIP_$1" + }, + "hom": { + "contact": { + "email": "bgee@sib.swiss", + "github": "fbastian", + "name": "Frederic Bastian", + "orcid": "0000-0002-9415-5104" + }, + "description": "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology.", + "download_owl": "http://purl.obolibrary.org/obo/hom.owl", + "example": "0000049", + "homepage": "https://github.com/BgeeDB/homology-ontology", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "HOM", + "biocontext": "HOM", + "bioportal": "HOM", + "fairsharing": "FAIRsharing.efv7gw", + "obofoundry": "hom", + "ols": "hom", + "ontobee": "HOM" + }, + "name": "Homology Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "HOM", + "publications": [ + { + "doi": "10.1016/j.tig.2009.12.012", + "pmc": null, + "pubmed": "20116127", + "title": "An ontology to clarify homology-related concepts.", + "year": 2010 + } + ], + "repository": "https://github.com/BgeeDB/homology-ontology", + "uri_format": "http://purl.obolibrary.org/obo/HOM_$1", + "version": "2015-01-07" + }, + "homd.seq": { + "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information.", + "example": "SEQF1003", + "homepage": "http://www.homd.org/index.php", + "keywords": [ + "genome", + "microbial" + ], + "mappings": { + "biocontext": "HOMD.SEQ", + "miriam": "homd.seq", + "n2t": "homd.seq", + "prefixcommons": "homd.seq" + }, + "name": "HOMD Sequence Metainformation", + "pattern": "^SEQF\\d+$", + "preferred_prefix": "homd.seq", + "publications": [ + { + "doi": "10.1093/database/baq013", + "pmc": "PMC2911848", + "pubmed": "20624719", + "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.", + "year": 2010 + } + ], + "uri_format": "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1" + }, + "homd.taxon": { + "description": "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information.", + "example": "811", + "homepage": "http://www.homd.org/index.php", + "keywords": [ + "microbial", + "taxonomy" + ], + "mappings": { + "biocontext": "HOMD.TAXON", + "miriam": "homd.taxon", + "n2t": "homd.taxon", + "ncbi": "HOMD", + "prefixcommons": "homd.taxon" + }, + "name": "Human Oral Microbiome Database", + "pattern": "^\\d+$", + "preferred_prefix": "homd.taxon", + "publications": [ + { + "doi": "10.1093/database/baq013", + "pmc": "PMC2911848", + "pubmed": "20624719", + "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.", + "year": 2010 + } + ], + "uri_format": "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1" + }, + "homologene": { + "description": "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.", + "example": "1000", + "homepage": "https://www.ncbi.nlm.nih.gov/homologene/", + "keywords": [ + "gene", + "genome", + "life science" + ], + "mappings": { + "biocontext": "HOMOLOGENE", + "fairsharing": "FAIRsharing.mzc066", + "miriam": "homologene", + "n2t": "homologene", + "prefixcommons": "homologene", + "wikidata": "P593" + }, + "name": "HomoloGene", + "pattern": "^\\d+$", + "preferred_prefix": "homologene", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Bio2RDF", + "homepage": "http://homologene.bio2rdf.org/fct", + "name": "Bio2RDF", + "uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkq1172", + "pmc": "PMC3013733", + "pubmed": "21097890", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2010 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1" + }, + "horizon_discovery": { + "description": "Cell line collections", + "example": "HD+118-001", + "homepage": "https://horizondiscovery.com/", + "mappings": { + "cellosaurus": "Horizon_Discovery" + }, + "name": "Horizon Discovery cell line collection", + "preferred_prefix": "horizon_discovery", + "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" + }, + "hovergen": { + "contact": { + "email": "duret@biomserv.univ-lyon1.fr", + "github": null, + "name": "Laurent Duret", + "orcid": "0000-0003-2836-3463" + }, + "description": "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.", + "example": "HBG004341", + "homepage": "https://pbil.univ-lyon1.fr/databases/hovergen.php", + "keywords": [ + "dna", + "gene", + "life science", + "protein" + ], + "mappings": { + "biocontext": "HOVERGEN", + "fairsharing": "FAIRsharing.dg1f0e", + "miriam": "hovergen", + "n2t": "hovergen", + "prefixcommons": "hovergen" + }, + "name": "Homologous Vertebrate Genes Database", + "pattern": "^HBG\\d+$", + "preferred_prefix": "hovergen", + "publications": [ + { + "doi": "10.1093/bioinformatics/bti325", + "pmc": null, + "pubmed": "15713731", + "title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.", + "year": 2005 + } + ], + "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN" + }, + "hp": { + "appears_in": [ + "chiro", + "maxo", + "scdo" + ], + "banana": "HP", + "contact": { + "email": "dr.sebastian.koehler@gmail.com", + "github": "drseb", + "name": "Sebastian Koehler", + "orcid": "0000-0002-5316-1399" + }, + "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", + "download_json": "http://purl.obolibrary.org/obo/hp.json", + "download_obo": "http://purl.obolibrary.org/obo/hp.obo", + "download_owl": "http://purl.obolibrary.org/obo/hp.owl", + "example": "0011140", + "homepage": "http://www.human-phenotype-ontology.org/", + "keywords": [ + "biomedical science", + "genetics", + "obo", + "ontology", + "phenomics", + "preclinical studies" + ], + "license": "hpo", + "mappings": { + "aberowl": "HP_O", + "bartoc": "1937", + "biocontext": "HPO", + "bioportal": "HP_O", + "fairsharing": "FAIRsharing.kbtt7f", + "hl7": "2.16.840.1.113883.6.339", + "miriam": "hp", + "n2t": "hp", + "obofoundry": "hp", + "ols": "hp", + "ontobee": "HP", + "wikidata": "P3841" + }, + "name": "Human Phenotype Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "HP", + "publications": [ + { + "doi": "10.1093/nar/gky1105", + "pmc": "PMC6324074", + "pubmed": "30476213", + "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw1039", + "pmc": "PMC5210535", + "pubmed": "27899602", + "title": "The Human Phenotype Ontology in 2017.", + "year": 2016 + }, + { + "doi": "10.1016/j.ajhg.2015.05.020", + "pmc": "PMC4572507", + "pubmed": "26119816", + "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkt1026", + "pmc": "PMC3965098", + "pubmed": "24217912", + "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.", + "year": 2013 + }, + { + "doi": "10.1111/j.1399-0004.2010.01436.x", + "pmc": null, + "pubmed": "20412080", + "title": "The human phenotype ontology.", + "year": 2010 + }, + { + "doi": "10.1016/j.ajhg.2008.09.017", + "pmc": "PMC2668030", + "pubmed": "18950739", + "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.", + "year": 2008 + } + ], + "repository": "https://github.com/obophenotype/human-phenotype-ontology", + "synonyms": [ + "hpo" + ], + "twitter": "hp_ontology", + "uri_format": "https://hpo.jax.org/app/browse/term/HP:$1", + "version": "2022-06-11" + }, + "hpa": { + "contact": { + "email": "mathias.uhlen@scilifelab.se", + "github": null, + "name": "Mathias Uhlen", + "orcid": "0000-0002-4858-8056" + }, + "description": "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. 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This collection references proteins.", + "example": "1968", + "homepage": "http://www.humanproteomemap.org/index.php", + "mappings": { + "biocontext": "HPM.PROTEIN", + "miriam": "hpm.protein", + "n2t": "hpm.protein", + "ncbi": "HPM" + }, + "name": "Human Proteome Map", + "pattern": "^\\d+$", + "preferred_prefix": "hpm.protein", + "uri_format": "http://www.humanproteomemap.org/protein.php?hpm_id=$1" + }, + "hprd": { + "contact": { + "email": "pandey@jhmi.edu", + "github": null, + "name": "Akhilesh Pandey", + "orcid": "0000-0001-9943-6127" + }, + "description": "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.", + "example": "00001", + "homepage": "http://www.hprd.org/", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "biocontext": "HPRD", + 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It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas.", + "example": "5621", + "homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb", + "mappings": { + "wikidata": "P2062" + }, + "name": "Hazardous Substances Data Bank", + "pattern": "^\\d+$", + "preferred_prefix": "hsdb", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1" + }, + "hso": { + "contact": { + "email": "fernanda.dorea@sva.se", + "github": "nandadorea", + "name": "Fernanda Dorea", + "orcid": "0000-0001-8638-8525" + }, + "depends_on": [ + "bfo", + "ncbitaxon", + "obi", + "ro", + "uberon" + ], + "description": "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance.", + "download_owl": "http://purl.obolibrary.org/obo/hso.owl", + "example": "0000062", + "homepage": "https://w3id.org/hso", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "HSO", + "bioportal": "HSO", + "obofoundry": "hso", + "ols": "hso", + "ontobee": "HSO" + }, + "name": "Health Surveillance Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "HSO", + "repository": "https://github.com/SVA-SE/HSO", + "uri_format": "http://purl.obolibrary.org/obo/HSO_$1", + "version": "2021-12-13" + }, + "hssp": { + "description": "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.", + "example": "102l", + "homepage": "http://swift.cmbi.kun.nl/swift/hssp/", + "keywords": [ + "clustering", + "protein", + "sequence" + ], + "mappings": { + "biocontext": "HSSP", + "miriam": "hssp", + "n2t": "hssp", + "ncbi": "HSSP", + "prefixcommons": "hssp" + }, + "name": "Database of homology-derived secondary structure of proteins", + "pattern": "^\\w{4}$", + "preferred_prefix": "hssp", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "HSSP at CMBI", + "homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/", + "name": "HSSP at CMBI", + "uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2" + } + ], + "publications": [ + { + "doi": "10.1093/nar/24.1.201", + "pmc": "PMC145595", + "pubmed": "8594579", + "title": "The HSSP database of protein structure-sequence alignments.", + "year": 1996 + }, + 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"aberowl": "IAO", + "biocontext": "IAO", + "bioportal": "IAO", + "fairsharing": "FAIRsharing.gq1xtx", + "go": "IAO", + "miriam": "iao", + "n2t": "iao", + "obofoundry": "iao", + "ols": "iao", + "ontobee": "IAO" + }, + "name": "Information Artifact Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "IAO", + "providers": [ + { + "code": "legacy", + "description": "A URI from the semanticweb.og", + "homepage": "http://www.semanticweb.org", + "name": "Legacy URI", + "uri_format": "http://www.semanticweb.org/ontologies/2011/9/Ontology1317751904226.owl#IAO_$1" + } + ], + "publications": [ + { + "doi": "10.3233/978-1-61499-101-4-68", + "pmc": null, + "pubmed": "22874154", + "title": "An information artifact ontology perspective on data collections and associated representational artifacts.", + "year": 2012 + } + ], + "repository": "https://github.com/information-artifact-ontology/IAO", + "uri_format": "http://purl.obolibrary.org/obo/IAO_$1", + "version": "2020-12-09" + }, + "icd10": { + "contact": { + "email": "info@who.int", + "github": null, + "name": "World Health Organization", + "orcid": null + }, + "contributor_extras": [ + { + "email": null, + "github": "joeflack4", + "name": "Joe Flack", + "orcid": "0000-0002-2906-7319" + }, + { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nico Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + ], + "description": "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States.", + "example": "C34", + "example_decoys": [ + "G00X", + "C34.90", + "C4A.8", + "C91.Z", + "C91.Z0" + ], + "example_extras": [ + "V20", + "G00", + "A01.1", + "XVIII", + "R25-R29", + "R25", + "R25.3" + ], + "homepage": "https://icd.who.int/browse10", + "keywords": [ + "biomedical science", + "classification", + "disease", + "epidemiology", + "global health", + "health science", + "ontology", + "taxonomy" + ], + "mappings": { + "aberowl": "ICD10", + "bartoc": "447", + "biocontext": "ICD", + "biolink": "ICD10", + "bioportal": "ICD10", + "edam": "2611", + "fairsharing": "FAIRsharing.nj16g", + "hl7": "2.16.840.1.113883.6.3", + "miriam": "icd", + "n2t": "icd", + "prefixcommons": "icd", + "wikidata": "P494" + }, + "name": "International Classification of Diseases, 10th Revision", + "pattern": "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$", + "preferred_prefix": "icd10", + "providers": [ + { + "code": "icd10_2008", + "description": "The 2008 revision of ICD-10", + "homepage": "https://icd.who.int/browse10/2008/en#", + "name": "ICD-10 Version 2008", + "uri_format": "https://icd.who.int/browse10/2008/en#/$1" + }, + { + "code": "icd10_2010", + "description": "The 2010 revision of ICD-10", + "homepage": "https://icd.who.int/browse10/2010/en#", + "name": "ICD-10 Version 2010", + "uri_format": "https://icd.who.int/browse10/2010/en#/$1" + }, + { + "code": "icd10_2014", + "description": "The 2014 revision of ICD-10", + "homepage": "https://icd.who.int/browse10/2014/en#", + "name": "ICD-10 Version 2014", + "uri_format": "https://icd.who.int/browse10/2014/en#/$1" + }, + { + "code": "icd10_2015", + "description": "The 2015 revision of ICD-10", + "homepage": "https://icd.who.int/browse10/2015/en#", + "name": "ICD-10 Version 2015", + "uri_format": "https://icd.who.int/browse10/2015/en#/$1" + }, + { + "code": "icd10_2016", + "description": "The 2016 revision of ICD-10", + "homepage": "https://icd.who.int/browse10/2016/en#", + "name": "ICD-10 Version 2016", + "uri_format": "https://icd.who.int/browse10/2016/en#/$1" + }, + { + "code": "icdcodelookup", + "description": "This site is dedicated exclusively to helping you look up ICD-10 codes, quickly access the codes you use most, and become more comfortable with the new code set in general.", + "homepage": "https://icdcodelookup.com/icd-10/codes", + "name": "ICD Code Lookup", + "uri_format": "https://icdcodelookup.com/icd-10/codes/$1" + } + ], + "synonyms": [ + "ICD", + "ICD-10", + "ICD10", + "ICD10WHO" + ], + "uri_format": "https://icd.who.int/browse10/2019/en#/$1" + }, + "icd10cm": { + "contact": { + "email": "pbrooks@hcfa.gov", + "github": null, + "name": "Patricia Brooks", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS).", + "example": "F45.21", + "example_decoys": [ + "C000", + "c00", + "C00-D499", + "C00-99", + "C34.90000" + ], + "example_extras": [ + "C00-D49", + "U49", + "C34", + "C34.90", + "C4A.8", + "C91.Z", + "C91.Z0", + "T37.0X1A" + ], + "homepage": "https://www.icd10data.com/ICD10CM", + "keywords": [ + "biomedical science", + "health science", + "medicine", + "ontology" + ], + "mappings": { + "aberowl": "ICD10CM", + "bioportal": "ICD10CM", + "fairsharing": "FAIRsharing.hpvbxb", + "hl7": "2.16.840.1.113883.6.90", + "wikidata": "P4229" + }, + "name": "International Classification of Diseases, 10th Revision, Clinical Modification", + "pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$", + "preferred_prefix": "icd10cm", + "synonyms": [ + "ICD10CM" + ], + "uri_format": "https://icd.codes/icd10cm/$1" + }, + "icd10pcs": { + "contact": { + "email": "patricia.brooks2@cms.hhs.gov", + "github": null, + "name": "Pat Brooks", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records.", + "example": "01N50ZZ", + "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS", + "keywords": [ + "biomedical science", + "epidemiology", + "health science", + "ontology" + ], + "mappings": { + "aberowl": "ICD10PCS", + "bioportal": "ICD10PCS", + "fairsharing": "FAIRsharing.85k1jm", + "hl7": "2.16.840.1.113883.6.4", + "wikidata": "P1690" + }, + "name": "International Classification of Diseases, 10th Revision, Procedure Coding System", + "preferred_prefix": "icd10pcs", + "uri_format": "https://www.findacode.com/code.php?set=ICD10PCS&c=$1" + }, + "icd11": { + "comment": "The codes, such as RA00.0, need their own namespace.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease.", + "example": "402558626", + "homepage": "https://icd.who.int/", + "keywords": [ + "biomedical science", + "epidemiology", + "global health", + "health science" + ], + "mappings": { + "fairsharing": "FAIRsharing.97805c", + "hl7": "2.16.840.1.113883.6.347", + "wikidata": "P7807" + }, + "name": "International Classification of Diseases, 11th Revision", + "pattern": "^[1-9]\\d*$", + "preferred_prefix": "icd11", + "synonyms": [ + "ICD-11" + ], + "uri_format": "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1" + }, + "icd9": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics.", + "example": "277.9", + "homepage": "https://www.cdc.gov/nchs/icd/icd9.htm", + "mappings": { + "biolink": "ICD9", + "hl7": "2.16.840.1.113883.6.42", + "wikidata": "P493" + }, + "name": "International Classification of Diseases, 9th Revision", + "pattern": "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$", + "preferred_prefix": "icd9", + "synonyms": [ + "ICD9", + "ICD9_2005", + "MTHICD9_2006" + ], + "uri_format": "http://www.icd9data.com/getICD9Code.ashx?icd9=$1" + }, + "icd9cm": { + "contact": { + "email": "pbrooks@hcfa.gov", + "github": null, + "name": "Patricia Brooks", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States.", + "example": "784", + "homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm", + "keywords": [ + "biomedical science", + "epidemiology", + "health science", + "medicine", + "ontology", + "preclinical studies" + ], + "mappings": { + "aberowl": "ICD9CM", + "bioportal": "ICD9CM", + "fairsharing": "FAIRsharing.10zsxb", + "hl7": "2.16.840.1.113883.6.2", + "wikidata": "P1692" + }, + "name": "International Classification of Diseases, 9th Revision, Clinical Modification", + "pattern": "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$", + "preferred_prefix": "icd9cm", + "synonyms": [ + "IC9CM", + "ICD9CM", + "ICD9CM_2005", + "ICD9CM_2006", + "ICDCM_2005" + ], + "uri_format": "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1" + }, + "icdc": { + "contact": { + "email": "annika.jahnke-bornemann@uni-hamburg.de", + "github": null, + "name": "Annika Jahnke-Bornemann", + "orcid": "0000-0001-7815-151X" + }, + "description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.", + "example": "000009", + "homepage": "https://caninecommons.cancer.gov/#/", + "keywords": [ + "atmospheric science", + "earth science", + "meteorology", + "oceanography", + "remote sensing", + "social science" + ], + "mappings": { + "fairsharing": "FAIRsharing.d95034", + "miriam": "icdc" + }, + "name": "Integrated Canine Data Commons", + "pattern": "^\\d{6}$", + "preferred_prefix": "icdc", + "twitter": "ICDC_Hamburg", + "uri_format": "https://caninecommons.cancer.gov/#/study/$1" + }, + "icdo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases", + "download_owl": "http://aber-owl.net/media/ontologies/ICDO/12/icdo.owl", + "example": "9861/3", + "homepage": "https://www.who.int/classifications/icd/adaptations/oncology/en/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "ICDO", + "bartoc": "445", + "hl7": "2.16.840.1.113883.6.43", + "prefixcommons": "icdo", + "wikidata": "P563" + }, + "name": "International Classification of Diseases for Oncology", + "pattern": "^[8-9]\\d{3}(/[0-3])?$", + "preferred_prefix": "icdo", + "synonyms": [ + "ICD-O", + "ICDO" + ], + "uri_format": "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1" + }, + "iceberg.cime": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.", + "example": "6", + "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_CIME.php?type=alpha&alpha=100", + "keywords": [ + "biology", + "genomics" + ], + "name": "ICEberg cis-integrative and mobilizable element", + "part_of": "iceberg", + "pattern": "^\\d+$", + "preferred_prefix": "iceberg.cime", + "publications": [ + { + "doi": "10.1093/nar/gky1123", + "pmc": "PMC6323972", + "pubmed": "30407568", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkr846", + "pmc": "PMC3244999", + "pubmed": "22009673", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "year": 2011 + } + ], + "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME" + }, + "iceberg.element": { + "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", + "example": "100", + "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=alpha&alpha=100", + "mappings": { + "biocontext": "ICEBERG.ELEMENT", + "miriam": "iceberg.element", + "n2t": "iceberg.element" + }, + "name": "ICEberg integrative and conjugative element", + "part_of": "iceberg", + "pattern": "^\\d+$", + "preferred_prefix": "iceberg.element", + "publications": [ + { + "doi": "10.1093/nar/gky1123", + "pmc": "PMC6323972", + "pubmed": "30407568", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkr846", + "pmc": "PMC3244999", + "pubmed": "22009673", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "year": 2011 + } + ], + "synonyms": [ + "iceberg.ice" + ], + "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1" + }, + "iceberg.family": { + "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", + "example": "1", + "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_fam.php", + "mappings": { + "biocontext": "ICEBERG.FAMILY", + "miriam": "iceberg.family", + "n2t": "iceberg.family" + }, + "name": "ICEberg family", + "part_of": "iceberg", + "pattern": "^\\d+$", + "preferred_prefix": "iceberg.family", + "publications": [ + { + "doi": "10.1093/nar/gky1123", + "pmc": "PMC6323972", + "pubmed": "30407568", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkr846", + "pmc": "PMC3244999", + "pubmed": "22009673", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "year": 2011 + } + ], + "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1" + }, + "iceberg.ime": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements.", + "example": "1", + "homepage": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_IME.php?type=alpha&alpha=100", + "keywords": [ + "biology", + "genomics" + ], + "name": "ICEberg integrative and mobilizable element", + "part_of": "iceberg", + "pattern": "^\\d+$", + "preferred_prefix": "iceberg.ime", + "publications": [ + { + "doi": "10.1093/nar/gky1123", + "pmc": "PMC6323972", + "pubmed": "30407568", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkr846", + "pmc": "PMC3244999", + "pubmed": "22009673", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "year": 2011 + } + ], + "uri_format": "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME" + }, + "iceo": { + "contact": { + "email": "liumeng94@sjtu.edu.cn", + "github": "Lemon-Liu", + "name": "Meng LIU", + "orcid": "0000-0003-3781-6962" + }, + "description": "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning.", + "download_owl": "http://purl.obolibrary.org/obo/iceo.owl", + "example": "0000712_1", + "example_extras": [ + "0000712" + ], + "homepage": "https://github.com/ontoice/ICEO", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ICEO", + "bioportal": "ICEO", + "obofoundry": "iceo", + "ols": "iceo", + "ontobee": "ICEO" + }, + "name": "Integrative and Conjugative Element Ontology", + "pattern": "^\\d{7}(_\\d)?$", + "preferred_prefix": "ICEO", + "publications": [ + { + "doi": "10.1038/s41597-021-01112-5", + "pmc": "PMC8776819", + "pubmed": "35058462", + "title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements.", + "year": 2022 + } + ], + "repository": "https://github.com/ontoice/ICEO", + "uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", + "version": "2.1" + }, + "icepo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ", + "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo", + "example": "0000002", + "homepage": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/", + "keywords": [ + "ontology" + ], + "name": "Ion Channel Electrophysiology Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "icepo", + "publications": [ + { + "doi": null, + "pmc": "PMC4823818", + "pubmed": null, + "title": "ICEPO: the ion channel electrophysiology ontology", + "year": null + } + ], + "twitter": "neXtProt_news", + "uri_format": "https://biopragmatics.github.io/providers/icepo/$1" + }, + "icf": { + "comment": "This might be possible to roll directly into ICD11", + "contact": { + "email": "info@who.int", + "github": null, + "name": "The World Health Organization", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels.", + "download_owl": "http://aber-owl.net/media/ontologies/ICF/3/icf.owl", + "example": "326705068", + "homepage": "https://icd.who.int/dev11/l-icf/en", + "keywords": [ + "biomedical science", + "health science", + "medicine", + "ontology", + "primary health care" + ], + "mappings": { + "aberowl": "ICF", + "bioportal": "ICF", + "fairsharing": "FAIRsharing.7rngj0", + "hl7": "2.16.840.1.113883.6.254" + }, + "name": "International Classification of Functioning, Disability and Health", + "pattern": "^\\d+$", + "preferred_prefix": "icf", + "uri_format": "http://id.who.int/icd/entity/$1" + }, + "iclc": { + "description": "Cell line collections", + "example": "ATL98012", + "homepage": "http://www.iclc.it", + "mappings": { + "cellosaurus": "ICLC" + }, + "name": "Interlab Cell Line Collection", + "preferred_prefix": "iclc", + "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" + }, + "ico": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "description": "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.", + "download_owl": "http://purl.obolibrary.org/obo/ico.owl", + "example": "0000066", + "homepage": "https://github.com/ICO-ontology/ICO", + "keywords": [ + "biomedical science", + "clinical studies", + "health science", + "medicine", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "ICO", + "biocontext": "ICO", + "bioportal": "ICO", + "fairsharing": "FAIRsharing.b9znd5", + "obofoundry": "ico", + "ols": "ico", + "ontobee": "ICO" + }, + "name": "Informed Consent Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ICO", + "repository": "https://github.com/ICO-ontology/ICO", + "uri_format": "http://purl.obolibrary.org/obo/ICO_$1", + "version": "1.0.187" + }, + "ideal": { + "description": "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments.", + "example": "IID00001", + "homepage": "https://www.ideal-db.org", + "keywords": [ + "biology" + ], + "mappings": { + "biocontext": "IDEAL", + "fairsharing": "FAIRsharing.h3y42f", + "miriam": "ideal", + "n2t": "ideal", + "uniprot": "DB-0251" + }, + "name": "Intrinsically Disordered proteins with Extensive Annotations and Literature", + "pattern": "^IID\\d+$", + "preferred_prefix": "ideal", + "publications": [ + { + "doi": "10.1093/nar/gkt1010", + "pmc": "PMC3965115", + "pubmed": "24178034", + "title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners.", + "year": 2013 + } + ], + "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1" + }, + "ido": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "Lindsay.Cowell@utsouthwestern.edu", + "github": "lgcowell", + "name": "Lindsay Cowell", + "orcid": "0000-0003-1617-8244" + }, + "description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.", + "download_owl": "http://purl.obolibrary.org/obo/ido.owl", + "example": "0000504", + "homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology", + "keywords": [ + "biomedical science", + "molecular infection biology", + "obo", + "ontology", + "preclinical studies" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "IDO", + "biocontext": "IDO", + "bioportal": "IDO", + "fairsharing": "FAIRsharing.aae3v6", + "miriam": "ido", + "n2t": "ido", + "obofoundry": "ido", + "ols": "ido", + "ontobee": "IDO" + }, + "name": "Infectious Disease Ontology", + "pattern": "^[0-9]+$", + "preferred_prefix": "IDO", + "providers": [ + { + "code": "obo.1", + "description": "This incorrect encoding was found inside IDO-COVID-19", + "homepage": "http://purl.obolibrary.org", + "name": "Nonstandard OBO PURL", + "uri_format": "http://purl.obolibrary.org/obo/ido.owl/IDO_$1" + } + ], + "publications": [ + { + "doi": "10.1186/s13326-021-00245-1", + "pmc": "PMC8286442", + "pubmed": "34275487", + "title": "The Infectious Disease Ontology in the age of COVID-19.", + "year": 2021 + } + ], + "repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1", + "version": "2017-11-03" + }, + "idocovid19": { + "contact": { + "email": "johnbeverley2021@u.northwestern.edu", + "github": "johnbeve", + "name": "John Beverly", + "orcid": "0000-0002-1118-1738" + }, + "description": "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease.", + "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-covid-19/master/ontology/ido%20covid-19", + "example": "0001191", + "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "IDO-COVID-19", + "bioportal": "IDO-COVID-19", + "ols": "idocovid19" + }, + "name": "The COVID-19 Infectious Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "idocovid19", + "providers": [ + { + "code": "obo1", + "description": "This variation uses incorrect usage of dashes instead of underscores", + "homepage": "http://purl.obolibrary.org", + "name": "Incorrect OBO PURL variation 1", + "uri_format": "http://purl.obolibrary.org/obo/IDO-COVID-19_$1" + } + ], + "repository": "https://github.com/infectious-disease-ontology-extensions/ido-covid-19", + "uri_format": "http://purl.obolibrary.org/obo/COVIDO_$1", + "version": "2020-07-21" + }, + "idoden": { + "contact": { + "email": "elvira@imbb.forth.gr", + "github": null, + "name": "Elvira Mitraka", + "orcid": "0000-0003-0719-3485" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology for dengue fever.", + "download_owl": "http://aber-owl.net/media/ontologies/IDODEN/6/idoden.owl", + "example": "0003463", + "homepage": "https://bioportal.bioontology.org/ontologies/IDODEN", + "keywords": [ + "medicine", + "ontology" + ], + "mappings": { + "aberowl": "IDODEN", + "bioportal": "IDODEN", + "fairsharing": "FAIRsharing.askzq4" + }, + "name": "Dengue Fever Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "idoden", + "references": [ + "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003479" + ], + "uri_format": "http://purl.bioontology.org/ontology/IDODEN_$1" + }, + "idog": { + "contact": { + "email": "baoym@big.ac.cn", + "github": null, + "name": "Yiming Bao", + "orcid": "0000-0002-9922-9723" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses.", + "example": "4", + "homepage": "https://ngdc.cncb.ac.cn/idog/", + "license": "CC-BY-4.0", + "mappings": { + "re3data": "r3d100012176" + }, + "name": "Integrated Resource for Domestic Dog", + "pattern": "^\\d+$", + "preferred_prefix": "idog", + "publications": [ + { + "doi": "10.1093/nar/gky1041", + "pmc": "PMC6323916", + "pubmed": "30371881", + "title": "iDog: an integrated resource for domestic dogs and wild canids", + "year": 2019 + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/pull/725" + ], + "uri_format": "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1" + }, + "idomal": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "topalis@imbb.forth.gr", + "github": null, + "name": "Pantelis Topalis", + "orcid": "0000-0002-1635-4810" + }, + "deprecated": true, + "description": "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it.", + "download_obo": "http://purl.obolibrary.org/obo/idomal.obo", + "download_owl": "http://purl.obolibrary.org/obo/idomal.owl", + "example": "0002350", + "example_extras": [ + "50000015" + ], + "homepage": "https://www.vectorbase.org/ontology-browser", + "keywords": [ + "biomedical science", + "life science", + "molecular infection biology", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "IDOMAL", + "biocontext": "IDOMAL", + "bioportal": "IDOMAL", + "fairsharing": "FAIRsharing.2q8c28", + "obofoundry": "idomal", + "ols": "idomal", + "ontobee": "IDOMAL" + }, + "name": "Malaria Ontology", + "pattern": "^(5?)\\d{7}$", + "preferred_prefix": "IDOMAL", + "publications": [ + { + "doi": "10.1186/2041-1480-4-16", + "pmc": "PMC3848731", + "pubmed": "24034841", + "title": "IDOMAL: the malaria ontology revisited.", + "year": 2013 + }, + { + "doi": "10.1186/1475-2875-9-230", + "pmc": "PMC2925367", + "pubmed": "20698959", + "title": "IDOMAL: an ontology for malaria.", + "year": 2010 + } + ], + "repository": "https://github.com/VEuPathDB-ontology/IDOMAL", + "twitter": "VectorBase", + "uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", + "version": "2015-03-16" + }, + "idoo": { + "description": "Identifiers.org Ontology", + "example": "DataCollection", + "homepage": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology", + "mappings": { + "miriam": "idoo", + "n2t": "idoo" + }, + "name": "Identifiers.org Ontology", + "pattern": "^[0-9a-zA-Z]+$", + "preferred_prefix": "idoo", + "uri_format": "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1" + }, + "idot": { + "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", + "example": "identifierPattern", + "homepage": "http://biomodels.net/vocab/idot.rdf", + "mappings": { + "biocontext": "idot", + "miriam": "idot", + "n2t": "idot" + }, + "name": "Identifiers.org Terms", + "pattern": "^[A-Za-z]+$", + "preferred_prefix": "idot", + "uri_format": "https://biomodels.net/vocab/idot.rdf#$1" + }, + "idpo": { + "contact": { + "email": "f.quaglia@ibiom.cnr.it", + "github": "federicaquaglia", + "name": "Federica Quaglia", + "orcid": "0000-0002-0341-4888" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR.", + "example": "00056", + "homepage": "https://www.disprot.org/ontology", + "keywords": [ + "protein structure", + "proteins", + "structural biochemistry", + "structural bioinformatics" + ], + "name": "Intrinsically Disordered Proteins Ontology", + "pattern": "^\\d{5}$", + "preferred_prefix": "idpo", + "uri_format": "https://www.disprot.org/idpo/IDPO:$1" + }, + "idr": { + "contact": { + "email": "j.a.moore@dundee.ac.uk", + "github": null, + "name": "Josh Moore", + "orcid": "0000-0003-4028-811X" + }, + "description": "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools.", + "example": "0001", + "homepage": "https://idr.openmicroscopy.org", + "keywords": [ + "biomedical science", + "botany", + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.6wf1zw", + "miriam": "idr", + "re3data": "r3d100012435" + }, + "name": "Image Data Resource", + "pattern": "^[0-9]{4}$", + "preferred_prefix": "idr", + "publications": [ + { + "doi": "10.1038/nmeth.4326", + "pmc": "PMC5536224", + "pubmed": "28775673", + "title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform.", + "year": 2017 + } + ], + "twitter": "openmicroscopy", + "uri_format": "https://idr.openmicroscopy.org/search/?query=Name:idr$1" + }, + "iedb": { + "description": "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes.", + "example": "1038233", + "homepage": "https://www.lji.org/", + "keywords": [ + "bioinformatics", + "immunology", + "life science", + "protein", + "small molecule" + ], + "mappings": { + "fairsharing": "FAIRsharing.c886cd", + "miriam": "iedb", + "prefixcommons": "tied", + "re3data": "r3d100012702" + }, + "name": "Immune Epitope Database", + "pattern": "^[0-9]+$", + "preferred_prefix": "iedb", + "publications": [ + { + "doi": "10.1093/nar/gku938", + "pmc": "PMC4384014", + "pubmed": "25300482", + "title": "The immune epitope database (IEDB) 3.0.", + "year": 2014 + }, + { + "doi": "10.1111/j.1365-2567.2012.03611.x", + "pmc": "PMC3461392", + "pubmed": "22681406", + "title": "The immune epitope database: a historical retrospective of the first decade.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkp1004", + "pmc": "PMC2808938", + "pubmed": "19906713", + "title": "The immune epitope database 2.0.", + "year": 2009 + }, + { + "doi": null, + "pmc": null, + "pubmed": "16312048", + "title": "The immune epitope database and analysis resource: from vision to blueprint.", + "year": 2004 + } + ], + "uri_format": "https://www.iedb.org/reference/$1" + }, + "ietf.language": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Shorthand representations of languages and their subtypes", + "example": "en-GB", + "example_extras": [ + "en", + "ar-SA", + "aaf" + ], + "homepage": "http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry", + "mappings": { + "wikidata": "P305" + }, + "name": "Internet Engineering Task Force Language Tag", + "pattern": "^\\w{2,3}(-\\w+)?$", + "preferred_prefix": "ietf.language", + "synonyms": [ + "bcp47" + ] + }, + "iev": { + "deprecated": true, + "description": "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.", + "example": "0000000", + "homepage": "http://www.inoh.org", + "keywords": [ + "obo", + "ontology", + "pathway", + "structure" + ], + "mappings": { + "biocontext": "IEV", + "obofoundry": "iev", + "prefixcommons": "iev" + }, + "name": "Event (INOH pathway ontology)", + "pattern": "^\\d{7}$", + "preferred_prefix": "IEV", + "uri_format": "http://purl.obolibrary.org/obo/IEV_$1" + }, + "igrhcellid": { + "description": "Cell line databases/resources", + "example": "ACHN", + "homepage": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi", + "mappings": { + "cellosaurus": "IGRhCellID" + }, + "name": "Integrated Genomic Resources of human Cell Lines for Identification", + "preferred_prefix": "igrhcellid", + "uri_format": "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1" + }, + "igsn": { + "description": "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents.", + "example": "AU124", + "homepage": "http://www.geosamples.org/", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.c7f365", + "miriam": "igsn", + "n2t": "igsn" + }, + "name": "International Geo Sample Number", + "pattern": "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$", + "preferred_prefix": "igsn", + "uri_format": "http://igsn.org/$1" + }, + "igsr": { + "description": "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project.", + "example": "NA06985", + "homepage": "https://www.internationalgenome.org/", + "keywords": [ + "comparative genomics", + "genomics" + ], + "mappings": { + "cellosaurus": "IGSR", + "fairsharing": "FAIRsharing.4Vs9VM", + "re3data": "r3d100010180" + }, + "name": "International Genome Sample Resource", + "preferred_prefix": "igsr", + "publications": [ + { + "doi": "10.1093/nar/gkz836", + "pmc": "PMC6943028", + "pubmed": "31584097", + "title": "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources.", + "year": 2020 + }, + { + "doi": "10.1038/nature15393", + "pmc": "PMC4750478", + "pubmed": "26432245", + "title": "A global reference for human genetic variation.", + "year": 2015 + } + ], + "twitter": "1000genomes", + "uri_format": "https://www.internationalgenome.org/data-portal/sample/$1" + }, + "ihw": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics.", + "example": "IHW09326", + "homepage": "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html", + "mappings": { + "cellosaurus": "IHW" + }, + "name": "International Histocompatibility Workshop cell lines", + "pattern": "^IHW\\d+$", + "preferred_prefix": "ihw" + }, + "illumina.probe": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip.", + "example": "ILMN_129894", + "homepage": "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt", + "keywords": [ + "transcriptomics" + ], + "name": "Illumina Probe Identifier", + "pattern": "^ILMN_\\d+$", + "preferred_prefix": "illumina.probe", + "references": [ + "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-9184/A-GEOD-9184_comments.txt" + ] + }, + "imanis": { + "description": "Cell line collections", + "example": "CL070", + "homepage": "https://www.imanislife.com/collections/cell-lines/", + "mappings": { + "cellosaurus": "Imanis" + }, + "name": "Imanis Life Sciences cell line products", + "preferred_prefix": "imanis", + "uri_format": "https://www.imanislife.com/?s=$1" + }, + "imdrf": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence.", + "homepage": "http://www.imdrf.org/", + "name": "International Medical Device Regulators Forum", + "no_own_terms": true, + "preferred_prefix": "imdrf", + "references": [ + "https://www.fda.gov/medical-devices/mandatory-reporting-requirements-manufacturers-importers-and-device-user-facilities/mdr-adverse-event-codes" + ] + }, + "imex": { + "banana": "IM", + "banana_peel": "-", + "description": "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources.", + "example": "19210-3", + "example_extras": [ + "19210" + ], + "homepage": "https://www.imexconsortium.org/", + "keywords": [ + "interaction", + "molecule" + ], + "mappings": { + "biocontext": "IMEX", + "miriam": "imex", + "n2t": "imex", + "prefixcommons": "imex", + "re3data": "r3d100010669" + }, + "name": "International Molecular Exchange", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^\\d+(-\\d+)?$", + "preferred_prefix": "imex", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "IMEx Consortium though Intact", + "homepage": "https://www.ebi.ac.uk/intact/", + "name": "IMEx Consortium though Intact", + "uri_format": "https://imexcentral.org/icentral/imex/rec/$1" + }, + { + "code": "intact.search", + "description": "Search page on IntAct", + "homepage": "https://www.ebi.ac.uk/intact", + "name": "IntAct Search", + "uri_format": "https://www.ebi.ac.uk/intact/search?query=IM-$1" + } + ], + "publications": [ + { + "doi": "10.1002/pmic.200700286", + "pmc": null, + "pubmed": "17893861", + "title": "Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.", + "year": 2007 + } + ], + "uri_format": "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1" + }, + "img.gene": { + "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information.", + "example": "638309541", + "homepage": "http://img.jgi.doe.gov/", + "keywords": [ + "gene", + "genome" + ], + "mappings": { + "biocontext": "IMG.GENE", + "miriam": "img.gene", + "n2t": "img.gene", + "prefixcommons": "img.gene" + }, + "name": "Integrated Microbial Genomes Gene", + "pattern": "^\\d+$", + "preferred_prefix": "img.gene", + "publications": [ + { + "doi": "10.1093/nar/gkm846", + "pmc": "PMC2238897", + "pubmed": "17933782", + "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.", + "year": 2007 + } + ], + "uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1" + }, + "img.taxon": { + "description": "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information.", + "example": "648028003", + "homepage": "http://img.jgi.doe.gov/", + "keywords": [ + "genome", + "taxonomy" + ], + "mappings": { + "biocontext": "IMG.TAXON", + "miriam": "img.taxon", + "n2t": "img.taxon", + "prefixcommons": "img.taxon" + }, + "name": "Integrated Microbial Genomes Taxon", + "pattern": "^\\d+$", + "preferred_prefix": "img.taxon", + "publications": [ + { + "doi": "10.1093/nar/gkm846", + "pmc": "PMC2238897", + "pubmed": "17933782", + "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.", + "year": 2007 + } + ], + "uri_format": "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1" + }, + "imgt.hla": { + "contact": { + "email": "steven.marsh@ucl.ac.uk", + "github": null, + "name": "Steven G. E. 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This collection references allele information through the WHO nomenclature.", + "example": "A*01:01:01:01", + "homepage": "https://www.ebi.ac.uk/imgt/hla/allele.html", + "keywords": [ + "biomedical science", + "dna", + "immunogenetics", + "immunology", + "protein", + "rna" + ], + "mappings": { + "biocontext": "IMGT.HLA", + "cellosaurus": "IPD-IMGT/HLA", + "edam": "2773", + "fairsharing": "FAIRsharing.e28v7g", + "go": "IMGT_HLA", + "miriam": "imgt.hla", + "n2t": "imgt.hla", + "ncbi": "IMGT/HLA", + "prefixcommons": "imgthla", + "re3data": "r3d100010804" + }, + "name": "IMGT/HLA human major histocompatibility complex sequence database", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^[A-Z0-9*:]+$", + "preferred_prefix": "imgt.hla", + "publications": [ + { + "doi": "10.1093/nar/gkz950", + "pmc": "PMC7145640", + "pubmed": "31667505", + "title": "IPD-IMGT/HLA Database.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gku1161", + "pmc": "PMC4383959", + "pubmed": "25414341", + "title": "The IPD and IMGT/HLA database: allele variant databases.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkn662", + "pmc": "PMC2686596", + "pubmed": "18838392", + "title": "The IMGT/HLA database.", + "year": 2008 + }, + { + "doi": "10.1007/978-1-60327-118-9_3", + "pmc": null, + "pubmed": "18449991", + "title": "The IMGT/HLA database.", + "year": 2007 + }, + { + "doi": "10.1002/humu.20406", + "pmc": null, + "pubmed": "16944494", + "title": "The IMGT/HLA and IPD databases.", + "year": 2006 + }, + { + "doi": "10.1093/nar/gkj088", + "pmc": "PMC1347451", + "pubmed": "16381979", + "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.", + "year": 2006 + }, + { + "doi": "10.1093/nar/gkg070", + "pmc": "PMC165517", + "pubmed": "12520010", + "title": "IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.", + "year": 2003 + }, + { + "doi": "10.1093/nar/29.1.210", + "pmc": "PMC29780", + "pubmed": "11125094", + "title": "IMGT/HLA Database--a sequence database for the human major histocompatibility complex.", + "year": 2001 + }, + { + "doi": "10.1034/j.1399-0039.2000.550314.x", + "pmc": null, + "pubmed": "10777106", + "title": "IMGT/HLA database--a sequence database for the human major histocompatibility complex.", + "year": 2000 + } + ], + "synonyms": [ + "IPD-IMGT/HLA" + ], + "uri_format": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1" + }, + "imgt.ligm": { + "description": "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates.", + "example": "M94112", + "homepage": "http://www.imgt.org/", + "keywords": [ + "dna" + ], + "mappings": { + "biocontext": "IMGT.LIGM", + "go": "IMGT_LIGM", + "miriam": "imgt.ligm", + "n2t": "imgt.ligm", + "ncbi": "IMGT/LIGM", + "prefixcommons": "imgt.ligm" + }, + "name": "ImMunoGeneTics database covering immunoglobulins and T-cell receptors", + "pattern": "^M\\d+$", + "preferred_prefix": "imgt.ligm", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "IMGT LIGM through DKFZ (SRS)", + "homepage": "http://genius.embnet.dkfz-heidelberg.de/", + "name": "IMGT LIGM through DKFZ (SRS)", + "uri_format": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1']" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkj088", + "pmc": "PMC1347451", + "pubmed": "16381979", + "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.", + "year": 2006 + } + ], + "uri_format": "http://www.imgt.org/ligmdb/view?id=$1" + }, + "imgt.primerdb": { + "description": "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR).", + "example": "IPP900099", + "homepage": "http://imgt.org/IMGTPrimerDB/", + "keywords": [ + "dna" + ], + "mappings": { + "prefixcommons": "imgt.primerdb", + "re3data": "r3d100012535" + }, + "name": "IMGT/PRIMER-DB", + "preferred_prefix": "imgt.primerdb", + "uri_format": "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList" + }, + "imotdb": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members.", + "example": "53784", + "homepage": "http://caps.ncbs.res.in/imotdb/", + "keywords": [ + "interaction", + "protein" + ], + "mappings": { + "prefixcommons": "imotdb" + }, + "name": "Database of Spatially Interacting Motifs in Proteins", + "preferred_prefix": "imotdb", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1" + }, + "imr": { + "contact": { + "email": "curator@inoh.org", + "github": null, + "name": "INOH curators", + "orcid": null + }, + "deprecated": true, + "description": "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.", + "example": "0000001", + "homepage": "http://www.inoh.org", + "keywords": [ + "obo", + "ontology", + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "IMR", + "obofoundry": "imr", + "prefixcommons": "imr" + }, + "name": "Molecule role (INOH Protein name/family name ontology)", + "pattern": "^\\d{7}$", + "preferred_prefix": "IMR", + "uri_format": "http://purl.obolibrary.org/obo/IMR_$1" + }, + "inaturalist.observation": { + "contributor": { + "email": null, + "github": "oolonek", + "name": "Pierre-Marie Allard", + "orcid": "0000-0003-3389-2191" + }, + "description": "The identifier for an observation in iNaturalist", + "example": "36010371", + "github_request_issue": 517, + "homepage": "https://www.inaturalist.org/observations", + "mappings": { + "wikidata": "P5683" + }, + "name": "iNaturalist Observation", + "pattern": "^[1-9]\\d*$", + "preferred_prefix": "inaturalist.observation", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.inaturalist.org/observations/$1" + }, + "inaturalist.place": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Identifier for a place in iNaturalist", + "example": "7207", + "homepage": "https://www.inaturalist.org/places", + "mappings": { + "wikidata": "P7471" + }, + "name": "iNaturalist Place", + "pattern": "^[1-9]\\d*$", + "preferred_prefix": "inaturalist.place", + "uri_format": "https://www.inaturalist.org/places/$1" + }, + "inaturalist.taxon": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Identifier for a species in iNaturalist", + "example": "21723", + "homepage": "https://www.inaturalist.org/taxa", + "mappings": { + "wikidata": "P3151" + }, + "name": "iNaturalist Taxonomy", + "pattern": "^[1-9]\\d{0,6}$", + "preferred_prefix": "inaturalist.taxon", + "uri_format": "https://www.inaturalist.org/taxa/$1" + }, + "inaturalist.user": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Identifier for a user in iNaturalist", + "example": "1426686", + "homepage": "https://www.inaturalist.org/users", + "keywords": [ + "person" + ], + "name": "iNaturalist User", + "pattern": "^[1-9]\\d*$", + "preferred_prefix": "inaturalist.user", + "uri_format": "https://www.inaturalist.org/users/$1" + }, + "inchi": { + "description": "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier.", + "example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3", + "homepage": "http://www.chemspider.com/", + "keywords": [ + "cheminformatics", + "chemistry", + "knowledge and information systems" + ], + "mappings": { + "biocontext": "INCHI", + "fairsharing": "FAIRsharing.ddk9t9", + "miriam": "inchi", + "n2t": "inchi", + "wikidata": "P234" + }, + "name": "InChI", + "pattern": "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$", + "preferred_prefix": "inchi", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "InChI through NIST", + "homepage": "http://webbook.nist.gov/chemistry", + "name": "InChI through NIST", + "uri_format": "http://webbook.nist.gov/cgi/cbook.cgi?$1" + }, + { + "code": "ebi", + "description": "InChI through ChEBI", + "homepage": "https://www.ebi.ac.uk/chebi/", + "name": "InChI through ChEBI", + "uri_format": "https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString=$1" + }, + { + "code": "um", + "description": "InChI through RDF Open Molecules", + "homepage": "http://rdf.openmolecules.net/", + "name": "InChI through RDF Open Molecules", + "uri_format": "http://rdf.openmolecules.net/?$1" + } + ], + "publications": [ + { + "doi": "10.1186/s13321-021-00517-z", + "pmc": "PMC8147039", + "pubmed": "34030732", + "title": "InChI version 1.06: now more than 99.99% reliable.", + "year": 2021 + }, + { + "doi": "10.1186/s13321-015-0068-4", + "pmc": "PMC4486400", + "pubmed": "26136848", + "title": "InChI, the IUPAC International Chemical Identifier.", + "year": 2015 + }, + { + "doi": "10.1007/s10822-015-9854-3", + "pmc": null, + "pubmed": "26081259", + "title": "Many InChIs and quite some feat.", + "year": 2015 + } + ], + "twitter": "inchi_trust", + "uri_format": "http://www.chemspider.com/$1" + }, + "inchikey": { + "description": "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI.", + "example": "RYYVLZVUVIJVGH-UHFFFAOYSA-N", + "homepage": "http://www.chemspider.com/", + "mappings": { + "biocontext": "INCHIKEY", + "miriam": "inchikey", + "n2t": "inchikey", + "wikidata": "P235" + }, + "name": "InChIKey", + "pattern": "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$", + "preferred_prefix": "inchikey", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/inchikey/$1" + } + ], + "uri_format": "http://www.chemspider.com/inchikey=$1" + }, + "inhand": { + "comment": "This nomenclature is available via email. Truly a disgrace.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.", + "homepage": "https://www.goreni.org/gr3_nomenclature.php", + "keywords": [ + "biomedical science" + ], + "mappings": { + "fairsharing": "FAIRsharing.9gqfpm" + }, + "name": "The International Harmonization of Nomenclature and Diagnostic criteria", + "preferred_prefix": "inhand", + "proprietary": true, + "publications": [ + { + "doi": "10.1177/0192623309353423", + "pmc": null, + "pubmed": "20032296", + "title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract.", + "year": 2009 + } + ] + }, + "inn": { + "comment": "can not find a place to resolve to", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO.", + "example": "fluticasone", + "homepage": "https://www.who.int/teams/health-product-and-policy-standards/inn", + "mappings": { + "wikidata": "P2275" + }, + "name": "International Nonproprietary Names", + "preferred_prefix": "inn", + "synonyms": [ + "INN_ID" + ], + "uri_format": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1" + }, + "innatedb": { + "description": "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation.", + "example": "20021", + "homepage": "http://www.innatedb.ca/", + "keywords": [ + "gene", + "immunology", + "interaction", + "life science", + "pathway", + "protein" + ], + "mappings": { + "fairsharing": "FAIRsharing.rb2drw", + "prefixcommons": "innatedb", + "re3data": "r3d100010676" + }, + "name": "A Knowledge Resource for Innate Immunity Interactions and Pathways", + "preferred_prefix": "innatedb", + "publications": [ + { + "doi": "10.1093/nar/gks1147", + "pmc": "PMC3531080", + "pubmed": "23180781", + "title": "InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.", + "year": 2012 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "twitter": "innatedb", + "uri_format": "http://www.innatedb.ca/getGeneCard.do?id=$1" + }, + "ino": { + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "description": "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles.", + "download_owl": "http://purl.obolibrary.org/obo/ino.owl", + "example": "0000003", + "homepage": "https://github.com/INO-ontology/ino", + "keywords": [ + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "INO", + "biolink": "INO", + "bioportal": "INO", + "fairsharing": "FAIRsharing.mm72as", + "obofoundry": "ino", + "ols": "ino", + "ontobee": "INO" + }, + "name": "Interaction Network Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "INO", + "publications": [ + { + "doi": "10.1186/s13040-016-0118-0", + "pmc": "PMC5168857", + "pubmed": "28031747", + "title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.", + "year": 2016 + }, + { + "doi": "10.1186/2041-1480-6-2", + "pmc": "PMC4362819", + "pubmed": "25785184", + "title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.", + "year": 2015 + }, + { + "doi": "10.1186/2041-1480-2-s2-s8", + "pmc": "PMC3102897", + "pubmed": "21624163", + "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.", + "year": 2011 + } + ], + "repository": "https://github.com/INO-ontology/ino", + "uri_format": "http://purl.obolibrary.org/obo/INO_$1", + "version": "1.1.13" + }, + "insdc": { + "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", + "example": "X58356", + "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", + "keywords": [ + "dna" + ], + "mappings": { + "biocontext": "INSDC", + "miriam": "insdc", + "n2t": "insdc", + "prefixcommons": "insdc" + }, + "name": "Nucleotide Sequence Database", + "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", + "preferred_prefix": "insdc", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "INSDC through GenBank", + "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", + "name": "INSDC through GenBank", + "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" + }, + { + "code": "CURATOR_REVIEW", + "description": "INSDC through DDBJ", + "homepage": "http://www.ddbj.nig.ac.jp/", + "name": "INSDC through DDBJ", + "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1" + }, + { + "code": "ebi", + "description": "INSDC through European Nucleotide Archive (ENA)", + "homepage": "https://www.ebi.ac.uk/ena/", + "name": "INSDC through European Nucleotide Archive (ENA)", + "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/18.6.1517", + "pmc": "PMC330520", + "pubmed": "2326192", + "title": "Recent changes in the GenBank On-line Service.", + "year": 1990 + }, + { + "doi": "10.1093/nar/gkl986", + "pmc": "PMC1781245", + "pubmed": "17202161", + "title": "GenBank.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkl913", + "pmc": "PMC1897316", + "pubmed": "17148479", + "title": "EMBL Nucleotide Sequence Database in 2006.", + "year": 2006 + }, + { + "doi": "10.1126/science.298.5597.1333b", + "pmc": null, + "pubmed": "12436968", + "title": "Nucleotide sequence database policies.", + "year": 2002 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" + }, + "insdc.cds": { + "description": "The coding sequence or protein identifiers as maintained in INSDC.", + "example": "AAA35559", + "has_canonical": "ncbiprotein", + "homepage": "http://getentry.ddbj.nig.ac.jp", + "mappings": { + "biocontext": "INSDC.CDS", + "miriam": "insdc.cds", + "n2t": "insdc.cds" + }, + "name": "INSDC CDS", + "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", + "preferred_prefix": "insdc.cds", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "INSDC CDS through ENA", + "homepage": "https://www.ebi.ac.uk/ena", + "name": "INSDC CDS through ENA", + "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" + }, + { + "code": "CURATOR_REVIEW", + "description": "INSDC CDS through NCBI", + "homepage": "https://www.ncbi.nlm.nih.gov/protein/", + "name": "INSDC CDS through NCBI", + "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" + } + ], + "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1" + }, + "insdc.gca": { + "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage.", + "example": "GCA_000155495.1", + "has_canonical": "ncbi.assembly", + "homepage": "https://www.ebi.ac.uk/ena/browse/genome-assembly-database", + "mappings": { + "biocontext": "INSDC.GCA", + "miriam": "insdc.gca", + "n2t": "insdc.gca" + }, + "name": "Genome assembly database", + "pattern": "^GC[AF]_[0-9]{9}\\.[0-9]+$", + "preferred_prefix": "insdc.gca", + "providers": [ + { + "code": "ncbi", + "description": "Genome assembly database NCBI", + "homepage": "https://www.ncbi.nlm.nih.gov/assembly/", + "name": "Genome assembly database NCBI", + "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" + } + ], + "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" + }, + "insdc.run": { + "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --", + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "An experimental run, served thrugh the ENA", + "example": "ERR436051", + "github_request_issue": 131, + "has_canonical": "ena.embl", + "homepage": "https://www.insdc.org/", + "name": "International Nucleotide Sequence Database Collaboration (INSDC) Run", + "pattern": "^(E|D|S)RR[0-9]{6,}$", + "preferred_prefix": "insdc.run", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1" + }, + "insdc.sra": { + "description": "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.", + "example": "SRX000007", + "homepage": "https://www.ncbi.nlm.nih.gov/sra", + "keywords": [ + "biology", + "epidemiology", + "genomics", + "virology" + ], + "mappings": { + "biocontext": "INSDC.SRA", + "fairsharing": "FAIRsharing.g7t2hv", + "miriam": "insdc.sra", + "n2t": "insdc.sra", + "re3data": "r3d100010775" + }, + "name": "Sequence Read Archive", + "pattern": "^[SED]R[APRSXZ]\\d+$", + "preferred_prefix": "insdc.sra", + "providers": [ + { + "code": "ddbj", + "description": "DDBJ Sequence Read Archive (DRA)", + "homepage": "http://trace.ddbj.nig.ac.jp/dra/", + "name": "DDBJ Sequence Read Archive (DRA)", + "uri_format": "http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1" + }, + { + "code": "ebi", + "description": "European Nucleotide Archive (ENA)", + "homepage": "https://www.ebi.ac.uk/ena", + "name": "European Nucleotide Archive (ENA)", + "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" + } + ], + "publications": [ + { + "doi": "10.1186/s13742-015-0064-7", + "pmc": "PMC4425880", + "pubmed": "25960871", + "title": "Investigation into the annotation of protocol sequencing steps in the sequence read archive.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkr854", + "pmc": "PMC3245110", + "pubmed": "22009675", + "title": "The Sequence Read Archive: explosive growth of sequencing data.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkm1000", + "pmc": "PMC2238880", + "pubmed": "18045790", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2007 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/sra/$1" + }, + "intact": { + "contact": { + "email": "orchard@ebi.ac.uk", + "github": null, + "name": "Sandra Orchard", + "orcid": "0000-0002-8878-3972" + }, + "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data.", + "example": "EBI-2307691", + "homepage": "https://www.ebi.ac.uk/intact/", + "keywords": [ + "biology", + "interaction", + "protein" + ], + "mappings": { + "biocontext": "INTACT", + "fairsharing": "FAIRsharing.d05nwx", + "go": "IntAct", + "miriam": "intact", + "n2t": "intact", + "prefixcommons": "intact", + "re3data": "r3d100010671", + "uniprot": "DB-0051" + }, + "name": "IntAct protein interaction database", + "owners": [ + { + "name": "European Bioinformatics Institute", + "partnered": false, + "ror": "02catss52", + "wikidata": null + } + ], + "pattern": "^EBI\\-[0-9]+$", + "preferred_prefix": "intact", + "publications": [ + { + "doi": "10.1093/nar/gkt1115", + "pmc": "PMC3965093", + "pubmed": "24234451", + "title": "The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.", + "year": 2013 + }, + { + "doi": "10.1038/nmeth.1637", + "pmc": "PMC3246345", + "pubmed": "21716279", + "title": "PSICQUIC and PSISCORE: accessing and scoring molecular interactions.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkp878", + "pmc": "PMC2808934", + "pubmed": "19850723", + "title": "The IntAct molecular interaction database in 2010.", + "year": 2009 + }, + { + "doi": "10.1186/1741-7007-5-44", + "pmc": "PMC2189715", + "pubmed": "17925023", + "title": "Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkh052", + "pmc": "PMC308786", + "pubmed": "14681455", + "title": "IntAct: an open source molecular interaction database.", + "year": 2004 + } + ], + "twitter": "intact_project", + "uri_format": "https://www.ebi.ac.uk/intact/interaction/$1" + }, + "intact.molecule": { + "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", + "example": "EBI-366083", + "homepage": "https://www.ebi.ac.uk/intact/", + "mappings": { + "biocontext": "INTACT.MOLECULE", + "miriam": "intact.molecule", + "n2t": "intact.molecule" + }, + "name": "IntAct Molecule", + "pattern": "^EBI\\-[0-9]+$", + "preferred_prefix": "intact.molecule", + "uri_format": "https://www.ebi.ac.uk/intact/search?query=$1" + }, + "interfil": { + "description": "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants.", + "example": "NM_006262", + "homepage": "http://www.interfil.org", + "keywords": [ + "genome" + ], + "mappings": { + "prefixcommons": "interfil" + }, + "name": "Human Intermediate Filament Database", + "preferred_prefix": "interfil", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.interfil.org/details.php?id=$1" + }, + "interlex": { + "description": "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ", + "example": "0101963", + "homepage": "https://www.fdilab.org", + "keywords": [ + "anatomy", + "biomedical science", + "neurobiology" + ], + "mappings": { + "fairsharing": "FAIRsharing.67sssf", + "miriam": "ilx", + "wikidata": "P696" + }, + "name": "InterLex", + "pattern": "^[0-9]+$", + "preferred_prefix": "interlex", + "publications": [ + { + "doi": "10.3389/fninf.2013.00018", + "pmc": "PMC3757470", + "pubmed": "24009581", + "title": "NeuroLex.org: an online framework for neuroscience knowledge.", + "year": 2013 + } + ], + "references": [ + "https://github.com/AllenInstitute/nomenclature" + ], + "synonyms": [ + "ILX" + ], + "uri_format": "https://scicrunch.org/scicrunch/interlex/view/ilx_$1" + }, + "interpro": { + "contact": { + "email": "interhelp@ebi.ac.uk", + "github": null, + "name": "InterPro Help", + "orcid": null + }, + "description": "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.", + "example": "IPR016380", + "homepage": "http://www.ebi.ac.uk/interpro/index.html", + "keywords": [ + "bioinformatics", + "biology", + "domain", + "obo", + "ontology", + "protein" + ], + "mappings": { + "biocontext": "IPR", + "biolink": "interpro", + "edam": "1133", + "fairsharing": "FAIRsharing.pda11d", + "go": "InterPro", + "miriam": "interpro", + "n2t": "interpro", + "ncbi": "InterPro", + "obofoundry": "ipr", + "prefixcommons": "interpro", + "re3data": "r3d100010798", + "uniprot": "DB-0052", + "wikidata": "P2926" + }, + "name": "InterPro", + "pattern": "^IPR\\d{6}$", + "preferred_prefix": "interpro", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Bio2RDF", + "homepage": "http://interpro.bio2rdf.org/fct/", + "name": "Bio2RDF", + "uri_format": "http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkaa977", + "pmc": "PMC7778928", + "pubmed": "33156333", + "title": "The InterPro protein families and domains database: 20 years on.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gky1100", + "pmc": "PMC6323941", + "pubmed": "30398656", + "title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gki106", + "pmc": "PMC540060", + "pubmed": "15608177", + "title": "InterPro, progress and status in 2005.", + "year": 2005 + } + ], + "repository": "https://proteinswebteam.github.io/interpro-blog/", + "synonyms": [ + "IP", + "IPR", + "InterPro" + ], + "twitter": "InterProDB", + "uri_format": "https://www.ebi.ac.uk/interpro/entry/$1" + }, + "iobc": { + "contact": { + "email": "kushida@biosciencedbc.jp", + "github": "kushidatatsuya", + "name": "Tatsuya Kushida", + "orcid": "0000-0002-0784-4113" + }, + "description": "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\".", + "download_owl": "http://aber-owl.net/media/ontologies/IOBC/25/iobc.owl", + "example": "200906038218908385", + "example_extras": [ + "AC21_cat", + "AC21", + "OWLClass_00000000000000000321" + ], + "homepage": "https://github.com/kushidat/IOBC", + "keywords": [ + "ontology" + ], + "license": "CC-BY-NC-4.0", + "mappings": { + "aberowl": "IOBC", + "bioportal": "IOBC" + }, + "name": "Interlinking Ontology for Biological Concepts", + "preferred_prefix": "iobc", + "publications": [ + { + "doi": "10.1007/s00354-019-00074-y", + "pmc": null, + "pubmed": null, + "title": "Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts", + "year": 2019 + } + ], + "repository": "https://github.com/kushidat/IOBC", + "uri_format": "http://purl.jp/bio/4/id/$1" + }, + "ipi": { + "deprecated": true, + "description": "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers.", + "example": "IPI00000001", + "homepage": "http://www.ebi.ac.uk/IPI", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "IPI", + "prefixcommons": "ipi" + }, + "name": "International Protein Index", + "preferred_prefix": "ipi", + "publications": [ + { + "doi": "10.1002/pmic.200300721", + "pmc": null, + "pubmed": "15221759", + "title": "The International Protein Index: an integrated database for proteomics experiments.", + "year": 2004 + } + ], + "uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default" + }, + "ird.segment": { + "description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).", + "example": "CY077097", + "homepage": "http://www.fludb.org/", + "keywords": [ + "gene", + "protein" + ], + "mappings": { + "biocontext": "IRD.SEGMENT", + "miriam": "ird.segment", + "n2t": "ird.segment", + "prefixcommons": "ird.segment" + }, + "name": "IRD Segment Sequence", + "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", + "preferred_prefix": "ird.segment", + "publications": [ + { + "doi": "10.1093/nar/gkm905", + "pmc": "PMC2238987", + "pubmed": "17965094", + "title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.", + "year": 2007 + } + ], + "uri_format": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1" + }, + "irefweb": { + "description": "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived.", + "example": "617102", + "homepage": "http://wodaklab.org/iRefWeb/", + "keywords": [ + "interaction", + "life science", + "protein" + ], + "mappings": { + "biocontext": "IREFWEB", + "fairsharing": "FAIRsharing.t31wcb", + "miriam": "irefweb", + "n2t": "irefweb", + "prefixcommons": "irefweb", + "re3data": "r3d100012725" + }, + "name": "iRefWeb", + "pattern": "^\\d+$", + "preferred_prefix": "irefweb", + "publications": [ + { + "doi": "10.1093/database/baq023", + "pmc": "PMC2963317", + "pubmed": "20940177", + "title": "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.", + "year": 2010 + } + ], + "twitter": "wodaklab", + "uri_format": "http://wodaklab.org/iRefWeb/interaction/show/$1" + }, + "iresite": { + "description": "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.", + "example": "322", + "homepage": "http://www.iresite.org", + "keywords": [ + "life science", + "regulation", + "rna" + ], + "mappings": { + "fairsharing": "FAIRsharing.kd39j4", + "prefixcommons": "iresite" + }, + "name": "Database of experimentally verified IRES structures", + "preferred_prefix": "iresite", + "publications": [ + { + "doi": "10.1093/nar/gkp981", + "pmc": "PMC2808886", + "pubmed": "19917642", + "title": "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkj081", + "pmc": "PMC1347444", + "pubmed": "16381829", + "title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org).", + "year": 2006 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1" + }, + "iro": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "example": "0000008", + "name": "Insect Resistance Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "iro", + "uri_format": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1" + }, + "isbn": { + "description": "The International Standard Book Number (ISBN) is for identifying printed books.", + "example": "9781584885658", + "homepage": "http://isbndb.com/", + "keywords": [ + "bibliography" + ], + "mappings": { + "biocontext": "ISBN-13", + "biolink": "isbn", + "edam": "2634", + "go": "ISBN", + "miriam": "isbn", + "n2t": "isbn", + "prefixcommons": "isbn" + }, + "name": "International Standard Book Number", + "pattern": "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$", + "preferred_prefix": "isbn", + "providers": [ + { + "code": "worldcat", + "description": "ISBN database at WorldCat", + "homepage": "http://www.worldcat.org/", + "name": "ISBN database at WorldCat", + "uri_format": "http://www.worldcat.org/isbn/$1" + } + ], + "synonyms": [ + "ISBN-10", + "ISBN-13" + ], + "uri_format": "http://isbndb.com/search-all.html?kw=$1" + }, + "ised": { + "description": "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea.", + "example": "AY209920", + "homepage": "http://influenza.korea.ac.kr", + "keywords": [ + "protein" + ], + "mappings": { + "prefixcommons": "ised" + }, + "name": "Influenza Sequence and Epitope Database", + "preferred_prefix": "ised" + }, + "isfinder": { + "description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.", + "example": "ISA1083-2", + "homepage": "http://www-is.biotoul.fr/i", + "keywords": [ + "gene", + "life science", + "sequence" + ], + "mappings": { + "biocontext": "ISFINDER", + "fairsharing": "FAIRsharing.xhpc3h", + "miriam": "isfinder", + "n2t": "isfinder", + "ncbi": "ISFinder", + "prefixcommons": "isfinder" + }, + "name": "Insertion sequence elements database", + "pattern": "^IS\\w+(\\-\\d)?$", + "preferred_prefix": "isfinder", + "publications": [ + { + "doi": "10.1093/nar/gkj014", + "pmc": "PMC1347377", + "pubmed": "16381877", + "title": "ISfinder: the reference centre for bacterial insertion sequences.", + "year": 2006 + } + ], + "uri_format": "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1" + }, + "isni": { + "description": "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. 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cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.", + "example": "78", + "homepage": "http://www.guidetopharmacology.org/", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "IUPHAR.FAMILY", + "miriam": "iuphar.family", + "n2t": "iuphar.family", + "prefixcommons": "iuphar.family" + }, + "name": "IUPHAR family", + "pattern": "^\\d+$", + "preferred_prefix": "iuphar.family", + "synonyms": [ + "IUPHARfam" + ], + "uri_format": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1" + }, + "iuphar.ligand": { + "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. 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It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits.", + "example": "101", + "homepage": "http://www.guidetopharmacology.org/targets.jsp", + "mappings": { + "biocontext": "IUPHAR.RECEPTOR", + "go": "IUPHAR_RECEPTOR", + "miriam": "iuphar.receptor", + "n2t": "iuphar.receptor", + "uniprot": "DB-0182", + "wikidata": "P5458" + }, + "name": "Guide to Pharmacology Target", + "pattern": "^\\d+$", + "preferred_prefix": "iuphar.receptor", + "publications": [ + { + "doi": "10.1093/nar/gkab1010", + "pmc": "PMC8689838", + "pubmed": "34718737", + "title": "The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials.", + "year": 2022 + }, + { + "doi": "10.1111/j.1476-5381.2012.02141.x", + "pmc": "PMC3575771", + "pubmed": "23003568", + "title": "GuideToPharmacology.org--an update.", + "year": 2012 + } + ], + "synonyms": [ + "IUPHAR_GPCR", + "IUPHARobj" + ], + "uri_format": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1" + }, + "ivdb": { + "description": "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively.", + "example": "E13035", + "homepage": "http://influenza.psych.ac.cn/", + "keywords": [ + "dna", + "gene", + "genome" + ], + "mappings": { + "prefixcommons": "ivdb" + }, + "name": "Influenza Virus Database", + "preferred_prefix": "ivdb", + "uri_format": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1" + }, + "jax": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Information about the C57BL/6J. 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This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.", + "example": "JCGG-STR008690", + "homepage": "http://jcggdb.jp/index_en.html", + "mappings": { + "biocontext": "JCGGDB", + "miriam": "jcggdb", + "n2t": "jcggdb" + }, + "name": "Japan Consortium for Glycobiology and Glycotechnology Database", + "pattern": "^JCGG-STR\\d{6}$", + "preferred_prefix": "jcggdb", + "uri_format": "http://jcggdb.jp/idb/jcggdb/$1" + }, + "jcm": { + "description": "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2.", + "example": "17254", + "homepage": "http://www.jcm.riken.go.jp/", + "keywords": [ + "life science", + "microbial", + "taxonomy" + ], + "mappings": { + "biocontext": "JCM", + "fairsharing": "FAIRsharing.h2wrt2", + "miriam": "jcm", + "n2t": "jcm", + "ncbi": "JCM", + "prefixcommons": "jcm" + }, + "name": "Japan Collection of Microorganisms", + "pattern": "^\\d+$", + "preferred_prefix": "jcm", + "uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1" + }, + "jcrb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Cell line collections", + "example": "JCRB1355", + "homepage": "https://cellbank.nibiohn.go.jp", + "mappings": { + "cellosaurus": "JCRB" + }, + "name": "JRBC Cell Bank", + "preferred_prefix": "jcrb", + "uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1" + }, + "jcsd": { + "description": "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST).", + "example": "J55.713G", + "homepage": "http://jglobal.jst.go.jp/en/", + "keywords": [ + "chemical", + "structure" + ], + "mappings": { + "biocontext": "JCSD", + "miriam": "jcsd", + "n2t": "jcsd", + "prefixcommons": "jcsd" + }, + "name": "Japan Chemical Substance Dictionary", + "pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$", + "preferred_prefix": "jcsd", + "uri_format": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1" + }, + "jstor": { + "description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.", + "example": "3075966", + "homepage": "http://www.jstor.org/", + "mappings": { + "biocontext": "JSTOR", + "go": "JSTOR", + "miriam": "jstor", + "n2t": "jstor" + }, + "name": "Digital archive of scholarly articles", + "pattern": "^\\d+$", + "preferred_prefix": "jstor", + "uri_format": "http://www.jstor.org/stable/$1" + }, + "jws": { + "description": "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser.", + "example": "achcar11", + "homepage": "http://jjj.biochem.sun.ac.za/models/", + "keywords": [ + "model", + "pathway" + ], + "mappings": { + "biocontext": "JWS", + "miriam": "jws", + "n2t": "jws", + "prefixcommons": "jws" + }, + "name": "JWS Online", + "pattern": "^\\w+$", + "preferred_prefix": "jws", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "JWS Online Model Repository at Manchester", + "homepage": "http://jjj.mib.ac.uk/index.html", + "name": "JWS Online Model Repository at Manchester", + "uri_format": "http://jjj.mib.ac.uk/models/$1" + }, + { + "code": "CURATOR_REVIEW", + "description": "JWS Online Model Repository at Amsterdam", + "homepage": "http://jjj.bio.vu.nl/models/", + "name": "JWS Online Model Repository at Amsterdam", + "uri_format": "http://jjj.bio.vu.nl/models/$1/" + } + ], + "publications": [ + { + "doi": "10.1093/bioinformatics/bth200", + "pmc": null, + "pubmed": "15072998", + "title": "Web-based kinetic modelling using JWS Online.", + "year": 2004 + } + ], + "uri_format": "https://jjj.bio.vu.nl/models/$1" + }, + "kaggle": { + "description": "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions.", + "example": "nasa/kepler-exoplanet-search-results", + "homepage": "https://kaggle.com", + "mappings": { + "miriam": "kaggle", + "n2t": "kaggle", + "re3data": "r3d100012705" + }, + "name": "Kaggle", + "pattern": "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$", + "preferred_prefix": "kaggle", + "uri_format": "https://www.kaggle.com/$1" + }, + "kclb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Cell line collections", + "example": "10020.2", + "homepage": "https://cellbank.snu.ac.kr/english", + "mappings": { + "cellosaurus": "KCLB" + }, + "name": "Korean Cell Line Bank", + "preferred_prefix": "kclb", + "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1" + }, + "kegg": { + "comment": "KEGG prefix has been split into several others", + "deprecated": true, + "description": "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.", + "example": "hsa00190", + "homepage": "http://www.kegg.jp/", + "mappings": { + "biocontext": "KEGG", + "cheminf": "000409", + "go": "KEGG", + "miriam": "kegg", + "n2t": "kegg", + "uniprot": "DB-0053" + }, + "name": "Kyoto Encyclopedia of Genes and Genomes", + "pattern": "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$", + "preferred_prefix": "kegg", + "publications": [ + { + "doi": "10.1093/nar/gkw1092", + "pmc": "PMC5210567", + "pubmed": "27899662", + "title": "KEGG: new perspectives on genomes, pathways, diseases and drugs.", + "year": 2016 + } + ], + "synonyms": [ + "KEGG" + ], + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.brite": { + "description": "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships.", + "example": "ko00071", + "homepage": "http://www.genome.jp/kegg/brite.html", + "keywords": [ + "classification", + "ontology", + "pathway" + ], + "mappings": { + "biolink": "KEGG.BRITE", + "prefixcommons": "kegg.brite" + }, + "name": "KEGG BRITE", + "part_of": "kegg", + "preferred_prefix": "kegg.brite", + "uri_format": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1" + }, + "kegg.compound": { + "description": "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life.", + "example": "C12345", + "homepage": "https://www.genome.jp/kegg/ligand.html", + "keywords": [ + "small molecule" + ], + "mappings": { + "biocontext": "KEGG.COMPOUND", + "edam": "2605", + "miriam": "kegg.compound", + "n2t": "kegg.compound", + "prefixcommons": "kegg.compound", + "wikidata": "P665" + }, + "name": "KEGG Compound", + "part_of": "kegg", + "pattern": "^C\\d+$", + "preferred_prefix": "kegg.compound", + "publications": [ + { + "doi": "10.1002/0471250953.bi0112s38", + "pmc": null, + "pubmed": "22700311", + "title": "Using the KEGG database resource.", + "year": 2012 + } + ], + "synonyms": [ + "KEGG COMPOUND", + "KEGG.COMPOUND" + ], + "uri_format": "https://www.kegg.jp/entry/$1" + }, + "kegg.dgroup": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries.", + "example": "DG00301", + "homepage": "http://www.genome.jp/kegg/reaction/", + "mappings": { + "biolink": "KEGG.DGROUP" + }, + "name": "KEGG Drug Group", + "part_of": "kegg", + "pattern": "^DG\\d+$", + "preferred_prefix": "kegg.dgroup", + "references": [ + "https://github.com/prefixcommons/prefixes/pull/4" + ], + "synonyms": [ + "KEGG_DGROUP", + "KEGG_DRUG_GROUP" + ] + }, + "kegg.disease": { + "description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.", + "example": "H00076", + "homepage": "http://www.genome.jp/kegg/disease/", + "keywords": [ + "classification" + ], + "mappings": { + "biocontext": "KEGG.DISEASE", + "miriam": "kegg.disease", + "n2t": "kegg.disease", + "prefixcommons": "kegg.disease" + }, + "name": "KEGG Disease", + "part_of": "kegg", + "pattern": "^H\\d+$", + "preferred_prefix": "kegg.disease", + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.drug": { + "description": "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules.", + "example": "D00123", + "homepage": "https://www.genome.jp/kegg/drug/", + "keywords": [ + "small molecule" + ], + "mappings": { + "biocontext": "KEGG.DRUG", + "edam": "2609", + "miriam": "kegg.drug", + "n2t": "kegg.drug", + "prefixcommons": "kegg.drug", + "wikidata": "P665" + }, + "name": "KEGG Drug", + "part_of": "kegg", + "pattern": "^D\\d+$", + "preferred_prefix": "kegg.drug", + "publications": [ + { + "doi": "10.1093/nar/gkj102", + "pmc": "PMC1347464", + "pubmed": "16381885", + "title": "From genomics to chemical genomics: new developments in KEGG.", + "year": 2006 + } + ], + "synonyms": [ + "KEGG DRUG", + "KEGG.DRUG" + ], + "uri_format": "https://www.kegg.jp/entry/$1" + }, + "kegg.environ": { + "deprecated": true, + "description": "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable.", + "example": "ev:E00032", + "homepage": "http://www.genome.jp/kegg/drug/environ.html", + "mappings": { + "biocontext": "KEGG.ENVIRON", + "miriam": "kegg.environ", + "n2t": "kegg.environ" + }, + "name": "KEGG Environ", + "part_of": "kegg", + "pattern": "^(ev\\:)?E\\d+$", + "preferred_prefix": "kegg.environ", + "synonyms": [ + "KEGG.EDRUG" + ], + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.enzyme": { + "description": "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links.", + "homepage": "http://www.genome.jp/dbget-bin/www_bfind?enzyme", + "mappings": { + "biolink": "KEGG.ENZYME", + "go": "KEGG_ENZYME" + }, + "name": "KEGG Enzyme", + "part_of": "kegg", + "preferred_prefix": "kegg.enzyme", + "provides": "eccode", + "uri_format": "http://www.genome.jp/dbget-bin/www_bget?ec:$1" + }, + "kegg.genes": { + "description": "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources.", + "example": "bsu:BSU01340", + "homepage": "http://www.genome.jp/kegg/genes.html", + "keywords": [ + "dna", + "gene", + "protein" + ], + "mappings": { + "biocontext": "KEGG.GENES", + "biolink": "KEGG.GENE", + "miriam": "kegg.genes", + "n2t": "kegg.genes", + "prefixcommons": "kegg.gene", + "wikidata": "P665" + }, + "name": "KEGG Genes", + "part_of": "kegg", + "pattern": "^\\w+:[\\w\\d\\.-]*$", + "preferred_prefix": "kegg.genes", + "publications": [ + { + "doi": "10.1093/nar/gkj102", + "pmc": "PMC1347464", + "pubmed": "16381885", + "title": "From genomics to chemical genomics: new developments in KEGG.", + "year": 2006 + } + ], + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.genome": { + "description": "KEGG Genome is a collection of organisms whose genomes have been completely sequenced.", + "example": "T06648", + "homepage": "http://www.genome.jp/kegg/catalog/org_list.html", + "mappings": { + "biocontext": "KEGG.GENOME", + "miriam": "kegg.genome", + "n2t": "kegg.genome", + "prefixcommons": "kegg.genome", + "wikidata": "P665" + }, + "name": "KEGG Genome", + "part_of": "kegg", + "pattern": "^(T0\\d+|\\w{3,5})$", + "preferred_prefix": "kegg.genome", + "publications": [ + { + "doi": "10.1093/nar/gkr988", + "pmc": "PMC3245020", + "pubmed": "22080510", + "title": "KEGG for integration and interpretation of large-scale molecular data sets.", + "year": 2011 + } + ], + "synonyms": [ + "kegg_genome", + "kegg_genomes" + ], + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.glycan": { + "description": "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.", + "example": "G00123", + "homepage": "https://www.genome.jp/kegg/glycan/", + "keywords": [ + "small molecule" + ], + "mappings": { + "biocontext": "KEGG.GLYCAN", + "edam": "2613", + "miriam": "kegg.glycan", + "n2t": "kegg.glycan", + "prefixcommons": "kegg.glycan" + }, + "name": "KEGG Glycan", + "part_of": "kegg", + "pattern": "^G\\d+$", + "preferred_prefix": "kegg.glycan", + "publications": [ + { + "doi": "10.1093/glycob/cwj010", + "pmc": null, + "pubmed": "16014746", + "title": "KEGG as a glycome informatics resource.", + "year": 2005 + } + ], + "uri_format": "https://www.kegg.jp/entry/$1" + }, + "kegg.ligand": { + "comment": "This database has been discontinued by KEGG. It now lives inside the compound database", + "deprecated": true, + "homepage": "http://www.genome.ad.jp/kegg/docs/upd_ligand.html", + "mappings": { + "go": "KEGG_LIGAND" + }, + "name": "KEGG LIGAND", + "part_of": "kegg", + "preferred_prefix": "kegg.ligand", + "uri_format": "http://www.genome.jp/dbget-bin/www_bget?cpd:$1" + }, + "kegg.metagenome": { + "description": "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species.", + "example": "T30002", + "homepage": "http://www.genome.jp/kegg/catalog/org_list3.html", + "keywords": [ + "genome" + ], + "mappings": { + "biocontext": "KEGG.METAGENOME", + "miriam": "kegg.metagenome", + "n2t": "kegg.metagenome", + "prefixcommons": "kegg.metagenome" + }, + "name": "KEGG Metagenome", + "part_of": "kegg", + "pattern": "^T3\\d+$", + "preferred_prefix": "kegg.metagenome", + "publications": [ + { + "doi": "10.1093/nar/gkr988", + "pmc": "PMC3245020", + "pubmed": "22080510", + "title": "KEGG for integration and interpretation of large-scale molecular data sets.", + "year": 2011 + } + ], + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.module": { + "description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.", + "example": "M00002", + "homepage": "http://www.kegg.jp/kegg/module.html", + "mappings": { + "biocontext": "KEGG.MODULE", + "miriam": "kegg.module", + "n2t": "kegg.module" + }, + "name": "KEGG Module", + "part_of": "kegg", + "pattern": "^([a-z]{3,5}_)?M\\d{5}$", + "preferred_prefix": "kegg.module", + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.orthology": { + "description": "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms.", + "example": "K00001", + "homepage": "http://www.genome.jp/kegg/ko.html", + "keywords": [ + "classification", + "pathway" + ], + "mappings": { + "biocontext": "KEGG.ORTHOLOGY", + "miriam": "kegg.orthology", + "n2t": "kegg.orthology", + "prefixcommons": "kegg.orthology" + }, + "name": "KEGG Orthology", + "part_of": "kegg", + "pattern": "^K\\d+$", + "preferred_prefix": "kegg.orthology", + "uri_format": "http://www.kegg.jp/entry/$1" + }, + "kegg.pathway": { + "description": "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.", + "example": "rsk00410", + "homepage": "https://www.genome.jp/kegg/pathway.html", + "keywords": [ + "pathway" + ], + "mappings": { + "biocontext": "KEGG.PATHWAY", + "biolink": "KEGG.PATHWAY", + "edam": "2343", + "go": "KEGG_PATHWAY", + "miriam": "kegg.pathway", + "n2t": "kegg.pathway", + "prefixcommons": "kegg.pathway", + "wikidata": "P665" + }, + "name": "KEGG Pathways Database", + "part_of": "kegg", + "pattern": "^\\w{2,4}\\d{5}$", + "preferred_prefix": "kegg.pathway", + "publications": [ + { + "doi": "10.1002/0471250953.bi0112s38", + "pmc": null, + "pubmed": "22700311", + "title": "Using the KEGG database resource.", + "year": 2012 + } + ], + "synonyms": [ + "KEGG-path", + "KEGG_PATHWAY" + ], + "uri_format": "https://www.kegg.jp/entry/$1" + }, + "kegg.rclass": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns.", + "example": "RC00001", + "homepage": "http://www.genome.jp/kegg/reaction/", + "mappings": { + "biolink": "KEGG.RCLASS" + }, + "name": "KEGG Reaction Class", + "part_of": "kegg", + "pattern": "^RC\\d+$", + "preferred_prefix": "kegg.rclass", + "references": [ + "https://github.com/prefixcommons/prefixes/pull/2" + ], + "synonyms": [ + "KEGG_RCLASS", + "KEGG_REACTION_CLASS" + ] + }, + "kegg.reaction": { + "description": "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life.", + "example": "R00100", + "homepage": "https://www.genome.jp/kegg/reaction/", + "keywords": [ + "enzyme", + "pathway" + ], + "mappings": { + "biocontext": "KEGG.REACTION", + "edam": "2608", + "go": "KEGG_REACTION", + "miriam": "kegg.reaction", + "n2t": "kegg.reaction", + "prefixcommons": "kegg.reaction", + "wikidata": "P665" + }, + "name": "KEGG Reaction", + "part_of": "kegg", + "pattern": "^R\\d+$", + "preferred_prefix": "kegg.reaction", + "publications": [ + { + "doi": "10.1002/0471250953.bi0112s38", + "pmc": null, + "pubmed": "22700311", + "title": "Using the KEGG database resource.", + "year": 2012 + } + ], + "synonyms": [ + "KEGG_REACTION" + ], + "uri_format": "https://www.kegg.jp/entry/$1" + }, + "kerafast": { + "description": "Cell line collections", + "example": "EJH014", + "homepage": "https://www.kerafast.com/", + "mappings": { + "cellosaurus": "Kerafast" + }, + "name": "Kerafast cell lines", + "preferred_prefix": "kerafast", + "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" + }, + "knapsack": { + "description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.", + "example": "C00000001", + "homepage": "http://www.knapsackfamily.com/KNApSAcK/", + "mappings": { + "biocontext": "KNAPSACK", + "miriam": "knapsack", + "n2t": "knapsack", + "wikidata": "P2064" + }, + "name": "KNApSAcK", + "pattern": "^C\\d{8}$", + "preferred_prefix": "knapsack", + "uri_format": "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1" + }, + "kupo": { + "appears_in": [ + "cl" + ], + "comment": "Website is down, now it redirects to something else that is not related", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "example": "0001009", + "homepage": "http://www.kupkb.org/", + "name": "Kidney and Urinary Pathway Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "kupo", + "references": [ + "https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S7" + ] + }, + "kyinno": { + "description": "Cell line collections", + "example": "KC-0979", + "homepage": "https://www.kyinno.com/", + "mappings": { + "cellosaurus": "KYinno" + }, + "name": "KYinno cell lines", + "preferred_prefix": "kyinno", + "uri_format": "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf" + }, + "labo": { + "contact": { + "email": "paul.fabry@usherbrooke.ca", + "github": "pfabry", + "name": "Paul Fabry", + "orcid": "0000-0002-3336-2476" + }, + "depends_on": [ + "iao", + "obi", + "ogms", + "omiabis", + "omrse", + "opmi" + ], + "description": "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents.", + "download_owl": "http://purl.obolibrary.org/obo/labo.owl", + "example": "0000124", + "homepage": "https://github.com/OpenLHS/LABO", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "LABO", + "bioportal": "LABO", + "obofoundry": "labo", + "ols": "labo", + "ontobee": "LABO" + }, + "name": "clinical LABoratory Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "LABO", + "publications": [ + { + "doi": "10.5281/zenodo.6522019", + "pmc": null, + "pubmed": null, + "title": "LABO: An ontology for laboratory test prescription and reporting", + "year": 2019 + } + ], + "repository": "https://github.com/OpenLHS/LABO", + "uri_format": "http://purl.obolibrary.org/obo/LABO_$1", + "version": "2021-06-08" + }, + "langual": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases", + "example": "B2067", + "github_request_issue": 507, + "homepage": "https://www.langual.org", + "name": "Langua aLimentaria Thesaurus", + "pattern": "^B\\d+$", + "preferred_prefix": "langual", + "uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1" + }, + "lbo": { + "contact": { + "email": "caripark@iastate.edu", + "github": "caripark", + "name": "Carissa Park", + "orcid": "0000-0002-2346-5201" + }, + "description": "A vocabulary for cattle, chicken, horse, pig, and sheep breeds.", + "download_obo": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo", + "download_owl": "https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl", + "example": "0000487", + "homepage": "http://bioportal.bioontology.org/ontologies/LBO", + "keywords": [ + "animal breeding", + "animal husbandry", + "genetics", + "genomics", + "ontology" + ], + "mappings": { + "aberowl": "LBO", + "agroportal": "LBO", + "bioportal": "LBO", + "fairsharing": "FAIRsharing.309v57", + "ols": "lbo" + }, + "name": "Livestock Breed Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "lbo", + "repository": "https://github.com/AnimalGenome/livestock-breed-ontology", + "uri_format": "http://purl.obolibrary.org/obo/LBO_$1" + }, + "leafsnap": { + "description": "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide", + "example": "Amelanchier laevis", + "homepage": "http://leafsnap.com/", + "mappings": { + "wikidata": "P10538" + }, + "name": "Leafsnap", + "preferred_prefix": "leafsnap", + "uri_format": "http://leafsnap.com/species/$1/" + }, + "lei": { + "description": "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland.", + "example": "HWUPKR0MPOU8FGXBT394", + "homepage": "https://www.gleif.org/", + "mappings": { + "miriam": "lei", + "n2t": "lei" + }, + "name": "Global LEI Index", + "pattern": "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$", + "preferred_prefix": "lei", + "uri_format": "https://www.gleif.org/lei/$1" + }, + "lepao": { + "contact": { + "email": "lagonzalezmo@unal.edu.co", + "github": "luis-gonzalez-m", + "name": "Luis A. Gonzalez-Montana", + "orcid": "0000-0002-9136-9932" + }, + "depends_on": [ + "aism", + "bfo", + "bspo", + "caro", + "pato", + "ro", + "uberon" + ], + "description": "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research.", + "download_obo": "http://purl.obolibrary.org/obo/lepao.obo", + "download_owl": "http://purl.obolibrary.org/obo/lepao.owl", + "example": "0000005", + "homepage": "https://github.com/insect-morphology/lepao", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "LEPAO", + "bioportal": "LEPAO", + "obofoundry": "lepao", + "ols": "lepao", + "ontobee": "LEPAO" + }, + "name": "Lepidoptera Anatomy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "LEPAO", + "repository": "https://github.com/insect-morphology/lepao", + "uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", + "version": "2021-11-20" + }, + "lgai.cede": { + "description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).", + "example": "LGCEDe-S-000002244", + "homepage": "https://www.lgresearch.ai", + "mappings": { + "miriam": "lgai.cede" + }, + "name": "LG Chemical Entity Detection Dataset (LGCEDe)", + "pattern": "^LGCEDe-S-\\d{9}$", + "preferred_prefix": "lgai.cede", + "uri_format": "https://s3.us-east-2.amazonaws.com/lg.cede/$1" + }, + "lgic": { + "comment": "Website is gone", + "deprecated": true, + "description": "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available.", + "example": "5HT3Arano", + "homepage": "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php", + "keywords": [ + "gene", + "protein", + "sequence" + ], + "mappings": { + "biocontext": "LGIC", + "miriam": "lgic", + "n2t": "lgic", + "prefixcommons": "lgicdb" + }, + "name": "Ligand-Gated Ion Channel database", + "pattern": "^\\w+$", + "preferred_prefix": "lgic", + "publications": [ + { + "doi": "10.1093/nar/27.1.340", + "pmc": "PMC148177", + "pubmed": "9847222", + "title": "The Ligand Gated Ion Channel Database.", + "year": 1999 + } + ], + "uri_format": "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php" + }, + "licebase": { + "contact": { + "email": "Inge.Jonassen@uib.no", + "github": null, + "name": "Inge Jonassen", + "orcid": "0000-0003-4110-0748" + }, + "description": "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects.", + "example": "EMLSAT00000003403", + "homepage": "https://licebase.org", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "LICEBASE", + "fairsharing": "FAIRsharing.c7w81a", + "miriam": "licebase", + "n2t": "licebase", + "re3data": "r3d100013547" + }, + "name": "LiceBase", + "pattern": "^[A-Za-z0-9\\-\\/]+$", + "preferred_prefix": "licebase", + "uri_format": "https://licebase.org/?q=$1" + }, + "ligandbook": { + "description": "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community.", + "example": "785", + "homepage": "https://ligandbook.org/", + "mappings": { + "miriam": "ligandbook", + "n2t": "ligandbook" + }, + "name": "LigandBook", + "pattern": "^[0-9]+$", + "preferred_prefix": "ligandbook", + "uri_format": "https://ligandbook.org/package/$1" + }, + "ligandbox": { + "description": "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.", + "example": "D00001", + "homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en", + "mappings": { + "biocontext": "LIGANDBOX", + "miriam": "ligandbox", + "n2t": "ligandbox" + }, + "name": "LigandBox", + "pattern": "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$", + "preferred_prefix": "ligandbox", + "uri_format": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1" + }, + "ligandexpo": { + "contact": { + "email": "jwest@rcsb.rutgers.edu", + "github": null, + "name": "John Westbrook", + "orcid": "0000-0002-6686-5475" + }, + "description": "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids.", + "example": "ABC", + "homepage": "http://ligand-depot.rutgers.edu/index.html", + "keywords": [ + "chemical", + "interaction", + "life science", + "nucleic acid", + "protein", + "structure" + ], + "mappings": { + "biocontext": "LIGANDEXPO", + "fairsharing": "FAIRsharing.2ma4gq", + "miriam": "ligandexpo", + "n2t": "ligandexpo", + "prefixcommons": "ligandexpo" + }, + "name": "Ligand Expo", + "pattern": "^(\\w){3}$", + "preferred_prefix": "ligandexpo", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Ligand Expo at Rutgers", + "homepage": "http://ligand-expo.rcsb.org/", + "name": "Ligand Expo at Rutgers", + "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" + } + ], + "publications": [ + { + "doi": "10.1093/bioinformatics/bth214", + "pmc": null, + "pubmed": "15059838", + "title": "Ligand Depot: a data warehouse for ligands bound to macromolecules.", + "year": 2004 + } + ], + "uri_format": "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" + }, + "ligea": { + "comment": "This might just be a provider for CCLE", + "description": "Polymorphism and mutation databases", + "example": "CCLE_867", + "homepage": "http://hpc-bioinformatics.cineca.it/fusion/main", + "mappings": { + "cellosaurus": "LiGeA" + }, + "name": "Cancer cell LInes GEne fusions portAl", + "preferred_prefix": "ligea", + "uri_format": "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1" + }, + "limore": { + "description": "Cell line databases/resources", + "example": "Li7", + "homepage": "https://www.picb.ac.cn/limore/home", + "mappings": { + "cellosaurus": "LIMORE" + }, + "name": "Liver Cancer Model Repository", + "preferred_prefix": "limore", + "uri_format": "https://www.picb.ac.cn/limore/cellLines/single?para=$1" + }, + "lincs.cell": { + "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", + "example": "LCL-2085", + "homepage": "http://lincsportal.ccs.miami.edu/cells/", + "mappings": { + "biocontext": "LINCS.CELL", + "cellosaurus": "LINCS_LDP", + "miriam": "lincs.cell", + "n2t": "lincs.cell" + }, + "name": "LINCS Cell", + "pattern": "^(LCL|LDC|ES|LSC|LPC)-\\d+$", + "preferred_prefix": "lincs.cell", + "synonyms": [ + "LINCS_LDP" + ], + "uri_format": "http://lincsportal.ccs.miami.edu/cells/#/view/$1" + }, + "lincs.data": { + "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level).", + "example": "LDS-1110", + "homepage": "http://lincsportal.ccs.miami.edu/datasets/", + "mappings": { + "biocontext": "LINCS.DATA", + "miriam": "lincs.data", + "n2t": "lincs.data" + }, + "name": "LINCS Data", + "pattern": "^[EL]D[SG]-\\d+$", + "preferred_prefix": "lincs.data", + "providers": [ + { + "code": "omicsdi", + "description": "Lincs through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "Lincs through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/lincs/$1" + } + ], + "uri_format": "http://lincsportal.ccs.miami.edu/datasets/#/view/$1" + }, + "lincs.protein": { + "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", + "example": "200282", + "homepage": "http://lincs.hms.harvard.edu/db/proteins/", + "mappings": { + "biocontext": "LINCS.PROTEIN", + "miriam": "lincs.protein", + "n2t": "lincs.protein" + }, + "name": "LINCS Protein", + "pattern": "^\\d+$", + "preferred_prefix": "lincs.protein", + "uri_format": "https://lincs.hms.harvard.edu/db/proteins/$1" + }, + "lincs.smallmolecule": { + "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", + "example": "LSM-6306", + "homepage": "http://lincsportal.ccs.miami.edu/SmallMolecules/", + "mappings": { + "biocontext": "LINCS.SMALLMOLECULE", + "miriam": "lincs.smallmolecule", + "n2t": "lincs.smallmolecule" + }, + "name": "LINCS Small Molecule", + "pattern": "^LSM-\\d+$", + "preferred_prefix": "lincs.smallmolecule", + "synonyms": [ + "lincs" + ], + "uri_format": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1" + }, + "linguist": { + "description": "Registry of programming languages for the Linguist program for detecting and highlighting programming languages.", + "example": "Python", + "homepage": "https://github.com/github/linguist", + "mappings": { + "miriam": "linguist" + }, + "name": "Linguist", + "pattern": "^[a-zA-Z0-9 +#'*]+$", + "preferred_prefix": "linguist", + "repository": "https://github.com/github/linguist", + "uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1" + }, + "linkml": { + "comment": "Closes #508", + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.", + "example": "SchemaDefinition", + "github_request_issue": 512, + "homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/", + "keywords": [ + "data integration", + "ontology and terminology" + ], + "mappings": { + "biolink": "linkml", + "fairsharing": "FAIRsharing.cb7086" + }, + "name": "LinkML", + "preferred_prefix": "linkml", + "publications": [ + { + "doi": "10.5281/zenodo.5598314", + "pmc": null, + "pubmed": null, + "title": "linkml/linkml-model: v1.5.0rc2", + "year": 2023 + } + ], + "repository": "https://github.com/linkml/", + "twitter": "linkml_data", + "uri_format": "https://w3id.org/linkml/$1" + }, + "lipidbank": { + "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", + "example": "BBA0001", + "homepage": "http://lipidbank.jp/index.html", + "keywords": [ + "life science", + "lipid", + "molecule", + "structure" + ], + "mappings": { + "biocontext": "LIPIDBANK", + "edam": "2665", + "fairsharing": "FAIRsharing.bdn9br", + "miriam": "lipidbank", + "n2t": "lipidbank", + "prefixcommons": "lipidbank" + }, + "name": "LipidBank", + "pattern": "^\\w+\\d+$", + "preferred_prefix": "lipidbank", + "publications": [ + { + "doi": null, + "pmc": null, + "pubmed": "12058481", + "title": "[LIPIDBANK for Web, the newly developed lipid database].", + "year": 2002 + } + ], + "uri_format": "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1" + }, + "lipidmaps": { + "description": "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy.", + "example": "LMPR0102010012", + "homepage": "http://www.lipidmaps.org", + "keywords": [ + "biomedical science", + "endocrinology", + "life science", + "lipid", + "structure", + "systems biology", + "taxonomy" + ], + "mappings": { + "biocontext": "LIPIDMAPS", + "cheminf": "000564", + "edam": "2625", + "fairsharing": "FAIRsharing.cpneh8", + "miriam": "lipidmaps", + "n2t": "lipidmaps", + "prefixcommons": "lipidmaps", + "re3data": "r3d100012315", + "wikidata": "P2063" + }, + "name": "LIPID MAPS", + "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", + "preferred_prefix": "lipidmaps", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/lipidmaps/$1" + } + ], + "publications": [ + { + "doi": "10.1194/jlr.r800095-jlr200", + "pmc": "PMC2674711", + "pubmed": "19098281", + "title": "Update of the LIPID MAPS comprehensive classification system for lipids.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkm324", + "pmc": "PMC1933166", + "pubmed": "17584797", + "title": "LIPID MAPS online tools for lipid research.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkl838", + "pmc": "PMC1669719", + "pubmed": "17098933", + "title": "LMSD: LIPID MAPS structure database.", + "year": 2006 + }, + { + "doi": "10.1194/jlr.e400004-jlr200", + "pmc": null, + "pubmed": "15722563", + "title": "A comprehensive classification system for lipids.", + "year": 2005 + } + ], + "synonyms": [ + "LIPID MAPS", + "LIPID_MAPS_class", + "LIPID_MAPS_instance" + ], + "twitter": "lipidmaps", + "uri_format": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1" + }, + "lipro": { + "contact": { + "email": "bakerc@unb.ca", + "github": null, + "name": "Christopher Baker", + "orcid": "0000-0003-4004-6479" + }, + "deprecated": true, + "description": "An ontology representation of the LIPIDMAPS nomenclature classification.", + "download_owl": "http://aber-owl.net/media/ontologies/LIPRO/4/lipro.owl", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "aberowl": "LIPRO", + "biocontext": "LIPRO", + "bioportal": "LIPRO", + "obofoundry": "lipro" + }, + "name": "Lipid Ontology", + "preferred_prefix": "LIPRO", + "uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1" + }, + "lncipedia": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A comprehensive compendium of human long non-coding RNAs", + "example": "SNHG3", + "homepage": "https://lncipedia.org", + "keywords": [ + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.84c1a7" + }, + "name": "LNCipedia", + "preferred_prefix": "lncipedia", + "publications": [ + { + "doi": "10.1093/nar/gkv295", + "pmc": "PMC4417186", + "pubmed": "25829178", + "title": "An update on LNCipedia: a database for annotated human lncRNA sequences.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gku1060", + "pmc": "PMC4383901", + "pubmed": "25378313", + "title": "An update on LNCipedia: a database for annotated human lncRNA sequences.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks915", + "pmc": "PMC3531107", + "pubmed": "23042674", + "title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures.", + "year": 2012 + } + ] + }, + "loggerhead": { + "contact": { + "email": "peteremidford@yahoo.com", + "github": null, + "name": "Peter Midford", + "orcid": "0000-0001-6512-3296" + }, + "deprecated": true, + "homepage": 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The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.", + "example": "ThoracicArtery", + "homepage": "http://www.molecularconnections.com", + "keywords": [ + "ontology" + ], + "mappings": { + "bioportal": "MCCL" + }, + "name": "Cell Line Ontology [derivative]", + "preferred_prefix": "mcc", + "uri_format": "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1" + }, + "mco": { + "contact": { + "email": "citlalli.mejiaalmonte@gmail.com", + "github": "citmejia", + "name": "Citlalli Mejía-Almonte", + "orcid": "0000-0002-0142-5591" + }, + "depends_on": [ + "bfo", + "chebi", + "cl", + "clo", + "micro", + "ncbitaxon", + "ncit", + "obi", + "omit", + "omp", + "pato", + "peco", + "uberon", + "zeco" + ], + "description": "Microbial Conditions Ontology is an ontology...", + "download_obo": "http://purl.obolibrary.org/obo/mco.obo", + "download_owl": "http://purl.obolibrary.org/obo/mco.owl", + "example": "0000858", + "homepage": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MCO", + "bioportal": "MCO", + "obofoundry": "mco", + "ols": "mco", + "ontobee": "MCO" + }, + "name": "Microbial Conditions Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "MCO", + "repository": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", + "uri_format": "http://purl.obolibrary.org/obo/MCO_$1", + "version": "2019-05-15" + }, + "mdm": { + "contact": { + "email": "bernd.mueller@zbmed.de", + "github": null, + "name": "Bernd Müller", + "orcid": "0000-0003-3062-8192" + }, + "description": "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. 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The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems.", + "download_owl": "http://aber-owl.net/media/ontologies/MDM/4/mdm.owl", + "example": "4776", + "homepage": "https://medical-data-models.org/", + "keywords": [ + "biomedical science", + "medicine", + "ontology", + "translational medicine" + ], + "mappings": { + "aberowl": "MDM", + "biocontext": "MDM", + "bioportal": "MDM", + "fairsharing": "FAIRsharing.wnk2eq", + "miriam": "mdm", + "n2t": "mdm", + "re3data": "r3d100013816" + }, + "name": "Medical Data Models", + "pattern": "^\\d+$", + "preferred_prefix": "mdm", + "publications": [ + { + "doi": "10.1093/database/bav121", + "pmc": "PMC4750548", + "pubmed": "26868052", + "title": "Portal of medical data models: information infrastructure for medical research and healthcare.", + "year": 2016 + } + ], + "uri_format": "https://medical-data-models.org/forms/$1" + }, + "meddra": { + "contact": { + "email": "mssohelp@meddra.org", + "github": null, + "name": "MedDRA MSSO", + "orcid": null + }, + "description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. 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The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).", + "example": "10015919", + "homepage": "http://bioportal.bioontology.org/ontologies/MEDDRA", + "keywords": [ + "biomedical science", + "medicine", + "ontology", + "preclinical studies" + ], + "mappings": { + "aberowl": "MEDDRA", + "bartoc": "1237", + "biocontext": "MEDDRA", + "bioportal": "MEDDRA", + "fairsharing": "FAIRsharing.ad3137", + "hl7": "2.16.840.1.113883.6.163", + "miriam": "meddra", + "n2t": "meddra", + "wikidata": "P3201" + }, + "name": "Medical Dictionary for Regulatory Activities Terminology", + "pattern": "^\\d+$", + "preferred_prefix": "meddra", + "publications": [ + { + "doi": "10.1016/s1386-5056(00)00062-9", + "pmc": null, + "pubmed": "10961570", + "title": "The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM).", + "year": 2000 + }, + { + "doi": "10.2165/00002018-199920020-00002", + "pmc": null, + "pubmed": "10082069", + "title": "The medical dictionary for regulatory activities (MedDRA).", + "year": 1999 + } + ], + "synonyms": [ + "MEDRA", + "MeDRA", + "MedDRA", + "Medical Dictionary for Regulatory Activities" + ], + "uri_format": "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1" + }, + "medgen": { + "description": "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder.", + "example": "760050", + "homepage": "https://www.ncbi.nlm.nih.gov/medgen/", + "mappings": { + "biocontext": "MedGen", + "biolink": "medgen", + "miriam": "medgen", + "n2t": "medgen", + "ncbi": "MedGen" + }, + "name": "Human Medical Genetics", + "pattern": "^[CN]*\\d{4,7}$", + "preferred_prefix": "medgen", + "uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1" + }, + "medlineplus": { + "contact": { + "email": "custserv@nlm.nih.gov", + "github": null, + "name": "NLM Customer Service", + "orcid": null + }, + "description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. 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These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families.", + "example": "S1", + "homepage": "http://merops.sanger.ac.uk/index.htm", + "mappings": { + "biocontext": "MEROPS.FAMILY", + "miriam": "merops.family", + "n2t": "merops.family" + }, + "name": "MEROPS Family", + "part_of": "merops", + "pattern": "^[SCTAGMNU]\\d+$", + "preferred_prefix": "merops.family", + "publications": [ + { + "doi": "10.1093/nar/gkx1134", + "pmc": "PMC5753285", + "pubmed": "29145643", + "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.", + "year": 2018 + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/439" + ], + "uri_format": "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1" + }, + "mesh": { + "contact": { + "email": "custserv@nlm.nih.gov", + "github": null, + "name": "NLM Customer Service", + "orcid": null + }, + "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.", + "example": "C063233", + "example_extras": [ + "D000001" + ], + "homepage": "http://id.nlm.nih.gov/mesh/", + "keywords": [ + "bioinformatics", + "biomedical science", + "classification", + "life science", + "metascience", + "ontology", + "topics" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "MESH", + "bartoc": "391", + "biocontext": "MESH", + "biolink": "MESH", + "bioportal": "MESH", + "cellosaurus": "MeSH", + "edam": "1177", + "fairsharing": "FAIRsharing.qnkw45", + "go": "MeSH", + "hl7": "2.16.840.1.113883.6.177", + "miriam": "mesh", + "n2t": "mesh", + "prefixcommons": "mesh", + "wikidata": "P486" + }, + "name": "Medical Subject Headings", + "pattern": "^(C|D)\\d{6,9}$", + "preferred_prefix": "mesh", + "publications": [ + { + "doi": null, + "pmc": "PMC197951", + "pubmed": "13982385", + "title": "Medical subject headings.", + "year": 1963 + } + ], + "synonyms": [ + "MESH", + "MESHA", + "MESHC", + "MESHCS", + "MESHD", + "MESHPP", + "MESH_DESCRIPTOR_UI", + "MESH_SUPPLEMENTAL_RECORD_UI", + "MSH", + "MSH2010_2010_02_22" + ], + "uri_format": "https://meshb.nlm.nih.gov/record/ui?ui=$1" + }, + "mesh.2012": { + "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. 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This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.", + "example": "17165", + "homepage": "http://www.nlm.nih.gov/mesh/", + "mappings": { + "biocontext": "MESH.2013", + "miriam": "mesh.2013", + "n2t": "mesh.2013" + }, + "name": "MeSH 2013", + "pattern": "^[A-Za-z0-9]+$", + "preferred_prefix": "mesh.2013", + "provides": "mesh", + "uri_format": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded" + }, + "mesh.vocab": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump", + "example": "term", + "homepage": "https://hhs.github.io/meshrdf/", + "name": "Medical Subject Headings Vocabulary", + "part_of": "mesh", + "preferred_prefix": "mesh.vocab", + "references": [ + "https://id.nlm.nih.gov/mesh/query" + ], + "repository": "https://github.com/HHS/meshrdf", + "uri_format": "http://id.nlm.nih.gov/mesh/vocab#$1" + }, + "metabolights": { + "description": "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies.", + "example": "MTBLS1", + "homepage": "https://www.ebi.ac.uk/metabolights/", + "mappings": { + "biocontext": "METABOLIGHTS", + "cellosaurus": "MetaboLights", + "miriam": "metabolights", + "n2t": "metabolights", + "re3data": "r3d100011556", + "wikidata": "P3890" + }, + "name": "MetaboLights Compound", + "pattern": "^MTBLS\\d+$", + "preferred_prefix": "metabolights", + "providers": [ + { + "code": "omicsdi", + "description": "MataboLights through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "MataboLights through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/metabolights_dataset/$1" + } + ], + "uri_format": "https://www.ebi.ac.uk/metabolights/$1" + }, + "metacyc.compound": { + "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", + "example": "CPD-10330", + "homepage": "https://metacyc.org", + "keywords": [ + "life science", + "metabolomics", + "systems biology" + ], + "mappings": { + "biocontext": "METACYC.COMPOUND", + "biolink": "MetaCyc", + "fairsharing": "FAIRsharing.yytevr", + "go": "MetaCyc", + "miriam": "metacyc.compound", + "n2t": "metacyc.compound", + "re3data": "r3d100011294" + }, + "name": "Metabolic Encyclopedia of metabolic and other pathways", + "pattern": "^[A-Za-z0-9+_.%-:]+$", + "preferred_prefix": "metacyc.compound", + "publications": [ + { + "doi": "10.1093/nar/gkv1164", + "pmc": "PMC4702838", + "pubmed": "26527732", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkt1103", + "pmc": "PMC3964957", + "pubmed": "24225315", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkr1014", + "pmc": "PMC3245006", + "pubmed": "22102576", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.", + "year": 2011 + } + ], + "synonyms": [ + "MetaCyc" + ], + "twitter": "BioCyc", + "uri_format": "https://metacyc.org/compound?orgid=META&id=$1" + }, + "metacyc.reaction": { + "description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.", + "example": "RXN-14904", + "homepage": "https://metacyc.org", + "mappings": { + "biocontext": "METACYC.REACTION", + "biolink": "metacyc.reaction", + "miriam": "metacyc.reaction", + "n2t": "metacyc.reaction" + }, + "name": "MetaCyc Reaction", + "pattern": "^[A-Za-z0-9+_.%-:]+$", + "preferred_prefix": "metacyc.reaction", + "uri_format": "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1" + }, + "metanetx.chemical": { + "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.", + "example": "MNXM1723", + "homepage": "https://www.metanetx.org/", + "mappings": { + "biocontext": "METANETX.CHEMICAL", + "miriam": "metanetx.chemical", + "n2t": "metanetx.chemical" + }, + "name": "MetaNetX chemical", + "pattern": "^(MNXM\\d+|BIOMASS|WATER)$", + "preferred_prefix": "metanetx.chemical", + "uri_format": "https://www.metanetx.org/chem_info/$1" + }, + "metanetx.compartment": { + "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments.", + "example": "MNXC15", + "homepage": "https://www.metanetx.org/", + "mappings": { + "biocontext": "METANETX.COMPARTMENT", + "miriam": "metanetx.compartment", + "n2t": "metanetx.compartment" + }, + "name": "MetaNetX compartment", + "pattern": "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$", + "preferred_prefix": "metanetx.compartment", + "uri_format": "https://www.metanetx.org/comp_info/$1" + }, + "metanetx.reaction": { + "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions.", + "example": "MNXR101574", + "homepage": "https://www.metanetx.org/", + "mappings": { + "biocontext": "METANETX.REACTION", + "biolink": "METANETX.REACTION", + "miriam": "metanetx.reaction", + "n2t": "metanetx.reaction" + }, + "name": "MetaNetX reaction", + "pattern": "^(MNXR\\d+|EMPTY)$", + "preferred_prefix": "metanetx.reaction", + "uri_format": "https://www.metanetx.org/equa_info/$1" + }, + "metatlas": { + "contact": { + "email": "mihail.anton@chalmers.se", + "github": "mihai-sysbio", + "name": "Mihail Anton", + "orcid": "0000-0002-7753-9042" + }, + "contributor": { + "email": "mihail.anton@chalmers.se", + "github": "mihai-sysbio", + "name": "Mihail Anton", + "orcid": "0000-0002-7753-9042" + }, + "description": "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.", + "example": "MAM01234c", + "example_decoys": [ + "MAR11851c" + ], + "example_extras": [ + "MAR11851" + ], + "github_request_issue": 495, + "homepage": "https://metabolicatlas.org", + "keywords": [ + "chemistry", + "metabolites", + "reactions" + ], + "mappings": { + "miriam": "metatlas" + }, + "name": "Metabolic Atlas", + "pattern": "^(MAM\\d{5}\\w)|(MAR\\d{5})$", + "preferred_prefix": "metatlas", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" + }, + "metatlas.metabolite": { + "contact": { + "email": "mihail.anton@chalmers.se", + "github": "mihai-sysbio", + "name": "Mihail Anton", + "orcid": "0000-0002-7753-9042" + }, + "contributor": { + "email": "mihail.anton@chalmers.se", + "github": "mihai-sysbio", + "name": "Mihail Anton", + "orcid": "0000-0002-7753-9042" + }, + "description": "A subspace of Metabolic Atlas for compartment-specific records for metabolites.", + "example": "MAM01234c", + "github_request_issue": 495, + "homepage": "https://metabolicatlas.org", + "keywords": [ + "chemistry", + "metabolites" + ], + "name": "Metabolic Atlas Metabolite", + "part_of": "metatlas", + "pattern": "^MAM\\d{5}\\w$", + "preferred_prefix": "metatlas.metabolite", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" + }, + "metatlas.reaction": { + "contact": { + "email": "mihail.anton@chalmers.se", + "github": "mihai-sysbio", + "name": "Mihail Anton", + "orcid": "0000-0002-7753-9042" + }, + "contributor": { + "email": "mihail.anton@chalmers.se", + "github": "mihai-sysbio", + "name": "Mihail Anton", + "orcid": "0000-0002-7753-9042" + }, + "description": "A subspace of Metabolic Atlas for reactions.", + "example": "MAR11851", + "github_request_issue": 495, + "homepage": "https://metabolicatlas.org", + "keywords": [ + "chemistry", + "reactions" + ], + "name": "Metabolic Atlas Reaction", + "part_of": "metatlas", + "pattern": "^MAR\\d{5}$", + "preferred_prefix": "metatlas.reaction", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://metabolicatlas.org/identifier/MetabolicAtlas/$1" + }, + "metlin": { + "description": "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry.", + "example": "1455", + "homepage": "http://masspec.scripps.edu/", + "mappings": { + "biocontext": "METLIN", + "miriam": "metlin", + "n2t": "metlin", + "re3data": "r3d100012311" + }, + "name": "Metabolite and Tandem Mass Spectrometry Database", + "pattern": "^\\d{4}$", + "preferred_prefix": "metlin", + "uri_format": "http://metlin.scripps.edu/metabo_info.php?molid=$1" + }, + "metnetdb": { + "description": "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another.", + "example": "377369", + "homepage": "http://www.metnetdb.org/MetNet_db.htm", + "keywords": [ + "dna", + "interaction", + "pathway", + "protein", + "regulation", + "rna", + "small molecule" + ], + "mappings": { + "prefixcommons": "metnetdb" + }, + "name": "Metabolic Network Exchange Database", + "preferred_prefix": "metnetdb", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://metnetonline.org/browse_pathway2.php?pthID=$1" + }, + "mex": { + "description": "A public place to process, interpret and share GC/MS metabolomics datasets.", + "example": "36", + "homepage": "https://www.metabolome-express.org/", + "mappings": { + "biocontext": "MEX", + "miriam": "mex", + "n2t": "mex" + }, + "name": "Metabolome Express", + "pattern": "^\\d+$", + "preferred_prefix": "mex", + "providers": [ + { + "code": "omicsdi", + "description": "Metabolome Express through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "Metabolome Express through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/metabolome_express/MEX$1" + } + ], + "uri_format": "https://www.metabolome-express.org/datasetview.php?datasetid=$1" + }, + "mf": { + "contact": { + "email": "janna.hastings@gmail.com", + "github": "jannahastings", + "name": "Janna Hastings", + "orcid": "0000-0002-3469-4923" + }, + "description": "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning.", + "download_owl": "http://purl.obolibrary.org/obo/mf.owl", + "example": "0000091", + "homepage": "https://github.com/jannahastings/mental-functioning-ontology", + "keywords": [ + "biomedical science", + "cognitive neuroscience", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MF", + "biocontext": "MF", + "bioportal": "MF", + "fairsharing": "FAIRsharing.4gm9gt", + "obofoundry": "mf", + "ols": "mf", + "ontobee": "MF" + }, + "name": "Mental Functioning Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MF", + "repository": "https://github.com/jannahastings/mental-functioning-ontology", + "uri_format": "http://purl.obolibrary.org/obo/MF_$1", + "version": "2021-11-17" + }, + "mfmo": { + "contact": { + "email": "druzinsk@uic.edu", + "github": "RDruzinsky", + "name": "Robert Druzinsky", + "orcid": "0000-0002-1572-1316" + }, + "depends_on": [ + "uberon" + ], + "description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.", + "download_owl": "http://purl.obolibrary.org/obo/mfmo.owl", + "example": "0000208", + "homepage": "https://github.com/rdruzinsky/feedontology", + "keywords": [ + "anatomy", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MFMO", + "biocontext": "MFMO", + "bioportal": "MFMO", + "fairsharing": "FAIRsharing.669cnk", + "obofoundry": "mfmo", + "ols": "mfmo", + "ontobee": "MFMO" + }, + "name": "Mammalian Feeding Muscle Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MFMO", + "providers": [ + { + "code": "conflated", + "description": "A conflated URL with parts.", + "homepage": "http://purl.obolibrary.org", + "name": "OBO PURL Parts", + "uri_format": "http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1" + } + ], + "repository": "https://github.com/RDruzinsky/feedontology", + "uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", + "version": "2013-11-16" + }, + "mfo": { + "contact": { + "email": "Thorsten.Henrich@embl-heidelberg.de", + "github": null, + "name": "Thorsten Henrich", + "orcid": null + }, + "deprecated": true, + "description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.", + "download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo", + "download_owl": "http://purl.obolibrary.org/obo/mfo.owl", + "example": "MFO_0000001", + "homepage": "http://ani.embl.de:8080/mepd/", + "keywords": [ + "anatomy", + "development", + "fish", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "MFO", + "biocontext": "MFO", + "bioportal": "MFO", + "obofoundry": "mfo", + "prefixcommons": "mfo" + }, + "name": "Medaka fish anatomy and development", + "preferred_prefix": "MFO", + "uri_format": "http://purl.obolibrary.org/obo/MFO_$1" + }, + "mfoem": { + "contact": { + "email": "janna.hastings@gmail.com", + "github": "jannahastings", + "name": "Janna Hastings", + "orcid": "0000-0002-3469-4923" + }, + "description": "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings.", + "download_owl": "http://purl.obolibrary.org/obo/mfoem.owl", + "example": "000204", + "homepage": "https://github.com/jannahastings/emotion-ontology", + "keywords": [ + "biomedical science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MFOEM", + "biocontext": "MFOEM", + "bioportal": "MFOEM", + "fairsharing": "FAIRsharing.dx30m8", + "obofoundry": "mfoem", + "ols": "mfoem", + "ontobee": "MFOEM" + }, + "name": "Emotion Ontology", + "pattern": "^\\d{6}$", + "preferred_prefix": "MFOEM", + "publications": [ + { + "doi": "10.1186/2041-1480-5-38", + "pmc": "PMC4417517", + "pubmed": "25937879", + "title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.", + "year": 2014 + } + ], + "repository": "https://github.com/jannahastings/emotion-ontology", + "uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", + "version": "2021-11-17" + }, + "mfomd": { + "contact": { + "email": "janna.hastings@gmail.com", + "github": "jannahastings", + "name": "Janna Hastings", + "orcid": "0000-0002-3469-4923" + }, + "description": "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF).", + "download_owl": "http://purl.obolibrary.org/obo/mfomd.owl", + "example": "0000046", + "homepage": "https://github.com/jannahastings/mental-functioning-ontology", + "keywords": [ + "obo", + "ontology", + "psychiatry" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MFOMD", + "biocontext": "MFOMD", + "bioportal": "MFOMD", + "fairsharing": "FAIRsharing.q053vb", + "obofoundry": "mfomd", + "ols": "mfomd", + "ontobee": "MFOMD" + }, + "name": "Mental Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MFOMD", + "repository": "https://github.com/jannahastings/mental-functioning-ontology", + "uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", + "version": "2020-04-26" + }, + "mge": { + "banana": "mge", + "deprecated": true, + "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", + "example": "2", + "homepage": "http://aclame.ulb.ac.be/", + "keywords": [ + "gene", + "genome", + "life science" + ], + "mappings": { + "biocontext": "ACLAME", + "edam": "2631", + "fairsharing": "FAIRsharing.5tfcy8", + "miriam": "mge", + "n2t": "mge", + "prefixcommons": "aclame" + }, + "name": "Aclame", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "mge", + "publications": [ + { + "doi": "10.1093/nar/gkp938", + "pmc": "PMC2808911", + "pubmed": "19933762", + "title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkh084", + "pmc": "PMC308818", + "pubmed": "14681355", + "title": "ACLAME: a CLAssification of Mobile genetic Elements.", + "year": 2004 + } + ], + "synonyms": [ + "aclame" + ], + "uri_format": "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1" + }, + "mgi": { + "banana": "MGI", + "description": "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data.", + "example": "6017782", + "homepage": "http://www.informatics.jax.org/", + "keywords": [ + "expression", + "life science", + "ontology and terminology", + "phenotype", + "sequence" + ], + "mappings": { + "biocontext": "MGI", + "cellosaurus": "MGI", + "edam": "3274", + "fairsharing": "FAIRsharing.fcwyhz", + "go": "MGI", + "miriam": "mgi", + "n2t": "mgi", + "ncbi": "MGI", + "prefixcommons": "mgi", + "re3data": "r3d100010266", + "uniprot": "DB-0060", + "wikidata": "P671" + }, + "name": "Mouse Genome Informatics", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "MGI", + "providers": [ + { + "code": "agr", + "description": "MGI through the Alliance of Genome Resources", + "homepage": "https://www.alliancegenome.org", + "name": "MGI through the Alliance of Genome Resources", + "uri_format": "https://www.alliancegenome.org/gene/MGI:$1" + }, + { + "code": "mgi.marker", + "description": "MGI Marker", + "homepage": "http://www.informatics.jax.org/marker", + "name": "MGI Marker", + "uri_format": "http://www.informatics.jax.org/marker/MGI:$1" + } + ], + "publications": [ + { + "doi": "10.1126/science.8091224", + "pmc": null, + "pubmed": "8091224", + "title": "A database for mouse development.", + "year": 1994 + }, + { + "doi": "10.1093/nar/gky1056", + "pmc": "PMC6323923", + "pubmed": "30407599", + "title": "Mouse Genome Database (MGD) 2019.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gky922", + "pmc": "PMC6324054", + "pubmed": "30335138", + "title": "The mouse Gene Expression Database (GXD): 2019 update.", + "year": 2019 + }, + { + "doi": "10.1093/ilar/ilx013", + "pmc": "PMC5886341", + "pubmed": "28838066", + "title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.", + "year": 2017 + }, + { + "doi": "10.1007/978-1-4939-6427-7_3", + "pmc": null, + "pubmed": "27933520", + "title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.", + "year": 2017 + }, + { + "doi": "10.1093/nar/gkw1040", + "pmc": "PMC5210536", + "pubmed": "27899570", + "title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkt1225", + "pmc": "PMC3964950", + "pubmed": "24285300", + "title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gks1115", + "pmc": "PMC3531104", + "pubmed": "23175610", + "title": "The mouse genome database: genotypes, phenotypes, and models of human disease.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkr974", + "pmc": "PMC3245042", + "pubmed": "22075990", + "title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gki113", + "pmc": "PMC540067", + "pubmed": "15608240", + "title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.", + "year": 2005 + } + ], + "synonyms": [ + "MGD", + "MGI" + ], + "twitter": "mgi_mouse", + "uri_format": "http://www.informatics.jax.org/accession/MGI:$1" + }, + "mgnify.analysis": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Analyses of microbiome data within MGnify", + "example": "MGYA00002270", + "homepage": "https://www.ebi.ac.uk/metagenomics/", + "name": "MGnify Analysis", + "pattern": "^MGYA\\d+$", + "preferred_prefix": "mgnify.analysis", + "uri_format": "https://www.ebi.ac.uk/metagenomics/analyses/$1" + }, + "mgnify.proj": { + "description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", + "example": "ERP004492", + "homepage": "https://www.ebi.ac.uk/metagenomics", + "mappings": { + "miriam": "mgnify.proj", + "n2t": "mgnify.proj" + }, + "name": "MGnify Project", + "pattern": "^[A-Z]+[0-9]+$", + "preferred_prefix": "mgnify.proj", + "uri_format": "https://www.ebi.ac.uk/metagenomics/projects/$1" + }, + "mgnify.samp": { + "description": "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.", + "example": "SRS086444", + "homepage": "https://www.ebi.ac.uk/metagenomics", + "mappings": { + "miriam": "mgnify.samp", + "n2t": "mgnify.samp" + }, + "name": "MGnify Sample", + "pattern": "^[A-Z]+[0-9]+$", + "preferred_prefix": "mgnify.samp", + "uri_format": "https://www.ebi.ac.uk/metagenomics/samples/$1" + }, + "mi": { + "banana": "MI", + "contact": { + "email": "pporras@ebi.ac.uk", + "github": "pporrasebi", + "name": "Pablo Porras Millán", + "orcid": "0000-0002-8429-8793" + }, + "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", + "download_obo": "http://purl.obolibrary.org/obo/mi.obo", + "download_owl": "http://purl.obolibrary.org/obo/mi.owl", + "example": "0058", + "homepage": "https://github.com/HUPO-PSI/psi-mi-CV", + "keywords": [ + "interaction", + "life science", + "molecule", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "MI", + "biocontext": "PSIMI", + "biolink": "MI", + "bioportal": "MI", + "fairsharing": "FAIRsharing.8qzmtr", + "go": "PSI-MI", + "miriam": "mi", + "n2t": "psimi", + "obofoundry": "mi", + "ols": "mi", + "ontobee": "MI", + "prefixcommons": "psi.mi" + }, + "name": "Molecular Interactions Controlled Vocabulary", + "namespace_in_lui": true, + "pattern": "^\\d{4}$", + "preferred_prefix": "MI", + "publications": [ + { + "doi": "10.1038/nbt926", + "pmc": null, + "pubmed": "14755292", + "title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.", + "year": 2004 + } + ], + "repository": "https://github.com/HUPO-PSI/psi-mi-CV", + "synonyms": [ + "PSI-MI" + ], + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1" + }, + "miaa": { + "comment": "same as MAT", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "name": "Minimal Information About Anatomy ontology", + "preferred_prefix": "miaa", + "references": [ + "https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/rols/inst/doc/rols.pdf" + ] + }, + "miapa": { + "contact": { + "email": "hilmar.lapp@duke.edu", + "github": "hlapp", + "name": "Hilmar Lapp", + "orcid": "0000-0001-9107-0714" + }, + "description": "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.", + "download_owl": "http://purl.obolibrary.org/obo/miapa.owl", + "example": "0000010", + "homepage": "http://www.evoio.org/wiki/MIAPA", + "keywords": [ + "life science", + "obo", + "ontology", + "phylogenetics", + "phylogeny" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "MIAPA", + "biocontext": "MIAPA", + "bioportal": "MIAPA", + "fairsharing": "FAIRsharing.ca48xs", + "obofoundry": "miapa", + "ols": "miapa", + "ontobee": "MIAPA" + }, + "name": "Minimum Anformation About a Phylogenetic Analysis Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MIAPA", + "publications": [ + { + "doi": "10.1089/omi.2006.10.231", + "pmc": "PMC3167193", + "pubmed": "16901231", + "title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).", + "year": 2006 + } + ], + "repository": "https://github.com/evoinfo/miapa", + "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1", + "version": "2017-05-09" + }, + "micro": { + "appears_in": [ + "mco" + ], + "contact": { + "email": "carrine.blank@umontana.edu", + "github": "carrineblank", + "name": "Carrine Blank", + "orcid": "0000-0002-2100-6351" + }, + "description": "An ontology of prokaryotic phenotypic and metabolic characters", + "download_owl": "http://purl.obolibrary.org/obo/micro.owl", + "example": "0002999", + "homepage": "https://github.com/carrineblank/MicrO", + "keywords": [ + "bioinformatics", + "microbiology", + "obo", + "ontology" + ], + "license": "CC BY 2.0", + "mappings": { + "aberowl": "MICRO", + "biocontext": "MICRO", + "fairsharing": "FAIRsharing.brhpb0", + "obofoundry": "micro", + "ols": "micro", + "ontobee": "MICRO" + }, + "name": "Ontology of Prokaryotic Phenotypic and Metabolic Characters", + "pattern": "^\\d{7}$", + "preferred_prefix": "MICRO", + "publications": [ + { + "doi": "10.1186/s13326-016-0060-6", + "pmc": "PMC4830071", + "pubmed": "27076900", + "title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.", + "year": 2016 + } + ], + "repository": "https://github.com/carrineblank/MicrO", + "uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", + "version": "1.5.1" + }, + "microscope": { + "description": "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis.", + "example": "5601141", + "homepage": "http://www.genoscope.cns.fr/agc/microscope", + "keywords": [ + "comparative genomics", + "life science" + ], + "mappings": { + "biocontext": "MICROSCOPE", + "fairsharing": "FAIRsharing.3t5qc3", + "miriam": "microscope", + "n2t": "microscope", + "re3data": "r3d100012928" + }, + "name": "MicroScope", + "pattern": "^\\d+$", + "preferred_prefix": "microscope", + "publications": [ + { + "doi": "10.1093/nar/gks1194", + "pmc": "PMC3531135", + "pubmed": "23193269", + "title": "MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.", + "year": 2012 + } + ], + "uri_format": "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1" + }, + "microsporidia": { + "description": "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "ECU03_0820i", + "homepage": "http://microsporidiadb.org/micro/", + "keywords": [ + "eukaryotic", + "genome" + ], + "mappings": { + "biocontext": "MICROSPORIDIA", + "miriam": "microsporidia", + "n2t": "microsporidia", + "prefixcommons": "microsporidia" + }, + "name": "MicrosporidiaDB", + "pattern": "^\\w+$", + "preferred_prefix": "microsporidia", + "publications": [ + { + "doi": "10.1093/nar/gkp941", + "pmc": "PMC2808945", + "pubmed": "19914931", + "title": "EuPathDB: a portal to eukaryotic pathogen databases.", + "year": 2009 + } + ], + "uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" + }, + "millipore": { + "description": "Cell line collections", + "example": "SCC111", + "homepage": "https://www.merckmillipore.com/", + "mappings": { + "cellosaurus": "Millipore" + }, + "name": "Merck Millipore (EMD Millipore)", + "preferred_prefix": "millipore", + "uri_format": "https://www.merckmillipore.com/catalogue/item/$1" + }, + "mimodb": { + "description": "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank.", + "example": "1", + "homepage": "http://immunet.cn/bdb/", + "keywords": [ + "interaction", + "life science", + "protein" + ], + "mappings": { + "biocontext": "MIMODB", + "fairsharing": "FAIRsharing.bv0zjz", + "miriam": "mimodb", + "n2t": "mimodb", + "prefixcommons": "mimodb" + }, + "name": "MimoDB", + "pattern": "^\\d+$", + "preferred_prefix": "mimodb", + "publications": [ + { + "doi": "10.1093/nar/gkv1100", + "pmc": "PMC4702802", + "pubmed": "26503249", + "title": "BDB: biopanning data bank.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkr922", + "pmc": "PMC3245166", + "pubmed": "22053087", + "title": "MimoDB 2.0: a mimotope database and beyond.", + "year": 2011 + }, + { + "doi": "10.3390/molecules15118279", + "pmc": "PMC6259156", + "pubmed": "21079566", + "title": "MimoDB: a new repository for mimotope data derived from phage display technology.", + "year": 2010 + } + ], + "uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1" + }, + "minid": { + "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.", + "example": "b97957", + "homepage": "https://fair-research.org", + "mappings": { + "biocontext": "MINID", + "miriam": "minid", + "n2t": "minid" + }, + "name": "Minimal Viable Identifier", + "pattern": "^[A-Za-z0-9]+$", + "preferred_prefix": "minid", + "uri_format": "https://hdl.handle.net/hdl:20.500.12582/$1" + }, + "minid.test": { + "description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. ", + "example": "3SBPLMKKVEVR", + "homepage": "https://fair-research.org", + "mappings": { + "miriam": "minid.test" + }, + "name": "MINID Test", + "pattern": "^[A-Za-z0-9]+$", + "preferred_prefix": "minid.test", + "uri_format": "https://hdl.handle.net/hdl:20.500.12633/$1" + }, + "mint": { + "banana": "MINT", + "banana_peel": "-", + "contact": { + "email": "luana.licata@gmail.com", + "github": null, + "name": "Luana Licata", + "orcid": "0000-0001-5084-9000" + }, + "description": "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals.", + "example": "6978836", + "homepage": "https://mint.bio.uniroma2.it", + "keywords": [ + "interaction", + "life science", + "protein", + "proteomics" + ], + "mappings": { + "biocontext": "MINT", + "edam": "2615", + "fairsharing": "FAIRsharing.2bdvmk", + "miriam": "mint", + "n2t": "mint", + "prefixcommons": "mint", + "re3data": "r3d100010414", + "uniprot": "DB-0158" + }, + "name": "Molecular Interaction Database", + "pattern": "^\\d{1,7}$", + "preferred_prefix": "mint", + "providers": [ + { + "code": "ebi", + "description": "MINT subset through IntAct", + "homepage": "https://www.ebi.ac.uk/intact/", + "name": "MINT subset through IntAct", + "uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkr930", + "pmc": "PMC3244991", + "pubmed": "22096227", + "title": "MINT, the molecular interaction database: 2012 update.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkp983", + "pmc": "PMC2808973", + "pubmed": "19897547", + "title": "MINT, the molecular interaction database: 2009 update.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkl950", + "pmc": "PMC1751541", + "pubmed": "17135203", + "title": "MINT: the Molecular INTeraction database.", + "year": 2006 + }, + { + "doi": "10.1016/s0014-5793(01)03293-8", + "pmc": null, + "pubmed": "11911893", + "title": "MINT: a Molecular INTeraction database.", + "year": 2002 + } + ], + "twitter": "MINT_database", + "uri_format": "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1" + }, + "mipmod": { + "description": "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures.", + "example": "HOSAPI0399", + "homepage": "http://bioinfo.iitk.ac.in/MIPModDB", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "biocontext": "MIPMOD", + "miriam": "mipmod", + "n2t": "mipmod", + "prefixcommons": "mipmod" + }, + "name": "MIPModDB", + "pattern": "^\\w+$", + "preferred_prefix": "mipmod", + "publications": [ + { + "doi": "10.1093/nar/gkr914", + "pmc": "PMC3245135", + "pubmed": "22080560", + "title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins.", + "year": 2011 + } + ], + "uri_format": "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1" + }, + "mir": { + "banana": "MIR", + "description": "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources.", + "example": "00100037", + "homepage": "https://registry.identifiers.org/registry", + "mappings": { + "biocontext": "MIR", + "miriam": "mir", + "n2t": "mir" + }, + "name": "Identifiers.org Registry", + "namespace_in_lui": true, + "pattern": "^\\d{8}$", + "preferred_prefix": "mir", + "uri_format": "https://registry.identifiers.org/registry?query=MIR:$1" + }, + "mirbase": { + "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).", + "example": "MI0026471", + "homepage": "http://www.mirbase.org/", + "keywords": [ + "biology", + "gene", + "rna" + ], + "mappings": { + "biocontext": "MIRBASE", + "biolink": "mirbase", + "edam": "2642", + "fairsharing": "FAIRsharing.hmgte8", + "miriam": "mirbase", + "n2t": "mirbase", + "ncbi": "miRBase", + "prefixcommons": "mirbase", + "re3data": "r3d100010566", + "wikidata": "P2870" + }, + "name": "miRBase pre-miRNA", + "pattern": "^MI\\d{7}$", + "preferred_prefix": "mirbase", + "publications": [ + { + "doi": "10.1093/nar/gky1141", + "pmc": "PMC6323917", + "pubmed": "30423142", + "title": "miRBase: from microRNA sequences to function.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkt1181", + "pmc": "PMC3965103", + "pubmed": "24275495", + "title": "miRBase: annotating high confidence microRNAs using deep sequencing data.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkq1027", + "pmc": "PMC3013655", + "pubmed": "21037258", + "title": "miRBase: integrating microRNA annotation and deep-sequencing data.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkm952", + "pmc": "PMC2238936", + "pubmed": "17991681", + "title": "miRBase: tools for microRNA genomics.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkj112", + "pmc": "PMC1347474", + "pubmed": "16381832", + "title": "miRBase: microRNA sequences, targets and gene nomenclature.", + "year": 2006 + }, + { + "doi": "10.1093/nar/gkh023", + "pmc": "PMC308757", + "pubmed": "14681370", + "title": "The microRNA Registry.", + "year": 2004 + } + ], + "uri_format": "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1" + }, + "mirbase.family": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.", + "example": "MIPF0000002", + "homepage": "http://www.mirbase.org/", + "name": "miRBase Families", + "preferred_prefix": "mirbase.family", + "synonyms": [ + "MIRBASE_FAMILY" + ], + "uri_format": "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1" + }, + "mirbase.mature": { + "description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence.", + "example": "MIMAT0046872", + "homepage": "http://www.mirbase.org/", + "keywords": [ + "nucleotide", + "sequence" + ], + "mappings": { + "biocontext": "MIRBASE.MATURE", + "miriam": "mirbase.mature", + "n2t": "mirbase.mature", + "prefixcommons": "mirbase.mature", + "wikidata": "P2871" + }, + "name": "miRBase mature miRNA", + "pattern": "^MIMAT\\d{7}$", + "preferred_prefix": "mirbase.mature", + "synonyms": [ + "MIRBASEM" + ], + "uri_format": "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1" + }, + "mirex": { + "description": "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages.", + "example": "165a", + "homepage": "http://comgen.pl/mirex/?page=home", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "MIREX", + "fairsharing": "FAIRsharing.q3b39v", + "miriam": "mirex", + "n2t": "mirex" + }, + "name": "mirEX", + "pattern": "^\\d+(\\w+)?$", + "preferred_prefix": "mirex", + "publications": [ + { + "doi": "10.1186/s12870-015-0533-2", + "pmc": "PMC4490709", + "pubmed": "26141515", + "title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkr878", + "pmc": "PMC3245179", + "pubmed": "22013167", + "title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data.", + "year": 2011 + } + ], + "uri_format": "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes" + }, + "miriam": { + "contact": { + "email": "n.lenovere@gmail.com", + "github": null, + "name": "Nicolas Le Novère", + "orcid": "0000-0002-6309-7327" + }, + "description": "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain.", + "example": "pubmed", + "homepage": "https://www.ebi.ac.uk", + "keywords": [ + "biochemistry", + "biomedical science", + "life science" + ], + "mappings": { + "edam": "1162", + "fairsharing": "FAIRsharing.ap169a", + "miriam": "identifiers.namespace" + }, + "name": "Identifiers.org namespace", + "pattern": "^[0-9a-z_:\\.-]+$", + "preferred_prefix": "miriam", + "publications": [ + { + "doi": "10.1093/nar/gkr1097", + "pmc": "PMC3245029", + "pubmed": "22140103", + "title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.", + "year": 2011 + }, + { + "doi": "10.1186/1752-0509-1-58", + "pmc": "PMC2259379", + "pubmed": "18078503", + "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.", + "year": 2007 + }, + { + "doi": "10.1038/nbt1156", + "pmc": null, + "pubmed": "16333295", + "title": "Minimum information requested in the annotation of biochemical models (MIRIAM).", + "year": 2005 + } + ], + "synonyms": [ + "identifiers.namespace" + ], + "uri_format": "https://registry.identifiers.org/registry/$1" + }, + "miriam.collection": { + "banana": "MIR", + "deprecated": true, + "description": "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections.", + "example": "00000008", + "homepage": "https://www.ebi.ac.uk/miriam/", + "mappings": { + "biocontext": "MIRIAM.COLLECTION", + "miriam": "miriam.collection", + "n2t": "miriam.collection" + }, + "name": "MIRIAM Registry collection", + "part_of": "miriam", + "pattern": "^000\\d{5}$", + "preferred_prefix": "miriam.collection", + "uri_format": "https://www.ebi.ac.uk/miriam/main/$1" + }, + "miriam.resource": { + "banana": "MIR", + "deprecated": true, + "description": "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases.", + "example": "00100005", + "homepage": "https://www.ebi.ac.uk/miriam/", + "keywords": [ + "registry" + ], + "mappings": { + "biocontext": "MIRIAM.RESOURCE", + "miriam": "miriam.resource", + "n2t": "miriam.resource", + "prefixcommons": "miriam.resource" + }, + "name": "MIRIAM Legacy Registry Identifier", + "part_of": "miriam", + "pattern": "^001\\d{5}$", + "preferred_prefix": "miriam.resource", + "publications": [ + { + "doi": "10.1186/1752-0509-1-58", + "pmc": "PMC2259379", + "pubmed": "18078503", + "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.", + "year": 2007 + } + ], + "uri_format": "https://www.ebi.ac.uk/miriam/main/resources/$1" + }, + "mirnao": { + "contact": { + "email": "topalis@imbb.forth.gr", + "github": null, + "name": "Pantelis Topalis", + "orcid": "0000-0002-1635-4810" + }, + "deprecated": true, + "description": "An application ontology for use with miRNA databases.", + "download_owl": "http://purl.obolibrary.org/obo/mirnao.owl", + "homepage": "http://code.google.com/p/mirna-ontology/", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "MIRNAO", + "biocontext": "MIRNAO", + "bioportal": "MIRNAO", + "obofoundry": "mirnao", + "ontobee": "miRNAO" + }, + "name": "microRNA Ontology", + "preferred_prefix": "MIRNAO", + "uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1" + }, + "mirnest": { + "description": "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species.", + "example": "MNEST029358", + "homepage": "http://rhesus.amu.edu.pl/mirnest/copy/", + "keywords": [ + "expression", + "genomics", + "life science", + "prediction" + ], + "mappings": { + "biocontext": "MIRNEST", + "fairsharing": "FAIRsharing.5pfx4r", + "miriam": "mirnest", + "n2t": "mirnest", + "prefixcommons": "mirnest" + }, + "name": "miRNEST", + "pattern": "^MNEST\\d+$", + "preferred_prefix": "mirnest", + "publications": [ + { + "doi": "10.1093/nar/gkt1156", + "pmc": "PMC3965105", + "pubmed": "24243848", + "title": "miRNEST 2.0: a database of plant and animal microRNAs.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkr1159", + "pmc": "PMC3245016", + "pubmed": "22135287", + "title": "miRNEST database: an integrative approach in microRNA search and annotation.", + "year": 2011 + } + ], + "uri_format": "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1" + }, + "miro": { + "contact": { + "email": "louis@imbb.forth.gr", + "github": null, + "name": " Christos Louis", + "orcid": "0000-0003-2497-2210" + }, + "deprecated": true, + "description": "Application ontology for entities related to insecticide resistance in mosquitos", + "download_obo": "http://purl.obolibrary.org/obo/miro.obo", + "download_owl": "http://purl.obolibrary.org/obo/miro.owl", + "example": "40000617", + "homepage": "https://github.com/VEuPathDB-ontology/MIRO", + "keywords": [ + "life science", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "MIRO", + "biocontext": "MIRO", + "bioportal": "MIRO", + "fairsharing": "FAIRsharing.sjf113", + "obofoundry": "miro", + "ols": "miro", + "ontobee": "MIRO" + }, + "name": "Mosquito insecticide resistance", + "pattern": "^\\d{8}$", + "preferred_prefix": "MIRO", + "publications": [ + { + "doi": "10.1371/journal.pntd.0000465", + "pmc": "PMC2694272", + "pubmed": "19547750", + "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.", + "year": 2009 + } + ], + "repository": "https://github.com/VEuPathDB-ontology/MIRO", + "uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", + "version": "2014-05-14" + }, + "mirtarbase": { + "contact": { + "email": "ken.sd.hsu@gmail.com", + "github": null, + "name": "Sheng-Da Hsu", + "orcid": "0000-0002-8214-1696" + }, + "description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.", + "example": "MIRT000002", + "homepage": "http://mirtarbase.mbc.nctu.edu.tw/", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "MIRTARBASE", + "fairsharing": "FAIRsharing.f0bxfg", + "miriam": "mirtarbase", + "n2t": "mirtarbase", + "wikidata": "P2646" + }, + "name": "mirTarBase", + "pattern": "^MIRT\\d{6}$", + "preferred_prefix": "mirtarbase", + "publications": [ + { + "doi": "10.1093/nar/gkq1107", + "pmc": "PMC3013699", + "pubmed": "21071411", + "title": "miRTarBase: a database curates experimentally validated microRNA-target interactions.", + "year": 2010 + } + ], + "uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1" + }, + "mirte": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs", + "example": "miR-1", + "homepage": "http://www.russelllab.org/miRNAs/", + "name": "miRNA Target Prediction at EMBL", + "preferred_prefix": "mirte" + }, + "mixs": { + "comment": "Some things to be decided before granting - [ ] should the prefix be mixs, gsc.mixs, MIxS, MIXS, ...? - [ ] MIxS terms are most commonly identified by a short computable stable label, e.g ph_regm. The GSC CIG team are creating numeric identifiers, e.g. MIXS:0001056 - Should we support both schemes? - If we do, should these be different prefixes? I would strongly recommend this. E.g. mixs.term:ph_regm, mixs:0001056. We can then have different regex patterns for both Additional notes: - The http://gensc.org/ns/mixs/ will likely changes to a w3id.org URI that will also serve as a semweb identifier - It currently redirects to the tdwg wiki but this is I assume temporary", + "contact": { + "email": "rlwalls2008@gmail.com", + "github": "ramonawalls", + "name": "Ramona Walls", + "orcid": "0000-0001-8815-0078" + }, + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor_extras": [ + { + "email": "chris@gigasciencejournal.com", + "github": "only1chunts", + "name": "Chris Hunter", + "orcid": "0000-0002-1335-0881" + } + ], + "description": "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample.", + "download_owl": "http://aber-owl.net/media/ontologies/MIXS/5/mixs.owl", + "example": "0001056", + "homepage": "https://gensc.org/mixs/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "MIXS", + "bioportal": "MIXS", + "fairsharing": "FAIRsharing.9aa0zp" + }, + "name": "Minimal Information about any Sequence", + "pattern": "^\\d{7}$", + "preferred_prefix": "mixs", + "providers": [ + { + "code": "github", + "description": "MIxS LinkML schema", + "homepage": "https://genomicsstandardsconsortium.github.io/mixs", + "name": "MIxS LinkML schema", + "uri_format": "https://genomicsstandardsconsortium.github.io/mixs/$1" + } + ], + "publications": [ + { + "doi": "10.1038/nbt.1823", + "pmc": "PMC3367316", + "pubmed": "21552244", + "title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.", + "year": 2011 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://w3id.org/mixs/$1" + }, + "mlc": { + "description": "MLCommons Association artifacts, including benchmark results, datasets, and saved models.", + "example": "0.7-123", + "homepage": "https://mlcommons.org/en/", + "mappings": { + "miriam": "mlc" + }, + "name": "MLCommons Association", + "pattern": "^[0-9a-zA-Z\\.\\-\\_]+$", + "preferred_prefix": "mlc", + "uri_format": "https://www.mlcommons.org/mlc-id/$1" + }, + "mmdb": { + "description": "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites.", + "example": "50885", + "homepage": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure", + "keywords": [ + "dna", + "interaction", + "protein", + "small molecule", + "structure" + ], + "mappings": { + "biocontext": "MMDB", + "edam": "2667", + "miriam": "mmdb", + "n2t": "mmdb", + "prefixcommons": "mmdb" + }, + "name": "Molecular Modeling Database", + "pattern": "^\\d{1,5}$", + "preferred_prefix": "mmdb", + "publications": [ + { + "doi": "10.1093/nar/gkl952", + "pmc": "PMC1751549", + "pubmed": "17135201", + "title": "MMDB: annotating protein sequences with Entrez's 3D-structure database.", + "year": 2006 + } + ], + "uri_format": "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1" + }, + "mmmp.biomaps": { + "description": "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.", + "example": "37", + "homepage": "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp", + "keywords": [ + "interaction", + "molecule", + "pathway" + ], + "mappings": { + "biocontext": "MMMP:BIOMAPS", + "biolink": "mmmp.biomaps", + "miriam": "mmmp:biomaps", + "n2t": "biomaps", + "prefixcommons": "mmmp" + }, + "name": "Melanoma Molecular Map Project Biomaps", + "pattern": "^\\d+$", + "preferred_prefix": "mmmp.biomaps", + "synonyms": [ + "mmmp:biomaps" + ], + "uri_format": "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1" + }, + "mmo": { + "contact": { + "email": "jrsmith@mcw.edu", + "github": "jrsjrs", + "name": "Jennifer Smith", + "orcid": "0000-0002-6443-9376" + }, + "description": "A representation of the variety of methods used to make clinical and phenotype measurements. ", + "download_obo": "http://purl.obolibrary.org/obo/mmo.obo", + "download_owl": "http://purl.obolibrary.org/obo/mmo.owl", + "example": "0000574", + "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000", + "keywords": [ + "biomedical science", + "life science", + "obo", + "ontology", + "preclinical studies" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "MMO", + "biocontext": "MMO", + "bioportal": "MMO", + "fairsharing": "FAIRsharing.bgkyd7", + "obofoundry": "mmo", + "ols": "mmo", + "ontobee": "MMO" + }, + "name": "Measurement method ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MMO", + "publications": [ + { + "doi": "10.1186/2041-1480-4-26", + "pmc": "PMC3882879", + "pubmed": "24103152", + "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", + "year": 2013 + }, + { + "doi": "10.3389/fgene.2012.00087", + "pmc": "PMC3361058", + "pubmed": "22654893", + "title": "Three ontologies to define phenotype measurement data.", + "year": 2012 + } + ], + "repository": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology", + "twitter": "ratgenome", + "uri_format": "http://purl.obolibrary.org/obo/MMO_$1", + "version": "2019-03-27" + }, + "mmp.cat": { + "description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.", + "example": "MMP743597.11", + "homepage": "https://mmp.sfb.uit.no/databases/marcat/", + "mappings": { + "biocontext": "MMP.CAT", + "miriam": "mmp.cat", + "n2t": "mmp.cat" + }, + "name": "MarCat", + "pattern": "^MMP\\d+.\\d+$", + "preferred_prefix": "mmp.cat", + "uri_format": "https://mmp.sfb.uit.no/databases/marcat/#/records/$1" + }, + "mmp.db": { + "description": "MarDB includes all sequenced marine microbial genomes regardless of level of completeness.", + "example": "MMP02954345.1", + "homepage": "https://mmp.sfb.uit.no/databases/mardb/", + "mappings": { + "biocontext": "MMP.DB", + "miriam": "mmp.db", + "n2t": "mmp.db" + }, + "name": "MarDB", + "pattern": "^MMP\\d+.\\d+$", + "preferred_prefix": "mmp.db", + "uri_format": "https://mmp.sfb.uit.no/databases/mardb/#/records/$1" + }, + "mmp.fun": { + "description": "MarFun is manually curated database for marine fungi which is a part of the MAR databases.", + "example": "MMP3888430", + "homepage": "https://mmp.sfb.uit.no/databases/marfun", + "mappings": { + "miriam": "mmp.fun" + }, + "name": "MarFun", + "pattern": "^MMP\\d+.\\d+$", + "preferred_prefix": "mmp.fun", + "uri_format": "https://mmp.sfb.uit.no/databases/marfun/#/records/$1" + }, + "mmp.ref": { + "description": "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes.", + "example": "MMP3312982.2", + "homepage": "https://mmp.sfb.uit.no/databases/marref/", + "mappings": { + "biocontext": "MMP.REF", + "miriam": "mmp.ref", + "n2t": "mmp.ref" + }, + "name": "MarRef", + "pattern": "^MMP\\d+.\\d+$", + "preferred_prefix": "mmp.ref", + "uri_format": "https://mmp.sfb.uit.no/databases/marref/#/records/$1" + }, + "mmrrc": { + "description": "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections.", + "example": "70", + "homepage": "https://www.mmrrc.org", + "keywords": [ + "biology" + ], + "mappings": { + "biocontext": "MMRRC", + "cellosaurus": "MMRRC", + "fairsharing": "FAIRsharing.9dpd18", + "miriam": "mmrrc", + "n2t": "mmrrc", + "re3data": "r3d100013715" + }, + "name": "Mutant Mouse Resource and Research Centers", + "pattern": "^\\d+$", + "preferred_prefix": "mmrrc", + "publications": [ + { + "doi": null, + "pmc": null, + "pubmed": "12102564", + "title": "Mutant Mouse Regional Resource Center Program: a resource for distribution of mouse models for biomedical research.", + "year": 2002 + } + ], + "twitter": "mmrc", + "uri_format": "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1" + }, + "mmsinc": { + "description": "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats.", + "example": "MMs00000001", + "homepage": "http://mms.dsfarm.unipd.it/MMsINC", + "keywords": [ + "small molecule", + "structure" + ], + "mappings": { + "prefixcommons": "mmsinc" + }, + "name": "MMsINC", + "preferred_prefix": "mmsinc", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1" + }, + "mmsl": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included.", + "example": "3355", + "homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html", + "mappings": { + "hl7": "2.16.840.1.113883.6.175" + }, + "name": "Multum MediSource Lexicon", + "pattern": "^\\d+$", + "preferred_prefix": "mmsl", + "synonyms": [ + "MMSL_CODE" + ] + }, + "mmusdv": { + "contact": { + "email": "frederic.bastian@unil.ch", + "github": "fbastian", + "name": "Frédéric Bastian", + "orcid": "0000-0002-9415-5104" + }, + "description": "Life cycle stages for Mus Musculus", + "download_obo": "http://purl.obolibrary.org/obo/mmusdv.obo", + "download_owl": "http://purl.obolibrary.org/obo/mmusdv.owl", + "example": "0000066", + "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv", + "keywords": [ + "anatomy", + "developmental biology", + "embryology", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MMUSDV", + "biocontext": "MMUSDV", + "biolink": "MmusDv", + "bioportal": "MMUSDV", + "fairsharing": "FAIRsharing.zchb68", + "obofoundry": "mmusdv", + "ols": "mmusdv", + "ontobee": "MmusDv" + }, + "name": "Mouse Developmental Stages", + "pattern": "^\\d{7}$", + "preferred_prefix": "MmusDv", + "repository": "https://github.com/obophenotype/developmental-stage-ontologies", + "synonyms": [ + "MmusDv" + ], + "uri_format": "http://purl.obolibrary.org/obo/MMUSDV_$1", + "version": "2020-03-10" + }, + "mo": { + "contact": { + "email": "stoeckrt@pcbi.upenn.edu", + "github": null, + "name": "Chris Stoeckert", + "orcid": "0000-0002-5714-991X" + }, + "deprecated": true, + "description": "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data.", + "download_owl": "http://purl.obolibrary.org/obo/mo.owl", + "example": "ArrayGroup", + "homepage": "http://mged.sourceforge.net/ontologies/MGEDontology.php", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "aberowl": "MO", + "biocontext": "MO", + "bioportal": "MO", + "miriam": "mo", + "n2t": "mo", + "obofoundry": "mo" + }, + "name": "Microarray experimental conditions", + "pattern": "^\\w+$", + "preferred_prefix": "MO", + "providers": [ + { + "code": "ebi", + "description": "MGED Ontology at SourceForge", + "homepage": "https://mged.sourceforge.net/ontologies/MGEDontology.php", + "name": "MGED Ontology at SourceForge", + "uri_format": "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1" + } + ], + "uri_format": "http://purl.obolibrary.org/obo/MO_$1" + }, + "mobidb": { + "contact": { + "email": "silvio.tosatto@unipd.it", + "github": null, + "name": "Silvio C.E. 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It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways.", + "download_json": "http://purl.obolibrary.org/obo/mp.json", + "download_obo": "http://purl.obolibrary.org/obo/mp.obo", + "download_owl": "http://purl.obolibrary.org/obo/mp.owl", + "example": "0005452", + "homepage": "http://www.informatics.jax.org/searches/MP_form.shtml", + "keywords": [ + "developmental biology", + "life science", + "mammalian", + "obo", + "ontology", + "phenotype", + "physiology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "MP", + "biocontext": "MP", + "bioportal": "MP", + "fairsharing": "FAIRsharing.kg1x4z", + "miriam": "mp", + "n2t": "mp", + "obofoundry": "mp", + "ols": "mp", + "ontobee": "MP", + "prefixcommons": "mp" + }, + "name": "Mammalian Phenotype Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "MP", + "providers": [ + { + "code": "nextprot", + "description": "The neXtProt endpoint for exploring MP", + "homepage": "https://www.nextprot.org", + "name": "neXtProt MP Browser", + "uri_format": "https://www.nextprot.org/term/MP:$1" + } + ], + "publications": [ + { + "doi": "10.1186/s13326-015-0009-1", + "pmc": "PMC4378007", + "pubmed": "25825651", + "title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens.", + "year": 2015 + }, + { + "doi": "10.1007/s00335-012-9421-3", + "pmc": "PMC3463787", + "pubmed": "22961259", + "title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.", + "year": 2012 + }, + { + "doi": "10.1002/wsbm.44", + "pmc": "PMC2801442", + "pubmed": "20052305", + "title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis.", + "year": 2009 + }, + { + "doi": "10.1186/gb-2004-6-1-r7", + "pmc": "PMC549068", + "pubmed": "15642099", + "title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.", + "year": 2004 + } + ], + "repository": "https://github.com/mgijax/mammalian-phenotype-ontology", + "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1" + }, + "mpath": { + "contact": { + "email": "pns12@hermes.cam.ac.uk", + "github": "PaulNSchofield", + "name": "Paul Schofield", + "orcid": "0000-0002-5111-7263" + }, + "description": "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes", + "download_obo": "https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo", + "download_owl": "http://purl.obolibrary.org/obo/mpath.owl", + "example": "728", + "homepage": "http://www.pathbase.net", + "keywords": [ + "anatomy", + "biomedical science", + "mouse", + "obo", + "ontology", + "phenotype" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MPATH", + "biocontext": "MPATH", + "bioportal": "MPATH", + "fairsharing": "FAIRsharing.3wbgm0", + "obofoundry": "mpath", + "ols": "mpath", + "ontobee": "MPATH", + "prefixcommons": "mpath" + }, + "name": "Mouse pathology ontology", + "pattern": "^\\d+$", + "preferred_prefix": "MPATH", + "publications": [ + { + "doi": "10.1177/0300985810374845", + "pmc": "PMC3038412", + "pubmed": "20587689", + "title": "Pathbase and the MPATH ontology. 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The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts.", + "example": "172", + "homepage": "http://www.jcvi.org/mpidb/about.php", + "keywords": [ + "interaction", + "life science", + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "MPID", + "fairsharing": "FAIRsharing.eyjkws", + "miriam": "mpid", + "n2t": "mpid", + "prefixcommons": "mpi" + }, + "name": "Microbial Protein Interaction Database", + "pattern": "^\\d+$", + "preferred_prefix": "mpid", + "providers": [ + { + "code": "ebi", + "description": "Microbial Protein Interaction Database subset through IntAct", + "homepage": "https://www.ebi.ac.uk/intact/", + "name": "Microbial Protein Interaction Database subset through IntAct", + "uri_format": "https://www.ebi.ac.uk/intact/query/interaction_id:MPIDB-INT-$1" + } + ], + "publications": [ + { + "doi": "10.1093/bioinformatics/btn285", + "pmc": "PMC2638870", + "pubmed": "18556668", + "title": "MPIDB: the microbial protein interaction database.", + "year": 2008 + } + ], + "synonyms": [ + "mpidb" + ], + "uri_format": "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1" + }, + "mpio": { + "contact": { + "email": "mbrochhausen@uams.edu", + "github": "mbrochhausen", + "name": "Mathias Brochhausen", + "orcid": "0000-0003-1834-3856" + }, + "description": "An ontology of minimum information regarding potential drug-drug interaction information.", + "download_owl": "http://purl.obolibrary.org/obo/mpio.owl", + "example": "0000004", + "homepage": "https://github.com/MPIO-Developers/MPIO", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "MPIO", + "biocontext": "MPIO", + "bioportal": "MPIO", + "obofoundry": "mpio", + "ols": "mpio", + "ontobee": "MPIO" + }, + "name": "Minimum PDDI Information Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MPIO", + "repository": "https://github.com/MPIO-Developers/MPIO", + "uri_format": "http://purl.obolibrary.org/obo/MPIO_$1", + "version": "2019-01-30" + }, + "mro": { + "contact": { + "email": "bpeters@lji.org", + "github": "bpeters42", + "name": "Bjoern Peters", + "orcid": "0000-0002-8457-6693" + }, + "description": "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.", + "download_owl": "http://purl.obolibrary.org/obo/mro.owl", + "example": "0000634", + "homepage": "https://github.com/IEDB/MRO", + "keywords": [ + "immunology", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MRO", + "biocontext": "MRO", + "bioportal": "MRO", + "fairsharing": "FAIRsharing.k893xa", + "obofoundry": "mro", + "ols": "mro", + "ontobee": "MRO" + }, + "name": "MHC Restriction Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "MRO", + "publications": [ + { + "doi": "10.1186/s13326-016-0045-5", + "pmc": "PMC4709943", + "pubmed": "26759709", + "title": "An ontology for major histocompatibility restriction.", + "year": 2016 + } + ], + "repository": "https://github.com/IEDB/MRO", + "uri_format": "http://purl.obolibrary.org/obo/MRO_$1", + "version": "2022-06-17" + }, + "ms": { + "banana": "MS", + "contact": { + "email": "gerhard.mayer@rub.de", + "github": "germa", + "name": "Gerhard Mayer", + "orcid": "0000-0002-1767-2343" + }, + "depends_on": [ + "pato", + "uo" + ], + "description": "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance.", + "download_obo": "http://purl.obolibrary.org/obo/ms.obo", + "download_owl": "http://purl.obolibrary.org/obo/ms.owl", + "example": "1000560", + "homepage": "http://www.psidev.info/groups/controlled-vocabularies", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "MS", + "biocontext": "MS", + "bioportal": "MS", + "miriam": "ms", + "n2t": "ms", + "obofoundry": "ms", + "ols": "ms", + "ontobee": "MS" + }, + "name": "Mass spectrometry ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "MS", + "publications": [ + { + "doi": "10.1093/database/bat009", + "pmc": "PMC3594986", + "pubmed": "23482073", + "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.", + "year": 2013 + } + ], + "repository": "https://github.com/HUPO-PSI/psi-ms-CV", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1" + }, + "msigdb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can", + "example": "M1", + "homepage": "https://www.gsea-msigdb.org", + "mappings": { + "biolink": "MSigDB" + }, + "name": "Molecular Signatures Database", + "pattern": "^M\\d+$", + "preferred_prefix": "msigdb", + "synonyms": [ + "msig" + ], + "uri_format": "https://biopragmatics.github.io/providers/msigdb/$1" + }, + "msio": { + "description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.", + "download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl", + "example": "0000111", + "homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", + "keywords": [ + "ontology" + ], + "mappings": { + "ols": "msio" + }, + "name": "Metabolomics Standards Initiative Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "msio", + "repository": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO", + "uri_format": "http://purl.obolibrary.org/obo/MSIO_$1", + "version": "1.0.1" + }, + "mtbd": { + "description": "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors.", + "example": "1374", + "homepage": "http://tumor.informatics.jax.org", + "keywords": [ + "dna", + "gene expression" + ], + "mappings": { + "prefixcommons": "mtbd" + }, + "name": "Mouse Tumor Biology Database", + "preferred_prefix": "mtbd", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1" + }, + "multicellds": { + "contact": { + "email": "samuel.friedman@cammlab.org", + "github": null, + "name": "Samuel Friedman", + "orcid": "0000-0001-8003-6860" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", + "example": "MCDS_S_0000000001", + "homepage": "http://multicellds.org/MultiCellDB.php", + "keywords": [ + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.pqzyd5" + }, + "name": "MultiCellDS", + "preferred_prefix": "multicellds", + "uri_format": "http://multicellds.org/MultiCellDB/$1" + }, + "multicellds.cell_line": { + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata.", + "example": "MCDS_L_0000000001", + "homepage": "http://multicellds.org/MultiCellDB.php", + "mappings": { + "biocontext": "MULTICELLDS.CELL_LINE", + "miriam": "multicellds.cell_line", + "n2t": "multicellds.cell_line" + }, + "name": "MultiCellDS Digital Cell Line", + "part_of": "multicellds", + "pattern": "^MCDS_L_[a-zA-Z0-9]{1,10}$", + "preferred_prefix": "multicellds.cell_line", + "uri_format": "http://multicellds.org/MultiCellDB/$1" + }, + "multicellds.collection": { + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections).", + "example": "MCDS_C_0000000001", + "homepage": "http://multicellds.org/MultiCellDB.php", + "mappings": { + "biocontext": "MULTICELLDS.COLLECTION", + "miriam": "multicellds.collection", + "n2t": "multicellds.collection" + }, + "name": "MultiCellDS collection", + "part_of": "multicellds", + "pattern": "^MCDS_C_[a-zA-Z0-9]{1,10}$", + "preferred_prefix": "multicellds.collection", + "uri_format": "http://multicellds.org/MultiCellDB/$1" + }, + "multicellds.snapshot": { + "description": "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data.", + "example": "MCDS_S_0000000001", + "homepage": "http://multicellds.org/MultiCellDB.php", + "mappings": { + "biocontext": "MULTICELLDS.SNAPSHOT", + "miriam": "multicellds.snapshot", + "n2t": "multicellds.snapshot" + }, + "name": "MultiCellDS Digital snapshot", + "part_of": "multicellds", + "pattern": "^MCDS_S_[a-zA-Z0-9]{1,10}$", + "preferred_prefix": "multicellds.snapshot", + "uri_format": "http://multicellds.org/MultiCellDB/$1" + }, + "mw.project": { + "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", + "example": "PR000001", + "homepage": "http://www.metabolomicsworkbench.org/", + "mappings": { + "biocontext": "MW.PROJECT", + "miriam": "mw.project", + "n2t": "mw.project" + }, + "name": "Metabolomics Workbench Project", + "pattern": "^PR[0-9]{6}$", + "preferred_prefix": "mw.project", + "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1" + }, + "mw.study": { + "description": "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC).", + "example": "ST000900", + "homepage": "http://www.metabolomicsworkbench.org/", + "mappings": { + "biocontext": "MW.STUDY", + "miriam": "mw.study", + "n2t": "mw.study" + }, + "name": "Metabolomics Workbench Study", + "pattern": "^ST[0-9]{6}$", + "preferred_prefix": "mw.study", + "providers": [ + { + "code": "omicsdi", + "description": "Metabolomics Workbench Study through OmicsDI", + "homepage": "https://www.omicsdi.org/", + "name": "Metabolomics Workbench Study through OmicsDI", + "uri_format": "https://www.omicsdi.org/dataset/metabolomics_workbench/$1" + } + ], + "uri_format": "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1" + }, + "myco.lepra": { + "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information.", + "example": "ML0224", + "homepage": "http://mycobrowser.epfl.ch/leprosy.html", + "keywords": [ + "genome", + "sequence" + ], + "mappings": { + "biocontext": "MYCO.LEPRA", + "miriam": "myco.lepra", + "n2t": "myco.lepra", + "prefixcommons": "myco.lepra" + }, + "name": "MycoBrowser leprae", + "pattern": "^ML\\w+$", + "preferred_prefix": "myco.lepra", + "uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1" + }, + "myco.marinum": { + "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information.", + "example": "MMAR_2462", + "homepage": "http://mycobrowser.epfl.ch/marinolist.html", + "keywords": [ + "genome", + "sequence" + ], + "mappings": { + "biocontext": "MYCO.MARINUM", + "miriam": "myco.marinum", + "n2t": "myco.marinum", + "prefixcommons": "myco.marinum" + }, + "name": "MycoBrowser marinum", + "pattern": "^MMAR\\_\\d+$", + "preferred_prefix": "myco.marinum", + "uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1" + }, + "myco.smeg": { + "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information.", + "example": "MSMEG_3769", + "homepage": "http://mycobrowser.epfl.ch/smegmalist.html", + "keywords": [ + "genome", + "sequence" + ], + "mappings": { + "biocontext": "MYCO.SMEG", + "miriam": "myco.smeg", + "n2t": "myco.smeg", + "prefixcommons": "myco.smeg" + }, + "name": "MycoBrowser smegmatis", + "pattern": "^MSMEG\\w+$", + "preferred_prefix": "myco.smeg", + "uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1" + }, + "myco.tuber": { + "description": "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information.", + "example": "Rv1908c", + "homepage": "http://tuberculist.epfl.ch/", + "keywords": [ + "dna", + "genome", + "protein" + ], + "mappings": { + "biocontext": "MYCO.TUBER", + "miriam": "myco.tuber", + "n2t": "myco.tuber", + "ncbi": "TubercuList", + "prefixcommons": "tuberculist", + "uniprot": "DB-0106" + }, + "name": "TubercuList knowledge base", + "pattern": "^Rv\\d{4}(A|B|c)?$", + "preferred_prefix": "myco.tuber", + "publications": [ + { + "doi": "10.1016/j.tube.2010.09.006", + "pmc": null, + "pubmed": "20980200", + "title": "The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.", + "year": 2010 + } + ], + "synonyms": [ + "TubercuList" + ], + "uri_format": "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1" + }, + "mycobank": { + "description": "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations.", + "example": "349124", + "homepage": "http://www.mycobank.org/", + "keywords": [ + "biology", + "classification", + "taxonomy" + ], + "mappings": { + "biocontext": "MYCOBANK", + "fairsharing": "FAIRsharing.v8se8r", + "miriam": "mycobank", + "n2t": "mycobank", + "ncbi": "MycoBank", + "prefixcommons": "mycobank", + "re3data": "r3d100011222" + }, + "name": "Fungal Nomenclature and Species Bank", + "pattern": "^\\d+$", + "preferred_prefix": "mycobank", + "publications": [ + { + "doi": "10.5598/imafungus.2013.04.02.16", + "pmc": "PMC3905949", + "pubmed": "24563843", + "title": "MycoBank gearing up for new horizons.", + "year": 2013 + } + ], + "uri_format": "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1" + }, + "mzspec": { + "banana": "mzspec", + "description": "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it.", + "example": "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2", + "homepage": "http://proteomecentral.proteomexchange.org/", + "keywords": [ + "data governance", + "metabolomics", + "proteomics" + ], + "mappings": { + "biocontext": "MZSPEC", + "fairsharing": "FAIRsharing.b549b8", + "miriam": "mzspec", + "n2t": "mzspec" + }, + "name": "Universal Spectrum Identifier", + "namespace_in_lui": true, + "pattern": "^.+$", + "preferred_prefix": "mzspec", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Universal Spectrum Identifier through Peptide Atlas", + "homepage": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum", + "name": "Universal Spectrum Identifier through Peptide Atlas", + "uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ShowObservedSpectrum?usi=mzspec:$1" + } + ], + "publications": [ + { + "doi": "10.1038/s41592-021-01184-6", + "pmc": "PMC8405201", + "pubmed": "34183830", + "title": "Universal Spectrum Identifier for mass spectra.", + "year": 2021 + } + ], + "uri_format": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1" + }, + "n2t": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org", + "example": "chebi", + "homepage": "https://n2t.net", + "name": "Name-to-Thing", + "preferred_prefix": "n2t", + "uri_format": "https://n2t.net/$1:" + }, + "namerxn": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO).", + "example": "4.2.78", + "homepage": "https://www.nextmovesoftware.com/namerxn.html", + "keywords": [ + "chemistry", + "reactions", + "text mining" + ], + "name": "NameRXN", + "preferred_prefix": "namerxn", + "proprietary": true, + "publications": [ + { + "doi": "10.1021/acs.jmedchem.6b00153", + "pmc": null, + "pubmed": "27028220", + "title": "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter.", + "year": 2016 + }, + { + "doi": "10.1038/s42256-020-00284-w", + "pmc": null, + "pubmed": null, + "title": "Mapping the space of chemical reactions using attention-based neural networks", + "year": 2021 + } + ], + "references": [ + "https://www.nextmovesoftware.com/products/HazELNutPoster.pdf", + "https://twitter.com/cthoyt/status/1443929184745758723" + ] + }, + "napdi": { + "contact": { + "email": "rdb20@pitt.edu", + "github": null, + "name": "Richard Boyce", + "orcid": "0000-0002-2993-2085" + }, + "description": "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs).", + "example": "28", + "homepage": "https://repo.napdi.org/", + "keywords": [ + "biomedical science", + "pharmacology" + ], + "mappings": { + "biocontext": "NAPDI", + "fairsharing": "FAIRsharing.y9x8wk", + "miriam": "napdi", + "n2t": "napdi" + }, + "name": "Natural Product-Drug Interaction Research Data Repository", + "pattern": "^[0-9]+$", + "preferred_prefix": "napdi", + "publications": [ + { + "doi": "10.1186/s13326-018-0183-z", + "pmc": "PMC5944177", + "pubmed": "29743102", + "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.", + "year": 2018 + } + ], + "uri_format": "https://repo.napdi.org/study/$1" + }, + "napp": { + "contact": { + "email": "daniel.gautheret@u-psud.fr", + "github": null, + "name": "Daniel Gautheret", + "orcid": "0000-0002-1508-8469" + }, + "description": "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters.", + "example": "351", + "homepage": "http://napp.u-psud.fr/", + "keywords": [ + "clustering", + "genomics", + "nucleotide" + ], + "mappings": { + "biocontext": "NAPP", + "fairsharing": "FAIRsharing.vr52p3", + "miriam": "napp", + "n2t": "napp", + "prefixcommons": "napp" + }, + "name": "Nucleic Acids Phylogenetic Profiling", + "pattern": "^\\d+$", + "preferred_prefix": "napp", + "publications": [ + { + "doi": "10.1093/nar/gkr807", + "pmc": "PMC3245103", + "pubmed": "21984475", + "title": "NAPP: the Nucleic Acid Phylogenetic Profile Database.", + "year": 2011 + }, + { + "doi": "10.1101/gr.089714.108", + "pmc": "PMC2694484", + "pubmed": "19237465", + "title": "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles.", + "year": 2009 + } + ], + "uri_format": "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1" + }, + "narcis": { + "description": "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases.", + "example": "oai:cwi.nl:4725", + "homepage": "http://www.narcis.nl", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "biocontext": "NARCIS", + "fairsharing": "FAIRsharing.f63h4k", + "miriam": "narcis", + "n2t": "narcis" + }, + "name": "National Academic Research and Collaborations Information System", + "pattern": "^oai\\:cwi\\.nl\\:\\d+$", + "preferred_prefix": "narcis", + "uri_format": "http://www.narcis.nl/publication/RecordID/$1" + }, + "nasc": { + "contact": { + "email": "sean@arabidopsis.org.uk", + "github": null, + "name": "Sean May", + "orcid": "0000-0001-5282-3250" + }, + "description": "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.", + "example": "N1899", + "homepage": "http://arabidopsis.info/", + "keywords": [ + "genome", + "life science" + ], + "mappings": { + "biocontext": "NASC", + "fairsharing": "FAIRsharing.2sqcxs", + "miriam": "nasc", + "n2t": "nasc", + "prefixcommons": "nasc", + "re3data": "r3d100010906" + }, + "name": "NASC code", + "pattern": "^(\\w+)?\\d+$", + "preferred_prefix": "nasc", + "publications": [ + { + "doi": "10.1093/nar/gkh133", + "pmc": "PMC308867", + "pubmed": "14681484", + "title": "NASCArrays: a repository for microarray data generated by NASC's transcriptomics service.", + "year": 2004 + } + ], + "twitter": "NascArabidopsis", + "uri_format": "http://arabidopsis.info/StockInfo?NASC_id=$1" + }, + "nbn": { + "description": "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier.", + "example": "urn:nbn:fi:tkk-004781", + "homepage": "http://nbn-resolving.org/resolve_urn.htm", + "mappings": { + "biocontext": "NBN", + "miriam": "nbn", + "n2t": "nbn" + }, + "name": "National Bibliography Number", + "pattern": "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$", + "preferred_prefix": "nbn", + "uri_format": "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect" + }, + "nbo": { + "appears_in": [ + "ecto", + "maxo", + "pcl", + "scdo" + ], + "contact": { + "email": "g.gkoutos@bham.ac.uk", + "github": "gkoutos", + "name": "George Gkoutos", + "orcid": "0000-0002-2061-091X" + }, + "description": "An ontology of human and animal behaviours and behavioural phenotypes", + "download_obo": "https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo", + "download_owl": "http://purl.obolibrary.org/obo/nbo.owl", + "example": "0000564", + "homepage": "https://github.com/obo-behavior/behavior-ontology/", + "keywords": [ + "obo", + "ontology", + "social and behavioural science", + "systemic neuroscience" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "NBO", + "biocontext": "NBO", + "bioportal": "NBO", + "fairsharing": "FAIRsharing.pktgc6", + "obofoundry": "nbo", + "ols": "nbo", + "ontobee": "NBO" + }, + "name": "Neuro Behavior Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "NBO", + "publications": [ + { + "doi": "10.1007/s00335-013-9481-z", + "pmc": null, + "pubmed": "24177753", + "title": "Analyzing gene expression data in mice with the Neuro Behavior Ontology.", + "year": 2013 + }, + { + "doi": "10.1016/b978-0-12-388408-4.00004-6", + "pmc": null, + "pubmed": "23195121", + "title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.", + "year": 2012 + } + ], + "repository": "https://github.com/obo-behavior/behavior-ontology", + "uri_format": "http://purl.obolibrary.org/obo/NBO_$1", + "version": "2021-02-15" + }, + "nbrc": { + "description": "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.", + "example": "00001234", + "homepage": "http://www.nbrc.nite.go.jp/e/index.html", + "keywords": [ + "microbial", + "microbiology", + "taxonomy" + ], + "mappings": { + "biocontext": "NBRC", + "fairsharing": "FAIRsharing.ftamrc", + "miriam": "nbrc", + "n2t": "nbrc", + "ncbi": "NBRC", + "prefixcommons": "nbrc" + }, + "name": "NITE Biological Resource Center", + "pattern": "^\\d+$", + "preferred_prefix": "nbrc", + "uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1" + }, + "ncats.bioplanet": { + "contact": { + "email": "ruili.huang@nih.gov", + "github": null, + "name": "Ruili Huang", + "orcid": "0000-0001-8886-8311" + }, + "contributor": { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + }, + "description": "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays.", + "example": "3", + "github_request_issue": 445, + "homepage": "https://tripod.nih.gov/bioplanet/", + "mappings": { + "biolink": "ncats.bioplanet" + }, + "name": "National Center for Advancing Translation Sciences BioPlanet", + "pattern": "^\\d+$", + "preferred_prefix": "ncats.bioplanet", + "publications": [ + { + "doi": "10.3389/fphar.2019.00445", + "pmc": "PMC6524730", + "pubmed": "31133849", + "title": "The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics.", + "year": 2019 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "twitter": "ncats_nih_gov", + "uri_format": "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1" + }, + "ncats.drug": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + { + "email": null, + "github": "vdancik", + "name": "Vlado Dancik", + "orcid": "0000-0002-5970-6660" + }, + { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + } + ], + "description": "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances", + "example": "44259", + "example_extras": [ + "1IJV77EI07" + ], + "homepage": "https://drugs.ncats.io/", + "mappings": { + "biolink": "ncats.drug" + }, + "name": "NCATS Drugs", + "preferred_prefix": "ncats.drug", + "synonyms": [ + "inxight", + "inxight-drugs" + ], + "uri_format": "https://drugs.ncats.io/drug/$1" + }, + "ncbi.assembly": { + "description": "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.", + "example": "GCF_000005845.2", + "homepage": "https://www.ncbi.nlm.nih.gov/", + "mappings": { + "biocontext": "NCBIAssembly", + "miriam": "assembly", + "re3data": "r3d100012688" + }, + "name": "Assembly", + "pattern": "^[a-zA-Z0-9_\\.]+$", + "preferred_prefix": "ncbi.assembly", + "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" + }, + "ncbi.genome": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.", + "example": "51", + "homepage": "https://www.ncbi.nlm.nih.gov/genome", + "mappings": { + "biocontext": "NCBIGenome", + "edam": "2787", + "re3data": "r3d100010785" + }, + "name": "NCBI Genome", + "pattern": "^\\d+$", + "preferred_prefix": "ncbi.genome", + "uri_format": "https://www.ncbi.nlm.nih.gov/genome/$1" + }, + "ncbi.resource": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources", + "example": "ECOCYC", + "homepage": "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/", + "name": "NCBI Registry", + "preferred_prefix": "ncbi.resource", + "uri_format": "https://bioregistry.io/metaregistry/ncbi/$1" + }, + "ncbibook": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ", + "example": "NBK331", + "homepage": "https://www.ncbi.nlm.nih.gov/books", + "name": "NCBI Bookshelf", + "pattern": "^NBK\\d+$", + "preferred_prefix": "ncbibook", + "uri_format": "https://www.ncbi.nlm.nih.gov/books/$1" + }, + "ncbigene": { + "description": "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.", + "example": "100010", + "homepage": "https://www.ncbi.nlm.nih.gov/gene", + "keywords": [ + "dna", + "gene", + "genetics", + "genome", + "genomics" + ], + "mappings": { + "biocontext": "NCBIGene", + "biolink": "NCBIGene", + "edam": "1027", + "fairsharing": "FAIRsharing.5h3maw", + "go": "NCBIGene", + "hl7": "2.16.840.1.113883.6.340", + "miriam": "ncbigene", + "n2t": "ncbigene", + "ncbi": "GeneID", + "prefixcommons": "ncbigene", + "re3data": "r3d100010650", + "uniprot": "DB-0118", + "wikidata": "P351" + }, + "name": "Entrez Gene", + "owners": [ + { + "name": "National Center for Biotechnology Information", + "partnered": false, + "ror": "02meqm098", + "wikidata": null + } + ], + "pattern": "^\\d+$", + "preferred_prefix": "NCBIGene", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Bio2RDF", + "homepage": "http://ncbigene.bio2rdf.org/fct", + "name": "Bio2RDF", + "uri_format": "http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1" + }, + { + "code": "marrvel", + "description": "Helps browse potential orthologs in model organisms for a given gene", + "homepage": "http://marrvel.org", + "name": "Model organism Aggregated Resources for Rare Variant ExpLoration", + "uri_format": "http://marrvel.org/model/gene/$1" + }, + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/ncbi-gene/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkq1237", + "pmc": "PMC3013746", + "pubmed": "21115458", + "title": "Entrez Gene: gene-centered information at NCBI.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gki031", + "pmc": "PMC539985", + "pubmed": "15608257", + "title": "Entrez Gene: gene-centered information at NCBI.", + "year": 2005 + } + ], + "synonyms": [ + "EGID", + "EntrezGene", + "NCBIGene", + "NCBI_GeneID", + "entrez", + "entrez gene/locuslink" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/gene/$1" + }, + "ncbigi": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. 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This was done before most of the current standard ontology and identifier management practices had been developed.", + "example": "7123", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: External", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nif.ext", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NIFEXT" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nifext_$1" + }, + "nif.grossanatomy": { + "contact": { + "email": "smtifahim@gmail.com", + "github": null, + "name": "Fahim Imam", + "orcid": "0000-0003-4752-543X" + }, + "deprecated": true, + "homepage": "http://neuinfo.org/", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "NIF_GROSSANATOMY", + "obofoundry": "nif_grossanatomy" + }, + "name": "NIF Gross Anatomy", + "part_of": "nif", + "preferred_prefix": "NIF_GROSSANATOMY", + "uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1" + }, + "nif.std": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4801" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4801" + }, + "description": "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing.", + "download_owl": "http://aber-owl.net/media/ontologies/NIFSTD/23/nifstd.owl", + "example": "BAMSC981", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "neuroscience", + "ontology" + ], + "license": "CC BY-4.0", + "mappings": { + "aberowl": "NIFSTD", + "bioportal": "NIFSTD", + "fairsharing": "FAIRsharing.vgw1m6" + }, + "name": "NIF Standard Ontology", + "part_of": "nif", + "pattern": "^BAMSC\\d+$", + "preferred_prefix": "nif.std", + "publications": [ + { + "doi": "10.1007/s12021-008-9032-z", + "pmc": "PMC2743139", + "pubmed": "18975148", + "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.", + "year": 2008 + } + ], + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NIFSTD" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/$1" + }, + "nihreporter.project": { + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. 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The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species.", + "homepage": "https://webbook.nist.gov/chemistry/", + "name": "NIST Chemistry WebBook", + "no_own_terms": true, + "preferred_prefix": "nist", + "synonyms": [ + "NIST", + "NIST Chemistry WebBook" + ] + }, + "nlm": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings.", + "example": "101775319", + "homepage": "https://www.ncbi.nlm.nih.gov/nlmcatalog", + "mappings": { + "bartoc": "528", + "biolink": "NLMID" + }, + "name": "National Library of Medicine Catalog", + "pattern": "^\\d+$", + "preferred_prefix": "nlm", + "uri_format": "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1" + }, + "nlx.anat": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4804" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "NLXANAT covers anatomy terms. Almost all terms are also in Uberon.", + "example": "090201", + "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", + "keywords": [ + "anatomy" + ], + "name": "NeuroLex Anatomy", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.anat", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1" + }, + "nlx.br": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4804" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4804" + }, + "description": "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).", + "example": "145", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "anatomy", + "brain regions", + "neuroscience" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Brain Regions", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.br", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXBR" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1" + }, + "nlx.cell": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4805" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4805" + }, + "description": "NLXCELL conatins cell types with a focus on neuron types.", + "example": "91005", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "cell lines", + "cell types", + "cells", + "neuroscience" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Cell Types", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.cell", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXCELL" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1" + }, + "nlx.chem": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4806" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4806" + }, + "description": "NLXCHEM covers chemicals. Most classes are also in ChEBI.", + "example": "90801", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "chemistry" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Chemical", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.chem", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXCHEM" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1" + }, + "nlx.dys": { + "appears_in": [ + "mondo" + ], + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4804" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc.", + "example": "20090303", + "homepage": "https://scicrunch.org/scicrunch/interlex/dashboard", + "keywords": [ + "disease", + "disorders", + "phenotypes" + ], + "name": "NeuroLex Dysfunction", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.dys", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1" + }, + "nlx.func": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4808" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4808" + }, + "description": "NLXFUNC covers terms for cognitive function.", + "example": "90801", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "neuroscience" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Cognitive Function", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.func", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXFUNC" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1" + }, + "nlx.inv": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4809" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4809" + }, + "description": "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.", + "example": "90901", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "data analysis", + "funding agencies" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Investigations", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.inv", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "synonyms": [ + "NLXINV" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1" + }, + "nlx.mol": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4810" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4810" + }, + "description": "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.", + "example": "90806", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "biology", + "chemistry", + "neuroscience", + "proteins" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Molecules", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.mol", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXMOL" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1" + }, + "nlx.oen": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4811" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4811" + }, + "description": "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).", + "example": "0001000", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "neuroscience" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: OEN Terms in Neurolex", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.oen", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXOEN" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/oen_$1" + }, + "nlx.org": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4812" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4812" + }, + "description": "NLXORG covers organisms.", + "example": "090701", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "taxonomy" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Organisms", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.org", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXORG" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1" + }, + "nlx.qual": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4813" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4813" + }, + "description": "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).", + "example": "100810", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "dispositions", + "qualities" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Qualities", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.qual", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXQUAL" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1" + }, + "nlx.res": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4814" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4814" + }, + "description": "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites", + "example": "090924", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "software and information systems" + ], + "license": "CC BY-4.0", + "name": "NIF Standard Ontology: Digital Resources", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.res", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXRES" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1" + }, + "nlx.sub": { + "contact": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4815" + }, + "contributor": { + "email": "tgbugs@gmail.com", + "github": "tgbugs", + "name": "Tom Gillespie", + "orcid": "0000-0002-7509-4815" + }, + "description": "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).", + "example": "090803", + "homepage": "https://github.com/SciCrunch/NIF-Ontology", + "keywords": [ + "cellular components" + ], + "license": "CC BY-4.0", + "mappings": { + "go": "NIF_Subcellular" + }, + "name": "NIF Standard Ontology: Subcellular Entities", + "part_of": "nif", + "pattern": "^\\d+$", + "preferred_prefix": "nlx.sub", + "repository": "https://github.com/SciCrunch/NIF-Ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "NLXSUB", + "nif_subcellular" + ], + "twitter": "SciCrunch", + "uri_format": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1" + }, + "nmdc": { + "contact": { + "email": "donny@polyneme.xyz", + "github": "dwinston", + "name": "Donny Winston", + "orcid": "0000-0002-8424-0604" + }, + "contributor": { + "email": "donny@polyneme.xyz", + "github": "dwinston", + "name": "Donny Winston", + "orcid": "0000-0002-8424-0604" + }, + "description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.", + "example": "y3ax-8bq3-60", + "homepage": "https://microbiomedata.org/", + "keywords": [ + "microbiome" + ], + "mappings": { + "miriam": "nmdc" + }, + "name": "National Microbiome Data Collaborative", + "pattern": "^[\\w\\-.]{3,}$", + "preferred_prefix": "nmdc", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://drs.microbiomedata.org/objects/$1" + }, + "nmpdr": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.", + "example": "fig|306254.1.peg.183", + "homepage": "http://www.nmpdr.org", + "keywords": [ + "genome" + ], + "mappings": { + "ncbi": "NMPDR", + "prefixcommons": "nmpdr" + }, + "name": "National Microbial Pathogen Data Resource", + "preferred_prefix": "nmpdr", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1" + }, + "nmr": { + "banana": "NMR", + "contact": { + "email": "schober@imbi.uni-freiburg.de", + "github": "DSchober", + "name": "Daniel Schober", + "orcid": "0000-0001-8014-6648" + }, + "deprecated": true, + "description": "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi.", + "download_owl": "https://nmrml.org/cv/stable/nmrCV.owl", + "example": "1000003", + "homepage": "http://msi-ontology.sourceforge.net/", + "keywords": [ + "nmr", + "obo", + "ontology", + "owl" + ], + "mappings": { + "aberowl": "NMR", + "biocontext": "NMR", + "bioportal": "NMR", + "miriam": "nmr", + "n2t": "nmr", + "obofoundry": "nmr", + "ols": "nmrcv", + "prefixcommons": "nmr" + }, + "name": "NMR-instrument specific component of metabolomics investigations", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "NMR", + "synonyms": [ + "nmrcv" + ], + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1", + "version": "1.1.0" + }, + "nmrshiftdb2": { + "contact": { + "email": "stefan.kuhn@dmu.ac.uk", + "github": null, + "name": "Stefan Kuhn", + "orcid": "0000-0002-5990-4157" + }, + "description": "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties.", + "example": "234", + "homepage": "https://nmrshiftdb.nmr.uni-koeln.de", + "keywords": [ + "analytical chemistry" + ], + "mappings": { + "fairsharing": "FAIRsharing.nYaZ1N", + "miriam": "nmrshiftdb2", + "wikidata": "P9405" + }, + "name": "NMRShiftDB structure", + "pattern": "^[0-9]+$", + "preferred_prefix": "nmrshiftdb2", + "publications": [ + { + "doi": "10.1002/mrc.4263", + "pmc": null, + "pubmed": "25998807", + "title": "Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.", + "year": 2015 + }, + { + "doi": "10.1016/j.phytochem.2004.08.027", + "pmc": null, + "pubmed": "15464159", + "title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.", + "year": 2004 + }, + { + "doi": "10.1021/ci0341363", + "pmc": null, + "pubmed": "14632418", + "title": "NMRShiftDB-constructing a free chemical information system with open-source components.", + "year": 2003 + } + ], + "uri_format": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1" + }, + "noaa": { + "contributor": { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + }, + "description": "Identifier for a species on the noaa fisheries website", + "example": "long-finned-pilot-whale", + "github_request_issue": 456, + "homepage": "https://www.fisheries.noaa.gov/species-directory", + "mappings": { + "wikidata": "P6049" + }, + "name": "NOAA Fisheries Species Directory", + "pattern": "^[a-z]+(\\-[a-z]+)*$", + "preferred_prefix": "noaa", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.fisheries.noaa.gov/species/$1" + }, + "nomen": { + "contact": { + "email": "diapriid@gmail.com", + "github": "mjy", + "name": "Matt Yoder", + "orcid": "0000-0002-5640-5491" + }, + "description": "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature.", + "download_owl": "http://purl.obolibrary.org/obo/nomen.owl", + "example": "0000295", + "homepage": "https://github.com/SpeciesFileGroup/nomen", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "NOMEN", + "bioportal": "NOMEN", + "obofoundry": "nomen", + "ols": "nomen", + "ontobee": "NOMEN" + }, + "name": "A nomenclatural ontology for biological names", + "pattern": "^\\d{7}$", + "preferred_prefix": "NOMEN", + "repository": "https://github.com/SpeciesFileGroup/nomen", + "uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1" + }, + "noncodev3": { + "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.", + "example": "377550", + "homepage": "http://www.noncode.org/", + "keywords": [ + "expression", + "nucleotide" + ], + "mappings": { + "biocontext": "NONCODEV3", + "miriam": "noncodev3", + "n2t": "noncodev3", + "prefixcommons": "noncode" + }, + "name": "NONCODE v3", + "pattern": "^\\d+$", + "preferred_prefix": "noncodev3", + "publications": [ + { + "doi": "10.1093/nar/gkr1175", + "pmc": "PMC3245065", + "pubmed": "22135294", + "title": "NONCODE v3.0: integrative annotation of long noncoding RNAs.", + "year": 2011 + } + ], + "uri_format": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1" + }, + "noncodev4.gene": { + "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.", + "example": "NONHSAG00001", + "homepage": "http://www.bioinfo.org/NONCODEv4/", + "mappings": { + "biocontext": "NONCODEV4.GENE", + "miriam": "noncodev4.gene", + "n2t": "noncodev4.gene" + }, + "name": "NONCODE v4 Gene", + "pattern": "^NONHSAG\\d{5}$", + "preferred_prefix": "noncodev4.gene", + "uri_format": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1" + }, + "noncodev4.rna": { + "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.", + "example": "NONHSAT000001", + "homepage": "http://www.bioinfo.org/NONCODEv4/", + "mappings": { + "biocontext": "NONCODEV4.RNA", + "miriam": "noncodev4.rna", + "n2t": "noncodev4.rna" + }, + "name": "NONCODE v4 Transcript", + "pattern": "^NONHSAT\\d{6}$", + "preferred_prefix": "noncodev4.rna", + "uri_format": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1" + }, + "norine": { + "description": "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings.", + "example": "NOR00681", + "homepage": "http://bioinfo.lifl.fr/norine/", + "keywords": [ + "life science", + "protein" + ], + "mappings": { + "biocontext": "NORINE", + "fairsharing": "FAIRsharing.gf8yhy", + "miriam": "norine", + "n2t": "norine", + "prefixcommons": "norine" + }, + "name": "Nonribosomal Peptides Database", + "pattern": "^NOR\\d+$", + "preferred_prefix": "norine", + "publications": [ + { + "doi": "10.1093/nar/gkz1000", + "pmc": "PMC7145658", + "pubmed": "31691799", + "title": "Norine: update of the nonribosomal peptide resource.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gkm792", + "pmc": "PMC2238963", + "pubmed": "17913739", + "title": "NORINE: a database of nonribosomal peptides.", + "year": 2007 + } + ], + "uri_format": "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1" + }, + "novus": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A vendor of antibodies and other biologics", + "example": "nb100-56351", + "homepage": "https://www.novusbio.com", + "name": "Novus Biologicals", + "preferred_prefix": "novus", + "uri_format": "https://www.novusbio.com/products/$1" + }, + "npass": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n", + "example": "NPC139585", + "homepage": "http://bidd.group/NPASS/", + "name": "Natural Product Activity and Species Source Database", + "pattern": "^NPC\\d+$", + "preferred_prefix": "npass" + }, + "npo": { + "contact": { + "email": "nathan.baker@pnnl.gov", + "github": "sobolevnrm", + "name": "Nathan Baker", + "orcid": "0000-0002-5892-6506" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.", + "download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl", + "example": "1731", + "homepage": "https://bioportal.bioontology.org/ontologies/NPO", + "keywords": [ + "life science", + "ontology" + ], + "mappings": { + "aberowl": "NPO", + "bioportal": "NPO", + "fairsharing": "FAIRsharing.vy0p71" + }, + "name": "NanoParticle Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "npo", + "publications": [ + { + "doi": "10.1016/j.jbi.2010.03.001", + "pmc": "PMC3042056", + "pubmed": "20211274", + "title": "NanoParticle Ontology for cancer nanotechnology research.", + "year": 2010 + } + ], + "repository": "https://github.com/sobolevnrm/npo", + "uri_format": "http://purl.bioontology.org/ontology/npo#NPO_$1" + }, + "nsc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Identifier used by the Cancer Chemotherapy National Service Center.", + "example": "27223", + "homepage": "https://wiki.nci.nih.gov/display/NCIDTPdata/Chemical+Data", + "mappings": { + "cheminf": "000565" + }, + "name": "USA National Service Center Number", + "pattern": "^\\d+$", + "preferred_prefix": "nsc", + "references": [ + "https://pubchem.ncbi.nlm.nih.gov/source/DTP/NCI" + ], + "uri_format": "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1" + }, + "nsf.award": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research.", + "example": "1458400", + "homepage": "https://www.nsf.gov/awards/about.jsp", + "name": "National Science Foundation Award", + "pattern": "^\\d+$", + "preferred_prefix": "nsf.award", + "uri_format": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1" + }, + "nucc.characteristic": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan.", + "example": "2A", + "example_extras": [ + "11", + "10" + ], + "homepage": "https://nucc.org/index.php/code-sets-mainmenu-41/provider-characteristics-mainmenu-39", + "name": "National Uniform Claim Committee Characteristic", + "pattern": "^\\d(\\d|\\w)$", + "preferred_prefix": "nucc.characteristic" + }, + "nucc.taxonomy": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards.", + "example": "207LH0002X", + "homepage": "https://taxonomy.nucc.org", + "name": "National Uniform Claim Committee Taxonomy", + "pattern": "^\\d{3}\\w(\\w|\\d_)\\d{4}X$", + "preferred_prefix": "nucc.taxonomy", + "references": [ + "https://www.nucc.org/images/stories/CSV/nucc_taxonomy_221.csv", + "https://www.nucc.org" + ] + }, + "nucleardb": { + "comment": "Note that the typo from MIRIAM has spread to several other sources", + "description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.", + "example": "prgr_human", + "homepage": "http://www.receptors.org/nucleardb/", + "keywords": [ + "classification" + ], + "mappings": { + "biocontext": "NUCLEARBD", + "miriam": "nuclearbd", + "n2t": "nuclearbd", + "prefixcommons": "nucleardb" + }, + "name": "NucleaRDB", + "pattern": "^\\w+\\_\\w+$", + "preferred_prefix": "nucleardb", + "publications": [ + { + "doi": "10.1093/nar/gkr960", + "pmc": "PMC3245090", + "pubmed": "22064856", + "title": "NucleaRDB: information system for nuclear receptors.", + "year": 2011 + } + ], + "synonyms": [ + "nuclearbd" + ], + "uri_format": "http://www.receptors.org/nucleardb/proteins/$1" + }, + "nucleotide": { + "description": "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.", + "example": "880798137", + "has_canonical": "insdc", + "homepage": "https://www.ncbi.nlm.nih.gov/", + "mappings": { + "miriam": "nucleotide" + }, + "name": "Nucleotide", + "pattern": "^[a-zA-Z0-9_\\.]+$", + "preferred_prefix": "nucleotide", + "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" + }, + "oa": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture.", + "download_owl": "http://aber-owl.net/media/ontologies/OA/4/oa.owl", + "example": "sourceDateStart", + "homepage": "http://www.w3.org/ns/oa", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "OA", + "biocontext": "oa", + "bioportal": "OA" + }, + "name": "Web Annotation Ontology", + "preferred_prefix": "oa", + "uri_format": "http://www.w3.org/ns/oa#$1" + }, + "oae": { + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqunh He", + "orcid": "0000-0001-9189-9661" + }, + "description": "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.", + "download_owl": "http://purl.obolibrary.org/obo/oae.owl", + "example": "0002959", + "homepage": "https://github.com/OAE-ontology/OAE/", + "keywords": [ + "biomedical science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OAE", + "biocontext": "OAE", + "bioportal": "OAE", + "fairsharing": "FAIRsharing.tw4q8x", + "obofoundry": "oae", + "ols": "oae", + "ontobee": "OAE" + }, + "name": "Ontology of Adverse Events", + "pattern": "^\\d{7}$", + "preferred_prefix": "OAE", + "publications": [ + { + "doi": "10.1186/2041-1480-5-29", + "pmc": "PMC4120740", + "pubmed": "25093068", + "title": "OAE: The Ontology of Adverse Events.", + "year": 2014 + } + ], + "repository": "https://github.com/OAE-ontology/OAE", + "uri_format": "http://purl.obolibrary.org/obo/OAE_$1", + "version": "1.2.44" + }, + "oarcs": { + "contact": { + "email": "mjyoder@illinois.edu", + "github": "mjy", + "name": "Matt Yoder", + "orcid": "0000-0002-5640-5491" + }, + "description": "OArCS is an ontology describing the Arthropod ciruclatory system.", + "download_owl": "http://purl.obolibrary.org/obo/oarcs.owl", + "example": "0000029", + "homepage": "https://github.com/aszool/oarcs", + "keywords": [ + "anatomy", + "angiology", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OARCS", + "biocontext": "OARCS", + "bioportal": "OARCS", + "fairsharing": "FAIRsharing.yqn857", + "obofoundry": "oarcs", + "ols": "oarcs", + "ontobee": "OARCS" + }, + "name": "Ontology of Arthropod Circulatory Systems", + "pattern": "^\\d{7}$", + "preferred_prefix": "OARCS", + "publications": [ + { + "doi": "10.1093/sysbio/syw108", + "pmc": null, + "pubmed": "28123116", + "title": "The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.", + "year": 2017 + } + ], + "repository": "https://github.com/aszool/oarcs", + "uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", + "version": "2019-04-18" + }, + "oba": { + "appears_in": [ + "fovt" + ], + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO.", + "download_json": "http://purl.obolibrary.org/obo/oba.json", + "download_obo": "http://purl.obolibrary.org/obo/oba.obo", + "download_owl": "http://purl.obolibrary.org/obo/oba.owl", + "example": "0000001", + "example_extras": [ + "VT0003769" + ], + "homepage": "https://github.com/obophenotype/bio-attribute-ontology", + "keywords": [ + "biology", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "OBA", + "biocontext": "OBA", + "bioportal": "OBA", + "fairsharing": "FAIRsharing.mp0rwf", + "obofoundry": "oba", + "ols": "oba", + "ontobee": "OBA" + }, + "name": "Ontology of Biological Attributes", + "pattern": "^(VT)?\\d{7}$", + "preferred_prefix": "OBA", + "publications": [ + { + "doi": "10.1101/2023.01.26.525742", + "pmc": "PMC9900877", + "pubmed": "36747660", + "title": "The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences.", + "year": 2023 + } + ], + "repository": "https://github.com/obophenotype/bio-attribute-ontology", + "uri_format": "http://purl.obolibrary.org/obo/OBA_$1", + "version": "2022-11-26" + }, + "oban": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]", + "download_owl": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl", + "download_rdf": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.ttl", + "example": "provenance", + "homepage": "https://github.com/EBISPOT/OBAN", + "keywords": [ + "ontology" + ], + "mappings": { + "biocontext": "OBAN", + "biolink": "OBAN" + }, + "name": "Open Biomedical Annotations", + "pattern": "^\\w+$", + "preferred_prefix": "oban", + "repository": "https://github.com/EBISPOT/OBAN", + "uri_format": "http://purl.org/oban/$1" + }, + "obcs": { + "contact": { + "email": "jiezheng@pennmedicine.upenn.edu", + "github": "zhengj2007", + "name": "Jie Zheng", + "orcid": "0000-0002-2999-0103" + }, + "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ", + "download_owl": "http://purl.obolibrary.org/obo/obcs.owl", + "example": "0000121", + "homepage": "https://github.com/obcs/obcs", + "keywords": [ + "biology", + "biomedical science", + "medical informatics", + "medicine", + "obo", + "ontology", + "statistics" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OBCS", + "biocontext": "OBCS", + "bioportal": "OBCS", + "fairsharing": "FAIRsharing.5p12xh", + "obofoundry": "obcs", + "ols": "obcs", + "ontobee": "OBCS" + }, + "name": "Ontology of Biological and Clinical Statistics", + "pattern": "^\\d{7}$", + "preferred_prefix": "OBCS", + "publications": [ + { + "doi": "10.1186/s13326-016-0100-2", + "pmc": "PMC5024438", + "pubmed": "27627881", + "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.", + "year": 2016 + } + ], + "repository": "https://github.com/obcs/obcs", + "uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", + "version": "101" + }, + "obi": { + "appears_in": [ + "agro", + "foodon", + "hso", + "labo", + "maxo", + "mco", + "one", + "ons", + "proco", + "rbo", + "scdo" + ], + "banana": "OBI", + "banana_peel": ":", + "contact": { + "email": "bpeters@lji.org", + "github": "bpeters42", + "name": "Bjoern Peters", + "orcid": "0000-0002-8457-6693" + }, + "description": "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).", + "download_obo": "https://github.com/obi-ontology/obi/raw/master/views/obi.obo", + "download_owl": "http://purl.obolibrary.org/obo/obi.owl", + "example": "0400109", + "homepage": "http://obi-ontology.org", + "keywords": [ + "biomedical science", + "functional genomics", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OBI", + "biocontext": "OBI", + "bioportal": "OBI", + "fairsharing": "FAIRsharing.284e1z", + "go": "OBI", + "miriam": "obi", + "n2t": "obi", + "obofoundry": "obi", + "ols": "obi", + "ontobee": "OBI", + "prefixcommons": "obi" + }, + "name": "Ontology for Biomedical Investigations", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "OBI", + "publications": [ + { + "doi": "10.1371/journal.pone.0154556", + "pmc": "PMC4851331", + "pubmed": "27128319", + "title": "The Ontology for Biomedical Investigations.", + "year": 2016 + }, + { + "doi": "10.1093/database/bau132", + "pmc": "PMC4309925", + "pubmed": "25632945", + "title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.", + "year": 2015 + }, + { + "doi": "10.1186/2041-1480-4-s1-s6", + "pmc": "PMC3633001", + "pubmed": "23734660", + "title": "Query enhancement through the practical application of ontology: the IEDB and OBI.", + "year": 2013 + }, + { + "doi": "10.4056/sigs.1994602", + "pmc": "PMC3235517", + "pubmed": "22180825", + "title": "Minimum Information about a Genotyping Experiment (MIGEN).", + "year": 2011 + }, + { + "doi": "10.1186/2041-1480-1-s1-s7", + "pmc": "PMC2903726", + "pubmed": "20626927", + "title": "Modeling biomedical experimental processes with OBI.", + "year": 2010 + } + ], + "repository": "https://github.com/obi-ontology/obi", + "uri_format": "http://purl.obolibrary.org/obo/OBI_$1", + "version": "2022-07-11" + }, + "obib": { + "contact": { + "email": "jiezheng@pennmedicine.upenn.edu", + "github": "zhengj2007", + "name": "Jie Zheng", + "orcid": "0000-0002-2999-0103" + }, + "description": "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology.", + "download_owl": "http://purl.obolibrary.org/obo/obib.owl", + "example": "0000389", + "homepage": "https://github.com/biobanking/biobanking", + "keywords": [ + "health science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OBIB", + "biocontext": "OBIB", + "bioportal": "OBIB", + "fairsharing": "FAIRsharing.bxc508", + "obofoundry": "obib", + "ols": "obib", + "ontobee": "OBIB" + }, + "name": "Ontology for Biobanking", + "pattern": "^\\d{7}$", + "preferred_prefix": "OBIB", + "publications": [ + { + "doi": "10.1186/s13326-016-0068-y", + "pmc": "PMC4855778", + "pubmed": "27148435", + "title": "OBIB-a novel ontology for biobanking.", + "year": 2016 + } + ], + "repository": "https://github.com/biobanking/biobanking", + "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", + "version": "2021-11-12" + }, + "obo": { + "contact": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nico Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "description": "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.", + "homepage": "http://www.obofoundry.org/", + "keywords": [ + "ontology and terminology" + ], + "mappings": { + "biocontext": "OBO", + "fairsharing": "FAIRsharing.847069" + }, + "name": "Open Biological and Biomedical Ontologies", + "preferred_prefix": "obo", + "publications": [ + { + "doi": "10.1038/nbt1346", + "pmc": "PMC2814061", + "pubmed": "17989687", + "title": "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.", + "year": 2007 + } + ], + "repository": "https://github.com/OBOFoundry/OBOFoundry.github.io", + "twitter": "OBOFoundry", + "uri_format": "http://purl.obolibrary.org/obo/$1" + }, + "oboinowl": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties", + "download_obo": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo", + "download_owl": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.owl", + "example": "hasDbXref", + "homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib", + "keywords": [ + "life science", + "ontology" + ], + "mappings": { + "biocontext": "oboInOwl", + "biolink": "oboformat", + "fairsharing": "FAIRsharing.aa0eat" + }, + "name": "OBO in OWL", + "preferred_prefix": "oboInOwl", + "repository": "https://github.com/geneontology/go-ontology", + "synonyms": [ + "oboformat", + "oio" + ], + "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" + }, + "occ": { + "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", + "example": "br/1", + "homepage": "https://w3id.org/oc/corpus", + "mappings": { + "miriam": "occ", + "n2t": "occ" + }, + "name": "OpenCitations Corpus", + "pattern": "^[a-z][a-z]/[0-9]+$", + "preferred_prefix": "occ", + "uri_format": "https://w3id.org/oc/corpus/$1" + }, + "oci": { + "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.", + "example": "1-18", + "homepage": "http://opencitations.net", + "mappings": { + "biocontext": "OCI", + "miriam": "oci", + "n2t": "oci" + }, + "name": "Open Citation Identifier", + "pattern": "^[0-9]+-[0-9]+$", + "preferred_prefix": "oci", + "uri_format": "https://w3id.org/oc/oci/$1" + }, + "ocid": { + "banana": "ocid", + "description": "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology.", + "example": "190000021540", + "homepage": "https://ontochem.com/", + "mappings": { + "miriam": "ocid" + }, + "name": "Ontology Concept Identifiers", + "namespace_in_lui": true, + "pattern": "^[0-9]{12}$", + "preferred_prefix": "ocid", + "uri_format": "https://ocid.ontochem.com/prefname?ocid=$1" + }, + "oclc": { + "description": "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information.", + "example": "634515043", + "homepage": "https://www.oclc.org/en/about.html", + "mappings": { + "biocontext": "OCLC", + "miriam": "oclc", + "n2t": "oclc" + }, + "name": "Online Computer Library Center WorldCat", + "pattern": "^[0-9]+$", + "preferred_prefix": "oclc", + "uri_format": "https://www.worldcat.org/oclc/$1" + }, + "odam": { + "description": "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed.", + "example": "frim1", + "homepage": "https://metabolome.cgfb.u-bordeaux.fr/", + "mappings": { + "miriam": "odam" + }, + "name": "Open Data for Access and Mining", + "pattern": "^[A-Za-z0-9]+$", + "preferred_prefix": "odam", + "uri_format": "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1" + }, + "odc.sci": { + "contact": { + "email": "jgrethe@ucsd.edu", + "github": null, + "name": "Jeffrey Grethe", + "orcid": "0000-0001-5212-7052" + }, + "description": "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data.", + "example": "602", + "homepage": "https://odc-sci.org", + "keywords": [ + "biomedical science", + "neurobiology", + "neurology", + "neuroscience" + ], + "mappings": { + "fairsharing": "FAIRsharing.M6Ruz3", + "miriam": "odc.sci", + "re3data": "r3d100014071" + }, + "name": "Open Data Commons for Spinal Cord Injury", + "pattern": "^[0-9]*$", + "preferred_prefix": "odc.sci", + "publications": [ + { + "doi": "10.1089/neu.2019.6674", + "pmc": "PMC7071068", + "pubmed": "31608767", + "title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research.", + "year": 2019 + }, + { + "doi": "s0014-4886(17)30137-1", + "pmc": "PMC6448396", + "pubmed": "28576567", + "title": "Developing a data sharing community for spinal cord injury research.", + "year": null + }, + { + "doi": "10.1016/j.expneurol.2017.05.012", + "pmc": "PMC6448396", + "pubmed": "28576567", + "title": "Developing a data sharing community for spinal cord injury research.", + "year": 2017 + }, + { + "doi": "10.1038/ncomms9581", + "pmc": "PMC4634208", + "pubmed": "26466022", + "title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury.", + "year": 2015 + }, + { + "doi": "10.1038/nn.3838", + "pmc": "PMC4728080", + "pubmed": "25349910", + "title": "Big data from small data: data-sharing in the 'long tail' of neuroscience.", + "year": 2014 + }, + { + "doi": "10.1089/neu.2014.3399", + "pmc": "PMC4186058", + "pubmed": "25077610", + "title": "Development of a database for translational spinal cord injury research.", + "year": 2014 + }, + { + "doi": "10.1371/journal.pone.0059712", + "pmc": "PMC3609747", + "pubmed": "23544088", + "title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats.", + "year": 2013 + }, + { + "doi": "10.1007/s12975-011-0121-1", + "pmc": "PMC3236294", + "pubmed": "22207883", + "title": "Syndromics: a bioinformatics approach for neurotrauma research.", + "year": 2011 + } + ], + "uri_format": "https://odc-sci.org/data/$1" + }, + "odc.tbi": { + "description": "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data.", + "example": "408", + "homepage": "https://odc-tbi.org", + "mappings": { + "miriam": "odc.tbi" + }, + "name": "Open Data Commons for Traumatic Brain Injury", + "pattern": "^[0-9]*$", + "preferred_prefix": "odc.tbi", + "uri_format": "https://odc-tbi.org/data/$1" + }, + "odor": { + "description": "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors", + "example": "74", + "homepage": "http://senselab.med.yale.edu/OdorDB", + "mappings": { + "biocontext": "ODOR", + "miriam": "odor", + "n2t": "odor" + }, + "name": "Odor Molecules DataBase", + "pattern": "^\\d+$", + "preferred_prefix": "odor", + "uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5" + }, + "ogg": { + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ", + "download_owl": "http://purl.obolibrary.org/obo/ogg.owl", + "example": "3000887619", + "homepage": "https://bitbucket.org/hegroup/ogg", + "keywords": [ + "biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OGG", + "biocontext": "OGG", + "bioportal": "OGG", + "fairsharing": "FAIRsharing.zmx7nn", + "obofoundry": "ogg", + "ols": "ogg", + "ontobee": "OGG" + }, + "name": "The Ontology of Genes and Genomes", + "pattern": "^\\d+$", + "preferred_prefix": "OGG", + "repository": "https://bitbucket.org/hegroup/ogg", + "uri_format": "http://purl.obolibrary.org/obo/OGG_$1", + "version": "1.0.59" + }, + "ogi": { + "contact": { + "email": "linikujp@gmail.com", + "github": "linikujp", + "name": "Asiyah Yu Lin", + "orcid": "0000-0002-5379-5359" + }, + "deprecated": true, + "description": "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n", + "download_owl": "http://purl.obolibrary.org/obo/ogi.owl", + "example": "0000019", + "homepage": "https://code.google.com/archive/p/ontology-for-genetic-interval/", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "aberowl": "OGI", + "biocontext": "OGI", + "bioportal": "OGI", + "obofoundry": "ogi", + "ols": "ogi", + "ontobee": "OGI" + }, + "name": "Ontology for genetic interval", + "pattern": "^\\d{7}$", + "preferred_prefix": "OGI", + "synonyms": [ + "OGI.owl" + ], + "uri_format": "http://purl.obolibrary.org/obo/OGI_$1", + "version": "2.0" + }, + "ogms": { + "appears_in": [ + "labo", + "scdo" + ], + "contact": { + "email": "baeverma@jcvi.org", + "github": "BAevermann", + "name": "Brian Aevermann", + "orcid": "0000-0003-1346-1327" + }, + "description": "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.", + "download_obo": "http://purl.obolibrary.org/obo/ogms.obo", + "download_owl": "http://purl.obolibrary.org/obo/ogms.owl", + "example": "0000031", + "homepage": "https://github.com/OGMS/ogms", + "keywords": [ + "biomedical science", + "medicine", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OGMS", + "bartoc": "216", + "biocontext": "OGMS", + "bioportal": "OGMS", + "fairsharing": "FAIRsharing.rvz0m9", + "obofoundry": "ogms", + "ols": "ogms", + "ontobee": "OGMS" + }, + "name": "Ontology for General Medical Science", + "pattern": "^\\d{7}$", + "preferred_prefix": "OGMS", + "publications": [ + { + "doi": null, + "pmc": null, + "pubmed": "25991121", + "title": "Biomarkers in the ontology for general medical science.", + "year": 2015 + }, + { + "doi": "10.1186/2041-1480-4-42", + "pmc": "PMC4028878", + "pubmed": "24314207", + "title": "The neurological disease ontology.", + "year": 2013 + } + ], + "repository": "https://github.com/OGMS/ogms", + "synonyms": [ + "ogms/OMRE" + ], + "uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", + "version": "2021-08-19" + }, + "ogsf": { + "contact": { + "email": "linikujp@gmail.com", + "github": "linikujp", + "name": "Asiyah Yu Lin", + "orcid": "0000-0002-5379-5359" + }, + "description": "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process.", + "download_owl": "http://purl.obolibrary.org/obo/ogsf.owl", + "example": "0000025", + "homepage": "https://github.com/linikujp/OGSF", + "keywords": [ + "biomedical science", + "epidemiology", + "genetics", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OGSF", + "biocontext": "OGSF", + "bioportal": "OGSF", + "fairsharing": "FAIRsharing.egv2cz", + "obofoundry": "ogsf", + "ols": "ogsf", + "ontobee": "OGSF" + }, + "name": "Ontology of Genetic Susceptibility Factor", + "pattern": "^\\d{7}$", + "preferred_prefix": "OGSF", + "publications": [ + { + "doi": "10.1186/2041-1480-5-19", + "pmc": "PMC4068904", + "pubmed": "24963371", + "title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.", + "year": 2014 + }, + { + "doi": null, + "pmc": null, + "pubmed": "20847592", + "title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease.", + "year": 2009 + } + ], + "repository": "https://github.com/linikujp/OGSF", + "uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", + "version": "2.0" + }, + "ohd": { + "contact": { + "email": "wdduncan@gmail.com", + "github": "wdduncan", + "name": "Bill Duncan", + "orcid": "0000-0001-9625-1899" + }, + "description": "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies.", + "download_owl": "http://purl.obolibrary.org/obo/ohd.owl", + "example": "0000006", + "homepage": "https://purl.obolibrary.org/obo/ohd/home", + "keywords": [ + "dentistry", + "medicine", + "obo", + "ontology", + "oral surgery" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OHD", + "biocontext": "OHD", + "bioportal": "OHD", + "fairsharing": "FAIRsharing.bg7bb6", + "obofoundry": "ohd", + "ols": "ohd", + "ontobee": "OHD" + }, + "name": "Oral Health and Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "OHD", + "publications": [ + { + "doi": "10.1186/s13326-020-00222-0", + "pmc": "PMC7439527", + "pubmed": "32819435", + "title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology.", + "year": 2020 + } + ], + "repository": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology", + "uri_format": "http://purl.obolibrary.org/obo/OHD_$1", + "version": "2016-06-27" + }, + "ohmi": { + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "description": "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.", + "download_owl": "http://purl.obolibrary.org/obo/ohmi.owl", + "example": "0000460", + "homepage": "https://github.com/ohmi-ontology/ohmi", + "keywords": [ + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OHMI", + "biocontext": "OHMI", + "bioportal": "OHMI", + "fairsharing": "FAIRsharing.cz9cnp", + "obofoundry": "ohmi", + "ols": "ohmi", + "ontobee": "OHMI" + }, + "name": "Ontology of Host-Microbiome Interactions", + "pattern": "^\\d{7}$", + "preferred_prefix": "OHMI", + "repository": "https://github.com/ohmi-ontology/ohmi", + "uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", + "version": "2019-09-17" + }, + "ohpi": { + "contact": { + "email": "edong@umich.edu", + "github": "e4ong1031", + "name": "Edison Ong", + "orcid": "0000-0002-5159-414X" + }, + "description": "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).", + "download_owl": "http://purl.obolibrary.org/obo/ohpi.owl", + "example": "9001411", + "homepage": "https://github.com/OHPI/ohpi", + "keywords": [ + "bioinformatics", + "biomedical science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OHPI", + "bioportal": "OHPI", + "fairsharing": "FAIRsharing.vxpUJ6", + "obofoundry": "ohpi", + "ols": "ohpi", + "ontobee": "OHPI" + }, + "name": "Ontology of Host Pathogen Interactions", + "pattern": "^\\d+$", + "preferred_prefix": "OHPI", + "publications": [ + { + "doi": "10.1093/nar/gky999", + "pmc": "PMC6324020", + "pubmed": "30365026", + "title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens.", + "year": 2019 + } + ], + "repository": "https://github.com/OHPI/ohpi", + "uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", + "version": "2019-10-02" + }, + "oid": { + "contributor_extras": [ + { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + ], + "description": "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes.", + "example": "2.16.840", + "example_extras": [ + "2", + "2.16", + "2.16.840.1", + "2.16.840.1.113883", + "2.16.840.1.113883.6", + "2.16.840.1.113883.6.88" + ], + "homepage": "http://www.oid-info.com/introduction.htm", + "mappings": { + "miriam": "oid", + "n2t": "oid" + }, + "name": "ISO Object Identifier", + "pattern": "^[\\d.]+$", + "preferred_prefix": "oid", + "providers": [ + { + "code": "oid_www", + "description": "OID w/ WWW", + "homepage": "http://www.oid-info.com", + "name": "OID w/ WWW", + "uri_format": "http://www.oid-info.com/get/$1" + }, + { + "code": "orange", + "description": "Mirror of OID site from Orange", + "homepage": "https://oid-rep.orange-labs.fr", + "name": "Mirror of OID site from Orange", + "uri_format": "https://oid-rep.orange-labs.fr/get/$1" + } + ], + "references": [ + "https://en.wikipedia.org/wiki/Object_identifier" + ], + "uri_format": "http://oid-info.com/get/$1" + }, + "olatdv": { + "contact": { + "email": "frederic.bastian@unil.ch", + "github": "fbastian", + "name": "Frédéric Bastian", + "orcid": "0000-0002-9415-5104" + }, + "description": "Life cycle stages for Medaka", + "download_obo": "http://purl.obolibrary.org/obo/olatdv.obo", + "download_owl": "http://purl.obolibrary.org/obo/olatdv.owl", + "example": "0000210", + "homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv", + "keywords": [ + "aquaculture", + "developmental biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OLATDV", + "biocontext": "OLATDV", + "bioportal": "OLATDV", + "fairsharing": "FAIRsharing.c86z66", + "obofoundry": "olatdv", + "ols": "olatdv", + "ontobee": "OlatDv" + }, + "name": "Medaka Developmental Stages", + "pattern": "^\\d{7}$", + "preferred_prefix": "OlatDv", + "repository": "https://github.com/obophenotype/developmental-stage-ontologies", + "uri_format": "http://purl.obolibrary.org/obo/OLATDV_$1", + "version": "2020-03-10" + }, + "om": { + "contact": { + "email": "hajo.rijgersberg@wur.nl", + "github": null, + "name": "Hajo Rijgersberg", + "orcid": null + }, + "description": "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging", + "download_owl": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf", + "example": "Dimension", + "homepage": "https://github.com/HajoRijgersberg/OM", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "OM", + "agroportal": "OM", + "bioportal": "OM", + "ols": "om" + }, + "name": "Ontology of units of Measure", + "preferred_prefix": "om", + "repository": "https://github.com/HajoRijgersberg/OM", + "uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1", + "version": "2.0.38" + }, + "oma.grp": { + "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", + "example": "LCSCCPN", + "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", + "mappings": { + "biocontext": "OMA.GRP", + "miriam": "oma.grp", + "n2t": "oma.grp" + }, + "name": "OMA Group", + "pattern": "^[A-Z]+$", + "preferred_prefix": "oma.grp", + "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1" + }, + "oma.hog": { + "banana": "HOG", + "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ", + "example": "0459895", + "homepage": "https://omabrowser.org", + "mappings": { + "miriam": "oma.hog" + }, + "name": "OMA HOGs", + "namespace_in_lui": true, + "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", + "preferred_prefix": "oma.hog", + "uri_format": "https://omabrowser.org/oma/hog/HOG:$1" + }, + "oma.protein": { + "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records.", + "example": "HUMAN16963", + "homepage": "https://omabrowser.org/cgi-bin/gateway.pl", + "mappings": { + "biocontext": "OMA.PROTEIN", + "miriam": "oma.protein", + "n2t": "oma.protein" + }, + "name": "OMA Protein", + "pattern": "^[A-Z0-9]{5}\\d+$", + "preferred_prefix": "oma.protein", + "uri_format": "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1" + }, + "omia": { + "contact": { + "email": "imke.tammen@sydney.edu.au", + "github": "ImkeTammen", + "name": "Imke Tammen", + "orcid": "0000-0002-5520-6597" + }, + "contributor_extras": [ + { + "email": "imke.tammen@sydney.edu.au", + "github": "ImkeTammen", + "name": "Imke Tammen", + "orcid": "0000-0002-5520-6597" + } + ], + "description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in 363 animal species (other than human and mouse and rats and zebrafish, which have their own resources).", + "example": "1000", + "homepage": "https://omia.org", + "keywords": [ + "classification", + "disorders", + "gene", + "model organism database", + "traits" + ], + "mappings": { + "biocontext": "OMIA", + "miriam": "omia", + "n2t": "omia", + "prefixcommons": "omia" + }, + "name": "Online Mendelian Inheritance in Animals", + "pattern": "^\\d+$", + "preferred_prefix": "omia", + "uri_format": "https://omia.org/OMIA$1" + }, + "omiabis": { + "appears_in": [ + "labo" + ], + "contact": { + "email": "mbrochhausen@gmail.com", + "github": null, + "name": "Mathias Brochhausen", + "orcid": "0000-0003-1834-3856" + }, + "deprecated": true, + "description": "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)", + "download_owl": "http://purl.obolibrary.org/obo/omiabis.owl", + "example": "0001079", + "homepage": "https://github.com/OMIABIS/omiabis-dev", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OMIABIS", + "biocontext": "OMIABIS", + "bioportal": "OMIABIS", + "obofoundry": "omiabis", + "ols": "omiabis", + "ontobee": "OMIABIS" + }, + "name": "Ontologized MIABIS", + "pattern": "^\\d{7}$", + "preferred_prefix": "OMIABIS", + "repository": "https://github.com/OMIABIS/omiabis-dev", + "uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", + "version": "2014-05-28" + }, + "omim": { + "contact": { + "email": "ahamosh@jhmi.edu", + "github": "ahamosh", + "name": "Ada Hamosh", + "orcid": "0000-0002-1780-5230" + }, + "description": "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders.", + "example": "603903", + "homepage": "https://omim.org/", + "keywords": [ + "biomedical science", + "gene", + "gene expression", + "ontology" + ], + "mappings": { + "aberowl": "OMIM", + "biocontext": "OMIM", + "bioportal": "OMIM", + "edam": "1153", + "fairsharing": "FAIRsharing.b084yh", + "go": "OMIM", + "hl7": "2.16.840.1.113883.6.174", + "miriam": "mim", + "n2t": "mim", + "ncbi": "MIM", + "prefixcommons": "omim", + "uniprot": "DB-0062", + "wikidata": "P492" + }, + "name": "Online Mendelian Inheritance in Man", + "pattern": "^\\d+$", + "preferred_prefix": "omim", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "OMIM mirror at John Hopkins", + "homepage": "http://mirror.omim.org/", + "name": "OMIM mirror at John Hopkins", + "uri_format": "http://mirror.omim.org/entry/$1" + }, + { + "code": "legacy", + "description": "This is the actual endpoint for OMIM entries", + "homepage": "https://www.omim.org", + "name": "OMIM", + "uri_format": "https://www.omim.org/entry/$1" + }, + { + "code": "miriam_legacy", + "description": "Legacy URLs for identifiers.org", + "homepage": "http://identifiers.org", + "name": "MIRIAM Legacy", + "uri_format": "http://identifiers.org/omim/$1" + }, + { + "code": "ncbi.omim", + "description": "An NCBI endpoint for OMIM entries", + "homepage": "http://www.ncbi.nlm.nih.gov/omim", + "name": "NCBI", + "uri_format": "http://www.ncbi.nlm.nih.gov/omim/$1" + }, + { + "code": "purl", + "description": "An extra purl that was registred, but probably won't be used.", + "homepage": "https://www.omim.org", + "name": "OMIM PURL (not in use)", + "uri_format": "https://purl.org/mim/MIM:$1" + }, + { + "code": "purl2", + "description": "An extra purl that was registred, but probably won't be used.", + "homepage": "https://www.omim.org", + "name": "OMIM PURL (not in use)", + "uri_format": "https://omim.org/OMIM:$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gku1205", + "pmc": "PMC4383985", + "pubmed": "25428349", + "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gki033", + "pmc": "PMC539987", + "pubmed": "15608251", + "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.", + "year": 2005 + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/497" + ], + "synonyms": [ + "OMIM", + "mim" + ], + "uri_format": "https://omim.org/MIM:$1" + }, + "omim.ps": { + "banana": "PS", + "contact": { + "email": "ahamosh@jhmi.edu", + "github": "ahamosh", + "name": "Ada Hamosh", + "orcid": "0000-0002-1780-5230" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": null, + "github": "sierra-moxon", + "name": "Sierra Moxon", + "orcid": "0000-0002-8719-7760" + } + ], + "description": "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome.", + "example": "214100", + "homepage": "https://www.omim.org/phenotypicSeriesTitles/all", + "mappings": { + "biolink": "OMIM.PS" + }, + "name": "OMIM Phenotypic Series", + "part_of": "omim", + "pattern": "^\\d+$", + "preferred_prefix": "omim.ps", + "providers": [ + { + "code": "legacy", + "description": "This is the actual endpoint for OMIM phenotypic series entries", + "homepage": "https://www.omim.org", + "name": "OMIM", + "uri_format": "https://omim.org/phenotypicSeries/PS$1" + } + ], + "synonyms": [ + "MIMPS", + "OMIMPS", + "PS", + "mim.ps" + ], + "uri_format": "https://omim.org/MIM:PS$1" + }, + "omit": { + "appears_in": [ + "mco" + ], + "contact": { + "email": "huang@southalabama.edu", + "github": "Huang-OMIT", + "name": "Jingshan Huang", + "orcid": "0000-0003-2408-2883" + }, + "description": "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).", + "download_obo": "https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo", + "download_owl": "http://purl.obolibrary.org/obo/omit.owl", + "example": "0000069", + "homepage": "http://omit.cis.usouthal.edu/", + "keywords": [ + "biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OMIT", + "biocontext": "OMIT", + "bioportal": "OMIT", + "fairsharing": "FAIRsharing.mf91p5", + "miriam": "omit", + "n2t": "omit", + "obofoundry": "omit", + "ols": "omit", + "ontobee": "OMIT" + }, + "name": "Ontology for MicroRNA Target", + "pattern": "^\\d{7}$", + "preferred_prefix": "OMIT", + "publications": [ + { + "doi": "10.1186/s13326-016-0064-2", + "pmc": "PMC4863347", + "pubmed": "27175225", + "title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.", + "year": 2016 + }, + { + "doi": "10.1371/journal.pone.0100855", + "pmc": "PMC4099014", + "pubmed": "25025130", + "title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain.", + "year": 2014 + }, + { + "doi": "10.1007/s11095-011-0573-8", + "pmc": null, + "pubmed": "21879385", + "title": "OMIT: a domain-specific knowledge base for microRNA target prediction.", + "year": 2011 + } + ], + "repository": "https://github.com/OmniSearch/omit", + "synonyms": [ + "OMIT" + ], + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1", + "version": "2019-06-07" + }, + "omo": { + "appears_in": [ + "pcl" + ], + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).", + "download_owl": "http://purl.obolibrary.org/obo/omo.owl", + "homepage": "https://github.com/information-artifact-ontology/ontology-metadata", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "OMO", + "bioportal": "OMO", + "obofoundry": "omo", + "ols": "omo", + "ontobee": "OMO" + }, + "name": "OBO Metadata Ontology", + "no_own_terms": true, + "preferred_prefix": "OMO", + "repository": "https://github.com/information-artifact-ontology/ontology-metadata", + "uri_format": "http://purl.obolibrary.org/obo/OMO_$1", + "version": "2022-04-27" + }, + "omop": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nico Matentzoglu", + "orcid": "0000-0002-7356-1779" + } + ], + "description": "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.", + "example": "1", + "homepage": "https://www.ohdsi.org/data-standardization/the-common-data-model/", + "name": "Observational Medical Outcomes Partnership", + "pattern": "^\\d+$", + "preferred_prefix": "omop", + "providers": [ + { + "code": "ohdsi.api", + "description": "Programmatic access to OMOP terms", + "homepage": "http://api.ohdsi.org", + "name": "OHDSI API", + "uri_format": "http://api.ohdsi.org/WebAPI/vocabulary/concept/$1" + }, + { + "code": "ohdsi.data", + "description": " https://faircookbook.elixir-europe.org/content/recipes/applied-examples/ehden-ohdsi.html suggests https://data.ohdsi.org/concept/ as another uri expansion but it does not resolve.", + "homepage": "https://data.ohdsi.org/concept", + "name": "OHDSI Data Endpoint", + "uri_format": "https://data.ohdsi.org/concept/$1" + } + ], + "references": [ + "https://github.com/callahantiff/OMOP2OBO", + "https://github.com/biopragmatics/bioregistry/issues/599", + "https://github.com/biopragmatics/bioregistry/pull/600" + ], + "synonyms": [ + "OMOP" + ], + "uri_format": "https://athena.ohdsi.org/search-terms/terms/$1" + }, + "omp": { + "appears_in": [ + "mco" + ], + "contact": { + "email": "jimhu@tamu.edu", + "github": "jimhu-tamu", + "name": "James C. Hu", + "orcid": "0000-0001-9016-2684" + }, + "description": "An ontology of phenotypes covering microbes", + "download_obo": "http://purl.obolibrary.org/obo/omp.obo", + "download_owl": "http://purl.obolibrary.org/obo/omp.owl", + "example": "0005067", + "homepage": "http://microbialphenotypes.org", + "keywords": [ + "biology", + "data mining", + "microbiology", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OMP", + "biocontext": "OMP", + "bioportal": "OMP", + "fairsharing": "FAIRsharing.cc3f2x", + "obofoundry": "omp", + "ols": "omp", + "ontobee": "OMP" + }, + "name": "Ontology of Microbial Phenotypes", + "pattern": "^\\d{7}$", + "preferred_prefix": "OMP", + "publications": [ + { + "doi": "10.1186/s12866-014-0294-3", + "pmc": "PMC4287307", + "pubmed": "25433798", + "title": "An ontology for microbial phenotypes.", + "year": 2014 + } + ], + "repository": "https://github.com/microbialphenotypes/OMP-ontology", + "uri_format": "http://purl.obolibrary.org/obo/OMP_$1", + "version": "2022-08-05" + }, + "omrse": { + "appears_in": [ + "labo" + ], + "contact": { + "email": "hoganwr@gmail.com", + "github": "hoganwr", + "name": "Bill Hogan", + "orcid": "0000-0002-9881-1017" + }, + "description": "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations.", + "download_json": "http://purl.obolibrary.org/obo/omrse.json", + "download_obo": "https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo", + "download_owl": "http://purl.obolibrary.org/obo/omrse.owl", + "example": "00000022", + "homepage": "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview", + "keywords": [ + "biomedical science", + "demographics", + "health science", + "obo", + "ontology", + "social science" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OMRSE", + "biocontext": "OMRSE", + "bioportal": "OMRSE", + "fairsharing": "FAIRsharing.z0p37e", + "obofoundry": "omrse", + "ols": "omrse", + "ontobee": "OMRSE" + }, + "name": "Ontology of Medically Related Social Entities", + "pattern": "^\\d{8}$", + "preferred_prefix": "OMRSE", + "publications": [ + { + "doi": "10.1186/s13326-016-0087-8", + "pmc": "PMC4942889", + "pubmed": "27406187", + "title": "The ontology of medically related social entities: recent developments.", + "year": 2016 + } + ], + "repository": "https://github.com/ufbmi/OMRSE", + "uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", + "version": "2022-04-06" + }, + "oncotree": { + "appears_in": [ + "efo" + ], + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.", + "example": "BLL", + "homepage": "http://oncotree.mskcc.org", + "keywords": [ + "cancer", + "clinical decision support systems", + "oncology" + ], + "name": "OncoTree", + "preferred_prefix": "oncotree", + "uri_format": "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1" + }, + "one": { + "contact": { + "email": "chenyangnutrition@gmail.com", + "github": "cyang0128", + "name": "Chen Yang", + "orcid": "0000-0001-9202-5309" + }, + "depends_on": [ + "foodon", + "obi", + "ons" + ], + "description": "An ontology to standardize research output of nutritional epidemiologic studies.", + "download_owl": "http://purl.obolibrary.org/obo/one.owl", + "example": "0001021", + "homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", + "keywords": [ + "epidemiology", + "life science", + "nutritional science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ONE", + "bioportal": "ONE", + "fairsharing": "FAIRsharing.USxx0K", + "obofoundry": "one", + "ols": "one", + "ontobee": "ONE" + }, + "name": "Ontology for Nutritional Epidemiology", + "pattern": "^\\d{7}$", + "preferred_prefix": "ONE", + "publications": [ + { + "doi": "e1300", + "pmc": "PMC6628051", + "pubmed": "31181762", + "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.", + "year": null + }, + { + "doi": "10.3390/nu11061300", + "pmc": "PMC6628051", + "pubmed": "31181762", + "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.", + "year": 2019 + } + ], + "repository": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", + "uri_format": "http://purl.obolibrary.org/obo/ONE_$1" + }, + "ons": { + "appears_in": [ + "one" + ], + "contact": { + "email": "francesco.vitali@ibba.cnr.it", + "github": "FrancescoVit", + "name": "Francesco Vitali", + "orcid": "0000-0001-9125-4337" + }, + "depends_on": [ + "bfo", + "chebi", + "envo", + "foodon", + "ncbitaxon", + "obi", + "ro", + "uberon" + ], + "description": "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.", + "download_owl": "http://purl.obolibrary.org/obo/ons.owl", + "example": "0000060", + "homepage": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", + "keywords": [ + "biomedical science", + "nutritional science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ONS", + "bioportal": "ONS", + "fairsharing": "FAIRsharing.rfec93", + "obofoundry": "ons", + "ols": "ons", + "ontobee": "ONS" + }, + "name": "Ontology for Nutritional Studies", + "pattern": "^\\d{7}$", + "preferred_prefix": "ONS", + "publications": [ + { + "doi": "10.1186/s12263-018-0601-y", + "pmc": "PMC5928560", + "pubmed": "29736190", + "title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition.", + "year": 2018 + } + ], + "repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", + "uri_format": "http://purl.obolibrary.org/obo/ONS_$1", + "version": "Release version 1.2.3" + }, + "ontoavida": { + "contact": { + "email": "fortuna@ebd.csic.es", + "github": "miguelfortuna", + "name": "Miguel A. Fortuna", + "orcid": "0000-0002-8374-1941" + }, + "depends_on": [ + "fbcv", + "gsso", + "ncit", + "ro", + "stato" + ], + "description": "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html", + "download_obo": "http://purl.obolibrary.org/obo/ontoavida.obo", + "download_owl": "http://purl.obolibrary.org/obo/ontoavida.owl", + "example": "00000001", + "homepage": "https://gitlab.com/fortunalab/ontoavida", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ONTOAVIDA", + "bioportal": "ONTOAVIDA", + "obofoundry": "ontoavida", + "ols": "ontoavida", + "ontobee": "ONTOAVIDA" + }, + "name": "Ontology for Avida digital evolution platform", + "pattern": "^\\d{8}$", + "preferred_prefix": "ONTOAVIDA", + "repository": "https://gitlab.com/fortunalab/ontoavida", + "uri_format": "http://purl.obolibrary.org/obo/ONTOAVIDA_$1", + "version": "2022-03-15" + }, + "ontoneo": { + "contact": { + "email": "fernanda.farinelli@gmail.com", + "github": "FernandaFarinelli", + "name": "Fernanda Farinelli", + "orcid": "0000-0003-2338-8872" + }, + "description": "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby.", + "download_owl": "http://purl.obolibrary.org/obo/ontoneo.owl", + "example": "00000098", + "homepage": "http://ontoneo.com", + "keywords": [ + "obo", + "obstetrics", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "ONTONEO", + "biocontext": "ONTONEO", + "bioportal": "ONTONEO", + "fairsharing": "FAIRsharing.5a4y1y", + "obofoundry": "ontoneo", + "ols": "ontoneo", + "ontobee": "ONTONEO" + }, + "name": "Obstetric and Neonatal Ontology", + "pattern": "^\\d{8}$", + "preferred_prefix": "ONTONEO", + "publications": [ + { + "doi": "10.1002/asi.23900", + "pmc": null, + "pubmed": null, + "title": "Ontologies for the representation of electronic medical records: The obstetric and neonatal ontology", + "year": null + } + ], + "repository": "https://github.com/ontoneo-project/Ontoneo", + "uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", + "version": "v1.6" + }, + "oostt": { + "contact": { + "email": "mbrochhausen@gmail.com", + "github": "mbrochhausen", + "name": "Mathias Brochhausen", + "orcid": "0000-0003-1834-3856" + }, + "description": "An ontology built for representating the organizational components of trauma centers and trauma systems.", + "download_owl": "http://purl.obolibrary.org/obo/oostt.owl", + "example": "00000099", + "homepage": "https://github.com/OOSTT/OOSTT", + "keywords": [ + "obo", + "ontology", + "traumatology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OOSTT", + "biocontext": "OOSTT", + "bioportal": "OOSTT", + "fairsharing": "FAIRsharing.b4sa0w", + "obofoundry": "oostt", + "ols": "oostt", + "ontobee": "OOSTT" + }, + "name": "Ontology of Organizational Structures of Trauma centers and Trauma systems", + "pattern": "^\\d{8}$", + "preferred_prefix": "OOSTT", + "repository": "https://github.com/OOSTT/OOSTT", + "uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", + "version": "2021-01-11" + }, + "opb": { + "banana": "OPB", + "banana_peel": "_", + "contact": { + "email": "maxneal@gmail.com", + "github": null, + "name": "Maxwell L. 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It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.", + "download_owl": "http://aber-owl.net/media/ontologies/OPB/13/opb.owl", + "example": "00573", + "homepage": "http://bioportal.bioontology.org/ontologies/OPB", + "keywords": [ + "life science", + "ontology", + "physics", + "structure" + ], + "mappings": { + "aberowl": "OPB", + "biocontext": "OPB", + "bioportal": "OPB", + "fairsharing": "FAIRsharing.qcceez", + "miriam": "opb", + "n2t": "opb", + "prefixcommons": "opb" + }, + "name": "Ontology of Physics for Biology", + "pattern": "^\\d+$", + "preferred_prefix": "opb", + "publications": [ + { + "doi": "10.1186/2041-1480-4-41", + "pmc": "PMC3904761", + "pubmed": "24295137", + "title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes.", + "year": 2013 + }, + { + "doi": "10.1371/journal.pone.0028708", + "pmc": "PMC3246444", + "pubmed": "22216106", + "title": "Physical properties of biological entities: an introduction to the ontology of physics for biology.", + "year": 2011 + } + ], + "uri_format": "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1" + }, + "openalex": { + "contact": { + "email": "hpiwowar@gmail.com", + "github": "hpiwowar", + "name": "Heather Piwowar", + "orcid": "0000-0003-1613-5981" + }, + "contributor": { + "email": null, + "github": "dhimmel", + "name": "Daniel Himmelstein", + "orcid": "0000-0002-3012-7446" + }, + "description": "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other.", + "example": "W2741809807", + "github_request_issue": 280, + "homepage": "https://openalex.org/", + "keywords": [ + "knowledge graph", + "wikidata" + ], + "name": "OpenAlex", + "pattern": "^[WAICV]\\d{2,}$", + "preferred_prefix": "openalex", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://openalex.org/$1" + }, + "opl": { + "contact": { + "email": "jiezheng@pennmedicine.upenn.edu", + "github": "zhengj2007", + "name": "Jie Zheng", + "orcid": "0000-0002-2999-0103" + }, + "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.", + "download_owl": "http://purl.obolibrary.org/obo/opl.owl", + "example": "0000319", + "homepage": "https://github.com/OPL-ontology/OPL", + "keywords": [ + "anatomy", + "developmental biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "OPL", + "biocontext": "OPL", + "bioportal": "OPL", + "fairsharing": "FAIRsharing.ez2nhb", + "obofoundry": "opl", + "ols": "opl", + "ontobee": "OPL" + }, + "name": "Ontology for Parasite LifeCycle", + "pattern": "^\\d{7}$", + "preferred_prefix": "OPL", + "publications": [ + { + "doi": "10.1186/2041-1480-3-5", + "pmc": "PMC3488002", + "pubmed": "22621763", + "title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.", + "year": 2012 + } + ], + "repository": "https://github.com/OPL-ontology/OPL", + "uri_format": "http://purl.obolibrary.org/obo/OPL_$1", + "version": "2021-01-28" + }, + "opm": { + "description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.", + "example": "1h68", + "homepage": "http://opm.phar.umich.edu/", + "keywords": [ + "computer science", + "data management" + ], + "mappings": { + "biocontext": "OPM", + "fairsharing": "FAIRsharing.7c683b", + "miriam": "opm", + "n2t": "opm" + }, + "name": "Orientations of Proteins in Membranes Database", + "pattern": "^[0-9][A-Za-z0-9]{3}$", + "preferred_prefix": "opm", + "uri_format": "http://opm.phar.umich.edu/protein.php?pdbid=$1" + }, + "opmi": { + "appears_in": [ + "labo", + "scdo" + ], + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "description": "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. 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It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases.", + "example": "85163", + "homepage": "http://www.orpha.net/consor/", + "keywords": [ + "disease", + "drug", + "human", + "life science", + "ontology and terminology" + ], + "mappings": { + "biocontext": "Orphanet", + "biolink": "orphanet", + "fairsharing": "FAIRsharing.6bd5k6", + "miriam": "orphanet", + "n2t": "orphanet", + "prefixcommons": "orphanet", + "uniprot": "DB-0068", + "wikidata": "P1550" + }, + "name": "Orphanet", + "pattern": "^\\d+$", + "preferred_prefix": "orphanet", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Bio2RDF", + "homepage": "http://orphanet.bio2rdf.org/fct", + "name": "Bio2RDF", + "uri_format": "http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$1" + } + ], + "publications": [ + { + "doi": null, + "pmc": null, + "pubmed": "19058507", + "title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases].", + "year": 2008 + } + ], + "synonyms": [ + "ORPHA" + ], + "twitter": "orphanet", + "uri_format": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1" + }, + "orphanet.ordo": { + "banana": "Orphanet", + "banana_peel": "_", + "contact": { + "email": "ordo.orphanet@inserm.fr", + "github": null, + "name": "Ana Rath", + "orcid": "0000-0003-4308-6337" + }, + "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", + "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl", + "example": "C023", + "example_extras": [ + "478" + ], + "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo", + "keywords": [ + "biomedical science", + "health science", + "ontology" + ], + "mappings": { + "aberowl": "ordo", + "biocontext": "ORPHANET.ORDO", + "biolink": "ORPHA", + "bioportal": "ORDO", + "cellosaurus": "ORDO", + "fairsharing": "FAIRsharing.pbbnwa", + "miriam": "orphanet.ordo", + "n2t": "orphanet.ordo", + "ols": "ordo" + }, + "name": "Orphanet Rare Disease Ontology", + "pattern": "^C?\\d+$", + "preferred_prefix": "orphanet.ordo", + "publications": [ + { + "doi": null, + "pmc": null, + "pubmed": "22874158", + "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM.", + "year": 2012 + } + ], + "synonyms": [ + "ordo" + ], + "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1", + "version": "4.1" + }, + "orth": { + "contact": { + "email": "jfernand@um.es", + "github": "jesualdotomasfernandezbreis", + "name": "Jesualdo Tomás Fernández-Breis", + "orcid": "0000-0002-7558-2880" + }, + "description": "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way.", + "download_owl": "https://github.com/qfo/OrthologyOntology/raw/master/orthOntology_RC_v2_A.owl", + "example": "HomologyRelation", + "homepage": "https://github.com/qfo/OrthologyOntology", + "keywords": [ + "comparative genomics", + "ontology" + ], + "mappings": { + "aberowl": "ORTH", + "bioportal": "ORTH", + "fairsharing": "FAIRsharing.4877h0", + "ols": "orth" + }, + "name": "Orthology Ontology", + "preferred_prefix": "orth", + "publications": [ + { + "doi": "10.1186/s13326-016-0077-x", + "pmc": "PMC4893294", + "pubmed": "27259657", + "title": "The Orthology Ontology: development and applications.", + "year": 2016 + } + ], + "repository": "https://github.com/qfo/OrthologyOntology", + "uri_format": "http://purl.org/net/orth#$1", + "version": "This ontology is the second version of the orthology ontology first published in 2015 and available at http://purl.bioontology.org/ontology/ORTH .\n@authors T.M. de Farias, H. Chiba, J.T. Fernandez-Breis, E. Antezana, D. Kuznetsov, C. Dessimoz and F. Villiers." + }, + "orthodb": { + "description": "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups", + "example": "Q9P0K8", + "homepage": "https://www.orthodb.org", + "keywords": [ + "dna", + "eukaryotic", + "life science", + "protein" + ], + "mappings": { + "biocontext": "ORTHODB", + "fairsharing": "FAIRsharing.x989d5", + "miriam": "orthodb", + "n2t": "orthodb", + "prefixcommons": "orthodb", + "uniprot": "DB-0143" + }, + "name": "OrthoDB", + "pattern": "^\\w+$", + "preferred_prefix": "orthodb", + "provides": "uniprot", + "publications": [ + { + "doi": "10.1093/nar/gky1053", + "pmc": "PMC6323947", + "pubmed": "30395283", + "title": "OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gku1220", + "pmc": "PMC4383991", + "pubmed": "25428351", + "title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkq930", + "pmc": "PMC3013786", + "pubmed": "20972218", + "title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.", + "year": 2010 + } + ], + "uri_format": "http://cegg.unige.ch/orthodb/results?searchtext=$1" + }, + "oryzabase.gene": { + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", + "example": "117", + "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "mappings": { + "biocontext": "ORYZABASE.GENE", + "miriam": "oryzabase.gene", + "n2t": "oryzabase.gene" + }, + "name": "Oryzabase Gene", + "pattern": "^\\d+$", + "preferred_prefix": "oryzabase.gene", + "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1" + }, + "oryzabase.mutant": { + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.", + "example": "21393", + "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "mappings": { + "biocontext": "ORYZABASE.MUTANT", + "miriam": "oryzabase.mutant", + "n2t": "oryzabase.mutant" + }, + "name": "Oryzabase Mutant", + "pattern": "^\\d+$", + "preferred_prefix": "oryzabase.mutant", + "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1" + }, + "oryzabase.reference": { + "description": "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan.", + "example": "42840", + "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "mappings": { + "miriam": "oryzabase.reference", + "n2t": "oryzabase.reference" + }, + "name": "Oryzabase Reference", + "pattern": "^\\d+$", + "preferred_prefix": "oryzabase.reference", + "uri_format": "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1" + }, + "oryzabase.stage": { + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information.", + "example": "34", + "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "mappings": { + "biocontext": "ORYZABASE.STAGE", + "miriam": "oryzabase.stage", + "n2t": "oryzabase.stage" + }, + "name": "Oryzabase Stage", + "pattern": "^\\d+$", + "preferred_prefix": "oryzabase.stage", + "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1" + }, + "oryzabase.strain": { + "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information.", + "example": "1", + "homepage": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", + "mappings": { + "biocontext": "ORYZABASE.STRAIN", + "miriam": "oryzabase.strain", + "n2t": "oryzabase.strain" + }, + "name": "Oryzabase Strain", + "pattern": "^\\d+$", + "preferred_prefix": "oryzabase.strain", + "uri_format": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1" + }, + "oslc": { + "contact": { + "email": "jamsden@us.ibm.com", + "github": null, + "name": "Jim Amsden", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains.", + "example": "Property", + "homepage": "http://open-services.net/ns/core", + "name": "OASIS Open Services for Lifecycle Collaboration Core Vocabulary", + "preferred_prefix": "oslc", + "uri_format": "http://open-services.net/ns/core#$1" + }, + "otl": { + "description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.", + "example": "AADB12", + "homepage": "http://oryzatagline.cirad.fr/", + "keywords": [ + "dna", + "life science" + ], + "mappings": { + "biocontext": "OTL", + "fairsharing": "FAIRsharing.61c2x6", + "miriam": "otl", + "n2t": "otl", + "prefixcommons": "otl" + }, + "name": "Oryza Tag Line", + "pattern": "^A[A-Z]+\\d+$", + "preferred_prefix": "otl", + "publications": [ + { + "doi": "17947330", + "pmc": "PMC2238859", + "pubmed": "17947330", + "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.", + "year": null + }, + { + "doi": "10.1093/nar/gkm762", + "pmc": "PMC2238859", + "pubmed": "17947330", + "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.", + "year": 2007 + } + ], + "uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1" + }, + "otol": { + "contributor": { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + }, + "description": "Identifier for an entity in open tree of life", + "example": "3905431", + "github_request_issue": 470, + "homepage": "https://tree.opentreeoflife.org", + "mappings": { + "wikidata": "P9157" + }, + "name": "Open Tree of Life", + "pattern": "^[1-9]\\d*$", + "preferred_prefix": "otol", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://tree.opentreeoflife.org/taxonomy/browse?id=$1" + }, + "ovae": { + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqunh He", + "orcid": "0000-0001-9189-9661" + }, + "description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ", + "download_owl": "http://purl.obolibrary.org/obo/ovae.owl", + "example": "0000609", + "homepage": "http://www.violinet.org/ovae/", + "keywords": [ + "biomedical science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "OVAE", + "biocontext": "OVAE", + "bioportal": "OVAE", + "fairsharing": "FAIRsharing.w4x6n4", + "obofoundry": "ovae", + "ols": "ovae", + "ontobee": "OVAE" + }, + "name": "Ontology of Vaccine Adverse Events", + "pattern": "^\\d{7}$", + "preferred_prefix": "OVAE", + "publications": [ + { + "doi": "10.1186/2041-1480-4-40", + "pmc": "PMC4177204", + "pubmed": "24279920", + "title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.", + "year": 2013 + } + ], + "repository": "https://github.com/OVAE-Ontology/ovae", + "uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", + "version": "1.0.34" + }, + "owl": { + "contact": { + "email": "rmrich5@gmail.com", + "github": null, + "name": "Rafael Richards", + "orcid": "0000-0001-5699-0515" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. ", + "download_owl": "https://triplydb.com/w3c/owl/download.trig.gz", + "example": "Ontology", + "homepage": "https://www.w3.org/TR/owl-features/", + "keywords": [ + "computer science", + "informatics", + "ontology", + "ontology and terminology", + "subject agnostic" + ], + "mappings": { + "biocontext": "owl", + "fairsharing": "FAIRsharing.atygwy" + }, + "name": "Web Ontology Language", + "preferred_prefix": "owl", + "uri_format": "http://www.w3.org/2002/07/owl#$1" + }, + "owlstar": { + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]", + "download_rdf": "https://github.com/linkml/owlstar/raw/master/owlstar.ttl", + "example": "AllSomeInterpretation", + "homepage": "https://linkml.io/owlstar/", + "license": "CC0-1.0", + "mappings": { + "biolink": "os" + }, + "name": "Ontological Interpretations for Web Property Graphs", + "pattern": "^\\w+$", + "preferred_prefix": "owlstar", + "repository": "https://github.com/linkml/owlstar", + "uri_format": "http://w3id.org/owlstar/$1" + }, + "p3db.protein": { + "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites.", + "example": "70", + "homepage": "http://www.p3db.org/", + "keywords": [ + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "P3DB.PROTEIN", + "miriam": "p3db.protein", + "n2t": "p3db.protein", + "prefixcommons": "p3db" + }, + "name": "P3DB Protein", + "pattern": "^\\d+$", + "preferred_prefix": "p3db.protein", + "uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0" + }, + "p3db.site": { + "description": "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins.", + "example": "65", + "homepage": "http://www.p3db.org/", + "mappings": { + "biocontext": "P3DB.SITE", + "miriam": "p3db.site", + "n2t": "p3db.site" + }, + "name": "P3DB Site", + "pattern": "^\\d+$", + "preferred_prefix": "p3db.site", + "uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0" + }, + "paleodb": { + "description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.", + "example": "83088", + "homepage": "http://paleodb.org/", + "keywords": [ + "taxonomy" + ], + "mappings": { + "biocontext": "PALEODB", + "miriam": "paleodb", + "n2t": "paleodb", + "prefixcommons": "paleodb" + }, + "name": "Paleobiology Database", + "pattern": "^\\d+$", + "preferred_prefix": "paleodb", + "uri_format": "http://fossilworks.org/?a=taxonInfo&taxon_no=$1" + }, + "pandit": { + "description": "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.", + "example": "PF00004", + "homepage": "http://www.ebi.ac.uk/goldman-srv/pandit", + "keywords": [ + "dna", + "protein", + "structure" + ], + "mappings": { + "prefixcommons": "pandit", + "re3data": "r3d100011232" + }, + "name": "Protein and Associated NucleotideDomains with Inferred Trees", + "preferred_prefix": "pandit", + "provides": "pfam", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1" + }, + "panorama": { + "contact": { + "email": "brendanx@uw.edu", + "github": null, + "name": "Brendan MacLean", + "orcid": "0000-0002-9575-0255" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible.", + "example": "FxnI151FMs", + "homepage": "https://panoramaweb.org", + "keywords": [ + "life science", + "metabolomics", + "proteomics" + ], + "mappings": { + "fairsharing": "FAIRsharing.uBpQ1q" + }, + "name": "Panorama Public", + "preferred_prefix": "panorama", + "publications": [ + { + "doi": "10.1074/mcp.ra117.000543", + "pmc": "PMC5986241", + "pubmed": "29487113", + "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.", + "year": 2018 + }, + { + "doi": "10.1021/pr5006636", + "pmc": "PMC4156235", + "pubmed": "25102069", + "title": "Panorama: a targeted proteomics knowledge base.", + "year": 2014 + } + ], + "uri_format": "https://panoramaweb.org/$1.url" + }, + "panther.family": { + "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families.", + "example": "PTHR12345", + "homepage": "http://www.pantherdb.org/", + "keywords": [ + "classification", + "gene", + "ontology", + "pathway", + "protein" + ], + "mappings": { + "biocontext": "PANTHER.FAMILY", + "biolink": "PANTHER.FAMILY", + "go": "PANTHER", + "miriam": "panther.family", + "n2t": "panther.family", + "prefixcommons": "panther", + "uniprot": "DB-0069" + }, + "name": "PANTHER Family", + "part_of": "panther", + "pattern": "^PTHR\\d{5}(\\:SF\\d{1,3})?$", + "preferred_prefix": "panther.family", + "publications": [ + { + "doi": "10.1093/nar/gky1038", + "pmc": "PMC6323939", + "pubmed": "30407594", + "title": "PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.", + "year": 2019 + }, + { + "doi": "10.1101/gr.772403", + "pmc": "PMC403709", + "pubmed": "12952881", + "title": "PANTHER: a library of protein families and subfamilies indexed by function.", + "year": 2003 + } + ], + "uri_format": "http://www.pantherdb.org/panther/family.do?clsAccession=$1" + }, + "panther.node": { + "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes.", + "example": "PTN000000026", + "homepage": "http://pantree.org/", + "mappings": { + "biocontext": "PANTHER.NODE", + "miriam": "panther.node", + "n2t": "panther.node" + }, + "name": "PANTHER Node", + "part_of": "panther", + "pattern": "^PTN\\d{9}$", + "preferred_prefix": "panther.node", + "uri_format": "http://www.pantree.org/node/annotationNode.jsp?id=$1" + }, + "panther.pathway": { + "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components.", + "example": "P00024", + "homepage": "http://www.pantherdb.org/", + "mappings": { + "biocontext": "PANTHER.PATHWAY", + "edam": "1161", + "miriam": "panther.pathway", + "n2t": "panther.pathway" + }, + "name": "PANTHER Pathway", + "part_of": "panther", + "pattern": "^P\\d{5}$", + "preferred_prefix": "panther.pathway", + "uri_format": "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1" + }, + "panther.pthcmp": { + "description": "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", + "example": "P00266", + "homepage": "http://www.pantherdb.org/", + "mappings": { + "biocontext": "PANTHER.PTHCMP", + "miriam": "panther.pthcmp", + "n2t": "panther.pthcmp" + }, + "name": "PANTHER Pathway Component", + "part_of": "panther", + "pattern": "^(G|P|U|C|S)\\d{5}$", + "preferred_prefix": "panther.pthcmp", + "uri_format": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1" + }, + "pao": { + "contact": { + "email": "jaiswalp@science.oregonstate.edu", + "github": "jaiswalp", + "name": "Pankaj Jaiswal", + "orcid": "0000-0002-1005-8383" + }, + "deprecated": true, + "homepage": "http://www.plantontology.org", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "PAO", + "obofoundry": "pao" + }, + "name": "Plant Anatomy Ontology", + "preferred_prefix": "PAO", + "uri_format": "http://purl.obolibrary.org/obo/PAO_$1" + }, + "pass2": { + "deprecated": true, + "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", + "example": "46977", + "homepage": "http://caps.ncbs.res.in/pass2", + "keywords": [ + "classification", + "dna", + "genome", + "structure" + ], + "mappings": { + "biocontext": "PASS2", + "miriam": "pass2", + "n2t": "pass2", + "prefixcommons": "pass2" + }, + "name": "Protein Alignment organised as Structural Superfamily", + "pattern": "^\\d+$", + "preferred_prefix": "pass2", + "uri_format": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1" + }, + "pathbank": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana.", + "example": "SMP0000219", + "homepage": "https://pathbank.org", + "keywords": [ + "animal genetics", + "bioinformatics", + "biology", + "cell biology", + "cheminformatics", + "database management", + "drug metabolism", + "endocrinology", + "genetics", + "human genetics", + "medical informatics", + "metabolomics", + "microbiology", + "molecular biology", + "molecular microbiology", + "plant genetics", + "proteomics", + "systems biology", + "transcriptomics" + ], + "mappings": { + "fairsharing": "FAIRsharing.3xwMon" + }, + "name": "PathBank", + "pattern": "^(SMP|PW)\\d+$", + "preferred_prefix": "pathbank", + "uri_format": "https://pathbank.org/view/$1" + }, + "pathguide": { + "description": "Pathguide contains information about 325 biological related resources and molecular interaction related resources.", + "example": "49", + "homepage": "http://pathguide.org", + "keywords": [ + "gene", + "interaction", + "pathway", + "protein", + "small molecule" + ], + "mappings": { + "prefixcommons": "pathguide" + }, + "name": "Pathguide", + "preferred_prefix": "pathguide", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1" + }, + "pathoplant": { + "description": "PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.", + "example": "MO000027", + "homepage": "http://www.pathoplant.de", + "keywords": [ + "gene expression", + "interaction", + "pathway", + "protein", + "small molecule" + ], + "mappings": { + "prefixcommons": "pathoplant" + }, + "name": "PathoPlant®", + "preferred_prefix": "pathoplant", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.pathoplant.de/detail.php?accNo=$1" + }, + "pathwaycommons": { + "description": "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.", + "example": "485991", + "homepage": "http://www.pathwaycommons.org/pc/", + "keywords": [ + "pathway" + ], + "mappings": { + "biocontext": "PATHWAYCOMMONS", + "miriam": "pathwaycommons", + "n2t": "pathwaycommons", + "prefixcommons": "pathwaycommons", + "re3data": "r3d100012731", + "uniprot": "DB-0253" + }, + "name": "Pathway Commons", + "pattern": "^\\d+$", + "preferred_prefix": "pathwaycommons", + "publications": [ + { + "doi": "10.1093/nar/gkq1039", + "pmc": "PMC3013659", + "pubmed": "21071392", + "title": "Pathway Commons, a web resource for biological pathway data.", + "year": 2010 + } + ], + "uri_format": "http://www.pathwaycommons.org/pc/record2.do?id=$1" + }, + "pato": { + "appears_in": [ + "agro", + "aism", + "cdno", + "cl", + "colao", + "ecocore", + "ecto", + "fovt", + "lepao", + "mco", + "ms", + "pcl", + "pco", + "phipo", + "planp", + "proco", + "rbo", + "xpo", + "zp" + ], + "banana": "PATO", + "contact": { + "email": "g.gkoutos@gmail.com", + "github": "gkoutos", + "name": "George Gkoutos", + "orcid": "0000-0002-2061-091X" + }, + "description": "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation.", + "download_json": "http://purl.obolibrary.org/obo/pato.json", + "download_obo": "http://purl.obolibrary.org/obo/pato.obo", + "download_owl": "http://purl.obolibrary.org/obo/pato.owl", + "example": "0001998", + "homepage": "https://github.com/pato-ontology/pato/", + "keywords": [ + "biodiversity", + "biology", + "obo", + "ontology", + "phenotype", + "quality" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "PATO", + "agroportal": "PATO", + "biocontext": "PATO", + "bioportal": "PATO", + "fairsharing": "FAIRsharing.ezwdhz", + "go": "PATO", + "miriam": "pato", + "n2t": "pato", + "obofoundry": "pato", + "ols": "pato", + "ontobee": "PATO", + "prefixcommons": "pato" + }, + "name": "Phenotype And Trait Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "PATO", + "providers": [ + { + "code": "purl", + "description": "Legacy PURLs found in OAE", + "homepage": "http://purl.org/obo/owl/", + "name": "Legacy PURL", + "uri_format": "http://purl.org/obo/owl/PATO#PATO_$1" + } + ], + "publications": [ + { + "doi": "10.1093/bib/bbx035", + "pmc": "PMC6169674", + "pubmed": "28387809", + "title": "The anatomy of phenotype ontologies: principles, properties and applications.", + "year": 2018 + }, + { + "doi": "10.1186/gb-2010-11-1-r2", + "pmc": "PMC2847714", + "pubmed": "20064205", + "title": "Integrating phenotype ontologies across multiple species.", + "year": 2010 + }, + { + "doi": "10.1186/gb-2004-6-1-r8", + "pmc": "PMC549069", + "pubmed": "15642100", + "title": "Using ontologies to describe mouse phenotypes.", + "year": 2004 + } + ], + "repository": "https://github.com/pato-ontology/pato", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1", + "version": "2022-08-31" + }, + "pav": { + "contact": { + "email": "stian@soiland-reyes.com", + "github": null, + "name": "Stian Soiland-Reyes", + "orcid": "0000-0001-9842-9718" + }, + "contributor": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nico Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "contributor_extras": [ + { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + ], + "description": "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources.", + "download_owl": "http://aber-owl.net/media/ontologies/PAV/3/pav.owl", + "example": "authoredBy", + "github_request_issue": 186, + "homepage": "https://pav-ontology.github.io/pav/", + "keywords": [ + "data management", + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "PAV", + "biocontext": "pav", + "biolink": "pav", + "bioportal": "PAV", + "fairsharing": "FAIRsharing.nbfwwv" + }, + "name": "Provenance, Authoring, and Versioning Vocabulary", + "pattern": "^[a-z][a-zA-Z]+$", + "preferred_prefix": "pav", + "publications": [ + { + "doi": "10.1186/2041-1480-4-37", + "pmc": "PMC4177195", + "pubmed": "24267948", + "title": "PAV ontology: provenance, authoring and versioning.", + "year": 2013 + } + ], + "repository": "http://pav-ontology.github.io/pav/", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://purl.org/pav/$1" + }, + "paxdb.organism": { + "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species.", + "example": "9606", + "homepage": "http://pax-db.org/", + "mappings": { + "biocontext": "PAXDB.ORGANISM", + "miriam": "paxdb.organism", + "n2t": "paxdb.organism" + }, + "name": "PaxDb Organism", + "pattern": "^\\d+$", + "preferred_prefix": "paxdb.organism", + "uri_format": "http://pax-db.org/#!species/$1" + }, + "paxdb.protein": { + "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels.", + "example": "977869", + "homepage": "http://pax-db.org/", + "mappings": { + "biocontext": "PAXDB.PROTEIN", + "miriam": "paxdb.protein", + "n2t": "paxdb.protein" + }, + "name": "PaxDb Protein", + "pattern": "^\\d+$", + "preferred_prefix": "paxdb.protein", + "uri_format": "http://pax-db.org/#!protein/$1" + }, + "pazar": { + "contact": { + "email": "wyeth@cmmt.ubc.ca", + "github": null, + "name": "Wyeth W. Wasserman", + "orcid": "0000-0001-6098-6412" + }, + "description": "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors.", + "example": "TF0001053", + "homepage": "http://www.pazar.info/", + "keywords": [ + "dna", + "life science", + "regulation", + "rna" + ], + "mappings": { + "biocontext": "PAZAR", + "fairsharing": "FAIRsharing.33yggg", + "miriam": "pazar", + "n2t": "pazar", + "prefixcommons": "pazar" + }, + "name": "Pazar Transcription Factor", + "pattern": "^TF\\w+$", + "preferred_prefix": "pazar", + "publications": [ + { + "doi": "10.1093/nar/gkn783", + "pmc": "PMC2686574", + "pubmed": "18971253", + "title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.", + "year": 2008 + }, + { + "doi": "10.1186/gb-2007-8-10-r207", + "pmc": "PMC2246282", + "pubmed": "17916232", + "title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.", + "year": 2007 + } + ], + "uri_format": "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1" + }, + "pba": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A controlled vocabulary to support the study of transcription in the primate brain", + "download_obo": "https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo", + "example": "128011350", + "homepage": "https://www.blueprintnhpatlas.org/", + "keywords": [ + "ontology" + ], + "name": "Primate Brain Atlas", + "pattern": "^\\d+$", + "preferred_prefix": "PBA", + "uri_format": "https://biopragmatics.github.io/providers/pba/$1" + }, + "pcl": { + "contact": { + "email": "davidos@ebi.ac.uk", + "github": "dosumis", + "name": "David Osumi-Sutherland", + "orcid": "0000-0002-7073-9172" + }, + "depends_on": [ + "bfo", + "chebi", + "cl", + "go", + "nbo", + "ncbitaxon", + "omo", + "pato", + "pr", + "ro", + "so", + "uberon" + ], + "description": "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties.", + "download_json": "http://purl.obolibrary.org/obo/pcl.json", + "download_obo": "http://purl.obolibrary.org/obo/pcl.obo", + "download_owl": "http://purl.obolibrary.org/obo/pcl.owl", + "example": "0011124", + "homepage": "https://github.com/obophenotype/provisional_cell_ontology", + "keywords": [ + "anatomy", + "cell biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "PCL", + "bioportal": "PCL", + "fairsharing": "FAIRsharing.bfcfd0", + "obofoundry": "pcl", + "ols": "pcl", + "ontobee": "PCL" + }, + "name": "Provisional Cell Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PCL", + "publications": [ + { + "doi": "10.1101/2021.10.10.463703", + "pmc": null, + "pubmed": null, + "title": "Brain Data Standards - A method for building data-driven cell-type ontologies", + "year": 2021 + } + ], + "repository": "https://github.com/obophenotype/provisional_cell_ontology", + "uri_format": "http://purl.obolibrary.org/obo/PCL_$1", + "version": "2022-10-19" + }, + "pco": { + "appears_in": [ + "ecocore", + "envo" + ], + "contact": { + "email": "rlwalls2008@gmail.com", + "github": "ramonawalls", + "name": "Ramona Walls", + "orcid": "0000-0001-8815-0078" + }, + "depends_on": [ + "bfo", + "caro", + "envo", + "go", + "iao", + "ncbitaxon", + "pato", + "ro" + ], + "description": "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology.", + "download_obo": "http://purl.obolibrary.org/obo/pco.obo", + "download_owl": "http://purl.obolibrary.org/obo/pco.owl", + "example": "0000021", + "homepage": "https://github.com/PopulationAndCommunityOntology/pco", + "keywords": [ + "biodiversity", + "community care", + "ecology", + "obo", + "ontology", + "population genetics", + "social and behavioural science" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "PCO", + "agroportal": "PCO", + "biocontext": "PCO", + "bioportal": "PCO", + "ecoportal": "PCO", + "fairsharing": "FAIRsharing.vq28qp", + "obofoundry": "pco", + "ols": "pco", + "ontobee": "PCO" + }, + "name": "Population and Community Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PCO", + "repository": "https://github.com/PopulationAndCommunityOntology/pco", + "uri_format": "http://purl.obolibrary.org/obo/PCO_$1", + "version": "2021-05-03" + }, + "pd_st": { + "contact": { + "email": "henrich@embl.de", + "github": null, + "name": "Thorsten Heinrich", + "orcid": null + }, + "deprecated": true, + "homepage": "http://4dx.embl.de/platy", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "PD_ST", + "obofoundry": "pd_st" + }, + "name": "Platynereis stage ontology", + "preferred_prefix": "PD_ST", + "uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1" + }, + "pdb": { + "contact": { + "email": "harukin@protein.osaka-u.ac.jp", + "github": null, + "name": "Haruki Nakamura", + "orcid": "0000-0001-6690-5863" + }, + "description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.", + "example": "2gc4", + "homepage": "https://www.wwpdb.org/", + "keywords": [ + "bioinformatics", + "epidemiology", + "protein", + "proteomics", + "structural biology", + "structure", + "virology" + ], + "mappings": { + "biocontext": "PDB", + "edam": "1127", + "fairsharing": "FAIRsharing.rs2815", + "go": "PDB", + "miriam": "pdb", + "n2t": "pdb", + "ncbi": "PDB", + "prefixcommons": "pdbj", + "re3data": "r3d100010910", + "uniprot": "DB-0172", + "wikidata": "P638" + }, + "name": "PDB Structure", + "pattern": "^[0-9][A-Za-z0-9]{3}$", + "preferred_prefix": "pdb", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Proteopedia", + "homepage": "http://www.proteopedia.org/", + "name": "Proteopedia", + "uri_format": "http://proteopedia.org/wiki/index.php/$1" + }, + { + "code": "ebi", + "description": "Protein Databank through PDBsum", + "homepage": "https://www.ebi.ac.uk/pdbsum/", + "name": "Protein Databank through PDBsum", + "uri_format": "https://www.ebi.ac.uk/pdbsum/$1" + }, + { + "code": "pdbe", + "description": "Protein Databank in Europe (PDBe)", + "homepage": "http://www.pdbe.org/", + "name": "Protein Databank in Europe (PDBe)", + "uri_format": "https://www.ebi.ac.uk/pdbe/entry/pdb/$1" + }, + { + "code": "pdbj", + "description": "Protein Data Bank Japan (PDBj)", + "homepage": "http://www.pdbj.org/", + "name": "Protein Data Bank Japan (PDBj)", + "uri_format": "https://pdbj.org/mine/summary/$1" + }, + { + "code": "rcsb", + "description": "RCSB PDB", + "homepage": "https://www.rcsb.org/", + "name": "RCSB PDB", + "uri_format": "https://www.rcsb.org/structure/$1" + } + ], + "publications": [ + { + "doi": "10.1002/pro.4211", + "pmc": "PMC8740847", + "pubmed": "34664328", + "title": "Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.", + "year": 2021 + }, + { + "doi": "10.1002/pro.3273", + "pmc": "PMC5734392", + "pubmed": "28815765", + "title": "New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).", + "year": 2017 + }, + { + "doi": "10.1093/nar/gkw962", + "pmc": "PMC5210648", + "pubmed": "27789697", + "title": "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkr811", + "pmc": "PMC3245181", + "pubmed": "21976737", + "title": "Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.", + "year": 2011 + }, + { + "doi": "10.1007/s10822-011-9460-y", + "pmc": null, + "pubmed": "21796434", + "title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr.", + "year": 2011 + }, + { + "doi": "10.1093/database/baq021", + "pmc": "PMC2997606", + "pubmed": "20798081", + "title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.", + "year": 2010 + }, + { + "doi": null, + "pmc": null, + "pubmed": "12099029", + "title": "[Development of PDBj: Advanced database for protein structures].", + "year": 2002 + } + ], + "synonyms": [ + "RCSB_PDB", + "pdbe", + "pdbj", + "wwpdb" + ], + "twitter": "PDBj_en", + "uri_format": "https://www.wwpdb.org/pdb?id=$1" + }, + "pdb-ccd": { + "comment": "might be same as pdb.ligand, not sure though", + "contributor_extras": [ + { + "email": "bmeldal@ebi.ac.uk", + "github": "bmeldal-eg", + "name": "Birgit Meldal", + "orcid": "0000-0003-4062-6158" + } + ], + "description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.", + "example": "AB0", + "example_extras": [ + "A", + "PI" + ], + "has_canonical": "pdb.ligand", + "homepage": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/", + "keywords": [ + "chemical", + "classification" + ], + "mappings": { + "biocontext": "PDB-CCD", + "miriam": "pdb-ccd", + "n2t": "pdb-ccd", + "prefixcommons": "ccd" + }, + "name": "Chemical Component Dictionary", + "pattern": "^\\w{1,3}$", + "preferred_prefix": "pdb-ccd", + "publications": [ + { + "doi": "10.1038/nsb1203-980", + "pmc": null, + "pubmed": "14634627", + "title": "Announcing the worldwide Protein Data Bank.", + "year": 2003 + } + ], + "synonyms": [ + "pdbechem" + ], + "uri_format": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1" + }, + "pdb.ligand": { + "description": "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. 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"http://purl.obolibrary.org/obo/PGDSO_$1" + }, + "pgs": { + "description": "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation.", + "example": "PGS000018", + "homepage": "http://pgscatalog.org", + "mappings": { + "miriam": "pgs" + }, + "name": "Polygenic Score Catalog", + "pattern": "^PGS[0-9]{6}$", + "preferred_prefix": "pgs", + "uri_format": "https://www.pgscatalog.org/pgs/$1" + }, + "pgx": { + "contact": { + "email": "mbaudis@me.com", + "github": "mbaudis", + "name": "Michael Baudis", + "orcid": "0000-0002-9903-4248" + }, + "description": "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.", + "example": "pgxbs-kftva5zv", + "homepage": "https://progenetix.org/", + "keywords": [ + "biomedical science", + "genomics" + ], + "mappings": { + "biocontext": "PGX", + "cellosaurus": "Progenetix", + "fairsharing": "FAIRsharing.65tdnz", + "miriam": "pgx", + "n2t": "pgx", + "re3data": "r3d100012820" + }, + "name": "Progenetix", + "pattern": "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$", + "preferred_prefix": "pgx", + "publications": [ + { + "doi": "10.1093/nar/gku1123", + "pmc": "PMC4383937", + "pubmed": "25428357", + "title": "arrayMap 2014: an updated cancer genome resource.", + "year": 2014 + }, + { + "doi": "10.1186/1471-2164-15-82", + "pmc": "PMC3909908", + "pubmed": "24476156", + "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkt1108", + "pmc": "PMC3965091", + "pubmed": "24225322", + "title": "Progenetix: 12 years of oncogenomic data curation.", + "year": 2013 + }, + { + "doi": "10.1371/journal.pone.0036944", + "pmc": "PMC3356349", + "pubmed": "22629346", + "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies.", + "year": 2012 + }, + { + "doi": "10.1186/1471-2407-7-226", + "pmc": "PMC2225423", + "pubmed": "18088415", + "title": "Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data.", + "year": 2007 + }, + { + "doi": "10.2144/000112102", + "pmc": null, + "pubmed": "16568815", + "title": "Online database and bioinformatics toolbox to support data mining in cancer cytogenetics.", + "year": 2006 + }, + { + "doi": "10.1093/bioinformatics/17.12.1228", + "pmc": null, + "pubmed": "11751233", + "title": "Progenetix.net: an online repository for molecular cytogenetic aberration data.", + "year": 2001 + } + ], + "synonyms": [ + "Progenetix" + ], + "twitter": "progenetix", + "uri_format": "https://progenetix.org/services/ids/$1" + }, + "pharmacodb.cell": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line.", + "example": "22RV1_12_2019", + "homepage": "https://pharmacodb.ca/cell_lines", + "mappings": { + "cellosaurus": "PharmacoDB" + }, + "name": "PharmacoDB Cells", + "preferred_prefix": "pharmacodb.cell", + "uri_format": "https://pharmacodb.ca/cell_lines/$1" + }, + "pharmacodb.dataset": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset.", + "example": "1", + "homepage": "https://pharmacodb.ca/datasets", + "name": "PharmacoDB Datasets", + "pattern": "^\\d+$", + "preferred_prefix": "pharmacodb.dataset", + "uri_format": "https://pharmacodb.ca/datasets/$1" + }, + "pharmacodb.tissue": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue.", + "example": "13", + "homepage": "https://pharmacodb.ca/tissues", + "name": "PharmacoDB Tissues", + "pattern": "^\\d+$", + "preferred_prefix": "pharmacodb.tissue", + "uri_format": "https://pharmacodb.ca/tissues/$1" + }, + "pharmgkb.disease": { + "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", + "example": "PA447218", + "homepage": "http://www.pharmgkb.org/", + "keywords": [ + "pharmacogenomics" + ], + "mappings": { + "biocontext": "PHARMGKB.DISEASE", + "biolink": "PHARMGKB.DISEASE", + "edam": "2651", + "miriam": "pharmgkb.disease", + "n2t": "pharmgkb.disease", + "prefixcommons": "pharmgkb.disease", + "wikidata": "P7001" + }, + "name": "PharmGKB Disease", + "pattern": "^PA\\d+$", + "preferred_prefix": "pharmgkb.disease", + "publications": [ + { + "doi": "10.2217/bmm.11.94", + "pmc": "PMC3339046", + "pubmed": "22103613", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "year": 2011 + }, + { + "doi": "10.1038/sj.tpj.6500035", + "pmc": null, + "pubmed": "11908751", + "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.", + "year": 2001 + } + ], + "uri_format": "http://www.pharmgkb.org/disease/$1" + }, + "pharmgkb.drug": { + "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", + "example": "PA448710", + "homepage": "http://www.pharmgkb.org/", + "keywords": [ + "drug", + "pharmacogenomics" + ], + "mappings": { + "biocontext": "PHARMGKB.DRUG", + "edam": "2652", + "miriam": "pharmgkb.drug", + "n2t": "pharmgkb.drug", + "prefixcommons": "pharmgkb.drug", + "wikidata": "P7001" + }, + "name": "PharmGKB Drug", + "pattern": "^PA\\d+$", + "preferred_prefix": "pharmgkb.drug", + "publications": [ + { + "doi": "10.2217/bmm.11.94", + "pmc": "PMC3339046", + "pubmed": "22103613", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "year": 2011 + }, + { + "doi": "10.1038/sj.tpj.6500035", + "pmc": null, + "pubmed": "11908751", + "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.", + "year": 2001 + } + ], + "uri_format": "http://www.pharmgkb.org/drug/$1" + }, + "pharmgkb.gene": { + "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.", + "example": "PA131", + "homepage": "http://www.pharmgkb.org/", + "keywords": [ + "gene", + "ontology", + "pharmacogenomics" + ], + "mappings": { + "biocontext": "PHARMGKB.GENE", + "biolink": "PHARMGKB.GENE", + "bioportal": "PHARMGKB", + "go": "PharmGKB", + "miriam": "pharmgkb.gene", + "n2t": "pharmgkb.gene", + "prefixcommons": "pharmgkb.gene", + "uniprot": "DB-0074", + "wikidata": "P7001" + }, + "name": "PharmGKB Gene", + "pattern": "^PA\\w+$", + "preferred_prefix": "pharmgkb.gene", + "publications": [ + { + "doi": "10.2217/bmm.11.94", + "pmc": "PMC3339046", + "pubmed": "22103613", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "year": 2011 + }, + { + "doi": "10.1385/1-59259-957-5:179", + "pmc": null, + "pubmed": "16100408", + "title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base.", + "year": 2005 + } + ], + "uri_format": "http://www.pharmgkb.org/gene/$1" + }, + "pharmgkb.pathways": { + "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies.", + "example": "PA146123006", + "homepage": "http://www.pharmgkb.org/", + "keywords": [ + "pathway", + "pharmacogenomics" + ], + "mappings": { + "biocontext": "PHARMGKB.PATHWAYS", + "biolink": "PHARMGKB.PATHWAYS", + "edam": "2650", + "miriam": "pharmgkb.pathways", + "n2t": "pharmgkb.pathways", + "prefixcommons": "pharmgkb.pathways", + "wikidata": "P7001" + }, + "name": "PharmGKB", + "pattern": "^PA\\d+$", + "preferred_prefix": "pharmgkb.pathways", + "publications": [ + { + "doi": "10.2217/bmm.11.94", + "pmc": "PMC3339046", + "pubmed": "22103613", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "year": 2011 + }, + { + "doi": "10.1038/sj.tpj.6500035", + "pmc": null, + "pubmed": "11908751", + "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.", + "year": 2001 + } + ], + "uri_format": "http://www.pharmgkb.org/pathway/$1" + }, + "pharmvar": { + "description": "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium.", + "example": "CYP2A6", + "homepage": "https://www.pharmvar.org", + "keywords": [ + "gene", + "pharmacogenomics", + "variant" + ], + "mappings": { + "prefixcommons": "pharmvar" + }, + "name": "Pharmacogene Variation Consortium", + "preferred_prefix": "pharmvar", + "provides": "hgnc.symbol", + "publications": [ + { + "doi": "10.1002/cpt.910", + "pmc": "PMC5836850", + "pubmed": "29134625", + "title": "The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database.", + "year": 2017 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.pharmvar.org/gene/$1" + }, + "phenolexplorer": { + "description": "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis.", + "example": "75", + "homepage": "http://www.phenol-explorer.eu/foods/", + "mappings": { + "biocontext": "PHENOLEXPLORER", + "miriam": "phenolexplorer", + "n2t": "phenolexplorer", + "re3data": "r3d100012197" + }, + "name": "Phenol-Explorer", + "pattern": "^\\d+$", + "preferred_prefix": "phenolexplorer", + "uri_format": "http://phenol-explorer.eu/foods/$1" + }, + "phenx": { + "contact": { + "email": "yingqin@rti.org", + "github": null, + "name": "PhenX Admin", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.", + "download_owl": "http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl", + "example": "130502", + "github_request_issue": 503, + "homepage": "https://www.phenxtoolkit.org/", + "keywords": [ + "biomedical science", + "environmental science", + "life science", + "ontology" + ], + "mappings": { + "aberowl": "PHENX", + "bioportal": "PHENX", + "fairsharing": "FAIRsharing.y5jcwa" + }, + "name": "PhenX Toolkit", + "pattern": "^\\d+$", + "preferred_prefix": "phenx", + "publications": [ + { + "doi": "10.1038/gim.2016.199", + "pmc": "PMC5507752", + "pubmed": "28079902", + "title": "PhenX measures for phenotyping rare genetic conditions.", + "year": 2017 + }, + { + "doi": "10.1093/aje/kwr193", + "pmc": "PMC3141081", + "pubmed": "21749974", + "title": "The PhenX Toolkit: get the most from your measures.", + "year": 2011 + }, + { + "doi": "10.1097/mol.0b013e3283377395", + "pmc": "PMC8038872", + "pubmed": "20154612", + "title": "PhenX: a toolkit for interdisciplinary genetics research.", + "year": 2010 + } + ], + "synonyms": [ + "phenxtoolkit" + ], + "uri_format": "https://www.phenxtoolkit.org/protocols/view/$1" + }, + "phipo": { + "contact": { + "email": "alayne.cuzick@rothamsted.ac.uk", + "github": "CuzickA", + "name": "Alayne Cuzick", + "orcid": "0000-0001-8941-3984" + }, + "depends_on": [ + "pato" + ], + "description": "Ontology of species-neutral phenotypes observed in pathogen-host interactions.", + "download_obo": "http://purl.obolibrary.org/obo/phipo.obo", + "download_owl": "http://purl.obolibrary.org/obo/phipo.owl", + "example": "0000001", + "homepage": "https://github.com/PHI-base/phipo", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "PHIPO", + "bioportal": "PHIPO", + "obofoundry": "phipo", + "ols": "phipo", + "ontobee": "PHIPO" + }, + "name": "Pathogen Host Interaction Phenotype Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PHIPO", + "publications": [ + { + "doi": "10.1093/nar/gkab1037", + "pmc": "PMC8728202", + "pubmed": "34788826", + "title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.", + "year": 2022 + } + ], + "repository": "https://github.com/PHI-base/phipo", + "uri_format": "http://purl.obolibrary.org/obo/PHIPO_$1", + "version": "2021-07-14" + }, + "phosphopoint.kinase": { + "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.", + "example": "AURKA", + "homepage": "http://kinase.bioinformatics.tw/", + "mappings": { + "biocontext": "PHOSPHOPOINT.KINASE", + "miriam": "phosphopoint.kinase", + "n2t": "phosphopoint.kinase" + }, + "name": "PhosphoPoint Kinase", + "pattern": "^\\w+$", + "preferred_prefix": "phosphopoint.kinase", + "uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1" + }, + "phosphopoint.protein": { + "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information.", + "example": "AURKA", + "homepage": "http://kinase.bioinformatics.tw/", + "mappings": { + "biocontext": "PHOSPHOPOINT.PROTEIN", + "miriam": "phosphopoint.protein", + "n2t": "phosphopoint.protein" + }, + "name": "PhosphoPoint Phosphoprotein", + "pattern": "^\\w+$", + "preferred_prefix": "phosphopoint.protein", + "uri_format": "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0" + }, + "phosphosite.protein": { + "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database.", + "example": "12300", + "homepage": "http://www.phosphosite.org/homeAction.do", + "mappings": { + "biocontext": "PHOSPHOSITE.PROTEIN", + "miriam": "phosphosite.protein", + "n2t": "phosphosite.protein" + }, + "name": "PhosphoSite Protein", + "pattern": "^\\d{5}$", + "preferred_prefix": "phosphosite.protein", + "uri_format": "http://www.phosphosite.org/proteinAction.do?id=$1" + }, + "phosphosite.residue": { + "description": "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence.", + "example": "2842", + "homepage": "http://www.phosphosite.org/homeAction.do", + "mappings": { + "biocontext": "PHOSPHOSITE.RESIDUE", + "miriam": "phosphosite.residue", + "n2t": "phosphosite.residue" + }, + "name": "PhosphoSite Residue", + "pattern": "^\\d+$", + "preferred_prefix": "phosphosite.residue", + "uri_format": "http://www.phosphosite.org/siteAction.do?id=$1" + }, + "phosphosite.sitegroup": { + "comment": "Potentially could use a URI format like https://www.phosphosite.org/siteGroupAction.action?protOrg=1156&id=$1, but it's not obvious what the protOrg does.", + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur.", + "example": "447860", + "homepage": "https://www.phosphosite.org", + "keywords": [ + "biochemistry", + "grouping", + "post-translational modification" + ], + "name": "PhosphoSite Site Group", + "pattern": "^\\d+$", + "preferred_prefix": "phosphosite.sitegroup", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + }, + "phylomedb": { + "description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.", + "example": "Phy000CLXM_RAT", + "homepage": "http://phylomedb.org/", + "keywords": [ + "genome", + "life science", + "phylogenetics", + "phylogenomics", + "phylogeny", + "protein", + "taxonomy" + ], + "mappings": { + "biocontext": "PHYLOMEDB", + "fairsharing": "FAIRsharing.7hxxc4", + "miriam": "phylomedb", + "n2t": "phylomedb", + "prefixcommons": "phylomedb", + "uniprot": "DB-0144" + }, + "name": "PhylomeDB", + "pattern": "^\\w+$", + "preferred_prefix": "phylomedb", + "publications": [ + { + "doi": "10.1093/nar/gkab966", + "pmc": "PMC8728271", + "pubmed": "34718760", + "title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.", + "year": 2022 + }, + { + "doi": "10.1093/nar/gkt1177", + "pmc": "PMC3964985", + "pubmed": "24275491", + "title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkq1109", + "pmc": "PMC3013701", + "pubmed": "21075798", + "title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkm899", + "pmc": "PMC2238872", + "pubmed": "17962297", + "title": "PhylomeDB: a database for genome-wide collections of gene phylogenies.", + "year": 2007 + } + ], + "twitter": "phylomedb", + "uri_format": "http://phylomedb.org/?seqid=$1" + }, + "phytozome.locus": { + "description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.", + "example": "Glyma0021s00410", + "homepage": "http://www.phytozome.net/", + "mappings": { + "biocontext": "PHYTOZOME.LOCUS", + "miriam": "phytozome.locus", + "n2t": "phytozome.locus", + "ncbi": "Phytozome" + }, + "name": "Plant Genome Network", + "pattern": "^[A-Za-z0-9]+$", + "preferred_prefix": "phytozome.locus", + "synonyms": [ + "JGI Phytozome" + ], + "uri_format": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1" + }, + "pibase": { + "description": "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected.", + "example": "21692", + "homepage": "http://salilab.org/pibase", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "prefixcommons": "pibase" + }, + "name": "Database of structurally defined protein interfaces", + "preferred_prefix": "pibase", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1" + }, + "pictar": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "example": "hsa-let-7a", + "homepage": "https://pictar.mdc-berlin.de/", + "name": "PicTar", + "preferred_prefix": "pictar", + "synonyms": [ + "pictar-vert" + ] + }, + "pid.pathway": { + "description": "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information.", + "example": "eff796f3-6195-11e5-8ac5-06603eb7f303", + "homepage": "http://pid.nci.nih.gov/", + "keywords": [ + "gene", + "life science", + "pathway", + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "PID.PATHWAY", + "edam": "2344", + "fairsharing": "FAIRsharing.ncgh1j", + "miriam": "pid.pathway", + "n2t": "pid.pathway", + "prefixcommons": "pid" + }, + "name": "NCI Pathway Interaction Database: Pathway", + "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", + "preferred_prefix": "pid.pathway", + "publications": [ + { + "doi": "10.1093/nar/gkn653", + "pmc": "PMC2686461", + "pubmed": "18832364", + "title": "PID: the Pathway Interaction Database.", + "year": 2008 + } + ], + "synonyms": [ + "pid" + ], + "uri_format": "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1" + }, + "pigqtldb": { + "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs.", + "example": "14", + "homepage": "https://www.animalgenome.org/QTLdb", + "keywords": [ + "dna", + "genome" + ], + "mappings": { + "biocontext": "PIGQTLDB", + "miriam": "pigqtldb", + "n2t": "pigqtldb", + "prefixcommons": "pigqtldb" + }, + "name": "Animal Genome Pig QTL", + "part_of": "qtldb", + "pattern": "^\\d+$", + "preferred_prefix": "pigqtldb", + "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" + }, + "pina": { + "contact": { + "email": "wujm@bjmu.edu.cn", + "github": null, + "name": "Jianmin Wu", + "orcid": "0000-0002-8876-128X" + }, + "description": "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms.", + "example": "Q13485", + "homepage": "http://cbg.garvan.unsw.edu.au/pina/", + "keywords": [ + "data visualization", + "life science" + ], + "mappings": { + "biocontext": "PINA", + "fairsharing": "FAIRsharing.7q4gsz", + "miriam": "pina", + "n2t": "pina" + }, + "name": "Protein Interaction Network Analysis", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", + "preferred_prefix": "pina", + "provides": "uniprot", + "publications": [ + { + "doi": "10.1093/nar/gkaa1075", + "pmc": "PMC7779002", + "pubmed": "33231689", + "title": "PINA 3.0: mining cancer interactome.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gkr967", + "pmc": "PMC3244997", + "pubmed": "22067443", + "title": "PINA v2.0: mining interactome modules.", + "year": 2011 + }, + { + "doi": "10.1038/nmeth.1282", + "pmc": null, + "pubmed": "19079255", + "title": "Integrated network analysis platform for protein-protein interactions.", + "year": 2008 + } + ], + "uri_format": "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1" + }, + "piroplasma": { + "description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "TA14985", + "homepage": "http://piroplasmadb.org/", + "mappings": { + "biocontext": "PIROPLASMA", + "miriam": "piroplasma", + "n2t": "piroplasma" + }, + "name": "PiroplasmaDB", + "pattern": "^TA\\d+$", + "preferred_prefix": "piroplasma", + "uri_format": "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" + }, + "pirsf": { + "description": "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.", + "example": "PIRSF000100", + "homepage": "https://pir.georgetown.edu/", + "keywords": [ + "life science", + "protein", + "proteomics", + "structure" + ], + "mappings": { + "biocontext": "PIRSF", + "edam": "1136", + "fairsharing": "FAIRsharing.vssch2", + "go": "PIRSF", + "miriam": "pirsf", + "n2t": "pirsf", + "prefixcommons": "pirsf", + "uniprot": "DB-0079" + }, + "name": "PIR Superfamily Classification System", + "pattern": "^PIRSF\\d{6}$", + "preferred_prefix": "pirsf", + "publications": [ + { + "doi": "10.1093/nar/gkh097", + "pmc": "PMC308831", + "pubmed": "14681371", + "title": "PIRSF: family classification system at the Protein Information Resource.", + "year": 2004 + } + ], + "uri_format": "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1" + }, + "pkdb": { + "contact": { + "email": "konigmatt@googlemail.com", + "github": null, + "name": "Matthias König", + "orcid": "0000-0003-1725-179X" + }, + "description": "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ", + "example": "PKDB00198", + "homepage": "https://www.hu-berlin.de/?set_language=en&cl=en", + "keywords": [ + "clinical studies", + "clinical veterinary medicine", + "life science", + "personalized medicine", + "pharmacogenomics", + "pharmacology", + "preclinical studies" + ], + "mappings": { + "fairsharing": "FAIRsharing.AYegqK", + "miriam": "pkdb" + }, + "name": "PK-DB", + "pattern": "^PKDB[0-9]{5}$", + "preferred_prefix": "pkdb", + "publications": [ + { + "doi": "10.1093/nar/gkaa990", + "pmc": "PMC7779054", + "pubmed": "33151297", + "title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling.", + "year": 2021 + } + ], + "repository": "https://github.com/matthiaskoenig/pkdb/issues", + "uri_format": "https://pk-db.com/data/$1" + }, + "plana": { + "appears_in": [ + "planp" + ], + "contact": { + "email": "smr@stowers.org", + "github": "srobb1", + "name": "Sofia Robb", + "orcid": "0000-0002-3528-5267" + }, + "depends_on": [ + "ro", + "uberon" + ], + "description": "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.", + "download_obo": "http://purl.obolibrary.org/obo/plana.obo", + "download_owl": "http://purl.obolibrary.org/obo/plana.owl", + "example": "0000001", + "homepage": "https://github.com/obophenotype/planaria-ontology", + "keywords": [ + "anatomy", + "developmental biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "PLANA", + "biocontext": "PLANA", + "bioportal": "PLANA", + "fairsharing": "FAIRsharing.g1qrqs", + "obofoundry": "plana", + "ols": "plana", + "ontobee": "PLANA" + }, + "name": "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PLANA", + "publications": [ + { + "doi": "10.1242/dev.196097", + "pmc": "PMC8353266", + "pubmed": "34318308", + "title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.", + "year": 2021 + } + ], + "repository": "https://github.com/obophenotype/planaria-ontology", + "uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", + "version": "2022-03-02" + }, + "planp": { + "contact": { + "email": "smr@stowers.org", + "github": "srobb1", + "name": "Sofia Robb", + "orcid": "0000-0002-3528-5267" + }, + "depends_on": [ + "go", + "pato", + "plana", + "ro" + ], + "description": "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea.", + "download_obo": "http://purl.obolibrary.org/obo/planp.obo", + "download_owl": "http://purl.obolibrary.org/obo/planp.owl", + "example": "0000001", + "homepage": "https://github.com/obophenotype/planarian-phenotype-ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "PLANP", + "bioportal": "PLANP", + "obofoundry": "planp", + "ols": "planp", + "ontobee": "PLANP" + }, + "name": "Planarian Phenotype Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "PLANP", + "repository": "https://github.com/obophenotype/planarian-phenotype-ontology", + "uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", + "version": "2020-03-28" + }, + "planttfdb": { + "description": "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors.", + "example": "Ath_AT1G01030.1", + "homepage": "http://planttfdb.cbi.pku.edu.cn", + "keywords": [ + "dna", + "gene", + "life science", + "protein", + "regulation", + "rna", + "small molecule" + ], + "mappings": { + "biocontext": "PLANTTFDB", + "fairsharing": "FAIRsharing.ex3fqk", + "miriam": "planttfdb", + "n2t": "planttfdb", + "prefixcommons": "planttfdb", + "re3data": "r3d100011301" + }, + "name": "Plant Transcription Factor Database", + "pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$", + "preferred_prefix": "planttfdb", + "publications": [ + { + "doi": "10.1093/nar/gkw982", + "pmc": "PMC5210657", + "pubmed": "27924042", + "title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.", + "year": 2016 + }, + { + "doi": "10.1093/molbev/msv058", + "pmc": "PMC4476157", + "pubmed": "25750178", + "title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkt1016", + "pmc": "PMC3965000", + "pubmed": "24174544", + "title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors.", + "year": 2013 + } + ], + "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1" + }, + "plasmodb": { + "description": "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "PF11_0344", + "homepage": "http://plasmodb.org/plasmo/", + "keywords": [ + "genome", + "genomics", + "infectious disease medicine" + ], + "mappings": { + "biocontext": "PLASMODB", + "fairsharing": "FAIRsharing.g4n8sw", + "go": "PlasmoDB", + "miriam": "plasmodb", + "n2t": "plasmodb", + "ncbi": "ApiDB_PlasmoDB", + "prefixcommons": "plasmodb", + "re3data": "r3d100011569" + }, + "name": "PlasmoDB", + "pattern": "^\\w+$", + "preferred_prefix": "plasmodb", + "publications": [ + { + "doi": "10.1093/nar/gkn814", + "pmc": "PMC2686598", + "pubmed": "18957442", + "title": "PlasmoDB: a functional genomic database for malaria parasites.", + "year": 2008 + } + ], + "synonyms": [ + "ApiDB_PlasmoDB" + ], + "twitter": "VEuPathDB", + "uri_format": "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" + }, + "plo": { + "contact": { + "email": "mb4@sanger.ac.uk", + "github": null, + "name": "Matt Berriman", + "orcid": null + }, + "deprecated": true, + "homepage": "http://www.sanger.ac.uk/Users/mb4/PLO/", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "PLO", + "obofoundry": "plo" + }, + "name": "Plasmodium Life Cycle", + "preferred_prefix": "PLO", + "uri_format": "http://purl.obolibrary.org/obo/PLO_$1" + }, + "pmap.cutdb": { + "description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites).", + "example": "25782", + "homepage": "http://cutdb.burnham.org", + "keywords": [ + "enzyme", + "pathway", + "protein" + ], + "mappings": { + "biocontext": "PMAP.CUTDB", + "miriam": "pmap.cutdb", + "n2t": "pmap.cutdb", + "prefixcommons": "pmap.cutdb" + }, + "name": "CutDB", + "pattern": "^\\d+$", + "preferred_prefix": "pmap.cutdb", + "publications": [ + { + "doi": "10.1093/nar/gkl813", + "pmc": "PMC1669773", + "pubmed": "17142225", + "title": "CutDB: a proteolytic event database.", + "year": 2006 + } + ], + "uri_format": "http://cutdb.burnham.org/relation/show/$1" + }, + "pmap.substratedb": { + "description": "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates.", + "example": "1915", + "homepage": "http://substrate.burnham.org/", + "keywords": [ + "domain", + "protein", + "reaction" + ], + "mappings": { + "biocontext": "PMAP.SUBSTRATEDB", + "miriam": "pmap.substratedb", + "n2t": "pmap.substratedb", + "prefixcommons": "pmap.substratedb" + }, + "name": "SubstrateDB", + "pattern": "^\\d+$", + "preferred_prefix": "pmap.substratedb", + "publications": [ + { + "doi": "10.1093/nar/gkn683", + "pmc": "PMC2686432", + "pubmed": "18842634", + "title": "PMAP: databases for analyzing proteolytic events and pathways.", + "year": 2008 + } + ], + "uri_format": "http://substrate.burnham.org/protein/annotation/$1/html" + }, + "pmc": { + "description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.", + "example": "PMC3084216", + "homepage": "http://europepmc.org/", + "keywords": [ + "bibliography", + "biomedical science", + "earth science", + "environmental science", + "epidemiology", + "life science", + "virology" + ], + "mappings": { + "biocontext": "PMCID", + "fairsharing": "FAIRsharing.wpt5mp", + "go": "PMCID", + "miriam": "pmc", + "n2t": "pmc", + "prefixcommons": "pmc", + "wikidata": "P932" + }, + "name": "PubMed Central", + "pattern": "^PMC\\d+$", + "preferred_prefix": "pmc", + "providers": [ + { + "code": "ncbi", + "description": "PubMed Central", + "homepage": "https://www.ncbi.nlm.nih.gov/pmc/", + "name": "PubMed Central", + "uri_format": "https://www.ncbi.nlm.nih.gov/pmc/articles/$1/?tool=pubmed" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkr1184", + "pmc": "PMC3245031", + "pubmed": "22140104", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkq1172", + "pmc": "PMC3013733", + "pubmed": "21097890", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2010 + } + ], + "synonyms": [ + "PMC", + "PMCID" + ], + "uri_format": "http://europepmc.org/articles/$1" + }, + "pmdb": { + "description": "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques.", + "example": "PM0012345", + "homepage": "https://bioinformatics.cineca.it/PMDB/", + "keywords": [ + "protein", + "structural biology", + "structure" + ], + "mappings": { + "biocontext": "PMDB", + "fairsharing": "FAIRsharing.wkaakq", + "miriam": "pmdb", + "n2t": "pmdb", + "prefixcommons": "pmdb" + }, + "name": "Protein Model Database", + "pattern": "^PM\\d{7}$", + "preferred_prefix": "pmdb", + "publications": [ + { + "doi": "10.1093/nar/gkj105", + "pmc": "PMC1347467", + "pubmed": "16381873", + "title": "The PMDB Protein Model Database.", + "year": 2006 + } + ], + "uri_format": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1" + }, + "pmp": { + "description": "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers.", + "example": "Q0VCA6", + "homepage": "http://www.proteinmodelportal.org/", + "keywords": [ + "prediction", + "protein", + "structure" + ], + "mappings": { + "biocontext": "PMP", + "miriam": "pmp", + "n2t": "pmp", + "prefixcommons": "pmp" + }, + "name": "Protein Model Portal", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", + "preferred_prefix": "pmp", + "provides": "uniprot", + "publications": [ + { + "doi": "10.1007/s10969-008-9048-5", + "pmc": "PMC2704613", + "pubmed": "19037750", + "title": "The Protein Model Portal.", + "year": 2008 + } + ], + "uri_format": "http://www.proteinmodelportal.org/query/uniprot/$1" + }, + "pmr": { + "contact": { + "email": "laia.subirats@gmail.com", + "github": null, + "name": "Laia Subirats", + "orcid": "0000-0001-8646-5463" + }, + "description": 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Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation.", + "example": "PD000596", + "homepage": "https://www.probes-drugs.org", + "license": "CC BY-SA 4.0", + "mappings": { + "wikidata": "P11199" + }, + "name": "Probes and Drugs", + "pattern": "^PD\\d{6}$", + "preferred_prefix": "probesanddrugs", + "uri_format": "https://www.probes-drugs.org/compound/$1" + }, + "probonto": { + "banana": "PROB", + "banana_peel": "_", + "contact": { + "email": "pierre.grenon@ifomis.uni-saarland.de", + "github": "pgrenon", + "name": "Pierre Grenon", + "orcid": "0000-0003-4614-562X" + }, + "description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.", + "download_owl": "https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl", + "example": "c0000005", + "example_extras": [ + "k0001285" + ], + "homepage": "http://probonto.org", + "keywords": [ + "computational biology", + "mathematics", + "ontology", + "statistics", + "systems biology" + ], + "mappings": { + "biocontext": "PROBONTO", + "fairsharing": "FAIRsharing.8zqzm9", + "miriam": "probonto", + "n2t": "probonto", + "ols": "probonto" + }, + "name": "Probability Distribution Ontology", + "pattern": "^(c|k)\\d{7}$", + "preferred_prefix": "probonto", + "publications": [ + { + "doi": "10.1093/bioinformatics/btw170", + "pmc": "PMC5013898", + "pubmed": "27153608", + "title": "ProbOnto: ontology and knowledge base of probability distributions.", + "year": 2016 + } + ], + "repository": "https://github.com/probonto/ontology", + "uri_format": "http://www.probonto.org/ontology#PROB_$1", + "version": "2.5.0" + }, + "proco": { + "contact": { + "email": "wes_schafer@merck.com", + "github": "schaferw", + "name": "Wes Schafer", + "orcid": "0000-0002-8786-1756" + }, + "depends_on": [ + "chebi", + "cheminf", + "obi", + "pato", + "ro", + "sbo" + ], + "description": "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.", + "download_owl": "http://purl.obolibrary.org/obo/proco.owl", + "example": "0000001", + "homepage": "https://github.com/proco-ontology/PROCO", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "PROCO", + "obofoundry": "proco", + "ols": "proco", + "ontobee": "PROCO" + }, + "name": "Process Chemistry Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PROCO", + "repository": "https://github.com/proco-ontology/PROCO", + "uri_format": "http://purl.obolibrary.org/obo/PROCO_$1", + "version": "PROCO release 20220414" + }, + "prodom": { + "description": "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.", + "example": "PD10000", + "homepage": "http://prodom.prabi.fr/prodom/current/html/home.php", + "keywords": [ + "classification", + "life science", + "protein" + ], + "mappings": { + "biocontext": "PRODOM", + "fairsharing": "FAIRsharing.a8z6gz", + "miriam": "prodom", + "n2t": "prodom", + "prefixcommons": "prodom" + }, + "name": "ProDom", + "pattern": "^PD\\d+$", + "preferred_prefix": "prodom", + "publications": [ + { + "doi": "10.1093/nar/gki034", + "pmc": "PMC539988", + "pubmed": "15608179", + "title": "The ProDom database of protein domain families: more emphasis on 3D.", + "year": 2005 + }, + { + "doi": "10.1093/bib/3.3.246", + "pmc": null, + "pubmed": "12230033", + "title": "ProDom: automated clustering of homologous domains.", + "year": 2002 + } + ], + "uri_format": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1" + }, + "proglyc": { + "description": "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information.", + "example": "AC119", + "homepage": "http://www.proglycprot.org/", + "mappings": { + "biocontext": "PROGLYC", + "miriam": "proglyc", + "n2t": "proglyc" + }, + "name": "ProGlycProt", + "pattern": "^[A-Z]C\\d{1,3}$", + "preferred_prefix": "proglyc", + "uri_format": "http://www.proglycprot.org/detail.aspx?ProId=$1" + }, + "propreo": { + "contact": { + "email": "satyasahoo@ieee.org", + "github": null, + "name": "Satya S. Sahoo", + "orcid": "0000-0001-9190-4256" + }, + "deprecated": true, + "description": "A comprehensive proteomics data and process provenance ontology.", + "download_owl": "http://aber-owl.net/media/ontologies/PROPREO/2/propreo.owl", + "example": "protein", + "homepage": "http://lsdis.cs.uga.edu/projects/glycomics/propreo/", + "keywords": [ + "obo", + "ontology", + "owl", + "proteomics" + ], + "mappings": { + "aberowl": "PROPREO", + "biocontext": "PROPREO", + "bioportal": "PROPREO", + "obofoundry": "propreo", + "prefixcommons": "propreo" + }, + "name": "Proteomics data and process provenance", + "preferred_prefix": "PROPREO", + "uri_format": "http://purl.obolibrary.org/obo/PROPREO_$1" + }, + "prosite": { + "description": "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.", + "example": "PS00001", + "homepage": "https://www.expasy.org/prosite/", + "keywords": [ + "biology", + "protein", + "structure" + ], + "mappings": { + "biocontext": "PROSITE", + "fairsharing": "FAIRsharing.vwc6bd", + "go": "Prosite", + "miriam": "prosite", + "n2t": "prosite", + "prefixcommons": "prosite", + "uniprot": "DB-0084", + "wikidata": "P4355" + }, + "name": "PROSITE", + "pattern": "^PS\\d{5}$", + "preferred_prefix": "prosite", + "publications": [ + { + "doi": "10.1093/bioinformatics/btt129", + "pmc": "PMC3634184", + "pubmed": "23505298", + "title": "pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gks1067", + "pmc": "PMC3531220", + "pubmed": "23161676", + "title": "New and continuing developments at PROSITE.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkj063", + "pmc": "PMC1347426", + "pubmed": "16381852", + "title": "The PROSITE database.", + "year": 2006 + } + ], + "uri_format": "https://prosite.expasy.org/$1" + }, + "protclustdb": { + "description": "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.", + "example": "O80725", + "homepage": "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters", + "keywords": [ + "genetics", + "genomics", + "life science", + "protein", + "structure" + ], + "mappings": { + "biocontext": "PROTCLUSTDB", + "fairsharing": "FAIRsharing.da493y", + "miriam": "protclustdb", + "n2t": "protclustdb", + "prefixcommons": "protclustdb" + }, + "name": "ProtClustDB", + "pattern": "^\\w+$", + "preferred_prefix": "protclustdb", + "publications": [ + { + "doi": "10.1093/nar/gkn734", + "pmc": "PMC2686591", + "pubmed": "18940865", + "title": "The National Center for Biotechnology Information's Protein Clusters Database.", + "year": 2008 + } + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1" + }, + "protcom": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures).", + "example": "12e8LH", + "homepage": "http://www.ces.clemson.edu/compbio/protcom", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "prefixcommons": "protcom" + }, + "name": "Database of protein-protein complexes", + "preferred_prefix": "protcom", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1" + }, + "proteomicsdb.peptide": { + "comment": "The fact that this has .peptide as a subspace is a bit of a misnomer. Its original registration with MIRIAM uses a subview over the protein to point to peptides, but the identifiers in this semantic space seem to be about proteins.", + "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.", + "example": "53504", + "homepage": "https://www.proteomicsdb.org/#peptideSearch", + "mappings": { + "biocontext": "PROTEOMICSDB.PEPTIDE", + "miriam": "proteomicsdb.peptide", + "n2t": "proteomicsdb.peptide" + }, + "name": "ProteomicsDB Peptide", + "pattern": "^\\d+$", + "preferred_prefix": "proteomicsdb.peptide", + "uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1" + }, + "proteomicsdb.protein": { + "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.", + "example": "53504", + "homepage": "https://www.proteomicsdb.org/#human", + "mappings": { + "biocontext": "PROTEOMICSDB.PROTEIN", + "miriam": "proteomicsdb.protein", + "n2t": "proteomicsdb.protein" + }, + "name": "ProteomicsDB Protein", + "pattern": "^\\d+$", + "preferred_prefix": "proteomicsdb.protein", + "uri_format": "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary" + }, + "protonet.cluster": { + "description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information.", + "example": "4349895", + "homepage": "http://www.protonet.cs.huji.ac.il/", + "keywords": [ + "classification", + "clustering", + "protein" + ], + "mappings": { + "biocontext": "PROTONET.CLUSTER", + "miriam": "protonet.cluster", + "n2t": "protonet.cluster", + "prefixcommons": "protonet.cluster" + }, + "name": "ProtoNet Cluster", + "pattern": "^\\d+$", + "preferred_prefix": "protonet.cluster", + "publications": [ + { + "doi": "10.1110/ps.062185706", + "pmc": "PMC2242553", + "pubmed": "16672244", + "title": "Functional annotation prediction: all for one and one for all.", + "year": 2006 + } + ], + "uri_format": "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1" + }, + "protonet.proteincard": { + "description": "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information.", + "example": "16941567", + "homepage": "http://www.protonet.cs.huji.ac.il/", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "PROTONET.PROTEINCARD", + "miriam": "protonet.proteincard", + "n2t": "protonet.proteincard", + "prefixcommons": "protonet.proteincard" + }, + "name": "ProtoNet ProteinCard", + "pattern": "^\\d+$", + "preferred_prefix": "protonet.proteincard", + "publications": [ + { + "doi": "10.1110/ps.062185706", + "pmc": "PMC2242553", + "pubmed": "16672244", + "title": "Functional annotation prediction: all for one and one for all.", + "year": 2006 + } + ], + "uri_format": "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1" + }, + "prov": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.", + "download_owl": "http://www.w3.org/ns/prov-o-20130430", + "example": "Activity", + "homepage": "https://www.w3.org/ns/prov", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "PROV", + "biocontext": "prov", + "biolink": "prov", + "ols": "prov" + }, + "name": "PROV Namespace", + "preferred_prefix": "prov", + "uri_format": "http://www.w3.org/ns/prov#$1", + "version": "2013-04-30" + }, + "pscdb": { + "description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.", + "example": "051", + "homepage": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "PSCDB", + "fairsharing": "FAIRsharing.3d4jx0", + "miriam": "pscdb", + "n2t": "pscdb" + }, + "name": "Protein Structural Change Database", + "pattern": "^\\d+$", + "preferred_prefix": "pscdb", + "publications": [ + { + "doi": "10.1093/nar/gkr966", + "pmc": "PMC3245091", + "pubmed": "22080505", + "title": "PSCDB: a database for protein structural change upon ligand binding.", + "year": 2011 + }, + { + "doi": "10.1016/j.jmb.2011.02.058", + "pmc": null, + "pubmed": "21376729", + "title": "Classification and annotation of the relationship between protein structural change and ligand binding.", + "year": 2011 + } + ], + "uri_format": "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html" + }, + "psdo": { + "contact": { + "email": "zachll@umich.edu", + "github": "zachll", + "name": "Zach Landis-Lewis", + "orcid": "0000-0002-9117-9338" + }, + "depends_on": [ + "bfo", + "iao", + "ro", + "stato" + ], + "description": "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed.", + "download_owl": "http://purl.obolibrary.org/obo/psdo.owl", + "example": "0000055", + "homepage": "https://github.com/Display-Lab/psdo", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "PSDO", + "bioportal": "PSDO", + "obofoundry": "psdo", + "ols": "psdo", + "ontobee": "PSDO" + }, + "name": "Performance Summary Display Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PSDO", + "repository": "https://github.com/Display-Lab/psdo", + "uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", + "version": "1.0.0" + }, + "pseudogene": { + "contact": { + "email": "mark@gersteinlab.org", + "github": null, + "name": "Mark Gerstein", + "orcid": "0000-0002-9746-371" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase.", + "example": "PGOHUM00000289843", + "homepage": "http://www.pseudogene.org", + "keywords": [ + "gene", + "ontology" + ], + "mappings": { + "bioportal": "pseudo", + "prefixcommons": "pseudogene" + }, + "name": "PseudoGene", + "preferred_prefix": "pseudogene", + "synonyms": [ + "pseudogene.org" + ], + "uri_format": "http://tables.pseudogene.org/[?species_name]/$1" + }, + "pseudomonas": { + "description": "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.", + "example": "PSEEN0001", + "homepage": "http://www.pseudomonas.com/", + "mappings": { + "biocontext": "PSEUDOMONAS", + "miriam": "pseudomonas", + "n2t": "pseudomonas" + }, + "name": "Pseudomonas Genome Database", + "pattern": "^P\\w+$", + "preferred_prefix": "pseudomonas", + "uri_format": "http://www.pseudomonas.com/feature/show/?locus_tag=$1" + }, + "psipar": { + "banana": "PAR", + "comment": "This resource is no longer loaded on XML and the sourceforge link from the HUPO website to the psi-par.obo artifact is dead.", + "deprecated": true, + "description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.", + "example": "0116", + "homepage": "https://www.psidev.info/psi-par", + "mappings": { + "biocontext": "PSIPAR", + "miriam": "psipar", + "n2t": "psipar" + }, + "name": "Protein Affinity Reagents", + "pattern": "^\\d+$", + "preferred_prefix": "psipar", + "uri_format": "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1" + }, + "pso": { + "contact": { + "email": "cooperl@oregonstate.edu", + "github": "cooperl09", + "name": "Laurel Cooper", + "orcid": "0000-0002-6379-8932" + }, + "depends_on": [ + "ro" + ], + "description": "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter.", + "download_obo": "http://purl.obolibrary.org/obo/pso.obo", + "download_owl": "http://purl.obolibrary.org/obo/pso.owl", + "example": "0000013", + "homepage": "https://github.com/Planteome/plant-stress-ontology", + "keywords": [ + "medical informatics", + "obo", + "occupational medicine", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "PSO", + "bioportal": "PSO", + "fairsharing": "FAIRsharing.dyj433", + "obofoundry": "pso", + "ols": "pso", + "ontobee": "PSO" + }, + "name": "Plant Stress Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "PSO", + "publications": [ + { + "doi": "10.1093/nar/gkx1152", + "pmc": "PMC5753347", + "pubmed": "29186578", + "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.", + "year": 2018 + } + ], + "repository": "https://github.com/Planteome/plant-stress-ontology", + "uri_format": "http://purl.obolibrary.org/obo/PSO_$1", + "version": "2020-05-19" + }, + "pspub": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Documentation of the Phenoscape Curation Workflow", + "homepage": "https://wiki.phenoscape.org/wiki/Curation_workflow", + "name": "Phenoscape Publication", + "preferred_prefix": "pspub" + }, + "pubchem.bioassay": { + "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results.", + "example": "1018", + "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay", + "keywords": [ + "small molecule" + ], + "mappings": { + "biocontext": "PUBCHEM.BIOASSAY", + "edam": "2638", + "go": "PubChem_BioAssay", + "miriam": "pubchem.bioassay", + "n2t": "pubchem.bioassay", + "prefixcommons": "pubchem.bioassay" + }, + "name": "NCBI PubChem database of bioassay records", + "part_of": "pubchem", + "pattern": "^\\d+$", + "preferred_prefix": "pubchem.bioassay", + "publications": [ + { + "doi": "10.1093/nar/gkl1031", + "pmc": "PMC1781113", + "pubmed": "17170002", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2006 + } + ], + "twitter": "pubchem", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1" + }, + "pubchem.cell": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Cell Lines in PubChem", + "example": "31", + "homepage": "https://pubchem.ncbi.nlm.nih.gov", + "keywords": [ + "bioactivities", + "cell lines", + "chemistry" + ], + "name": "PubChem Cell Line", + "part_of": "pubchem", + "pattern": "^\\d+$", + "preferred_prefix": "pubchem.cell", + "twitter": "pubchem", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/cell/$1" + }, + "pubchem.classification": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records.", + "example": "87", + "homepage": "https://pubchem.ncbi.nlm.nih.gov/classification/", + "keywords": [ + "chemistry" + ], + "name": "PubChem Classification", + "part_of": "pubchem", + "pattern": "^\\d+$", + "preferred_prefix": "pubchem.classification", + "twitter": "pubchem", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1" + }, + "pubchem.compound": { + "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.", + "example": "100101", + "homepage": "https://pubchem.ncbi.nlm.nih.gov/", + "keywords": [ + "chemical", + "chemistry", + "epidemiology", + "metabolite", + "structure", + "virology" + ], + "mappings": { + "biocontext": "PUBCHEM.COMPOUND", + "biolink": "CID", + "cellosaurus": "PubChem", + "cheminf": "000140", + "edam": "2639", + "fairsharing": "FAIRsharing.qt3w7z", + "go": "PubChem_Compound", + "miriam": "pubchem.compound", + "n2t": "pubchem.compound", + "prefixcommons": "pubchem.compound", + "re3data": "r3d100010129", + "wikidata": "P662" + }, + "name": "PubChem CID", + "part_of": "pubchem", + "pattern": "^\\d+$", + "preferred_prefix": "pubchem.compound", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/pubchem/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkaa971", + "pmc": "PMC7778930", + "pubmed": "33151290", + "title": "PubChem in 2021: new data content and improved web interfaces.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gky1033", + "pmc": "PMC6324075", + "pubmed": "30371825", + "title": "PubChem 2019 update: improved access to chemical data.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw1118", + "pmc": "PMC5210581", + "pubmed": "27899599", + "title": "PubChem BioAssay: 2017 update.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gkt978", + "pmc": "PMC3965008", + "pubmed": "24198245", + "title": "PubChem BioAssay: 2014 update.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkr1132", + "pmc": "PMC3245056", + "pubmed": "22140110", + "title": "PubChem's BioAssay Database.", + "year": 2011 + }, + { + "doi": "10.1016/j.drudis.2010.10.003", + "pmc": "PMC3010383", + "pubmed": "20970519", + "title": "PubChem as a public resource for drug discovery.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkp456", + "pmc": "PMC2703903", + "pubmed": "19498078", + "title": "PubChem: a public information system for analyzing bioactivities of small molecules.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkl1031", + "pmc": "PMC1781113", + "pubmed": "17170002", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2006 + } + ], + "synonyms": [ + "CID", + "DSSTox_CID", + "PUBCHEM_CID", + "PubChem_Compound_CID", + "Pubchem", + "pubchem_id" + ], + "twitter": "pubchem", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/compound/$1" + }, + "pubchem.element": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number.", + "example": "1", + "homepage": "https://pubchem.ncbi.nlm.nih.gov/periodic-table", + "keywords": [ + "chemistry" + ], + "name": "PubChem Element", + "part_of": "pubchem", + "pattern": "^\\d+$", + "preferred_prefix": "pubchem.element", + "twitter": "pubchem", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/element/$1" + }, + "pubchem.substance": { + "description": "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records.", + "example": "100101", + "homepage": "https://pubchem.ncbi.nlm.nih.gov/", + "keywords": [ + "protein", + "small molecule", + "structure" + ], + "mappings": { + "biocontext": "PUBCHEM.SUBSTANCE", + "cheminf": "000141", + "go": "PubChem_Substance", + "miriam": "pubchem.substance", + "n2t": "pubchem.substance", + "prefixcommons": "pubchem.substance", + "wikidata": "P2153" + }, + "name": "PubChem Substance ID (SID)", + "part_of": "pubchem", + "pattern": "^\\d+$", + "preferred_prefix": "pubchem.substance", + "publications": [ + { + "doi": "10.1093/nar/gkl1031", + "pmc": "PMC1781113", + "pubmed": "17170002", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2006 + } + ], + "synonyms": [ + "DSSTox_Generic_SID" + ], + "twitter": "pubchem", + "uri_format": "https://pubchem.ncbi.nlm.nih.gov/substance/$1" + }, + "publons.publication": { + "description": "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)", + "example": "507568", + "homepage": "https://publons.com", + "mappings": { + "wikidata": "P3431" + }, + "name": "Publons publication", + "preferred_prefix": "publons.publication", + "uri_format": "https://publons.com/publon/$1" + }, + "publons.researcher": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work.", + "example": "1981638", + "homepage": "https://publons.com/researcher", + "mappings": { + "biolink": "ResearchID" + }, + "name": "Publons Researcher", + "pattern": "^\\d+$", + "preferred_prefix": "publons.researcher", + "uri_format": "https://publons.com/researcher/$1" + }, + "pubmed": { + "description": "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s.", + "example": "16333295", + "homepage": "https://www.ncbi.nlm.nih.gov/PubMed/", + "keywords": [ + "bibliography", + "biomedical science", + "earth science", + "environmental science", + "life science", + "traditional medicine" + ], + "mappings": { + "biocontext": "PUBMED", + "cellosaurus": "PubMed", + "cheminf": "000302", + "edam": "1187", + "fairsharing": "FAIRsharing.a5sv8m", + "go": "PMID", + "miriam": "pubmed", + "n2t": "pubmed", + "prefixcommons": "pubmed", + "wikidata": "P698" + }, + "name": "PubMed", + "pattern": "^\\d+$", + "preferred_prefix": "pubmed", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "PubMed through Linkedlife data", + "homepage": "http://linkedlifedata.com/", + "name": "PubMed through Linkedlife data", + "uri_format": "http://linkedlifedata.com/resource/pubmed/id/$1" + }, + { + "code": "epmc", + "description": "Europe PMC", + "homepage": "http://europepmc.org/", + "name": "Europe PMC", + "uri_format": "http://europepmc.org/abstract/MED/$1" + }, + { + "code": "hubmed", + "description": "HubMed", + "homepage": "http://www.hubmed.org/", + "name": "HubMed", + "uri_format": "http://www.hubmed.org/display.cgi?uids=$1" + }, + { + "code": "pubmed.new", + "description": "New-style link for pubmed", + "homepage": "https://pubmed.ncbi.nlm.nih.gov", + "name": "PubMed (new)", + "uri_format": "https://pubmed.ncbi.nlm.nih.gov/$1" + }, + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/pubmed/$1" + }, + { + "code": "uniprot.citation", + "description": "UniProt mints PURLs for citations identifiers", + "homepage": "https://uniprot.org/", + "name": "UniProt", + "uri_format": "http://purl.uniprot.org/citations/$1" + }, + { + "code": "uniprot.pubmed", + "description": "UniProt mints PURLs for PubMed identifiers", + "homepage": "https://uniprot.org/", + "name": "UniProt", + "uri_format": "http://purl.uniprot.org/pubmed/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkj158", + "pmc": "PMC1347520", + "pubmed": "16381840", + "title": "Database resources of the National Center for Biotechnology Information.", + "year": 2006 + } + ], + "synonyms": [ + "MEDLINE", + "PMID", + "PubMed", + "pmid" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/pubmed/$1" + }, + "puro": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians.", + "example": "RoleInTime", + "homepage": "http://www.sparontologies.net/ontologies/pro", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.3e88d6" + }, + "name": "Publishing Roles Ontology", + "preferred_prefix": "PuRO", + "publications": [ + { + "doi": "10.1145/2362499.2362502", + "pmc": null, + "pubmed": null, + "title": "Scholarly publishing and linked data", + "year": 2012 + } + ], + "repository": "https://github.com/sparontologies/pro", + "twitter": "sparontologies", + "uri_format": "http://purl.org/spar/pro/$1" + }, + "pw": { + "banana": "PW", + "contact": { + "email": "gthayman@mcw.edu", + "github": "gthayman", + "name": "G. Thomas Hayman", + "orcid": "0000-0002-9553-7227" + }, + "description": "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.", + "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo", + "download_owl": "http://purl.obolibrary.org/obo/pw.owl", + "example": "0000423", + "homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html", + "keywords": [ + "drug metabolism", + "human", + "life science", + "obo", + "ontology", + "pathway" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "PW", + "biocontext": "PW", + "bioportal": "PW", + "fairsharing": "FAIRsharing.f73xhd", + "miriam": "pw", + "n2t": "pw", + "obofoundry": "pw", + "ols": "pw", + "ontobee": "PW", + "prefixcommons": "pw", + "wikidata": "P7333" + }, + "name": "Pathway ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "PW", + "providers": [ + { + "code": "miriam_obo_legacy", + "description": "An old URI style for MIRIAM", + "homepage": "https://identifiers.org/", + "name": "MIRIAM OBO Legacy", + "uri_format": "http://identifiers.org/obo.pw/PW:$1" + } + ], + "publications": [ + { + "doi": "10.1186/s40246-014-0017-8", + "pmc": "PMC4191248", + "pubmed": "25265995", + "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.", + "year": 2014 + }, + { + "doi": "10.1186/2041-1480-5-7", + "pmc": "PMC3922094", + "pubmed": "24499703", + "title": "The pathway ontology - updates and applications.", + "year": 2014 + }, + { + "doi": "10.1093/database/bar010", + "pmc": "PMC3072770", + "pubmed": "21478484", + "title": "The Rat Genome Database pathway portal.", + "year": 2011 + } + ], + "repository": "https://github.com/rat-genome-database/PW-Pathway-Ontology", + "twitter": "ratgenome", + "uri_format": "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1", + "version": "2019-10-23" + }, + "pwo": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity.", + "example": "Workflow", + "homepage": "http://www.sparontologies.net/ontologies/pwo", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.c4e46c" + }, + "name": "Publishing Workflow Ontology", + "preferred_prefix": "PWO", + "publications": [ + { + "doi": "10.3233/sw-160230", + "pmc": null, + "pubmed": null, + "title": "The Publishing Workflow Ontology (PWO)", + "year": 2017 + } + ], + "repository": "https://github.com/sparontologies/pwo", + "twitter": "sparontologies", + "uri_format": "http://purl.org/spar/pwo/$1" + }, + "px": { + "description": "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination.", + "example": "PXD000500", + "homepage": "http://www.proteomexchange.org/", + "mappings": { + "biocontext": "PX", + "miriam": "px", + "n2t": "px" + }, + "name": "ProteomeXchange", + "pattern": "^(R)?PXD\\d{6}$", + "preferred_prefix": "px", + "uri_format": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1" + }, + "pypi": { + "description": "The Python Package Index (PyPI) is a repository for Python packages.", + "example": "numpy", + "homepage": "https://www.python.org/psf/", + "mappings": { + "miriam": "pypi" + }, + "name": "PyPI", + "pattern": "^[a-zA-Z_][a-zA-Z0-9\\-_]+$", + "preferred_prefix": "pypi", + "uri_format": "https://pypi.org/project/$1" + }, + "qb": { + "contact": { + "email": "richard@cyganiak.de", + "github": "cygri", + "name": "Richard Cyganiak", + "orcid": "0000-0001-9950-5209" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI).", + "download_rdf": "http://purl.org/linked-data/cube#", + "example": "Observation", + "homepage": "https://www.w3.org/TR/vocab-data-cube", + "name": "The data cube vocabulary", + "pattern": "^\\w+$", + "preferred_prefix": "qb", + "repository": "UKGovLD/publishing-statistical-data", + "uri_format": "http://purl.org/linked-data/cube#$1" + }, + "qtldb": { + "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent.", + "example": "4685", + "homepage": "https://www.animalgenome.org/QTLdb", + "mappings": { + "miriam": "qtldb" + }, + "name": "Animal Genome QTL", + "pattern": "^\\d+$", + "preferred_prefix": "qtldb", + "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" + }, + "qudt": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.", + "download_owl": "http://aber-owl.net/media/ontologies/QUDT/4/qudt.owl", + "download_rdf": "http://qudt.org/schema/qudt/", + "example": "baseDimensionEnumeration", + "homepage": "https://qudt.org", + "keywords": [ + "astrophysics and astronomy", + "ontology" + ], + "mappings": { + "aberowl": "QUDT", + "bartoc": "18206", + "biolink": "qud", + "bioportal": "QUDT", + "fairsharing": "FAIRsharing.d3pqw7" + }, + "name": "Quantities, Units, Dimensions, and Types Ontology", + "preferred_prefix": "qudt", + "repository": "https://github.com/qudt/qudt-public-repo", + "uri_format": "http://qudt.org/schema/qudt#$1" + }, + "radiomics": { + "contact": { + "email": "alberto.traverso@maastro.nl", + "github": null, + "name": "Alberto Traverso", + "orcid": "0000-0001-6183-4429" + }, + "description": "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]", + "example": "LK99", + "homepage": "http://www.radiomics.org/RO", + "keywords": [ + "ontology" + ], + "mappings": { + "bioportal": "RO" + }, + "name": "Radiomics Ontology", + "preferred_prefix": "radiomics", + "uri_format": "http://www.radiomics.org/RO/$1" + }, + "radlex": { + "contact": { + "email": "radlex-feedback@lists.rsna.org", + "github": null, + "name": "Radiological Society of North America", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project.", + "download_owl": "http://aber-owl.net/media/ontologies/RADLEX/37/radlex.owl", + "example": "RID1", + "homepage": "https://radlex.org", + "keywords": [ + "anatomy", + "biomedical science", + "clinical studies", + "medical informatics", + "ontology", + "radiology" + ], + "license": "http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf", + "mappings": { + "aberowl": "RADLEX", + "bioportal": "RADLEX", + "fairsharing": "FAIRsharing.shm2f2", + "hl7": "2.16.840.1.113883.6.256" + }, + "name": "RSNA Informatics RadLex", + "pattern": "^RID\\d+$", + "preferred_prefix": "radlex", + "publications": [ + { + "doi": "10.1016/j.jvir.2009.04.031", + "pmc": null, + "pubmed": "19560008", + "title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology.", + "year": 2009 + }, + { + "doi": "10.1016/j.jvir.2008.10.022", + "pmc": null, + "pubmed": "19081735", + "title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology.", + "year": 2008 + }, + { + "doi": "10.2214/ajr.174.5.1741463", + "pmc": null, + "pubmed": "10789815", + "title": "Radiology lexicon.", + "year": 2000 + } + ], + "uri_format": "https://radlex.org/RID/$1", + "version": "4.1" + }, + "rapdb.locus": { + "description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB.", + "example": "Os01g0883800", + "homepage": "https://rapdb.dna.affrc.go.jp/", + "mappings": { + "miriam": "rapdb.locus" + }, + "name": "RAP-DB Locus", + "pattern": "^Os\\S+g\\d{7}$", + "preferred_prefix": "rapdb.locus", + "synonyms": [ + "irgsp" + ], + "uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1" + }, + "rapdb.transcript": { + "description": "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB.", + "example": "Os01t0883800-02", + "homepage": "https://rapdb.dna.affrc.go.jp/", + "keywords": [ + "dna", + "genome" + ], + "mappings": { + "go": "RAP-DB", + "miriam": "rapdb.transcript", + "ncbi": "RAP-DB", + "prefixcommons": "rapdb" + }, + "name": "Rice annotation Project database", + "pattern": "^Os\\S+t\\d{7}-\\d{2}$", + "preferred_prefix": "rapdb.transcript", + "uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1" + }, + "ratmap": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters", + "example": "5", + "homepage": "http://ratmap.org", + "keywords": [ + "dna", + "gene", + "genome" + ], + "mappings": { + "ncbi": "RATMAP", + "prefixcommons": "ratmap" + }, + "name": "Rat Genome Database", + "preferred_prefix": "ratmap", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://ratmap.org/Showgene.php?gene_stable_id=$1" + }, + "rbk": { + "description": "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function.", + "example": "Q-2958", + "homepage": "https://www.rebuildingakidney.org/", + "keywords": [ + "cell biology", + "developmental biology", + "genomics", + "molecular biology" + ], + "mappings": { + "biocontext": "RBK", + "fairsharing": "FAIRsharing.78d3ad", + "miriam": "rbk", + "n2t": "rbk" + }, + "name": "Rebuilding a Kidney", + "pattern": "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$", + "preferred_prefix": "rbk", + "publications": [ + { + "doi": "10.1681/asn.2016101077", + "pmc": "PMC5407737", + "pubmed": "28096308", + "title": "(Re)Building a Kidney.", + "year": 2017 + } + ], + "repository": "https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets", + "uri_format": "https://www.rebuildingakidney.org/id/$1" + }, + "rbo": { + "contact": { + "email": "daniel.c.berrios@nasa.gov", + "github": "DanBerrios", + "name": "Daniel C. Berrios", + "orcid": "0000-0003-4312-9552" + }, + "depends_on": [ + "bfo", + "chmo", + "envo", + "obi", + "pato", + "ro", + "uo" + ], + "description": "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.", + "download_json": "http://purl.obolibrary.org/obo/rbo.json", + "download_obo": "http://purl.obolibrary.org/obo/rbo.obo", + "download_owl": "http://purl.obolibrary.org/obo/rbo.owl", + "example": "00000105", + "example_extras": [ + "010007" + ], + "homepage": "https://github.com/Radiobiology-Informatics-Consortium/RBO", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "RBO", + "bioportal": "RBO", + "obofoundry": "rbo", + "ols": "rbo", + "ontobee": "RBO" + }, + "name": "Radiation Biology Ontology", + "pattern": "^\\d{6,8}$", + "preferred_prefix": "RBO", + "repository": "https://github.com/Radiobiology-Informatics-Consortium/RBO", + "uri_format": "http://purl.obolibrary.org/obo/RBO_$1", + "version": "2022-06-02" + }, + "rcb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.", + "example": "RCB0002", + "homepage": "https://cell.brc.riken.jp/en/rcb", + "mappings": { + "cellosaurus": "RCB" + }, + "name": "RIKEN Bioresource Center Cell Bank", + "pattern": "^RCB\\d+$", + "preferred_prefix": "rcb", + "uri_format": "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1" + }, + "rdf": { + "contact": { + "email": "rmrich5@gmail.com", + "github": null, + "name": "Rafael Richards", + "orcid": "0000-0001-5699-0515" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts", + "example": "RDF", + "homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns", + "keywords": [ + "computer science", + "subject agnostic" + ], + "mappings": { + "biocontext": "rdf", + "fairsharing": "FAIRsharing.p77ph9" + }, + "name": "Resource Description Framework", + "preferred_prefix": "rdf", + "uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1" + }, + "rdfs": { + "contact": { + "email": "danbri@w3.org", + "github": null, + "name": "Dan Brickley", + "orcid": "0000-0002-6450-7041" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary.", + "download_owl": "https://triplydb.com/w3c/rdfs/download.trig.gz", + "example": "label", + "homepage": "https://www.w3.org/TR/rdf-schema/", + "keywords": [ + "bioinformatics", + "life science", + "linguistics", + "ontology", + "ontology and terminology" + ], + "mappings": { + "aberowl": "RDFS", + "biocontext": "rdfs", + "bioportal": "RDFS", + "fairsharing": "FAIRsharing.v9n3gk" + }, + "name": "RDF Schema", + "preferred_prefix": "rdfs", + "uri_format": "http://www.w3.org/2000/01/rdf-schema#$1" + }, + "rdo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms.", + "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.obo", + "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/RDO.owl", + "example": "9002859", + "homepage": "https://ratmine.mcw.edu/ontology/disease/", + "keywords": [ + "ontology" + ], + "name": "RGD Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "rdo", + "uri_format": "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1" + }, + "re3data": { + "description": "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines.", + "example": "r3d100010772", + "homepage": "https://datacite.org", + "mappings": { + "bartoc": "822", + "miriam": "re3data" + }, + "name": "re3data", + "pattern": "^r3d\\d{9,9}$", + "preferred_prefix": "re3data", + "uri_format": "https://www.re3data.org/repository/$1" + }, + "reactome": { + "description": "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.", + "example": "R-BTA-418592", + "homepage": "https://www.reactome.org/", + "keywords": [ + "human", + "pathway", + "reaction" + ], + "mappings": { + "biocontext": "REACTOME", + "cheminf": "000411", + "edam": "1155", + "go": "Reactome", + "miriam": "reactome", + "n2t": "reactome", + "prefixcommons": "reactome", + "re3data": "r3d100010861", + "wikidata": "P3937" + }, + "name": "Reactome", + "pattern": "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$", + "preferred_prefix": "reactome", + "providers": [ + { + "code": "pathwaycommons", + "description": "Pathway diagram drawn with Cytoscape", + "homepage": "https://www.pathwaycommons.org", + "name": "Pathway Commons", + "uri_format": "https://apps.pathwaycommons.org/pathways?uri=http%3A%2F%2Fidentifiers.org%2Freactome%2F$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gki072", + "pmc": "PMC540026", + "pubmed": "15608231", + "title": "Reactome: a knowledgebase of biological pathways.", + "year": 2005 + } + ], + "synonyms": [ + "RE", + "REACT" + ], + "uri_format": "https://reactome.org/content/detail/$1" + }, + "reaxys": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier.", + "example": "1257009", + "homepage": "https://www.reaxys.com", + "mappings": { + "edam": "1003", + "wikidata": "P1579" + }, + "name": "Reaxys", + "pattern": "^\\d+$", + "preferred_prefix": "reaxys", + "synonyms": [ + "Beilstein", + "Reaxys" + ] + }, + "rebase": { + "description": "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data.", + "example": "101", + "homepage": "http://rebase.neb.com/rebase/", + "keywords": [ + "dna", + "enzyme", + "genome", + "life science", + "protein", + "rna", + "small molecule", + "structure" + ], + "mappings": { + "biocontext": "REBASE", + "edam": "2325", + "fairsharing": "FAIRsharing.9sb9qh", + "go": "REBASE", + "miriam": "rebase", + "n2t": "rebase", + "prefixcommons": "rebase", + "re3data": "r3d100012171", + "uniprot": "DB-0089", + "wikidata": "P4866" + }, + "name": "REBASE Enzyme Number", + "pattern": "^\\d+$", + "preferred_prefix": "rebase", + "publications": [ + { + "doi": "10.1093/nar/gku1046", + "pmc": "PMC4383893", + "pubmed": "25378308", + "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkp874", + "pmc": "PMC2808884", + "pubmed": "19846593", + "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.", + "year": 2009 + } + ], + "uri_format": "http://rebase.neb.com/rebase/enz/$1.html" + }, + "receptome.family": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database.", + "example": "5.1", + "homepage": "http://www.receptome.org", + "keywords": [ + "protein" + ], + "mappings": { + "prefixcommons": "hpmr" + }, + "name": "Human Plasma Membrane Receptome Families", + "preferred_prefix": "receptome.family", + "uri_format": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1" + }, + "redfly": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs).", + "example": "8", + "homepage": "http://redfly.ccr.buffalo.edu", + "keywords": [ + "regulation" + ], + "mappings": { + "prefixcommons": "redfly" + }, + "name": "Regulatory Elements Database for Drosophila", + "preferred_prefix": "redfly", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1" + }, + "refseq": { + "contributor_extras": [ + { + "email": null, + "github": "slobentanzer", + "name": "Sebastian Lobentanzer", + "orcid": "0000-0003-3399-6695" + } + ], + "description": "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products.", + "example": "NP_012345", + "example_extras": [ + "WP_029104145.1" + ], + "has_canonical": "ncbiprotein", + "homepage": "https://www.ncbi.nlm.nih.gov/projects/RefSeq/", + "keywords": [ + "computational biology", + "dna", + "genetics", + "life science", + "protein", + "rna" + ], + "mappings": { + "biocontext": "RefSeq", + "edam": "1098", + "fairsharing": "FAIRsharing.4jg0qw", + "go": "RefSeq", + "hl7": "2.16.840.1.113883.6.280", + "miriam": "refseq", + "n2t": "refseq", + "prefixcommons": "refseq", + "re3data": "r3d100010285", + "uniprot": "DB-0117" + }, + "name": "Reference Sequence Collection", + "pattern": "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$", + "preferred_prefix": "refseq", + "publications": [ + { + "doi": "10.1093/nar/gkv1189", + "pmc": "PMC4702849", + "pubmed": "26553804", + "title": "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkl842", + "pmc": "PMC1716718", + "pubmed": "17130148", + "title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.", + "year": 2006 + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/545" + ], + "synonyms": [ + "REFSEQ_PROT" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" + }, + "reo": { + "comment": "From James O.: It was an ontology for \"reagents\" developed by @Matthew Brush. Since OBI was interested in reagents, Matt developed it in coordination with OBI and had plans to submit it to OBO. I believe that REO was once included in Ontobee, and OBI even started using some REO terms. But REO was never submitted to OBO. I believe it was abandoned.", + "contact": { + "email": "matt@tislab.org", + "github": "mbrush", + "name": "Matthew Brush", + "orcid": "0000-0002-1048-5019" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.", + "download_owl": "https://github.com/tis-lab/reagent-ontology/raw/master/reo/ontology_files/reo_pre-merged_or_reasoned_files/reo_reasoned_9-6-12.owl", + "example": "0000079", + "homepage": "https://github.com/tis-lab/reagent-ontology", + "keywords": [ + "ontology" + ], + "mappings": { + "ontobee": "REO" + }, + "name": "Reagent Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "reo", + "references": [ + "https://github.com/obi-ontology/obi/issues/1015", + "https://code.google.com/archive/p/reagent-ontology/", + "https://github.com/obi-ontology/obi/issues/1135" + ], + "repository": "https://github.com/tis-lab/reagent-ontology", + "uri_format": "http://purl.obolibrary.org/obo/REO_$11" + }, + "repeatsdb.protein": { + "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database.", + "example": "P29894", + "homepage": "https://repeatsdb.org/", + "mappings": { + "miriam": "repeatsdb.protein" + }, + "name": "RepeatsDB Protein", + "pattern": "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$", + "preferred_prefix": "repeatsdb.protein", + "provides": "uniprot", + "uri_format": "https://repeatsdb.org/protein/$1" + }, + "repeatsdb.structure": { + "description": "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database.", + "example": "2gc4E", + "homepage": "https://repeatsdb.org/", + "mappings": { + "miriam": "repeatsdb.structure" + }, + "name": "RepeatsDB Structure", + "pattern": "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$", + "preferred_prefix": "repeatsdb.structure", + "uri_format": "https://repeatsdb.org/structure/$1" + }, + "reproduceme": { + "contact": { + "email": "sheeba.samuel@uni-jena.de", + "github": null, + "name": "Sheeba Samuel", + "orcid": "0000-0002-7981-8504" + }, + "description": "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility.", + "download_owl": "https://sheeba-samuel.github.io/REPRODUCE-ME/doc/reproduce-me.xml", + "example": "MicrobeamManipulation", + "homepage": "https://w3id.org/reproduceme/research", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "REPRODUCE-ME", + "bioportal": "REPRODUCE-ME", + "ols": "reproduceme" + }, + "name": "REPRODUCE-ME Ontology", + "preferred_prefix": "reproduceme", + "uri_format": "https://w3id.org/reproduceme#$1", + "version": "1.1" + }, + "resid": { + "contact": { + "email": "john.garavelli@ebi.ac.uk", + "github": null, + "name": "John Garavelli", + "orcid": null + }, + "deprecated": true, + "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", + "example": "AA0001", + "homepage": "https://proteininformationresource.org/resid/", + "keywords": [ + "obo", + "ontology", + "protein", + "small molecule", + "structure" + ], + "mappings": { + "biocontext": "RESID", + "edam": "2619", + "go": "RESID", + "miriam": "resid", + "n2t": "resid", + "obofoundry": "resid", + "prefixcommons": "resid" + }, + "name": "Protein covalent bond", + "pattern": "^AA\\d{4}$", + "preferred_prefix": "RESID", + "publications": [ + { + "doi": "10.1002/pmic.200300764", + "pmc": null, + "pubmed": "15174124", + "title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base.", + "year": 2004 + } + ], + "uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1" + }, + "reto": { + "contact": { + "email": "vladimir.n.mironov@gmail.com", + "github": null, + "name": "Vladimir Mironov", + "orcid": null + }, + "description": "Regulation of Transcription", + "download_obo": "https://www.bio.ntnu.no/ontology/ReTO/reto.obo", + "download_owl": "https://www.bio.ntnu.no/ontology/ReTO/reto.owl", + "homepage": "http://www.semantic-systems-biology.org/apo", + "keywords": [ + "life science", + "ontology", + "transcriptomics" + ], + "mappings": { + "aberowl": "RETO", + "bioportal": "RETO", + "fairsharing": "FAIRsharing.4qyf0f", + "ols": "reto" + }, + "name": "Regulation of Transcription Ontology", + "no_own_terms": true, + "preferred_prefix": "reto", + "version": "2019-09-17" + }, + "rex": { + "contact": { + "email": "chebi-help@ebi.ac.uk", + "github": null, + "name": "Chebi Administrators", + "orcid": null + }, + "deprecated": true, + "description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.", + "download_owl": "http://purl.obolibrary.org/obo/rex.owl", + "example": "0000512", + "homepage": "https://www.ebi.ac.uk/chebi/", + "keywords": [ + "biochemistry", + "chemistry", + "life science", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "REX", + "biocontext": "REX", + "bioportal": "REX", + "fairsharing": "FAIRsharing.g0a7s0", + "obofoundry": "rex", + "ols": "rex", + "ontobee": "REX", + "prefixcommons": "rex" + }, + "name": "Physico-chemical process", + "part_of": "chebi", + "pattern": "^\\d{7}$", + "preferred_prefix": "REX", + "uri_format": "http://purl.obolibrary.org/obo/REX_$1", + "version": "2017-11-19" + }, + "rexo": { + "contact": { + "email": "kuiper@bio.ntnu.no", + "github": "makuintnu", + "name": "Martin Kuiper", + "orcid": "0000-0002-1171-9876" + }, + "description": "Regulation of Gene Expression", + "download_obo": "https://www.bio.ntnu.no/ontology/ReXO/rexo.obo", + "download_owl": "https://www.bio.ntnu.no/ontology/ReXO/rexo.owl", + "homepage": "http://www.semantic-systems-biology.org/apo", + "keywords": [ + "life science", + "ontology" + ], + "mappings": { + "aberowl": "REXO", + "bioportal": "REXO", + "fairsharing": "FAIRsharing.recas1", + "ols": "rexo" + }, + "name": "Regulation of Gene Expression Ontology", + "no_own_terms": true, + "preferred_prefix": "rexo", + "publications": [ + { + "doi": "10.1186/s12859-014-0386-y", + "pmc": "PMC4279962", + "pubmed": "25490885", + "title": "Finding gene regulatory network candidates using the gene expression knowledge base.", + "year": 2014 + } + ], + "version": "2019-04-11" + }, + "rfam": { + "description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.", + "example": "RF00230", + "homepage": "https://rfam.xfam.org/", + "keywords": [ + "genetics" + ], + "mappings": { + "biocontext": "RFAM", + "edam": "2356", + "fairsharing": "FAIRsharing.fex4c8", + "go": "Rfam", + "miriam": "rfam", + "n2t": "rfam", + "ncbi": "RFAM" + }, + "name": "Rfam database of RNA families", + "pattern": "^RF\\d{5}$", + "preferred_prefix": "rfam", + "publications": [ + { + "doi": "10.1093/nar/gkx1038", + "pmc": "PMC5753348", + "pubmed": "29112718", + "title": "Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gku1063", + "pmc": "PMC4383904", + "pubmed": "25392425", + "title": "Rfam 12.0: updates to the RNA families database.", + "year": 2014 + } + ], + "twitter": "RfamDB", + "uri_format": "https://rfam.xfam.org/family/$1" + }, + "rfc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Legacy site for IETF RFC proposals", + "example": "5013", + "homepage": "https://www.ietf.org/", + "mappings": { + "n2t": "rfc" + }, + "name": "Internet Standard -- IETF Request for Comments", + "pattern": "^\\d+$", + "preferred_prefix": "rfc", + "uri_format": "https://tools.ietf.org/rfc/rfc$1" + }, + "rgap": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data.", + "example": "LOC_Os02g13300", + "homepage": "http://rice.plantbiology.msu.edu/", + "keywords": [ + "dna", + "genome" + ], + "mappings": { + "prefixcommons": "rgap" + }, + "name": "Rice Genome Annotation Project", + "preferred_prefix": "rgap", + "publications": [ + { + "doi": "10.1093/nar/gkl976", + "pmc": "PMC1751532", + "pubmed": "17145706", + "title": "The TIGR Rice Genome Annotation Resource: improvements and new features.", + "year": 2006 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1" + }, + "rgd": { + "contact": { + "email": "jrsmith@mcw.edu", + "github": null, + "name": "Jennifer R Smith", + "orcid": "0000-0002-6443-9376" + }, + "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes.", + "example": "7499841", + "homepage": "http://rgd.mcw.edu/", + "keywords": [ + "biomedical science", + "comparative genomics", + "dna", + "gene", + "genome", + "genomics", + "molecular medicine", + "ontology", + "phenomics", + "quantitative genetics", + "translational medicine", + "veterinary medicine" + ], + "mappings": { + "aberowl": "RGD", + "biocontext": "RGD", + "bioportal": "RGD", + "cellosaurus": "RGD", + "edam": "2620", + "fairsharing": "FAIRsharing.pfg82t", + "go": "RGD", + "miriam": "rgd", + "n2t": "rgd", + "ncbi": "RGD", + "prefixcommons": "rgd", + "re3data": "r3d100010417", + "uniprot": "DB-0091", + "wikidata": "P3853" + }, + "name": "Rat Genome Database", + "pattern": "^\\d{4,}$", + "preferred_prefix": "rgd", + "providers": [ + { + "code": "agr", + "description": "RGD through the Alliance of Genome Resources", + "homepage": "https://www.alliancegenome.org", + "name": "RGD through the Alliance of Genome Resources", + "uri_format": "https://www.alliancegenome.org/gene/RGD:$1" + } + ], + "publications": [ + { + "doi": "10.1093/genetics/iyac005", + "pmc": "PMC8982048", + "pubmed": "35380657", + "title": "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses.", + "year": 2022 + }, + { + "doi": "10.1007/s00335-021-09932-x", + "pmc": "PMC8570235", + "pubmed": "34741192", + "title": "The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gkz1041", + "pmc": "PMC7145519", + "pubmed": "31713623", + "title": "The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.", + "year": 2020 + }, + { + "doi": "10.1007/978-1-4939-9581-3_3", + "pmc": null, + "pubmed": "31228152", + "title": "Rat Genome Databases, Repositories, and Tools.", + "year": 2019 + }, + { + "doi": "10.1007/978-1-4939-9581-3_2", + "pmc": null, + "pubmed": "31228151", + "title": "Rat Genome Assemblies, Annotation, and Variant Repository.", + "year": 2019 + }, + { + "doi": "10.1007/978-1-4939-9581-3_1", + "pmc": null, + "pubmed": "31228150", + "title": "The Rat: A Model Used in Biomedical Research.", + "year": 2019 + }, + { + "doi": "10.1093/database/baz037", + "pmc": "PMC6444380", + "pubmed": "30938777", + "title": "Quantitative phenotype analysis to identify, validate and compare rat disease models.", + "year": 2019 + }, + { + "doi": "10.1093/database/baz014", + "pmc": "PMC6369425", + "pubmed": "30753478", + "title": "Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.", + "year": 2019 + }, + { + "doi": "10.1007/978-1-4939-7737-6_8", + "pmc": "PMC6487669", + "pubmed": "29761460", + "title": "A Primer for the Rat Genome Database (RGD).", + "year": 2018 + }, + { + "doi": "10.1093/ilar/ilw041", + "pmc": "PMC6057551", + "pubmed": "28838068", + "title": "Rat Genome and Model Resources.", + "year": 2017 + }, + { + "doi": "10.1242/dmm.026021", + "pmc": "PMC5087824", + "pubmed": "27736745", + "title": "Exploring human disease using the Rat Genome Database.", + "year": 2016 + }, + { + "doi": "10.1016/j.csbj.2015.11.006", + "pmc": "PMC4700298", + "pubmed": "27602200", + "title": "Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.", + "year": 2015 + }, + { + "doi": "10.1152/physiolgenomics.00046.2016", + "pmc": "PMC5005459", + "pubmed": "27287925", + "title": "Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.", + "year": 2016 + }, + { + "doi": "10.1093/database/baw034", + "pmc": "PMC4805243", + "pubmed": "27009807", + "title": "The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gku1026", + "pmc": "PMC4383884", + "pubmed": "25355511", + "title": "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.", + "year": 2014 + }, + { + "doi": "10.1186/s40246-014-0017-8", + "pmc": "PMC4191248", + "pubmed": "25265995", + "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.", + "year": 2014 + }, + { + "doi": "10.1093/database/bat015", + "pmc": "PMC3630803", + "pubmed": "23603846", + "title": "PhenoMiner: quantitative phenotype curation at the rat genome database.", + "year": 2013 + }, + { + "doi": "10.1371/journal.pcbi.1000582", + "pmc": "PMC2775909", + "pubmed": "19956751", + "title": "The rat genome database curators: who, what, where, why.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkl988", + "pmc": "PMC1761441", + "pubmed": "17151068", + "title": "The Rat Genome Database, update 2007--easing the path from disease to data and back again.", + "year": 2006 + }, + { + "doi": null, + "pmc": null, + "pubmed": "10400928", + "title": "A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.", + "year": 1999 + } + ], + "synonyms": [ + "RGD" + ], + "twitter": "ratgenome", + "uri_format": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1" + }, + "rgd.qtl": { + "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes.", + "example": "1354581", + "homepage": "http://rgd.mcw.edu/", + "mappings": { + "biocontext": "RGD.QTL", + "miriam": "rgd.qtl", + "n2t": "rgd.qtl" + }, + "name": "Rat Genome Database qTL", + "pattern": "^\\d+$", + "preferred_prefix": "rgd.qtl", + "twitter": "ratgenome", + "uri_format": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1" + }, + "rgd.strain": { + "description": "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology.", + "example": "5688061", + "homepage": "http://rgd.mcw.edu/", + "mappings": { + "biocontext": "RGD.STRAIN", + "miriam": "rgd.strain", + "n2t": "rgd.strain" + }, + "name": "Rat Genome Database strain", + "pattern": "^\\d+$", + "preferred_prefix": "rgd.strain", + "twitter": "ratgenome", + "uri_format": "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1" + }, + "rhea": { + "contact": { + "email": "anne.morgat@sib.swiss", + "github": null, + "name": "Anne Morgat", + "orcid": "0000-0002-1216-2969" + }, + "description": " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB.", + "example": "12345", + "homepage": "https://www.rhea-db.org/", + "keywords": [ + "biochemistry", + "life science", + "reaction", + "small molecule" + ], + "mappings": { + "biocontext": "RHEA", + "edam": "2644", + "fairsharing": "FAIRsharing.pn1sr5", + "go": "RHEA", + "miriam": "rhea", + "n2t": "rhea", + "prefixcommons": "rhea", + "re3data": "r3d100010891" + }, + "name": "Rhea, the Annotated Reactions Database", + "pattern": "^\\d{5}$", + "preferred_prefix": "rhea", + "publications": [ + { + "doi": "10.1093/nar/gkab1016", + "pmc": "PMC8728268", + "pubmed": "34755880", + "title": "Rhea, the reaction knowledgebase in 2022.", + "year": 2022 + }, + { + "doi": "10.1093/bioinformatics/btz817", + "pmc": "PMC7162351", + "pubmed": "31688925", + "title": "Enzyme annotation in UniProtKB using Rhea.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gky876", + "pmc": "PMC6324061", + "pubmed": "30272209", + "title": "Updates in Rhea: SPARQLing biochemical reaction data.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw990", + "pmc": "PMC5210663", + "pubmed": "27789701", + "title": "Updates in Rhea - an expert curated resource of biochemical reactions.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gku961", + "pmc": "PMC4384025", + "pubmed": "25332395", + "title": "Updates in Rhea--a manually curated resource of biochemical reactions.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkr1126", + "pmc": "PMC3245052", + "pubmed": "22135291", + "title": "Rhea--a manually curated resource of biochemical reactions.", + "year": 2011 + } + ], + "synonyms": [ + "RHEA" + ], + "twitter": "rhea_db", + "uri_format": "https://www.rhea-db.org/rhea/$1" + }, + "ribocentre": { + "contact": { + "email": "huanglin36@mail.sysu.edu.cn", + "github": null, + "name": "Lin Huang", + "orcid": "0000-0002-2121-365X" + }, + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "Ribocentre is designed to contain comprehensive information of all natural ribozymes.", + "example": "hammer", + "github_request_issue": 611, + "homepage": "https://www.ribocentre.org/", + "name": "Ribocentre", + "pattern": "^[a-zA-Z0-9-]+$", + "preferred_prefix": "ribocentre", + "publications": [ + { + "doi": "10.1093/nar/gkac840", + "pmc": "PMC9825448", + "pubmed": "36177882", + "title": "Ribocentre: a database of ribozymes.", + "year": 2023 + } + ], + "repository": "https://github.com/ribocentre/ribocentre.github.io", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "ribocenter" + ], + "uri_format": "https://www.ribocentre.org/docs/$1" + }, + "ricecyc": { + "description": "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project", + "example": "PWY-1042", + "homepage": "http://www.gramene.org/pathway/ricecyc.html", + "keywords": [ + "gene", + "pathway" + ], + "mappings": { + "prefixcommons": "ricecyc" + }, + "name": "Rice Metabolic Pathways", + "preferred_prefix": "ricecyc", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1" + }, + "ricegap": { + "description": "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.", + "example": "LOC_Os02g13300", + "homepage": "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml", + "mappings": { + "biocontext": "RICEGAP", + "miriam": "ricegap", + "n2t": "ricegap" + }, + "name": "Rice Genome Annotation Project", + "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", + "preferred_prefix": "ricegap", + "uri_format": "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1" + }, + "ricenetdb.compound": { + "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", + "example": "OSC1416", + "homepage": "http://bis.zju.edu.cn/ricenetdb", + "mappings": { + "biocontext": "RICENETDB.COMPOUND", + "miriam": "ricenetdb.compound", + "n2t": "ricenetdb.compound" + }, + "name": "RiceNetDB Compound", + "pattern": "^OSC\\d{4}$", + "preferred_prefix": "ricenetdb.compound", + "uri_format": "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1" + }, + "ricenetdb.gene": { + "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", + "example": "LOC_Os01g49190.1", + "homepage": "http://bis.zju.edu.cn/ricenetdb/", + "mappings": { + "biocontext": "RICENETDB.GENE", + "miriam": "ricenetdb.gene", + "n2t": "ricenetdb.gene" + }, + "name": "RiceNetDB Gene", + "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$", + "preferred_prefix": "ricenetdb.gene", + "uri_format": "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1" + }, + "ricenetdb.mirna": { + "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", + "example": "osa-miR446", + "homepage": "http://bis.zju.edu.cn/ricenetdb", + "mappings": { + "biocontext": "RICENETDB.MIRNA", + "miriam": "ricenetdb.mirna", + "n2t": "ricenetdb.mirna" + }, + "name": "RiceNetDB miRNA", + "pattern": "^osa-miR\\d{3,5}[a-z]{0,1}$", + "preferred_prefix": "ricenetdb.mirna", + "uri_format": "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1" + }, + "ricenetdb.protein": { + "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", + "example": "LOC_Os01g49190", + "homepage": "http://bis.zju.edu.cn/ricenetdb/", + "mappings": { + "biocontext": "RICENETDB.PROTEIN", + "miriam": "ricenetdb.protein", + "n2t": "ricenetdb.protein" + }, + "name": "RiceNetDB Protein", + "pattern": "^LOC\\_Os\\d{1,2}g\\d{5}$", + "preferred_prefix": "ricenetdb.protein", + "uri_format": "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1" + }, + "ricenetdb.reaction": { + "description": "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping.", + "example": "OSR0818", + "homepage": "http://bis.zju.edu.cn/ricenetdb", + "mappings": { + "biocontext": "RICENETDB.REACTION", + "miriam": "ricenetdb.reaction", + "n2t": "ricenetdb.reaction" + }, + "name": "RiceNetDB Reaction", + "pattern": "^OSR\\d{4}$", + "preferred_prefix": "ricenetdb.reaction", + "uri_format": "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1" + }, + "rism": { + "description": "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project.", + "example": "people/11035", + "homepage": "https://rism.digital/", + "mappings": { + "miriam": "rism" + }, + "name": "RISM Online", + "pattern": "^[a-z]+/[0-9]+$", + "preferred_prefix": "rism", + "uri_format": "https://rism.online/$1" + }, + "rna_sstrand": { + "description": "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.", + "example": "CRW_00469", + "homepage": "http://www.rnasoft.ca/sstrand", + "keywords": [ + "rna", + "structure" + ], + "mappings": { + "prefixcommons": "rna_sstrand" + }, + "name": "RNA SSTRAND", + "preferred_prefix": "rna_sstrand", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1" + }, + "rnacentral": { + "contact": { + "email": "bsweeney@ebi.ac.uk", + "github": "blakesweeney", + "name": "Blake A Sweeney", + "orcid": "0000-0002-6497-2883" + }, + "description": "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.", + "example": "URS0000759CF4", + "homepage": "https://rnacentral.org/", + "keywords": [ + "bioinformatics", + "biology" + ], + "mappings": { + "biocontext": "RNACENTRAL", + "edam": "3856", + "fairsharing": "FAIRsharing.KcCjL7", + "go": "RNAcentral", + "miriam": "rnacentral", + "n2t": "rnacentral", + "ncbi": "RNAcentral", + "wikidata": "P8697" + }, + "name": "RNACentral", + "pattern": "^URS[0-9A-F]{10}(\\_\\d+)?$", + "preferred_prefix": "rnacentral", + "publications": [ + { + "doi": "10.1093/nar/gky1034", + "pmc": "PMC6324050", + "pubmed": "30395267", + "title": "RNAcentral: a hub of information for non-coding RNA sequences.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw1008", + "pmc": "PMC5210518", + "pubmed": "27794554", + "title": "RNAcentral: a comprehensive database of non-coding RNA sequences.", + "year": 2016 + } + ], + "repository": "https://github.com/RNAcentral/", + "synonyms": [ + "LNCRNADB" + ], + "twitter": "RNAcentral", + "uri_format": "https://rnacentral.org/rna/$1" + }, + "rnajunction": { + "description": "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. ", + "example": "8668", + "homepage": "http://rnajunction.abcc.ncifcrf.gov", + "keywords": [ + "rna", + "structural biology", + "structure" + ], + "mappings": { + "fairsharing": "FAIRsharing.zzgvrv", + "prefixcommons": "rnajunction" + }, + "name": "Database of RNA Junctions and Kissing loop Structures", + "preferred_prefix": "rnajunction", + "publications": [ + { + "doi": "10.1093/nar/gkm842", + "pmc": "PMC2238914", + "pubmed": "17947325", + "title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.", + "year": 2007 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1" + }, + "rnaloops": { + "contact": { + "email": "Maciej.Antczak@cs.put.poznan.pl", + "github": "mantczak", + "name": "Maciej Antczak", + "orcid": "0000-0002-5320-2023" + }, + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank.", + "example": "91792", + "github_request_issue": 601, + "homepage": "https://rnaloops.cs.put.poznan.pl", + "keywords": [ + "rna", + "structural bioinformatcs" + ], + "name": "RNAloops", + "pattern": "^\\d+$", + "preferred_prefix": "rnaloops", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://rnaloops.cs.put.poznan.pl/search/details/$1" + }, + "rnamod": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -", + "example": "051", + "homepage": "http://rna.rega.kuleuven.be/rnamods/", + "keywords": [ + "post-transcriptional modification", + "rna", + "structural bioinformatcs" + ], + "name": "The RNA Modification Database", + "pattern": "^\\d{3}$", + "preferred_prefix": "rnamod", + "uri_format": "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1" + }, + "rnamods": { + "description": "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA.", + "example": "101", + "homepage": "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm", + "keywords": [ + "rna", + "structure" + ], + "mappings": { + "biocontext": "RNAMODS", + "go": "RNAmods", + "miriam": "rnamods", + "n2t": "rnamods", + "prefixcommons": "rnamods" + }, + "name": "RNA Modification Database", + "pattern": "^\\d{3}$", + "preferred_prefix": "rnamods", + "uri_format": "http://mods.rna.albany.edu/mods/modifications/view/$1" + }, + "rnao": { + "contact": { + "email": "BatchelorC@rsc.org", + "github": null, + "name": "Colin Batchelor", + "orcid": "0000-0001-5985-7429" + }, + "deprecated": true, + "description": "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures.", + "download_obo": "http://purl.obolibrary.org/obo/rnao.obo", + "download_owl": "http://purl.obolibrary.org/obo/rnao.owl", + "example": "0000128", + "homepage": "https://github.com/bgsu-rna/rnao", + "keywords": [ + "biochemistry", + "life science", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "RNAO", + "biocontext": "RNAO", + "bioportal": "RNAO", + "fairsharing": "FAIRsharing.kqt2h2", + "obofoundry": "rnao", + "ols": "rnao", + "ontobee": "RNAO", + "prefixcommons": "rnao" + }, + "name": "RNA ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "RNAO", + "publications": [ + { + "doi": "10.1261/rna.2343206", + "pmc": "PMC1421088", + "pubmed": "16484377", + "title": "The RNA Ontology Consortium: an open invitation to the RNA community.", + "year": 2006 + }, + { + "doi": "10.3233/ao-2011-0082", + "pmc": null, + "pubmed": null, + "title": "The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data", + "year": 2011 + } + ], + "repository": "https://github.com/BGSU-RNA/rnao", + "uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", + "version": "2019-04-15" + }, + "rnavdb": { + "description": "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species.", + "example": "164750", + "homepage": "http://virus.zoo.ox.ac.uk/rnavirusdb/", + "keywords": [ + "genome", + "rna" + ], + "mappings": { + "prefixcommons": "rvd" + }, + "name": "RNA Virus Database", + "preferred_prefix": "rnavdb", + "uri_format": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1" + }, + "ro": { + "appears_in": [ + "agro", + "aism", + "cdno", + "cl", + "clao", + "clyh", + "colao", + "cteno", + "ecao", + "ecocore", + "ecto", + "envo", + "foodon", + "fovt", + "genepio", + "go", + "hso", + "lepao", + "maxo", + "ons", + "ontoavida", + "pcl", + "pco", + "plana", + "planp", + "poro", + "proco", + "psdo", + "pso", + "rbo", + "upa", + "xpo", + "zp" + ], + "banana": "RO", + "banana_peel": "_", + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies.", + "download_json": "http://purl.obolibrary.org/obo/ro.json", + "download_obo": "http://purl.obolibrary.org/obo/ro.obo", + "download_owl": "http://purl.obolibrary.org/obo/ro.owl", + "example": "0002533", + "homepage": "https://oborel.github.io/", + "keywords": [ + "natural science", + "obo", + "ontology", + "relations" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "RO", + "agroportal": "RO", + "biocontext": "RO", + "biolink": "RO", + "bioportal": "OBOREL", + "fairsharing": "FAIRsharing.cp0ybc", + "go": "RO", + "miriam": "ro", + "n2t": "ro", + "obofoundry": "ro", + "ols": "ro", + "ontobee": "RO", + "prefixcommons": "ro", + "wikidata": "P3590" + }, + "name": "Relation Ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "RO", + "publications": [ + { + "doi": "10.1186/2041-1480-5-41", + "pmc": "PMC4177597", + "pubmed": "25276335", + "title": "Structuring research methods and data with the research object model: genomics workflows as a case study.", + "year": 2014 + }, + { + "doi": "10.1186/gb-2005-6-5-r46", + "pmc": "PMC1175958", + "pubmed": "15892874", + "title": "Relations in biomedical ontologies.", + "year": 2005 + } + ], + "repository": "https://github.com/oborel/obo-relations", + "synonyms": [ + "RO_proposed_relation", + "obo_rel", + "oborel" + ], + "uri_format": "http://purl.obolibrary.org/obo/RO_$1", + "version": "2022-10-26" + }, + "roleo": { + "banana": "RoleO", + "banana_peel": "_", + "comment": "This resource doesn't exist on the web anymore", + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqun Oliver He", + "orcid": "0000-0001-9189-9661" + }, + "deprecated": true, + "description": "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.", + "download_owl": "http://aber-owl.net/media/ontologies/ROLEO/1/roleo.owl", + "example": "0000002", + "homepage": "http://sourceforge.net/projects/roleo", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "aberowl": "ROLEO", + "bioportal": "ROLEO", + "prefixcommons": "roleo" + }, + "name": "Role Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "RoleO", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://purl.obolibrary.org/obo/RoleO_$1" + }, + "ror": { + "contact": { + "email": "info@ror.org", + "github": null, + "name": "Maria Gould", + "orcid": "0000-0002-2916-3423" + }, + "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", + "example": "03yrm5c26", + "homepage": "https://ror.org", + "keywords": [ + "data management" + ], + "mappings": { + "fairsharing": "FAIRsharing.1jKfji", + "miriam": "ror", + "n2t": "ror" + }, + "name": "Research Organization Registry", + "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", + "preferred_prefix": "ror", + "repository": "https://github.com/ror-community", + "twitter": "ResearchOrgs", + "uri_format": "https://ror.org/$1" + }, + "rouge": { + "description": "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.", + "example": "mKIAA4200", + "homepage": "http://www.kazusa.or.jp/rouge/", + "keywords": [ + "dna", + "life science", + "protein" + ], + "mappings": { + "biocontext": "ROUGE", + "fairsharing": "FAIRsharing.vdbagq", + "miriam": "rouge", + "n2t": "rouge", + "prefixcommons": "rouge", + "uniprot": "DB-0092" + }, + "name": "Rodent Unidentified Gene-Encoded Large Proteins", + "pattern": "^m\\w+$", + "preferred_prefix": "rouge", + "publications": [ + { + "doi": "10.1093/nar/gkh035", + "pmc": "PMC308769", + "pubmed": "14681467", + "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.", + "year": 2004 + } + ], + "uri_format": "https://www.kazusa.or.jp/rouge/gfpage/$1" + }, + "rrid": { + "banana": "RRID", + "description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.", + "example": "AB_262044", + "homepage": "https://scicrunch.org/resolver", + "keywords": [ + "chemistry", + "life science" + ], + "mappings": { + "biocontext": "RRID", + "fairsharing": "FAIRsharing.ATwSZG", + "miriam": "rrid", + "n2t": "rrid" + }, + "name": "Research Resource Identification", + "namespace_in_lui": true, + "pattern": "^[a-zA-Z]+.+$", + "preferred_prefix": "rrid", + "publications": [ + { + "doi": "10.1038/nmeth.3995", + "pmc": null, + "pubmed": "27595404", + "title": "A proposal for validation of antibodies.", + "year": 2016 + }, + { + "doi": "10.1016/j.neuron.2016.04.030", + "pmc": "PMC5854161", + "pubmed": "27151636", + "title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods.", + "year": 2016 + }, + { + "doi": "10.1002/cne.23913", + "pmc": "PMC4684178", + "pubmed": "26599696", + "title": "The Resource Identification Initiative: A Cultural Shift in Publishing.", + "year": 2016 + }, + { + "doi": "10.12688/f1000research.6555.2", + "pmc": "PMC4648211", + "pubmed": "26594330", + "title": "The Resource Identification Initiative: A cultural shift in publishing.", + "year": 2015 + }, + { + "doi": "10.7717/peerj.148", + "pmc": "PMC3771067", + "pubmed": "24032093", + "title": "On the reproducibility of science: unique identification of research resources in the biomedical literature.", + "year": 2013 + } + ], + "uri_format": "https://scicrunch.org/resolver/RRID:$1" + }, + "rs": { + "contact": { + "email": "sjwang@mcw.edu", + "github": "shurjenw", + "name": "Shur-Jen Wang", + "orcid": "0000-0001-5256-8683" + }, + "description": "Ontology of rat strains", + "download_obo": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo", + "download_owl": "https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl", + "example": "0001807", + "homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html", + "keywords": [ + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "RS", + "biocontext": "RS", + "bioportal": "RS", + "fairsharing": "FAIRsharing.vajn3f", + "obofoundry": "rs", + "ols": "rs", + "ontobee": "RS", + "prefixcommons": "rs" + }, + "name": "Rat Strain Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "RS", + "publications": [ + { + "doi": "10.1186/2041-1480-4-36", + "pmc": "PMC4177145", + "pubmed": "24267899", + "title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.", + "year": 2013 + }, + { + "doi": "10.1093/database/bat015", + "pmc": "PMC3630803", + "pubmed": "23603846", + "title": "PhenoMiner: quantitative phenotype curation at the rat genome database.", + "year": 2013 + } + ], + "repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology", + "twitter": "ratgenome", + "uri_format": "http://purl.obolibrary.org/obo/RS_$1", + "version": "2019-12-13" + }, + "rtecs": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. 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"contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.).", + "example": "47419", + "homepage": "https://scop.berkeley.edu", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "biocontext": "SCOP", + "edam": "1042", + "miriam": "scop", + "n2t": "scop", + "prefixcommons": "scop" + }, + "name": "Structural Classification of Proteins - Unique Identifier", + "pattern": "^\\d+$", + "preferred_prefix": "scop", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "SCOP at Berkeley", + "homepage": "http://scop.berkeley.edu/", + "name": "SCOP at Berkeley", + "uri_format": "http://scop.berkeley.edu/sunid=$1" + }, + { + "code": "mrc", + "description": "SCOP at UK Medical Research council (MRC)", + "homepage": "https://scop.mrc-lmb.cam.ac.uk", + "name": "SCOP at UK Medical Research council (MRC)", + "uri_format": "https://scop.mrc-lmb.cam.ac.uk/term/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/27.1.254", + "pmc": "PMC148149", + "pubmed": "9847194", + "title": "SCOP: a Structural Classification of Proteins database.", + "year": 1999 + }, + { + "doi": "10.1093/nar/25.1.236", + "pmc": "PMC146380", + "pubmed": "9016544", + "title": "SCOP: a structural classification of proteins database.", + "year": 1997 + }, + { + "doi": "10.1093/nar/28.1.257", + "pmc": "PMC102479", + "pubmed": "10592240", + "title": "SCOP: a structural classification of proteins database.", + "year": 2000 + }, + { + "doi": "10.1107/s0907444998009172", + "pmc": null, + "pubmed": "10089491", + "title": "SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data.", + "year": 1998 + } + ], + "references": [ + "https://scop.berkeley.edu/help/#stableidentifiers" + ], + "synonyms": [ + "scop.sun", + "scop.sunid" + ], + "uri_format": "http://scop.berkeley.edu/sunid=$1" + }, + "scop.sccs": { + "contact": { + "email": "JMChandonia@lbl.gov", + "github": "jmchandonia", + "name": "John-Marc Chandonia", + "orcid": "0000-0002-5153-9079" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family.", + "example": "a.39.1.1", + "example_extras": [ + "a.39.1", + "a.39", + "a" + ], + "homepage": "https://scop.berkeley.edu", + "mappings": { + "edam": "1041" + }, + "name": "SCOP(e) concise classification string", + "preferred_prefix": "scop.sccs", + "references": [ + "https://scop.berkeley.edu/help/#stableidentifiers" + ], + "uri_format": "http://scop.berkeley.edu/sccs=$1" + }, + "scop.sid": { + "contact": { + "email": "JMChandonia@lbl.gov", + "github": "jmchandonia", + "name": "John-Marc Chandonia", + "orcid": "0000-0002-5153-9079" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": " A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1.", + "example": "d4akea1", + "example_extras": [ + "d9hvpa_", + "d1cph.1" + ], + "homepage": "https://scop.berkeley.edu", + "mappings": { + "edam": "1039" + }, + "name": "Structural Classification of Protein - Stable Domain Identifier", + "preferred_prefix": "scop.sid", + "references": [ + "https://scop.berkeley.edu/help/#stableidentifiers" + ], + "uri_format": "http://scop.berkeley.edu/sid=$1" + }, + "scopus": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research.", + "example": "56305849200", + "homepage": "https://www.scopus.com", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "biolink": "ScopusID", + "fairsharing": "FAIRsharing.0a674c" + }, + "name": "Scopus Researcher", + "pattern": "^\\d+$", + "preferred_prefix": "scopus", + "twitter": "Scopus" + }, + "scoro": { + "contact": { + "email": "silvio.peroni@unibo.it", + "github": "essepuntato", + "name": "Silvio Peroni", + "orcid": "0000-0003-0530-4305" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator).", + "example": "IntellectualContribution", + "homepage": "http://www.sparontologies.net/ontologies/scoro", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.c86b48" + }, + "name": "Scholarly Contributions and Roles Ontology", + "preferred_prefix": "SCoRO", + "publications": [ + { + "doi": "10.3233/sw-150177", + "pmc": null, + "pubmed": null, + "title": "The Document Components Ontology (DoCO)", + "year": 2016 + } + ], + "repository": "https://github.com/sparontologies/scoro", + "twitter": "sparontologies", + "uri_format": "http://purl.org/spar/scoro/$1" + }, + "scpd": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "Database containing promotor sequences found in Saccharomyces cerevisiae.", + "example": "CDC2", + "homepage": "http://rulai.cshl.edu/SCPD/", + "keywords": [ + "dna", + "rna" + ], + "mappings": { + "prefixcommons": "scpd" + }, + "name": "Saccharomyces cerevisiae promoter database", + "preferred_prefix": "scpd", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1" + }, + "scr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources.", + "example": "022586", + "github_request_issue": 421, + "homepage": "https://scicrunch.org/browse/resourcedashboard", + "keywords": [ + "life science", + "neurobiology" + ], + "mappings": { + "fairsharing": "FAIRsharing.kj4pvk" + }, + "name": "SciCrunch Registry", + "pattern": "^\\d+$", + "preferred_prefix": "scr", + "publications": [ + { + "doi": "10.1002/cne.23913", + "pmc": "PMC4684178", + "pubmed": "26599696", + "title": "The Resource Identification Initiative: A Cultural Shift in Publishing.", + "year": 2016 + } + ], + "synonyms": [ + "scicrunch" + ], + "uri_format": "http://scicrunch.org/resolver/SCR_$1" + }, + "scretf": { + "description": "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor.", + "example": "RSC3", + "homepage": "http://stormo.wustl.edu/ScerTF/", + "mappings": { + "biocontext": "SCRETF", + "miriam": "scretf", + "n2t": "scretf" + }, + "name": "ScerTF", + "pattern": "^\\w+$", + "preferred_prefix": "scretf", + "uri_format": "http://stormo.wustl.edu/ScerTF/details/$1" + }, + "sdap": { + "description": "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.", + "example": "610", + "homepage": "http://fermi.utmb.edu/SDAP", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "prefixcommons": "sdap" + }, + "name": "Structural Database of Allergenic Proteins", + "preferred_prefix": "sdap", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1" + }, + "sdbs": { + "description": "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra.", + "example": "4544", + "homepage": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi", + "mappings": { + "biocontext": "SDBS", + "miriam": "sdbs", + "n2t": "sdbs" + }, + "name": "Spectral Database for Organic Compounds", + "pattern": "^\\d+$", + "preferred_prefix": "sdbs", + "uri_format": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1" + }, + "sdgio": { + "contact": { + "email": "pier.buttigieg@awi.de", + "github": null, + "name": "Pier Luigi Buttigieg", + "orcid": "0000-0002-4366-3088" + }, + "description": "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators.", + "download_owl": "https://github.com/SDG-InterfaceOntology/sdgio/raw/master/sdgio.owl", + "example": "00020134", + "homepage": "https://github.com/SDG-InterfaceOntology/sdgio", + "keywords": [ + "environmental science", + "ontology" + ], + "mappings": { + "agroportal": "SDGIO", + "fairsharing": "FAIRsharing.d5ff6e", + "ols": "sdgio", + "ontobee": "SDGIO" + }, + "name": "Sustainable Development Goals Interface Ontology", + "pattern": "^\\d{8}$", + "preferred_prefix": "sdgio", + "publications": [ + { + "doi": "10.1186/s13326-016-0097-6", + "pmc": "PMC5035502", + "pubmed": "27664130", + "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.", + "year": 2016 + } + ], + "references": [ + "https://github.com/SDG-InterfaceOntology/sdgio/issues/233" + ], + "repository": "https://github.com/SDG-InterfaceOntology/sdgio", + "uri_format": "http://purl.unep.org/sdg/SDGIO_$1", + "version": "2018-08-10" + }, + "sdis": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Selventa legacy disease namespace used with the Biological Expression Language", + "example": "D0001", + "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt", + "keywords": [ + "bel", + "diseases", + "selventa" + ], + "name": "Selventa Diseases", + "pattern": "^D\\d{4}$", + "preferred_prefix": "sdis", + "uri_format": "https://biopragmatics.github.io/providers/sdis/$1" + }, + "sedml.format": { + "description": "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).", + "example": "csv", + "homepage": "http://sed-ml.org/", + "mappings": { + "miriam": "sedml.format" + }, + "name": "SED-ML data format", + "pattern": "^[a-z]+(\\..*?)?$", + "preferred_prefix": "sedml.format", + "uri_format": "https://sed-ml.org/urns.html#format:$1" + }, + "sedml.language": { + "description": "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML).", + "example": "sbml.level-3.version-2", + "homepage": "http://sed-ml.org/", + "mappings": { + "miriam": "sedml.language" + }, + "name": "SED-ML model format", + "pattern": "^[a-z]+(\\..*?)?$", + "preferred_prefix": "sedml.language", + "uri_format": "https://sed-ml.org/urns.html#language:$1" + }, + "seed": { + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "example": "Biotin_biosynthesis", + "homepage": "http://seed-viewer.theseed.org/seedviewer.cgi", + "keywords": [ + "earth science" + ], + "mappings": { + "biocontext": "SEED", + "fairsharing": "FAIRsharing.68b03f", + "go": "SEED", + "miriam": "seed", + "n2t": "seed", + "ncbi": "SEED" + }, + "name": "The SEED;", + "pattern": "^\\w+$", + "preferred_prefix": "seed", + "uri_format": "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1" + }, + "seed.compound": { + "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", + "example": "cpd15380", + "homepage": "http://modelseed.org/", + "mappings": { + "biocontext": "SEED.COMPOUND", + "miriam": "seed.compound", + "n2t": "seed.compound" + }, + "name": "SEED Compound", + "pattern": "^cpd\\d+$", + "preferred_prefix": "seed.compound", + "uri_format": "http://modelseed.org/biochem/compounds/$1" + }, + "seed.reaction": { + "description": "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions.", + "example": "rxn00001", + "homepage": "http://modelseed.org/biochem/reactions/", + "mappings": { + "biolink": "SEED.REACTION", + "miriam": "seed.reaction", + "n2t": "seed.reaction" + }, + "name": "SEED Reactions", + "pattern": "^rxn\\d+$", + "preferred_prefix": "seed.reaction", + "uri_format": "http://modelseed.org/biochem/reactions/$1" + }, + "seinet": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A vocabulary about species to support the environmental research community in Arizona and New Mexico", + "example": "762", + "github_request_issue": 653, + "homepage": "https://swbiodiversity.org/seinet/index.php", + "mappings": { + "wikidata": "P6209" + }, + "name": "Southwestern Environmental Information Network", + "pattern": "^\\d+$", + "preferred_prefix": "seinet", + "reviewer": { + "email": null, + "github": "callahantiff", + "name": "Tiffany J. Callahan", + "orcid": "0000-0002-8169-9049" + }, + "uri_format": "https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1" + }, + "semapv": { + "contact": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nico Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata.", + "download_owl": "https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl", + "example": "LexicalMatching", + "homepage": "https://mapping-commons.github.io/semantic-mapping-vocabulary/", + "keywords": [ + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "bartoc": "20428" + }, + "name": "Semantic Mapping Vocabulary", + "owners": [ + { + "name": "Semanticly", + "partnered": true, + "ror": null, + "wikidata": "Q115518213" + } + ], + "preferred_prefix": "semapv", + "references": [ + "https://github.com/biopragmatics/bioregistry/pull/714" + ], + "uri_format": "https://w3id.org/semapv/vocab/$1" + }, + "sep": { + "contact": { + "email": "psidev-gps-dev@lists.sourceforge.net", + "github": null, + "name": "SEP developers via the PSI and MSI mailing lists", + "orcid": null + }, + "deprecated": true, + "description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.", + "download_obo": "https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo", + "download_owl": "http://purl.obolibrary.org/obo/sep.owl", + "example": "00073", + "homepage": "https://psidev.info/sepcv", + "keywords": [ + "obo", + "ontology", + "protein" + ], + "mappings": { + "aberowl": "SEP", + "biocontext": "SEP", + "bioportal": "SEP", + "obofoundry": "sep", + "ontobee": "SEP", + "prefixcommons": "sep" + }, + "name": "Sample processing and separation techniques", + "pattern": "^\\d{5,6}$", + "preferred_prefix": "SEP", + "uri_format": "http://purl.obolibrary.org/obo/SEP_$1" + }, + "sepio": { + "contact": { + "email": "mhb120@gmail.com", + "github": "mbrush", + "name": "Matthew Brush", + "orcid": "0000-0002-1048-5019" + }, + "description": "An ontology for representing the provenance of scientific claims and the evidence that supports them.", + "download_owl": "http://purl.obolibrary.org/obo/sepio.owl", + "example": "0000048", + "homepage": "https://github.com/monarch-initiative/SEPIO-ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "SEPIO", + "biocontext": "SEPIO", + "bioportal": "SEPIO", + "obofoundry": "sepio", + "ols": "sepio", + "ontobee": "SEPIO" + }, + "name": "Scientific Evidence and Provenance Information Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "SEPIO", + "repository": "https://github.com/monarch-initiative/SEPIO-ontology", + "uri_format": "http://purl.obolibrary.org/obo/SEPIO_$1", + "version": "$Revision$" + }, + "sfam": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Selventa legacy protein family namespace used with the Biological Expression Language", + "example": "F0001", + "homepage": "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt", + "keywords": [ + "bel", + "protein families", + "selventa" + ], + "name": "Selventa Families", + "pattern": "^F\\d{4}$", + "preferred_prefix": "sfam", + "uri_format": "https://biopragmatics.github.io/providers/sfam/$1" + }, + "sgd": { + "description": "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae.", + "example": "S000002493", + "homepage": "https://www.yeastgenome.org/", + "keywords": [ + "epigenetics", + "eukaryotic", + "genome", + "life science", + "nucleotide", + "proteomics", + "transcriptomics" + ], + "mappings": { + "biocontext": "SGD", + "edam": "2632", + "fairsharing": "FAIRsharing.pzvw40", + "go": "SGD", + "miriam": "sgd", + "n2t": "sgd", + "ncbi": "SGD", + "prefixcommons": "sgd", + "re3data": "r3d100010419", + "uniprot": "DB-0095", + "wikidata": "P3406" + }, + "name": "Saccharomyces Genome Database", + "pattern": "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$", + "preferred_prefix": "sgd", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Bio2RDF", + "homepage": "http://sgd.bio2rdf.org/fct", + "name": "Bio2RDF", + "uri_format": "http://sgd.bio2rdf.org/describe/?url=http://bio2rdf.org/sgd:$1" + }, + { + "code": "agr", + "description": "SGD through the Alliance of Genome Resources", + "homepage": "https://www.alliancegenome.org", + "name": "SGD through the Alliance of Genome Resources", + "uri_format": "https://www.alliancegenome.org/gene/SGD:$1" + } + ], + "publications": [ + { + "doi": "10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g", + "pmc": "PMC3037831", + "pubmed": "9885151", + "title": "Expanding yeast knowledge online.", + "year": 1998 + }, + { + "doi": "10.1126/science.282.5396.2022", + "pmc": "PMC3057080", + "pubmed": "9851918", + "title": "Comparison of the complete protein sets of worm and yeast: orthology and divergence.", + "year": 1998 + }, + { + "doi": "10.1093/nar/27.1.74", + "pmc": "PMC148101", + "pubmed": "9847146", + "title": "Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.", + "year": 1999 + }, + { + "doi": "10.1093/nar/26.1.73", + "pmc": "PMC147204", + "pubmed": "9399804", + "title": "SGD: Saccharomyces Genome Database.", + "year": 1998 + }, + { + "doi": "10.1126/science.277.5330.1259", + "pmc": "PMC3039837", + "pubmed": "9297238", + "title": "Yeast as a model organism.", + "year": 1997 + }, + { + "doi": null, + "pmc": "PMC3057085", + "pubmed": "9169866", + "title": "Genetic and physical maps of Saccharomyces cerevisiae.", + "year": 1997 + }, + { + "doi": "10.1073/pnas.94.11.5506", + "pmc": "PMC34160", + "pubmed": "9159100", + "title": "Molecular linguistics: extracting information from gene and protein sequences.", + "year": 1997 + }, + { + "doi": null, + "pmc": null, + "pubmed": "7660459", + "title": "Genetic nomenclature guide. Saccharomyces cerevisiae.", + "year": 1995 + }, + { + "doi": "10.1093/database/baw020", + "pmc": "PMC4795930", + "pubmed": "26989152", + "title": "From one to many: expanding the Saccharomyces cerevisiae reference genome panel.", + "year": 2016 + }, + { + "doi": "10.1101/pdb.top083840", + "pmc": "PMC5673599", + "pubmed": "26631132", + "title": "The Saccharomyces Genome Database: A Tool for Discovery.", + "year": 2015 + }, + { + "doi": "10.1101/pdb.prot088922", + "pmc": "PMC5673602", + "pubmed": "26631126", + "title": "The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.", + "year": 2015 + }, + { + "doi": "10.1101/pdb.prot088914", + "pmc": "PMC5673600", + "pubmed": "26631125", + "title": "The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.", + "year": 2015 + }, + { + "doi": "10.1101/pdb.prot088906", + "pmc": "PMC5673598", + "pubmed": "26631124", + "title": "The Saccharomyces Genome Database: Advanced Searching 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ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.", + "example": "TripleExpression", + "homepage": "http://www.w3.org/ns/shex#", + "keywords": [ + "metadata", + "rdf", + "semantic web" + ], + "name": "Shape Expression Vocabulary", + "preferred_prefix": "shex", + "uri_format": "http://www.w3.org/ns/shex#$1" + }, + "shibase": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format.", + "example": "SDY2614", + "homepage": "http://www.mgc.ac.cn/ShiBASE/", + "keywords": [ + "genome" + ], + "mappings": { + "prefixcommons": "shibase" + }, + "name": "ShiBASE", + "preferred_prefix": "shibase", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1" + }, + "sibo": { + "contact": { + "email": "cjmungall@lbl.gov", + "github": null, + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "deprecated": true, + "description": "Social Behavior in insects", + "download_obo": "http://purl.obolibrary.org/obo/sibo.obo", + "download_owl": "http://purl.obolibrary.org/obo/sibo.owl", + "example": "0000509", + "homepage": "https://github.com/obophenotype/sibo", + "keywords": [ + "biology", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "SIBO", + "biocontext": "SIBO", + "bioportal": "SIBO", + "fairsharing": "FAIRsharing.q09hck", + "obofoundry": "sibo", + "ols": "sibo", + "ontobee": "SIBO" + }, + "name": "Social Insect Behavior Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "SIBO", + "repository": "https://github.com/obophenotype/sibo", + "uri_format": "http://purl.obolibrary.org/obo/SIBO_$1", + "version": "2015-06-15" + }, + "sider.drug": { + "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.", + "example": "2244", + "homepage": "http://sideeffects.embl.de/", + "mappings": { + "biocontext": "SIDER.DRUG", + "miriam": "sider.drug", + "n2t": "sider.drug" + }, + "name": "SIDER Drug", + "pattern": "^\\d+$", + "preferred_prefix": "sider.drug", + "uri_format": "http://sideeffects.embl.de/drugs/$1" + }, + "sider.effect": { + "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.", + "example": "C0017565", + "homepage": "http://sideeffects.embl.de/", + "mappings": { + "biocontext": "SIDER.EFFECT", + "miriam": "sider.effect", + "n2t": "sider.effect" + }, + "name": "SIDER Side Effect", + "pattern": "^C\\d+$", + "preferred_prefix": "sider.effect", + "provides": "umls", + "uri_format": "http://sideeffects.embl.de/se/$1" + }, + "sigmaaldrich": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Sigma Aldrich is a life sciences supply vendor.", + "example": "HPA000698", + "github_request_issue": 216, + "homepage": "https://www.sigmaaldrich.com", + "keywords": [ + "biology", + "chemistry", + "life sciences", + "vendor" + ], + "name": "Sigma Aldrich", + "preferred_prefix": "sigmaaldrich", + "uri_format": "https://www.sigmaaldrich.com/US/en/product/sigma/$1" + }, + "signaling-gateway": { + "description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.", + "example": "A001094", + "homepage": "http://www.signaling-gateway.org/molecule", + "keywords": [ + "pathway", + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "SIGNALING-GATEWAY", + "miriam": "signaling-gateway", + "n2t": "signaling-gateway", + "prefixcommons": "signaling-gateway" + }, + "name": "Signaling Gateway", + "pattern": "^A\\d{6}$", + "preferred_prefix": "signaling-gateway", + "publications": [ + { + "doi": "10.1093/bioinformatics/btr190", + "pmc": "PMC3106186", + "pubmed": "21505029", + "title": "Signaling gateway molecule pages--a data model perspective.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkm907", + "pmc": "PMC2238911", + "pubmed": "17965093", + "title": "The Molecule Pages database.", + "year": 2007 + }, + { + "doi": "10.1038/nature01307", + "pmc": null, + "pubmed": "12478304", + "title": "The Molecule Pages database.", + "year": 2002 + } + ], + "uri_format": "http://www.signaling-gateway.org/molecule/query?afcsid=$1" + }, + "signor": { + "contact": { + "email": "gianni.cesareni@torvergata.it", + "github": null, + "name": "Gianni Cesareni", + "orcid": "0000-0002-9528-6018" + }, + "description": "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature.", + "example": "SIGNOR-C41", + "homepage": "https://signor.uniroma2.it/", + "keywords": [ + "biology" + ], + "mappings": { + "fairsharing": "FAIRsharing.ss78t4", + "miriam": "signor", + "uniprot": "DB-0206" + }, + "name": "Signaling Network Open Resource", + "pattern": "^SIGNOR\\-[A-Z]+\\d+$", + "preferred_prefix": "signor", + "publications": [ + { + "doi": "10.1093/nar/gkv1048", + "pmc": "PMC4702784", + "pubmed": "26467481", + "title": "SIGNOR: a database of causal relationships between biological entities.", + "year": 2015 + } + ], + "synonyms": [ + "SIGNOR" + ], + "uri_format": "https://signor.uniroma2.it/relation_result.php?id=$1" + }, + "signor.relation": { + "comment": "Currently, you can put a SIGNOR relation ID into the main page search box and it will resolve, but there is not currently a way to resolve them via a URL pattern", + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "Identifiers for relationships between proteins and complexes, along with their type and provenance", + "example": "SIGNOR-252737", + "homepage": "https://signor.uniroma2.it", + "keywords": [ + "protein-protein interactions" + ], + "name": "SIGNOR Relation", + "part_of": "signor", + "pattern": "^SIGNOR-\\d+$", + "preferred_prefix": "signor.relation", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + }, + "sio": { + "banana": "SIO", + "banana_peel": "_", + "contact": { + "email": "michel.dumontier@gmail.com", + "github": "micheldumontier", + "name": "Michel Dumontier", + "orcid": "0000-0003-4727-9435" + }, + "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.", + "download_owl": "http://semanticscience.org/ontology/sio/v1.53/sio-release.owl", + "example": "000912", + "homepage": "https://github.com/micheldumontier/semanticscience", + "keywords": [ + "natural science", + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "SIO", + "agroportal": "SIO", + "biocontext": "SIO", + "biolink": "SIO", + "bioportal": "SIO", + "fairsharing": "FAIRsharing.dpkb5f", + "miriam": "sio", + "ols": "sio", + "ontobee": "SIO" + }, + "name": "Semanticscience Integrated Ontology", + "pattern": "^\\d{6}$", + "preferred_prefix": "sio", + "publications": [ + { + "doi": "10.1186/2041-1480-5-14", + "pmc": "PMC4015691", + "pubmed": "24602174", + "title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.", + "year": 2014 + } + ], + "repository": "https://github.com/micheldumontier/semanticscience", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1", + "version": "1.53" + }, + "siren": { + "comment": "appears in FOODON, there is no website other than the spreadsheet referenced below on langual's site", + "contact": { + "email": "patrice.buche@inrae.fr", + "github": null, + "name": "Patrice Buche", + "orcid": "0000-0002-9134-5404" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods", + "example": "F11903", + "homepage": "https://www.langual.org/langual_indexed_datasets.asp", + "mappings": { + "agroportal": "SIREN" + }, + "name": "Scientific Information Retrieval and Exchange Network", + "pattern": "^F\\d+$", + "preferred_prefix": "siren", + "publications": [ + { + "doi": "10.1093/jaoac/65.5.1268", + "pmc": null, + "pubmed": null, + "title": "SIREN: Data Base Approach to Scientific Information Handling in the Bureau of Foods, Food and Drug Administration", + "year": 1982 + } + ], + "references": [ + "https://github.com/FoodOntology/foodon/issues/267", + "https://www.langual.org/download/IndexedDatasets/FDA/SIREN%20(updated).TXT" + ], + "synonyms": [ + "SUBSET_SIREN" + ] + }, + "sisu": { + "contact": { + "email": "hannele.laivuori@helsinki.fi", + "github": null, + "name": "Hannele Laivuori", + "orcid": "0000-0003-3212-7826" + }, + "description": "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies.", + "example": "17:41223048", + "homepage": "http://www.sisuproject.fi/", + "keywords": [ + "biomedical science", + "epidemiology", + "genomics", + "medicine", + "preclinical studies" + ], + "mappings": { + "biocontext": "SISU", + "fairsharing": "FAIRsharing.t1a232", + "miriam": "sisu", + "n2t": "sisu" + }, + "name": "Sequencing Initiative Suomi", + "pattern": "^[0-9]+:[0-9]+$", + "preferred_prefix": "sisu", + "publications": [ + { + "doi": "10.1371/journal.pone.0128524", + "pmc": "PMC4452275", + "pubmed": "26030606", + "title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty.", + "year": 2015 + }, + { + "doi": "10.1371/journal.pgen.1004494", + "pmc": "PMC4117444", + "pubmed": "25078778", + "title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population.", + "year": 2014 + } + ], + "uri_format": "http://search.sisuproject.fi/#/variant/$1" + }, + "sitex": { + "description": "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments.", + "example": "1000", + "homepage": "http://www-bionet.sscc.ru/sitex/", + "keywords": [ + "domain", + "eukaryotic", + "life science", + "sequence", + "structure" + ], + "mappings": { + "biocontext": "SITEX", + "fairsharing": "FAIRsharing.5mr9c5", + "miriam": "sitex", + "n2t": "sitex", + "prefixcommons": "sitex" + }, + "name": "SitEx", + "pattern": "^\\d+$", + "preferred_prefix": "sitex", + "publications": [ + { + "doi": "10.1093/nar/gkr1187", + "pmc": "PMC3245165", + "pubmed": "22139920", + "title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes.", + "year": 2011 + } + ], + "uri_format": "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1" + }, + "skip": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine.", + "example": "SKIP001214", + "homepage": "https://skip.stemcellinformatics.org/en/", + "mappings": { + "cellosaurus": "SKIP" + }, + "name": "Stemcell Knowledge and Information Portal", + "pattern": "^SKIP\\d+$", + "preferred_prefix": "skip", + "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" + }, + "skm": { + "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", + "example": "rx00408", + "homepage": "http://www.nib.si/eng/", + "mappings": { + "miriam": "skm" + }, + "name": "Stress Knowledge Map", + "pattern": "^rx[0-9]{5}$", + "preferred_prefix": "skm", + "uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary" + }, + "skos": { + "contact": { + "email": "alistair.miles@linacre.ox.ac.uk", + "github": "alimanfoo", + "name": "Alistair Miles", + "orcid": "0000-0001-9018-4680" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web", + "download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl", + "example": "prefLabel", + "homepage": "https://www.w3.org/2004/02/skos/", + "keywords": [ + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "skos", + "biocontext": "skos", + "fairsharing": "FAIRsharing.48e326" + }, + "name": "Simple Knowledge Organization System", + "preferred_prefix": "skos", + "uri_format": "http://www.w3.org/2004/02/skos/core#$1" + }, + "skosxl": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.", + "example": "literalForm", + "homepage": "http://www.w3.org/2008/05/skos-xl#", + "keywords": [ + "data model", + "metadata", + "semantic web", + "skos" + ], + "name": "Simple Knowledge Organization System eXtension for Labels", + "preferred_prefix": "skosxl", + "uri_format": "http://www.w3.org/2008/05/skos-xl#$1" + }, + "slkbase": { + "description": "Cell line databases/resources", + "example": "3618", + "homepage": "https://sumlineknowledgebase.com/", + "mappings": { + "cellosaurus": "SLKBase" + }, + "name": "SUM Breast Cancer Cell Line Knowledge Base", + "pattern": "^\\d+$", + "preferred_prefix": "slkbase", + "uri_format": "https://sumlineknowledgebase.com/?page_id=$1" + }, + "smart": { + "description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.", + "example": "SM00015", + "homepage": "http://smart.embl-heidelberg.de/", + "keywords": [ + "domain", + "life science", + "protein", + "structure" + ], + "mappings": { + "biocontext": "SMART", + "fairsharing": "FAIRsharing.hsbpq3", + "go": "SMART", + "miriam": "smart", + "n2t": "smart", + "prefixcommons": "smart", + "uniprot": "DB-0097" + }, + "name": "Simple Modular Architecture Research Tool", + "pattern": "^SM\\d{5}$", + "preferred_prefix": "smart", + "publications": [ + { + "doi": "10.1093/nar/27.1.229", + "pmc": "PMC148142", + "pubmed": "9847187", + "title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences.", + "year": 1999 + }, + { + "doi": "10.1093/nar/gkx922", + "pmc": "PMC5753352", + "pubmed": "29040681", + "title": "20 years of the SMART protein domain annotation resource.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gku949", + "pmc": "PMC4384020", + "pubmed": "25300481", + "title": "SMART: recent updates, new developments and status in 2015.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkr931", + "pmc": "PMC3245027", + "pubmed": "22053084", + "title": "SMART 7: recent updates to the protein domain annotation resource.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkn808", + "pmc": "PMC2686533", + "pubmed": "18978020", + "title": "SMART 6: recent updates and new developments.", + "year": 2008 + }, + { + "doi": "10.1093/nar/gkj079", + "pmc": "PMC1347442", + "pubmed": "16381859", + "title": "SMART 5: domains in the context of genomes and networks.", + "year": 2006 + }, + { + "doi": "10.1093/nar/gkh088", + "pmc": "PMC308822", + "pubmed": "14681379", + "title": "SMART 4.0: towards genomic data integration.", + "year": 2004 + }, + { + "doi": "10.1093/nar/30.1.242", + "pmc": "PMC99073", + "pubmed": "11752305", + "title": "Recent improvements to the SMART domain-based sequence annotation resource.", + "year": 2002 + }, + { + "doi": "10.1093/nar/28.1.231", + "pmc": "PMC102444", + "pubmed": "10592234", + "title": "SMART: a web-based tool for the study of genetically mobile domains.", + "year": 2000 + }, + { + "doi": "10.1016/s0959-440x(99)80055-4", + "pmc": null, + "pubmed": "10361098", + "title": "Protein families in multicellular organisms.", + "year": 1999 + } + ], + "uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1" + }, + "smid": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. ", + "example": "137", + "homepage": "https://smid-db.org/", + "name": "C. elegans Small Molecule Identifier Database", + "pattern": "^\\d+$", + "preferred_prefix": "smid", + "synonyms": [ + "SMID-DB" + ], + "uri_format": "https://smid-db.org/smid/$1" + }, + "smiles": { + "contact": { + "email": "tim.vandermeersch@gmail.com", + "github": "timvdm", + "name": "Tim Vandermeersch", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.", + "example": "CC2(C)C\\1CCC(C)/C=C/12", + "homepage": "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html", + "keywords": [ + "chemistry", + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.qv4b3c", + "wikidata": "P233" + }, + "name": "Simplified molecular-input line-entry system", + "pattern": "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$", + "preferred_prefix": "smiles", + "publications": [ + { + "doi": "10.1186/1758-2946-4-24", + "pmc": "PMC3551648", + "pubmed": "23031664", + "title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code.", + "year": 2012 + }, + { + "doi": "10.1021/ci00067a005", + "pmc": null, + "pubmed": null, + "title": "SMILES. 3. DEPICT. Graphical depiction of chemical structures", + "year": 1990 + }, + { + "doi": "10.1021/ci00062a008", + "pmc": null, + "pubmed": null, + "title": "SMILES. 2. Algorithm for generation of unique SMILES notation", + "year": 1989 + }, + { + "doi": "10.1021/ci00057a005", + "pmc": null, + "pubmed": null, + "title": "SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules", + "year": 1988 + } + ], + "repository": "https://github.com/timvdm/OpenSMILES/blob/master/discussion_summary.txt", + "uri_format": "https://chemapps.stolaf.edu/jmol/jmol.php?model=$1" + }, + "smpdb": { + "description": "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.", + "example": "SMP0000219", + "homepage": "https://smpdb.ca/", + "keywords": [ + "chemical", + "human", + "life science", + "metabolite", + "pathway" + ], + "mappings": { + "biocontext": "SMPDB", + "biolink": "PathWhiz", + "edam": "2659", + "fairsharing": "FAIRsharing.y1zyaq", + "miriam": "smpdb", + "n2t": "smpdb", + "prefixcommons": "smpdb" + }, + "name": "Small Molecule Pathway Database", + "pattern": "^SMP\\d+$", + "preferred_prefix": "smpdb", + "publications": [ + { + "doi": "10.1093/nar/gkt1067", + "pmc": "PMC3965088", + "pubmed": "24203708", + "title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database.", + "year": 2013 + }, + { + "doi": "doi:10.1093/nar/gkp1002", + "pmc": "PMC2808928", + "pubmed": "19948758", + "title": "SMPDB: The Small Molecule Pathway Database.", + "year": null + }, + { + "doi": "10.1093/nar/gkp1002", + "pmc": "PMC2808928", + "pubmed": "19948758", + "title": "SMPDB: The Small Molecule Pathway Database.", + "year": 2009 + } + ], + "synonyms": [ + "SMP" + ], + "twitter": "WishartLab", + "uri_format": "https://smpdb.ca/view/$1" + }, + "snap": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality.", + "example": "Quality", + "homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", + "keywords": [ + "gene", + "interaction", + "pathway", + "protein" + ], + "mappings": { + "prefixcommons": "snap" + }, + "name": "Snapshot", + "preferred_prefix": "snap", + "uri_format": "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1" + }, + "snomedct": { + "contact": { + "email": "custserv@nlm.nih.gov", + "github": null, + "name": "NLM Customer Service", + "orcid": null + }, + "description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.", + "download_owl": "http://snomed.info/sct/900000000000207008/version/20200131", + "example": "284196006", + "homepage": "http://www.snomedbrowser.com/", + "keywords": [ + "biomedical science", + "health science", + "medicine", + "ontology", + "preclinical studies" + ], + "mappings": { + "aberowl": "SNOMEDCT", + "biocontext": "SNOMEDCT", + "biolink": "SNOMEDCT", + "bioportal": "SNOMEDCT", + "fairsharing": "FAIRsharing.d88s6e", + "hl7": "2.16.840.1.113883.6.96", + "miriam": "snomedct", + "n2t": "snomedct", + "ols": "snomed", + "prefixcommons": "snomedct", + "wikidata": "P5806" + }, + "name": "SNOMED CT (International Edition)", + "pattern": "^(\\w+)?\\d+$", + "preferred_prefix": "snomedct", + "publications": [ + { + "doi": "10.1097/00024665-200609000-00011", + "pmc": null, + "pubmed": "16980782", + "title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method.", + "year": 2006 + } + ], + "synonyms": [ + "SCTID", + "SCTID_2010_1_31", + "SNOMECT", + "SNOMED", + "SNOMEDCT", + "SNOMEDCTCT", + "SNOMEDCTCT_2018_03_01", + "SNOMEDCTCT_2019_03_01", + "SNOMEDCT_2005_07_31", + "SNOMEDCT_2010_1_31", + "SNOMEDCT_2020_03_01", + "SNOMEDCT_US", + "SNOMEDCT_US_2015_03_01", + "SNOMEDCT_US_2016_03_01", + "SNOMEDCT_US_2018_03_01", + "SNOMEDCT_US_2018_09_01", + "SNOMEDCT_US_2019_03_01", + "SNOMEDCT_US_2019_09_01", + "SNOMEDCT_US_2020_03_01", + "SNOMEDCT_US_2020_09_01", + "SNOMEDCT_US_2021_03_01", + "SNOMEDCT_US_2021_07_31", + "SNOMEDCT_US_2021_09_01", + "SNOMEDCT_US_2022_07_31", + "SNOMEDCT_US_2022_09_01", + "SNOMEDCT_US_2022_12_31", + "SNOMED_CT", + "SNOMED_CT_US_2018_03_01", + "SNOWMEDCT", + "SNOWMEDCT_US", + "SNOWMEDCT_US_2018_03_01" + ], + "uri_format": "http://www.snomedbrowser.com/Codes/Details/$1", + "version": "2020-01-31" + }, + "snornabase": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs.", + "example": "SR0000178", + "homepage": "https://www-snorna.biotoul.fr/", + "keywords": [ + "rna" + ], + "mappings": { + "prefixcommons": "snornalbmedb" + }, + "name": "snoRNABase", + "preferred_prefix": "snornabase", + "uri_format": "http://www-snorna.biotoul.fr/plus.php?id=$1" + }, + "snp2tfbs": { + "description": "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome.", + "example": "rs11603840", + "homepage": "https://ccg.epfl.ch/snp2tfbs/", + "mappings": { + "miriam": "snp2tfbs" + }, + "name": "SNP to Transcription Factor Binding Sites", + "pattern": "^rs[0-9]+$", + "preferred_prefix": "snp2tfbs", + "provides": "dbsnp", + "uri_format": "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1" + }, + "snp500cancer": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer.", + "example": "TP53-47", + "homepage": "http://snp500cancer.nci.nih.gov", + "keywords": [ + "dna" + ], + "mappings": { + "prefixcommons": "snp500cancer" + }, + "name": "SNP500Cancer", + "preferred_prefix": "snp500cancer", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1" + }, + "so": { + "appears_in": [ + "pcl" + ], + "banana": "SO", + "contact": { + "email": "keilbeck@genetics.utah.edu", + "github": "keilbeck", + "name": "Karen Eilbeck", + "orcid": "0000-0002-0831-6427" + }, + "description": "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.", + "download_obo": "https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo", + "download_owl": "http://purl.obolibrary.org/obo/so.owl", + "example": "0001157", + "homepage": "http://www.sequenceontology.org/", + "keywords": [ + "bioinformatics", + "biology", + "dna", + "life science", + "obo", + "ontology", + "rna", + "structure" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "SO", + "agroportal": "SO", + "biocontext": "SO", + "bioportal": "SO", + "fairsharing": "FAIRsharing.6bc7h9", + "go": "SO", + "miriam": "so", + "n2t": "so", + "obofoundry": "so", + "ols": "so", + "ontobee": "SO", + "prefixcommons": "so" + }, + "name": "Sequence types and features ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "SO", + "publications": [ + { + "doi": "10.1186/gb-2010-11-8-r88", + "pmc": "PMC2945790", + "pubmed": "20796305", + "title": "A standard variation file format for human genome sequences.", + "year": 2010 + }, + { + "doi": "10.1016/j.jbi.2010.03.002", + "pmc": "PMC3052763", + "pubmed": "20226267", + "title": "Evolution of the Sequence Ontology terms and relationships.", + "year": 2010 + }, + { + "doi": "10.1186/gb-2005-6-5-r44", + "pmc": "PMC1175956", + "pubmed": "15892872", + "title": "The Sequence Ontology: a tool for the unification of genome annotations.", + "year": 2005 + } + ], + "repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies", + "uri_format": "http://www.sequenceontology.org/miso/current_release/term/SO:$1", + "version": "2021-11-22" + }, + "sopharm": { + "contact": { + "email": "adrien.coulet@loria.fr", + "github": null, + "name": "Adrien Coulet", + "orcid": "0000-0002-1466-062X" + }, + "deprecated": true, + "description": "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. 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In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.", + "download_owl": "http://aber-owl.net/media/ontologies/SOPHARM/18/sopharm.owl", + "homepage": "http://www.loria.fr/~coulet/sopharm2.0_description.php", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "aberowl": "SOPHARM", + "biocontext": "SOPHARM", + "bioportal": "SOPHARM", + "obofoundry": "sopharm" + }, + "name": "Suggested Ontology for Pharmacogenomics", + "preferred_prefix": "SOPHARM", + "uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1" + }, + "soybase": { + "contact": { + "email": "Jacqueline.Campbell@usda.gov", + "github": null, + "name": "Jacqueline Campbell", + "orcid": "0000-0003-2787-3955" + }, + "description": "SoyBase is a repository for curated genetics, genomics and related data resources for soybean.", + "example": "BARC-013845-01256", + "homepage": "http://soybase.org/", + "keywords": [ + "agriculture", + "comparative genomics", + "development", + "life science", + "obo", + "phenotype", + "plant breeding", + "spider" + ], + "mappings": { + "biocontext": "SOYBASE", + "fairsharing": "FAIRsharing.z4agsr", + "miriam": "soybase", + "n2t": "soybase", + "ncbi": "SoyBase", + "prefixcommons": "soy", + "re3data": "r3d100010846" + }, + "name": "SoyBase", + "pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$", + "preferred_prefix": "soybase", + "publications": [ + { + "doi": "10.1093/nar/gkp798", + "pmc": "PMC2808871", + "pubmed": "20008513", + "title": "SoyBase, the USDA-ARS soybean genetics and genomics database.", + "year": 2009 + } + ], + "twitter": "SoyBaseDatabase", + "uri_format": "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1" + }, + "span": { + "comment": "see also snap. This ontology only exists in description in the paper and does not have an associated web resource", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.", + "homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", + "keywords": [ + "ontology", + "upper-level ontology" + ], + "name": "Span", + "preferred_prefix": "span" + }, + "spbase": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases.", + "example": "SPU_000001", + "homepage": "http://spbase.org", + "keywords": [ + "dna", + "genome", + "rna" + ], + "mappings": { + "prefixcommons": "spbase" + }, + "name": "SpBase", + "preferred_prefix": "spbase", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1" + }, + "spd": { + "contact": { + "email": "ramirez@macn.gov.ar", + "github": "martinjramirez", + "name": "Martin Ramirez", + "orcid": "0000-0002-0358-0130" + }, + "description": "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).", + "download_obo": "http://purl.obolibrary.org/obo/spd.obo", + "download_owl": "http://purl.obolibrary.org/obo/spd.owl", + "example": "0000001", + "homepage": "http://research.amnh.org/atol/files/", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology", + "spider" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "SPD", + "biocontext": "SPD", + "bioportal": "SPD", + "fairsharing": "FAIRsharing.yecp83", + "obofoundry": "spd", + "ols": "spd", + "ontobee": "SPD", + "prefixcommons": "spdo", + "wikidata": "P4537" + }, + "name": "Spider Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "SPD", + "publications": [ + { + "doi": "10.3390/d11100202", + "pmc": null, + "pubmed": null, + "title": "The Spider Anatomy Ontology (SPD)—A Versatile Tool to Link Anatomy with Cross-Disciplinary Data", + "year": 2019 + } + ], + "repository": "https://github.com/obophenotype/spider-ontology", + "uri_format": "http://purl.obolibrary.org/obo/SPD_$1", + "version": "2019-02-27" + }, + "spdx": { + "description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.", + "example": "CC-BY-1.0", + "homepage": "https://spdx.org/licenses", + "mappings": { + "miriam": "spdx", + "n2t": "spdx" + }, + "name": "Software Package Data Exchange License", + "pattern": "^[0-9A-Za-z\\-.]+$", + "preferred_prefix": "spdx", + "uri_format": "https://spdx.org/licenses/$1" + }, + "sphn": { + "contact": { + "email": "Sabine.Oesterle@sib.swiss", + "github": null, + "name": "Sabine Oesterle", + "orcid": "0000-0003-3248-7899" + }, + "contributor": { + "email": "deepak.unni3@gmail.com", + "github": "deepakunni3", + "name": "Deepak Unni", + "orcid": "0000-0002-3583-7340" + }, + "description": "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).", + "download_owl": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/ontology/sphn_ontology.owl?inline=false", + "download_rdf": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/ontology/sphn_ontology.ttl?inline=false", + "example": "Allergy", + "github_request_issue": 535, + "homepage": "https://www.sphn.ch", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "name": "Swiss Personalized Health Network Schema", + "pattern": "^\\S+$", + "preferred_prefix": "sphn", + "repository": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://biomedit.ch/rdf/sphn-ontology/sphn#$1" + }, + "spike.map": { + "description": "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps.", + "example": "spike00001", + "homepage": "http://www.cs.tau.ac.il/~spike/", + "keywords": [ + "dna", + "gene expression", + "pathway" + ], + "mappings": { + "biocontext": "SPIKE.MAP", + "miriam": "spike.map", + "n2t": "spike.map", + "prefixcommons": "spike" + }, + "name": "SPIKE Map", + "pattern": "^spike\\d{5}$", + "preferred_prefix": "spike.map", + "publications": [ + { + "doi": "10.1093/nar/gkq1167", + "pmc": "PMC3014840", + "pubmed": "21097778", + "title": "SPIKE: a database of highly curated human signaling pathways.", + "year": 2010 + }, + { + "doi": "10.1186/1471-2105-9-110", + "pmc": "PMC2263022", + "pubmed": "18289391", + "title": "SPIKE--a database, visualization and analysis tool of cellular signaling pathways.", + "year": 2008 + } + ], + "uri_format": "http://www.cs.tau.ac.il/~spike/maps/$1.html" + }, + "splash": { + "description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.", + "example": "splash10-0zq2000000-77302b0326a418630a84", + "homepage": "http://mona.fiehnlab.ucdavis.edu/", + "mappings": { + "biocontext": "SPLASH", + "miriam": "splash", + "n2t": "splash" + }, + "name": "Spectra Hash Code", + "pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$", + "preferred_prefix": "splash", + "uri_format": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1" + }, + "splicenest": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome.", + "example": "Hs635", + "homepage": "http://splicenest.molgen.mpg.de/", + "keywords": [ + "dna", + "gene", + "genome" + ], + "mappings": { + "prefixcommons": "splicenest" + }, + "name": "SpliceNest", + "preferred_prefix": "splicenest", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1" + }, + "spp": { + "contact": { + "email": "nmckenna@bcm.edu", + "github": null, + "name": "Neil McKenna", + "orcid": "0000-0001-6689-0104" + }, + "description": "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways.", + "example": "10.1621/vwN2g2HaX3", + "homepage": "https://www.signalingpathways.org/index.jsf", + "keywords": [ + "omics", + "transcriptomics" + ], + "mappings": { + "fairsharing": "FAIRsharing.WxI96O", + "miriam": "spp", + "re3data": "r3d100013650" + }, + "name": "Signaling Pathways Project", + "pattern": "^10.\\w{4}/\\w{10}$", + "preferred_prefix": "spp", + "publications": [ + { + "doi": "10.1038/s41597-019-0193-4", + "pmc": "PMC6823428", + "pubmed": "31672983", + "title": "The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways.", + "year": 2019 + } + ], + "twitter": "sigpathproject", + "uri_format": "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1" + }, + "srao": { + "contact": { + "email": "allyson.lister@oerc.ox.ac.uk", + "github": "allysonlister", + "name": "Allyson Lister", + "orcid": "0000-0002-7702-4495" + }, + "description": "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies.", + "download_owl": "https://raw.githubusercontent.com/FAIRsharing/subject-ontology/master/releases/SRAO.owl", + "example": "0000400", + "homepage": "https://github.com/FAIRsharing/subject-ontology", + "keywords": [ + "agriculture", + "biomedical science", + "computer science", + "earth science", + "environmental science", + "humanities", + "life science", + "metascience", + "natural science", + "ontology", + "topics" + ], + "mappings": { + "fairsharing": "FAIRsharing.b1xD9f", + "ols": "srao" + }, + "name": "FAIRsharing Subject Ontology", + "part_of": "fairsharing", + "pattern": "^\\d{7}$", + "preferred_prefix": "srao", + "repository": "https://github.com/FAIRsharing/subject-ontology", + "twitter": "FAIRsharing_org", + "uri_format": "http://www.fairsharing.org/ontology/subject/SRAO_$1", + "version": "0.3.0" + }, + "ssbd.dataset": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.", + "example": "1", + "homepage": "https://ssbd.riken.jp", + "keywords": [ + "cell biology", + "developmental biology", + "molecular dynamics" + ], + "mappings": { + "fairsharing": "FAIRsharing.we2r5a" + }, + "name": "System Science of Biological Dynamics dataset", + "pattern": "^\\d+$", + "preferred_prefix": "ssbd.dataset", + "publications": [ + { + "doi": "10.1093/bioinformatics/btw417", + "pmc": "PMC5181557", + "pubmed": "27412095", + "title": "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena.", + "year": 2016 + } + ], + "uri_format": "https://ssbd.riken.jp/database/dataset/$1" + }, + "ssbd.project": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations.", + "example": "1", + "homepage": "https://ssbd.riken.jp", + "name": "System Science of Biological Dynamics project", + "pattern": "^\\d+$", + "preferred_prefix": "ssbd.project", + "uri_format": "https://ssbd.riken.jp/database/project/$1" + }, + "sssom": { + "contact": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nicolas Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "contributor": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nicolas Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "description": "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace.", + "example": "mapping_justification", + "github_request_issue": 759, + "homepage": "https://w3id.org/sssom", + "license": "BSD-3-Clause", + "name": "Simple Standard for Sharing Ontological Mappings", + "pattern": "^[a-z_]+$", + "preferred_prefix": "sssom", + "repository": "https://github.com/mapping-commons/sssom", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://w3id.org/sssom/$1" + }, + "sstoss": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.", + "example": "01.01.005", + "homepage": "http://caps.ncbs.res.in/SSTOSS/index.htm", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "prefixcommons": "sstoss" + }, + "name": "Sequence-Structural Templates of Single-member Superfamilies", + "preferred_prefix": "sstoss", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1" + }, + "stap": { + "description": "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB).", + "example": "1a24", + "homepage": "http://psb.kobic.re.kr/STAP/refinement/", + "keywords": [ + "life science", + "statistics" + ], + "mappings": { + "biocontext": "STAP", + "fairsharing": "FAIRsharing.ja9cdq", + "miriam": "stap", + "n2t": "stap" + }, + "name": "Statistical Torsional Angles Potentials", + "pattern": "^[0-9][A-Za-z0-9]{3}$", + "preferred_prefix": "stap", + "publications": [ + { + "doi": "10.1093/bioinformatics/btv595", + "pmc": null, + "pubmed": "26504145", + "title": "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.", + "year": 2015 + }, + { + "doi": "10.1371/journal.pone.0108888", + "pmc": "PMC4184813", + "pubmed": "25279564", + "title": "Protein NMR structures refined without NOE data.", + "year": 2014 + }, + { + "doi": "10.1002/prot.24265", + "pmc": null, + "pubmed": "23408564", + "title": "Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkr1021", + "pmc": "PMC3245188", + "pubmed": "22102572", + "title": "STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures.", + "year": 2011 + } + ], + "uri_format": "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1" + }, + "stato": { + "appears_in": [ + "ontoavida", + "psdo", + "scdo" + ], + "contact": { + "email": "alejandra.gonzalez.beltran@gmail.com", + "github": "agbeltran", + "name": "Alejandra Gonzalez-Beltran", + "orcid": "0000-0003-3499-8262" + }, + "description": "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.", + "download_owl": "http://purl.obolibrary.org/obo/stato.owl", + "example": "0000288", + "homepage": "http://stato-ontology.org/", + "keywords": [ + "data visualization", + "obo", + "ontology", + "statistics" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "STATO", + "biocontext": "STATO", + "bioportal": "STATO", + "fairsharing": "FAIRsharing.na5xp", + "obofoundry": "stato", + "ols": "stato", + "ontobee": "STATO" + }, + "name": "The Statistical Methods Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "STATO", + "repository": "https://github.com/ISA-tools/stato", + "uri_format": "http://purl.obolibrary.org/obo/STATO_$1", + "version": "1.4" + }, + "stitch": { + "description": "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.", + "example": "BQJCRHHNABKAKU", + "homepage": "http://stitch.embl.de/", + "keywords": [ + "interaction", + "life science", + "protein", + "small molecule" + ], + "mappings": { + "biocontext": "STITCH", + "fairsharing": "FAIRsharing.zhwa8x", + "miriam": "stitch", + "n2t": "stitch", + "prefixcommons": "stitch" + }, + "name": "Search Tool for Interactions of Chemicals", + "pattern": "^\\w{14}$", + "preferred_prefix": "stitch", + "publications": [ + { + "doi": "10.1093/nar/gkt1207", + "pmc": "PMC3964996", + "pubmed": "24293645", + "title": "STITCH 4: integration of protein-chemical interactions with user data.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkr1011", + "pmc": "PMC3245073", + "pubmed": "22075997", + "title": "STITCH 3: zooming in on protein-chemical interactions.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkp937", + "pmc": "PMC2808890", + "pubmed": "19897548", + "title": "STITCH 2: an interaction network database for small molecules and proteins.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkm795", + "pmc": "PMC2238848", + "pubmed": "18084021", + "title": "STITCH: interaction networks of chemicals and proteins.", + "year": 2007 + } + ], + "uri_format": "http://stitch.embl.de/interactions/$1" + }, + "storedb": { + "banana": "STOREDB", + "contact": { + "email": "PNS12@cam.ac.uk", + "github": null, + "name": "Dr Paul Schofield", + "orcid": "0000-0002-5111-7263" + }, + "description": "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons.", + "example": "STUDY1040", + "homepage": "https://www.storedb.org/", + "keywords": [ + "biomedical science", + "ecology", + "epidemiology", + "life science", + "preclinical studies" + ], + "mappings": { + "biocontext": "STOREDB", + "fairsharing": "FAIRsharing.6h8d2r", + "miriam": "storedb", + "n2t": "storedb", + "re3data": "r3d100011049" + }, + "name": "Store DB", + "namespace_in_lui": true, + "pattern": "^(STUDY|FILE|DATASET)\\d+$", + "preferred_prefix": "storedb", + "uri_format": "https://www.storedb.org/?$1" + }, + "storedb.dataset": { + "comment": "Unfortunately, the resolver itself doesn't work since datasets are actually hierarchically assigned within studies.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "Datasets inside StoreDB", + "example": "1251", + "homepage": "https://www.storedb.org/", + "name": "STOREDB at University of Cambridge", + "part_of": "storedb", + "pattern": "^\\d+$", + "preferred_prefix": "storedb.dataset", + "uri_format": "https://www.storedb.org/?STOREDB:DATASET$1" + }, + "storedb.file": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "File inside StoreDB", + "example": "12929", + "homepage": "https://www.storedb.org/", + "name": "STOREDB at University of Cambridge", + "part_of": "storedb", + "pattern": "^\\d+$", + "preferred_prefix": "storedb.file", + "uri_format": "https://www.storedb.org/store_v3/download.jsp?fileId=$1" + }, + "storedb.study": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Study inside StoreDB", + "example": "1174", + "homepage": "https://www.storedb.org/", + "name": "STOREDB at University of Cambridge", + "part_of": "storedb", + "pattern": "^\\d+$", + "preferred_prefix": "storedb.study", + "providers": [ + { + "code": "doi", + "description": "DOIs for studies", + "homepage": "https://www.storedb.org/", + "name": "StoreDB DOI", + "uri_format": "http://dx.doi.org/doi:10.20348/STOREDB/$1" + } + ], + "uri_format": "https://www.storedb.org/store_v3/study.jsp?studyId=$1" + }, + "string": { + "contact": { + "email": "bork@embl.de", + "github": null, + "name": "Peer Bork", + "orcid": "0000-0002-2627-833X" + }, + "description": "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.", + "example": "P53350", + "homepage": "http://string.embl.de/", + "keywords": [ + "biology", + "interaction", + "life science", + "protein" + ], + "mappings": { + "biocontext": "STRING", + "edam": "2302", + "fairsharing": "FAIRsharing.9b7wvk", + "miriam": "string", + "n2t": "string", + "prefixcommons": "string", + "re3data": "r3d100010604", + "uniprot": "DB-0141" + }, + "name": "Search Tool for Retrieval of Interacting Genes/Proteins", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$", + "preferred_prefix": "string", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "STRING Mirror at Heidelberg", + "homepage": "http://string-db.org/", + "name": "STRING Mirror at Heidelberg", + "uri_format": "http://string-db.org/interactions/$1" + } + ], + "provides": "uniprot", + "publications": [ + { + "doi": "10.1093/nar/gky1131", + "pmc": "PMC6323986", + "pubmed": "30476243", + "title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.", + "year": 2019 + }, + { + "doi": "10.1093/nar/gkw937", + "pmc": "PMC5210637", + "pubmed": "27924014", + "title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.", + "year": 2016 + }, + { + "doi": "10.1093/bioinformatics/btv696", + "pmc": "PMC4896368", + "pubmed": "26614125", + "title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gku1003", + "pmc": "PMC4383874", + "pubmed": "25352553", + "title": "STRING v10: protein-protein interaction networks, integrated over the tree of life.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gks1094", + "pmc": "PMC3531103", + "pubmed": "23203871", + "title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkn760", + "pmc": "PMC2686466", + "pubmed": "18940858", + "title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms.", + "year": 2008 + } + ], + "uri_format": "http://string.embl.de/interactions/$1" + }, + "sty": { + "contact": { + "email": "support@bioontology.org", + "github": null, + "name": "bioportal", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.", + "example": "T039", + "homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "STY", + "agroportal": "STY", + "biolink": "UMLSSG", + "bioportal": "STY", + "ecoportal": "STY" + }, + "name": "UMLS Semantic Types Ontology", + "pattern": "^T\\d{3}$", + "preferred_prefix": "sty", + "synonyms": [ + "UMLSSG", + "umls.st", + "umls.sty" + ], + "uri_format": "http://purl.bioontology.org/ontology/STY/$1" + }, + "subtilist": { + "description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.", + "example": "BG11523", + "homepage": "http://genolist.pasteur.fr/SubtiList/", + "keywords": [ + "dna", + "genome", + "protein" + ], + "mappings": { + "biocontext": "SUBTILIST", + "fairsharing": "FAIRsharing.40j2vd", + "miriam": "subtilist", + "n2t": "subtilist", + "ncbi": "SubtiList", + "prefixcommons": "subtilist" + }, + "name": "Bacillus subtilis genome sequencing project", + "pattern": "^BG\\d+$", + "preferred_prefix": "subtilist", + "publications": [ + { + "doi": "10.1093/nar/30.1.62", + "pmc": "PMC99059", + "pubmed": "11752255", + "title": "SubtiList: the reference database for the Bacillus subtilis genome.", + "year": 2002 + } + ], + "uri_format": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1" + }, + "subtiwiki": { + "description": "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon.", + "example": "BSU29180", + "homepage": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page", + "keywords": [ + "dna", + "gene", + "life science", + "protein", + "rna" + ], + "mappings": { + "biocontext": "SUBTIWIKI", + "fairsharing": "FAIRsharing.2ck3st", + "miriam": "subtiwiki", + "n2t": "subtiwiki", + "prefixcommons": "subtiwiki" + }, + "name": "SubtiWiki", + "pattern": "^BSU\\d{5}$", + "preferred_prefix": "subtiwiki", + "publications": [ + { + "doi": "10.1093/nar/gkv1006", + "pmc": "PMC4702770", + "pubmed": "26433225", + "title": "SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis.", + "year": 2015 + }, + { + "doi": "10.1093/database/bap012", + "pmc": "PMC2790307", + "pubmed": "20157485", + "title": "A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.", + "year": 2009 + }, + { + "doi": "10.1099/mic.0.035790-0", + "pmc": null, + "pubmed": "19959575", + "title": "Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.", + "year": 2009 + } + ], + "uri_format": "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1" + }, + "sugarbind": { + "contact": { + "email": "frederique.lisacek@isb-sib.ch", + "github": null, + "name": "Frederique Lisacek", + "orcid": "0000-0002-0948-4537" + }, + "description": "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands.", + "example": "lectins/172", + "homepage": "http://sugarbind.expasy.org/", + "keywords": [ + "biomedical science", + "glycomics" + ], + "mappings": { + "biocontext": "SUGARBIND", + "fairsharing": "FAIRsharing.d064y6", + "miriam": "sugarbind", + "n2t": "sugarbind" + }, + "name": "SugarBind", + "pattern": "^[A-Za-z]+\\/[0-9]+$", + "preferred_prefix": "sugarbind", + "publications": [ + { + "doi": "10.1093/nar/gkv1247", + "pmc": "PMC4702881", + "pubmed": "26578555", + "title": "SugarBindDB, a resource of glycan-mediated host-pathogen interactions.", + "year": 2015 + }, + { + "doi": "10.1007/978-4-431-56454-6_13", + "pmc": null, + "pubmed": null, + "title": "SugarBindDB", + "year": 2016 + } + ], + "twitter": "ISBSIB", + "uri_format": "http://sugarbind.expasy.org/$1" + }, + "supfam": { + "description": "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt.", + "example": "SSF57615", + "homepage": "http://supfam.org/SUPERFAMILY/", + "keywords": [ + "classification", + "genome", + "protein", + "structure" + ], + "mappings": { + "biocontext": "SUPFAM", + "miriam": "supfam", + "n2t": "supfam", + "prefixcommons": "superfamily", + "uniprot": "DB-0155" + }, + "name": "SUPERFAMILY", + "pattern": "^\\w+$", + "preferred_prefix": "supfam", + "publications": [ + { + "doi": "10.1006/jmbi.2001.5080", + "pmc": null, + "pubmed": "11697912", + "title": "Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.", + "year": 2001 + } + ], + "uri_format": "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1" + }, + "sweetrealm": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).", + "download_obo": "https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo", + "example": "ANOVA", + "homepage": "https://bioportal.bioontology.org/ontologies/SWEET", + "keywords": [ + "ontology" + ], + "mappings": { + "bioportal": "SWEET" + }, + "name": "Semantic Web for Earth and Environment Technology Ontology", + "preferred_prefix": "sweetrealm", + "uri_format": "http://sweetontology.net/matrMineral/$1" + }, + "swh": { + "banana": "swh", + "description": "Software Heritage is the universal archive of software source code.", + "example": "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d", + "homepage": "https://archive.softwareheritage.org", + "mappings": { + "biocontext": "SWH", + "miriam": "swh", + "n2t": "swh" + }, + "name": "Software Heritage", + "namespace_in_lui": true, + "pattern": "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$", + "preferred_prefix": "swh", + "uri_format": "https://archive.softwareheritage.org/browse/swh:$1" + }, + "swiss-model": { + "contact": { + "email": "help-swissmodel@unibas.ch", + "github": null, + "name": "Torsten Schwede", + "orcid": "0000-0003-2715-335X" + }, + "description": "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences.", + "example": "P23298", + "homepage": "https://swissmodel.expasy.org", + "keywords": [ + "life science", + "protein", + "proteomics", + "structure" + ], + "mappings": { + "biocontext": "SWISS-MODEL", + "fairsharing": "FAIRsharing.vxz9pn", + "miriam": "swiss-model", + "n2t": "swiss-model", + "prefixcommons": "swissmodel", + "re3data": "r3d100010605" + }, + "name": "SWISS-MODEL Repository", + "pattern": "^\\w+$", + "preferred_prefix": "swiss-model", + "provides": "uniprot", + "publications": [ + { + "doi": "10.1093/nar/gkw1132", + "pmc": "PMC5210589", + "pubmed": "27899672", + "title": "The SWISS-MODEL Repository-new features and functionality.", + "year": 2016 + }, + { + "doi": "10.1093/nar/gku340", + "pmc": "PMC4086089", + "pubmed": "24782522", + "title": "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkn750", + "pmc": "PMC2686475", + "pubmed": "18931379", + "title": "The SWISS-MODEL Repository and associated resources.", + "year": 2008 + } + ], + "twitter": "SWISS_MODEL", + "uri_format": "https://swissmodel.expasy.org/repository/uniprot/$1" + }, + "swisslipid": { + "banana": "SLM", + "contact": { + "email": "swisslipids@isb-sib.ch", + "github": null, + "name": "Alan Bridge", + "orcid": "0000-0003-2148-9135" + }, + "description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.", + "example": "000000341", + "homepage": "http://www.swisslipids.org/#/", + "keywords": [ + "life science", + "metabolomics" + ], + "mappings": { + "biocontext": "SWISSLIPID", + "fairsharing": "FAIRsharing.pxr7x2", + "miriam": "slm", + "n2t": "swisslipid", + "re3data": "r3d100012603", + "uniprot": "DB-0197", + "wikidata": "P8691" + }, + "name": "SwissLipid", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "swisslipid", + "publications": [ + { + "doi": "10.1093/bioinformatics/btv285", + "pmc": "PMC4547616", + "pubmed": "25943471", + "title": "The SwissLipids knowledgebase for lipid biology.", + "year": 2015 + } + ], + "synonyms": [ + "slm", + "swisslipids" + ], + "uri_format": "https://www.swisslipids.org/#/entity/SLM:$1" + }, + "swissregulon": { + "contact": { + "email": "erik.vannimwegen@unibas.ch", + "github": null, + "name": "Erik van Nimwegen", + "orcid": "0000-0001-6338-1312" + }, + "description": "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form.", + "example": "AHR", + "homepage": "http://swissregulon.unibas.ch", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "SWISSREGULON", + "fairsharing": "FAIRsharing.7fnx38", + "miriam": "swissregulon", + "n2t": "swissregulon" + }, + "name": "SwissRegulon", + "pattern": "^[A-Za-z0-9]+$", + "preferred_prefix": "swissregulon", + "publications": [ + { + "doi": "10.1093/nar/gks1145", + "pmc": "PMC3531101", + "pubmed": "23180783", + "title": "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkl857", + "pmc": "PMC1716717", + "pubmed": "17130146", + "title": "SwissRegulon: a database of genome-wide annotations of regulatory sites.", + "year": 2006 + } + ], + "uri_format": "http://swissregulon.unibas.ch/query/$1" + }, + "swo": { + "contact": { + "email": "allyson.lister@oerc.ox.ac.uk", + "github": "allysonlister", + "name": "Allyson Lister", + "orcid": "0000-0002-7702-4495" + }, + "description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. 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It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]", + "example": "E5.11.2.0.0.0.4", + "homepage": "https://ifaa.unifr.ch/", + "mappings": { + "wikidata": "P1693" + }, + "name": "Terminologia Embryologica", + "preferred_prefix": "te", + "references": [ + "https://en.wikipedia.org/wiki/Terminologia_Embryologica" + ] + }, + "tfclass": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here..", + "example": "2.1.1", + "homepage": "http://tfclass.bioinf.med.uni-goettingen.de", + "keywords": [ + "bioinformatics", + "phylogenetics", + "transcriptomics" + ], + "mappings": { + "fairsharing": "FAIRsharing.XykycZ", + "go": "TFClass" + }, + "name": "Classification of Transcription Factors in Mammalia", + "preferred_prefix": "tfclass", + "publications": [ + { + "doi": "10.1093/nar/gkx987", + "pmc": "PMC5753292", + "pubmed": "29087517", + "title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs.", + "year": 2018 + } + ], + "uri_format": "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1" + }, + "tgd": { + "description": "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature.", + "example": "TTHERM_00648910", + "homepage": "http://ciliate.org/index.php/", + "keywords": [ + "genome" + ], + "mappings": { + "biocontext": "TGD", + "go": "TGD", + "miriam": "tgd", + "n2t": "tgd", + "prefixcommons": "tgd" + }, + "name": "Tetrahymena Genome Database", + "pattern": "^TTHERM\\_\\d+$", + "preferred_prefix": "tgd", + "uri_format": "http://ciliate.org/index.php/feature/details/$1" + }, + "tgma": { + "contact": { + "email": "topalis@imbb.forth.gr", + "github": null, + "name": "Pantelis Topalis", + "orcid": "0000-0002-1635-4810" + }, + "deprecated": true, + "description": "A structured controlled vocabulary of the anatomy of mosquitoes.", + "download_obo": "http://purl.obolibrary.org/obo/tgma.obo", + "download_owl": "http://purl.obolibrary.org/obo/tgma.owl", + "example": "0000984", + "homepage": "https://www.vectorbase.org/ontology-browser", + "keywords": [ + "anatomy", + "life science", + "mosquito", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "TGMA", + "biocontext": "TGMA", + "bioportal": "TGMA", + "fairsharing": "FAIRsharing.dqnfkg", + "obofoundry": "tgma", + "ols": "tgma", + "ontobee": "TGMA", + "prefixcommons": "tgma" + }, + "name": "Mosquito gross anatomy ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "TGMA", + "publications": [ + { + "doi": "10.1111/j.1365-2583.2008.00781.x", + "pmc": null, + "pubmed": "18237287", + "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase.", + "year": 2008 + } + ], + "repository": "https://github.com/VEuPathDB-ontology/TGMA", + "uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", + "version": "2013-06-03" + }, + "tgn": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "example": "1023371", + "homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/", + "mappings": { + "bartoc": "109" + }, + "name": "Getty Thesaurus of Geographic Names", + "pattern": "^\\d+$", + "preferred_prefix": "tgn", + "references": [ + "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638380238036200" + ], + "uri_format": "http://vocab.getty.edu/page/tgn/$1" + }, + "th": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]", + "example": "H3.03.00.0.00007", + "homepage": "https://ifaa.unifr.ch/", + "keywords": [ + "biology", + "cytology", + "histology", + "life sciences" + ], + "name": "Terminologia Histologica", + "preferred_prefix": "th", + "references": [ + "https://en.wikipedia.org/wiki/Terminologia_Histologica" + ] + }, + "thermofisher": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "ThermoFisher is a life sciences supply vendor.", + "example": "OSR00185W", + "homepage": "https://www.thermofisher.com", + "keywords": [ + "biology", + "chemistry", + "life sciences", + "vendor" + ], + "name": "Thermo Fisher Scientific", + "preferred_prefix": "thermofisher", + "uri_format": "https://www.thermofisher.com/antibody/product/$1" + }, + "tigrfam": { + "contributor_extras": [ + { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + } + ], + "description": "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins.", + "example": "TIGR00010", + "homepage": "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "TIGRFAM", + "edam": "1141", + "miriam": "tigrfam", + "n2t": "tigrfam", + "ncbi": "TIGRFAM", + "prefixcommons": "tigrfams" + }, + "name": "TIGR protein families", + "pattern": "^TIGR\\d+$", + "preferred_prefix": "tigrfam", + "references": [ + "https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt", + "https://github.com/biopragmatics/bioregistry/issues/366" + ], + "uri_format": "https://www.ncbi.nlm.nih.gov/cdd?term=$1" + }, + "time": { + "contact": { + "email": "simon.cox@csiro.au", + "github": "dr-shorthair", + "name": "Simon Cox", + "orcid": "0000-0002-3884-3420" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.", + "download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl", + "example": "DateTimeDescription", + "github_request_issue": 505, + "homepage": "https://www.w3.org/TR/owl-time/", + "keywords": [ + "ontology", + "subject agnostic" + ], + "mappings": { + "aberowl": "TIME", + "bioportal": "TIME", + "fairsharing": "FAIRsharing.hw3bh2" + }, + "name": "Time Ontology in OWL", + "preferred_prefix": "time", + "repository": "https://github.com/w3c/sdw/", + "uri_format": "http://www.w3.org/2006/time#$1" + }, + "tkg": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells.", + "example": "0221", + "homepage": "http://www2.idac.tohoku.ac.jp/dep/ccr/", + "mappings": { + "cellosaurus": "TKG" + }, + "name": "Tohoku University cell line catalog", + "pattern": "^\\d+$", + "preferred_prefix": "tkg", + "uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html" + }, + "tngb": { + "description": "Cell line collections", + "example": "67035", + "homepage": "http://biobanknetwork.telethon.it/", + "mappings": { + "cellosaurus": "TNGB" + }, + "name": "Telethon Network of Genetic Biobanks", + "pattern": "^\\d+$", + "preferred_prefix": "tngb", + "uri_format": "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1" + }, + "to": { + "appears_in": [ + "agro" + ], + "contact": { + "email": "jaiswalp@science.oregonstate.edu", + "github": "jaiswalp", + "name": "Pankaj Jaiswal", + "orcid": "0000-0002-1005-8383" + }, + "description": "A controlled vocabulary to describe phenotypic traits in plants.", + "download_obo": "http://purl.obolibrary.org/obo/to.obo", + "download_owl": "http://purl.obolibrary.org/obo/to.owl", + "example": "0000630", + "homepage": "http://browser.planteome.org/amigo", + "keywords": [ + "botany", + "obo", + "ontology", + "plant", + "trait" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "TO", + "agroportal": "TO", + "biocontext": "TO", + "bioportal": "PTO", + "fairsharing": "FAIRsharing.w69t6r", + "obofoundry": "to", + "ols": "to", + "ontobee": "TO", + "prefixcommons": "pto" + }, + "name": "Plant Trait Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "TO", + "publications": [ + { + "doi": "10.1093/nar/gkx1152", + "pmc": "PMC5753347", + "pubmed": "29186578", + "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.", + "year": 2018 + } + ], + "repository": "https://github.com/Planteome/plant-trait-ontology", + "uri_format": "http://purl.obolibrary.org/obo/TO_$1", + "version": "2022-04-13" + }, + "tokue": { + "deprecated": true, + "description": "Cell line databases/resources", + "homepage": "http://cell-lines.toku-e.com", + "mappings": { + "cellosaurus": "TOKU-E" + }, + "name": "TOKU-E Cell-culture Database", + "preferred_prefix": "tokue", + "uri_format": "http://cell-lines.toku-e.com/Cell-Lines_$1.html" + }, + "tol": { + "contributor_extras": [ + { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + } + ], + "description": "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.", + "example": "98034", + "homepage": "http://tolweb.org/tree/", + "mappings": { + "bartoc": "400", + "biocontext": "TOL", + "miriam": "tol", + "n2t": "tol", + "wikidata": "P5221" + }, + "name": "Tree of Life Web Project", + "pattern": "^\\d+$", + "preferred_prefix": "tol", + "synonyms": [ + "tol.webproj" + ], + "uri_format": "http://tolweb.org/$1" + }, + "topdb": { + "description": "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases.", + "example": "AP00378", + "homepage": "http://topdb.enzim.hu/", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "TOPDB", + "edam": "2789", + "miriam": "topdb", + "n2t": "topdb", + "prefixcommons": "topdb" + }, + "name": "Topology Data Bank of Transmembrane Proteins", + "pattern": "^[A-Z0-9]+$", + "preferred_prefix": "topdb", + "uri_format": "http://topdb.enzim.hu/?m=show&id=$1" + }, + "topfind": { + "description": "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.", + "example": "Q9UKQ2", + "homepage": "https://topfind.clip.msl.ubc.ca", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "TOPFIND", + "fairsharing": "FAIRsharing.rkpmhn", + "miriam": "topfind", + "n2t": "topfind", + "re3data": "r3d100012721" + }, + "name": "TopFind", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", + "preferred_prefix": "topfind", + "provides": "uniprot", + "publications": [ + { + "doi": "10.1093/nar/gku1012", + "pmc": "PMC4383881", + "pubmed": "25332401", + "title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkr1025", + "pmc": "PMC3244998", + "pubmed": "22102574", + "title": "TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function.", + "year": 2011 + }, + { + "doi": "10.1038/nmeth.1669", + "pmc": null, + "pubmed": "21822272", + "title": "TopFIND, a knowledgebase linking protein termini with function.", + "year": 2011 + } + ], + "uri_format": "http://clipserve.clip.ubc.ca/topfind/proteins/$1" + }, + "toxoplasma": { + "description": "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "TGME49_053730", + "homepage": "http://toxodb.org/toxo/", + "mappings": { + "biocontext": "TOXOPLASMA", + "miriam": "toxoplasma", + "n2t": "toxoplasma" + }, + "name": "ToxoDB", + "pattern": "^\\w+$", + "preferred_prefix": "toxoplasma", + "uri_format": "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" + }, + "trans": { + "contact": { + "email": "lynn.schriml@gmail.com", + "github": "lschriml", + "name": "Lynn Schriml", + "orcid": "0000-0001-8910-9851" + }, + "description": "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.", + "download_obo": "http://purl.obolibrary.org/obo/trans.obo", + "download_owl": "http://purl.obolibrary.org/obo/trans.owl", + "example": "0000024", + "homepage": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", + "keywords": [ + "health science", + "obo", + "ontology", + "pathogen" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "TRANS", + "biocontext": "TRANS", + "bioportal": "TRANS", + "fairsharing": "FAIRsharing.nygmp7", + "obofoundry": "trans", + "ols": "trans", + "ontobee": "TRANS", + "prefixcommons": "pt" + }, + "name": "Pathogen Transmission Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "TRANS", + "publications": [ + { + "doi": "10.1093/nar/gkab1063", + "pmc": "PMC8728220", + "pubmed": "34755882", + "title": "The Human Disease Ontology 2022 update.", + "year": 2022 + }, + { + "doi": "10.1093/nar/gkp832", + "pmc": "PMC2808878", + "pubmed": "19850722", + "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database.", + "year": 2009 + } + ], + "repository": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", + "uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", + "version": "2020-08-04" + }, + "transportdb": { + "description": "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.", + "example": "MMP0523", + "homepage": "http://www.membranetransport.org", + "keywords": [ + "protein" + ], + "mappings": { + "prefixcommons": "transportdb" + }, + "name": "TransportDB", + "preferred_prefix": "transportdb", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1" + }, + "transyt": { + "description": "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes.", + "example": "TR0000001", + "homepage": "https://www.bio.di.uminho.pt/", + "mappings": { + "miriam": "transyt" + }, + "name": "Transport Systems Tracker", + "pattern": "^T[A-Z]\\d{7}$", + "preferred_prefix": "transyt", + "uri_format": "https://transyt.bio.di.uminho.pt/reactions/$1" + }, + "tred": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present.", + "example": "21552", + "homepage": "http://rulai.cshl.edu/TRED", + "keywords": [ + "dna", + "regulation" + ], + "mappings": { + "prefixcommons": "tred" + }, + "name": "Transcriptional Regulatory Element Database", + "preferred_prefix": "tred", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1" + }, + "treebase": { + "contact": { + "email": "rutgeraldo@gmail.com", + "github": "rvosa", + "name": "Rutger Vos", + "orcid": "0000-0001-9254-7318" + }, + "description": "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc.", + "example": "TB2:S1000", + "homepage": "http://treebase.org/", + "keywords": [ + "classification", + "phylogenetics", + "phylogenomics" + ], + "mappings": { + "biocontext": "TREEBASE", + "fairsharing": "FAIRsharing.zcn4w4", + "miriam": "treebase", + "n2t": "treebase", + "prefixcommons": "treebase", + "re3data": "r3d100010170" + }, + "name": "TreeBASE", + "pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$", + "preferred_prefix": "treebase", + "publications": [ + { + "doi": "10.1186/1471-2148-9-93", + "pmc": "PMC2685121", + "pubmed": "19426482", + "title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment.", + "year": 2009 + } + ], + "repository": "https://github.com/TreeBASE/treebase/issues", + "twitter": "treebase", + "uri_format": "http://purl.org/phylo/treebase/phylows/study/$1?format=html" + }, + "treefam": { + "description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.", + "example": "TF101014", + "homepage": "http://www.treefam.org/", + "keywords": [ + "classification", + "gene" + ], + "mappings": { + "biocontext": "TREEFAM", + "miriam": "treefam", + "n2t": "treefam", + "prefixcommons": "treefam", + "uniprot": "DB-0185" + }, + "name": "TreeFam", + "pattern": "^\\w{1,2}\\d+$", + "preferred_prefix": "treefam", + "publications": [ + { + "doi": "10.1093/nar/gkt1055", + "pmc": "PMC3965059", + "pubmed": "24194607", + "title": "TreeFam v9: a new website, more species and orthology-on-the-fly.", + "year": 2013 + } + ], + "uri_format": "http://www.treefam.org/family/$1" + }, + "trichdb": { + "contact": { + "email": "oharb@pcbi.upenn.edu", + "github": null, + "name": "Omar Harb", + "orcid": "0000-0003-4446-6200" + }, + "description": "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "TVAG_386080", + "homepage": "http://trichdb.org/trichdb/", + "keywords": [ + "genomics" + ], + "mappings": { + "biocontext": "TRICHDB", + "fairsharing": "FAIRsharing.pv0ezt", + "miriam": "trichdb", + "n2t": "trichdb", + "re3data": "r3d100012461" + }, + "name": "TrichDB", + "pattern": "^\\w+$", + "preferred_prefix": "trichdb", + "publications": [ + { + "doi": "10.1093/nar/gkn631", + "pmc": "PMC2686445", + "pubmed": "18824479", + "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.", + "year": 2008 + } + ], + "twitter": "eupathdb", + "uri_format": "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" + }, + "tritrypdb": { + "contact": { + "email": "oharb@pcbi.upenn.edu", + "github": null, + "name": "Omar Harb", + "orcid": "0000-0003-4446-6200" + }, + "description": "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.", + "example": "Tb927.8.620", + "homepage": "http://tritrypdb.org/tritrypdb/", + "keywords": [ + "comparative genomics", + "genomics", + "infectious disease medicine" + ], + "mappings": { + "biocontext": "TRITRYPDB", + "fairsharing": "FAIRsharing.fs1z27", + "go": "TriTrypDB", + "miriam": "tritrypdb", + "n2t": "tritrypdb", + "re3data": "r3d100011479" + }, + "name": "TriTrypDB", + "pattern": "^\\w+(\\.)?\\w+(\\.)?\\w+$", + "preferred_prefix": "tritrypdb", + "publications": [ + { + "doi": "10.1093/nar/gkp851", + "pmc": "PMC2808979", + "pubmed": "19843604", + "title": "TriTrypDB: a functional genomic resource for the Trypanosomatidae.", + "year": 2009 + } + ], + "twitter": "VEuPathDB", + "uri_format": "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1" + }, + "trnadbce": { + "comment": "requires authentication to access", + "description": "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones.", + "example": "265912", + "homepage": "http://trna.nagahama-i-bio.ac.jp", + "keywords": [ + "dna", + "gene", + "genome", + "rna" + ], + "mappings": { + "prefixcommons": "trnadbce" + }, + "name": "tRNA Gene Database", + "preferred_prefix": "trnadbce", + "proprietary": true, + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1" + }, + "ttd.drug": { + "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", + "example": "DAP000773", + "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", + "mappings": { + "biocontext": "TTD.DRUG", + "edam": "2653", + "miriam": "ttd.drug", + "n2t": "ttd.drug" + }, + "name": "TTD Drug", + "pattern": "^DAP\\d+$", + "preferred_prefix": "ttd.drug", + "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1" + }, + "ttd.target": { + "description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.", + "example": "TTDS00056", + "homepage": "http://bidd.nus.edu.sg/group/ttd/ttd.asp", + "mappings": { + "biocontext": "TTD.TARGET", + "edam": "2654", + "miriam": "ttd.target", + "n2t": "ttd.target" + }, + "name": "TTD Target", + "pattern": "^TTDS\\d+$", + "preferred_prefix": "ttd.target", + "uri_format": "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1" + }, + "tto": { + "contact": { + "email": "balhoff@renci.org", + "github": "balhoff", + "name": "Jim Balhoff", + "orcid": "0000-0002-8688-6599" + }, + "description": "An ontology covering the taxonomy of teleosts (bony fish)", + "download_obo": "http://purl.obolibrary.org/obo/tto.obo", + "download_owl": "http://purl.obolibrary.org/obo/tto.owl", + "example": "1058367", + "homepage": "https://github.com/phenoscape/teleost-taxonomy-ontology", + "keywords": [ + "fish", + "life science", + "obo", + "ontology", + "phenotype" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "TTO", + "biocontext": "TTO", + "bioportal": "TTO", + "fairsharing": "FAIRsharing.1rj558", + "obofoundry": "tto", + "ols": "tto", + "ontobee": "TTO", + "prefixcommons": "tto" + }, + "name": "Teleost taxonomy ontology", + "pattern": "^\\d+$", + "preferred_prefix": "TTO", + "publications": [ + { + "doi": "10.1038/npre.2010.4629.1", + "pmc": null, + "pubmed": null, + "title": "The Teleost Taxonomy Ontology", + "year": 2010 + } + ], + "repository": "https://github.com/phenoscape/teleost-taxonomy-ontology", + "uri_format": "http://purl.obolibrary.org/obo/TTO_$1", + "version": "2018-03-26" + }, + "txpo": { + "contact": { + "email": "yuki.yamagata@riken.jp", + "github": "yuki-yamagata", + "name": "Yuki Yamagata", + "orcid": "0000-0002-9673-1283" + }, + "description": "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp", + "download_owl": "http://purl.obolibrary.org/obo/txpo.owl", + "example": "0002066", + "homepage": "https://toxpilot.nibiohn.go.jp/", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "TXPO", + "bioportal": "TXPO", + "obofoundry": "txpo", + "ols": "txpo", + "ontobee": "TXPO" + }, + "name": "Toxic Process Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "TXPO", + "publications": [ + { + "doi": "10.1038/s41598-020-71370-7", + "pmc": "PMC7471325", + "pubmed": "32883995", + "title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management.", + "year": 2020 + } + ], + "repository": "https://github.com/txpo-ontology/TXPO", + "uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", + "version": "2020-07-09" + }, + "uberon": { + "appears_in": [ + "aism", + "amphx", + "chiro", + "cl", + "clo", + "clyh", + "colao", + "cteno", + "ecao", + "ecocore", + "ecto", + "envo", + "foodon", + "fovt", + "genepio", + "go", + "hso", + "lepao", + "maxo", + "mco", + "mfmo", + "ons", + "pcl", + "plana", + "poro", + "zp" + ], + "banana": "UBERON", + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "depends_on": [ + "chebi", + "cl", + "go", + "pr" + ], + "description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.", + "download_json": "http://purl.obolibrary.org/obo/uberon.json", + "download_obo": "http://purl.obolibrary.org/obo/uberon/basic.obo", + "download_owl": "http://purl.obolibrary.org/obo/uberon.owl", + "example": "2005080", + "homepage": "http://uberon.org", + "keywords": [ + "anatomy", + "developmental biology", + "life science", + "obo", + "ontology", + "taxonomy" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "UBERON", + "biocontext": "UBERON", + "bioportal": "UBERON", + "cellosaurus": "UBERON", + "fairsharing": "FAIRsharing.4c0b6b", + "go": "UBERON", + "miriam": "uberon", + "n2t": "uberon", + "obofoundry": "uberon", + "ols": "uberon", + "ontobee": "UBERON", + "wikidata": "P1554" + }, + "name": "Uber Anatomy Ontology", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "UBERON", + "providers": [ + { + "code": "cellxgene", + "description": "Explore single cell data through the CZ CELLxGENE portal", + "homepage": "https://onto.cellxgene-labs.prod.si.czi.technology", + "name": "CELLxGENE", + "uri_format": "https://onto.cellxgene-labs.prod.si.czi.technology/a/ontology/UBERON/UBERON:$1" + } + ], + "publications": [ + { + "doi": "10.1186/2041-1480-5-21", + "pmc": "PMC4089931", + "pubmed": "25009735", + "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.", + "year": 2014 + }, + { + "doi": "10.1186/gb-2012-13-1-r5", + "pmc": "PMC3334586", + "pubmed": "22293552", + "title": "Uberon, an integrative multi-species anatomy ontology.", + "year": 2012 + } + ], + "repository": "https://github.com/obophenotype/uberon", + "synonyms": [ + "UBERON", + "Uber-anatomy ontology", + "Uberon" + ], + "twitter": "uberanat", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=UBERON:$1", + "version": "2022-09-30" + }, + "ubio.namebank": { + "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", + "example": "2555646", + "homepage": "http://www.ubio.org", + "mappings": { + "biocontext": "UBIO.NAMEBANK", + "miriam": "ubio.namebank", + "n2t": "ubio.namebank" + }, + "name": "uBio NameBank", + "pattern": "^\\d+$", + "preferred_prefix": "ubio.namebank", + "uri_format": "http://www.ubio.org/browser/details.php?namebankID=$1" + }, + "ubprop": { + "comment": "All of these are typedefs in uberon now", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "name": "Uberon Property", + "preferred_prefix": "ubprop", + "synonyms": [ + "UBPROP", + "UBREL" + ] + }, + "ucas": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An identifier for institutions in the United Kingdom, used in GRID and ROR.", + "example": "N21", + "homepage": "https://www.ucas.com", + "keywords": [ + "bibliometrics", + "institution" + ], + "name": "UK Universities and Colleges Admissions Service", + "pattern": "^\\w\\d+$", + "preferred_prefix": "ucas" + }, + "ucsc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.", + "example": "uc001rvw.5", + "homepage": "https://genome.ucsc.edu/", + "mappings": { + "biocontext": "UCSC", + "uniprot": "DB-0139", + "wikidata": "P2576" + }, + "name": "UCSC Genome Browser", + "preferred_prefix": "ucsc", + "publications": [ + { + "doi": "10.1093/nar/gky1095", + "pmc": "PMC6323953", + "pubmed": "30407534", + "title": "The UCSC Genome Browser database: 2019 update.", + "year": 2019 + } + ], + "uri_format": "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1" + }, + "ucum": { + "contact": { + "email": "dr.shorthair@pm.me", + "github": "dr-shorthair", + "name": "Simon Cox", + "orcid": "0000-0002-3884-3420" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.", + "example": "aBq", + "example_extras": [ + "/A/s3/cg3/T3", + "/g", + "/m3", + "%", + "Cel.d-1", + "dL/g", + "dlm", + "dlx", + "Em.s-2", + "g.cm-3", + "K2", + "kW/h", + "m/s", + "m.s-2", + "m/s/d", + "mmol.mL-1", + "mol.L-1", + "mol.um", + "ng-1", + "pA", + "ug.mL-1", + "umol.L-1", + "us", + "Wb" + ], + "homepage": "https://ucum.org", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "bartoc": "1895", + "fairsharing": "FAIRsharing.27w8k0", + "hl7": "2.16.840.1.113883.6.8" + }, + "name": "Unified Code for Units of Measure", + "preferred_prefix": "ucum", + "publications": [ + { + "doi": "10.1136/jamia.1999.0060151", + "pmc": "PMC61354", + "pubmed": "10094068", + "title": "Units of measure in clinical information systems.", + "year": 1999 + } + ], + "references": [ + "https://units-of-measurement.org/" + ], + "repository": "https://github.com/ucum-org/ucum", + "uri_format": "https://units-of-measurement.org/$1" + }, + "ukprn": { + "comment": "Added because of appearance in ROR", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "identifier for an educational organization issued by the UK Register of Learning Providers", + "example": "10007835", + "homepage": "https://www.ukrlp.co.uk", + "mappings": { + "wikidata": "P4971" + }, + "name": "UK Provider Reference Number", + "pattern": "^[1-9]\\d*$", + "preferred_prefix": "ukprn", + "synonyms": [ + "ukprns" + ], + "uri_format": "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L" + }, + "umbbd.compound": { + "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information.", + "example": "c0001", + "homepage": "http://umbbd.ethz.ch/", + "mappings": { + "biocontext": "UMBBD.COMPOUND", + "miriam": "umbbd.compound", + "n2t": "umbbd.compound", + "wikidata": "P8121" + }, + "name": "UM-BBD compound", + "part_of": "umbbd", + "pattern": "^c\\d+$", + "preferred_prefix": "umbbd.compound", + "synonyms": [ + "UM-BBD_compID" + ], + "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1" + }, + "umbbd.enzyme": { + "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information.", + "example": "e0333", + "homepage": "http://umbbd.ethz.ch/", + "mappings": { + "biocontext": "UMBBD.ENZYME", + "go": "UM-BBD_enzymeID", + "miriam": "umbbd.enzyme", + "n2t": "umbbd.enzyme" + }, + "name": "EAWAG Biocatalysis/Biodegradation Database", + "part_of": "umbbd", + "pattern": "^e\\d+$", + "preferred_prefix": "umbbd.enzyme", + "synonyms": [ + "UM-BBD_enzymeID" + ], + "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1" + }, + "umbbd.pathway": { + "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information.", + "example": "ala", + "homepage": "http://umbbd.ethz.ch/", + "mappings": { + "biocontext": "UMBBD.PATHWAY", + "go": "UM-BBD_pathwayID", + "miriam": "umbbd.pathway", + "n2t": "umbbd.pathway" + }, + "name": "EAWAG Biocatalysis/Biodegradation Database", + "part_of": "umbbd", + "pattern": "^\\w+$", + "preferred_prefix": "umbbd.pathway", + "providers": [ + { + "code": "eawag", + "description": "Graphical depiction of pathway", + "homepage": "http://eawag-bbd.ethz.ch", + "name": "Pathway map diagram", + "uri_format": "http://eawag-bbd.ethz.ch/$1/$1_map.html" + } + ], + "synonyms": [ + "UM-BBD_pathwayID" + ], + "uri_format": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1" + }, + "umbbd.reaction": { + "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information.", + "example": "r0001", + "homepage": "http://umbbd.ethz.ch/", + "mappings": { + "biocontext": "UMBBD.REACTION", + "go": "UM-BBD_reactionID", + "miriam": "umbbd.reaction", + "n2t": "umbbd.reaction" + }, + "name": "EAWAG Biocatalysis/Biodegradation Database", + "part_of": "umbbd", + "pattern": "^r\\d+$", + "preferred_prefix": "umbbd.reaction", + "synonyms": [ + "UM-BBD_reactionID" + ], + "uri_format": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1" + }, + "umbbd.rule": { + "description": "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules.", + "example": "bt0001", + "homepage": "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules", + "mappings": { + "biocontext": "UMBBD.RULE", + "go": "UM-BBD_ruleID", + "miriam": "umbbd.rule", + "n2t": "umbbd.rule" + }, + "name": "EAWAG Biocatalysis/Biodegradation Database", + "part_of": "umbbd", + "pattern": "^bt\\d+$", + "preferred_prefix": "umbbd.rule", + "synonyms": [ + "UM-BBD_ruleID" + ], + "uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1" + }, + "umls": { + "description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.", + "example": "C2584994", + "homepage": "https://www.nlm.nih.gov/research/umls", + "mappings": { + "bartoc": "20052", + "biocontext": "UMLS", + "edam": "1181", + "hl7": "2.16.840.1.113883.6.86", + "miriam": "umls", + "n2t": "umls", + "wikidata": "P2892" + }, + "name": "Unified Medical Language System Concept Unique Identifier", + "pattern": "^C\\d+$", + "preferred_prefix": "umls", + "synonyms": [ + "UMLS", + "UMLS CUI", + "UMLS_CUI", + "umls.cui" + ], + "uri_format": "http://linkedlifedata.com/resource/umls/id/$1" + }, + "umls.aui": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus.", + "example": "A0118748", + "homepage": "https://www.nlm.nih.gov/research/umls", + "name": "Unified Medical Language System Atomic Unique Identifier", + "pattern": "^A\\d+$", + "preferred_prefix": "umls.aui", + "synonyms": [ + "UMLS_ICD9CM_2005_AUI" + ] + }, + "unichem": { + "description": "identifier of a compound in the UniChem database", + "example": "161671", + "homepage": "https://chembl.gitbook.io/unichem/downloads", + "mappings": { + "wikidata": "P11089" + }, + "name": "UniChem compound", + "pattern": "^\\d+$", + "preferred_prefix": "unichem", + "uri_format": "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1" + }, + "unigene": { + "deprecated": true, + "description": "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.", + "example": "4900", + "homepage": "http://www.ncbi.nlm.nih.gov/unigene", + "keywords": [ + "dna", + "gene", + "gene expression", + "life science", + "protein" + ], + "mappings": { + "biocontext": "UNIGENE", + "fairsharing": "FAIRsharing.ge1c3p", + "miriam": "unigene", + "n2t": "unigene", + "prefixcommons": "unigene", + "re3data": "r3d100010774" + }, + "name": "UniGene", + "pattern": "^\\d+$", + "preferred_prefix": "unigene", + "publications": [ + { + "doi": "10.1093/nar/gkg033", + "pmc": "PMC165480", + "pubmed": "12519941", + "title": "Database resources of the National Center for Biotechnology.", + "year": 2003 + } + ], + "uri_format": "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1" + }, + "unii": { + "description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.", + "example": "3G6A5W338E", + "homepage": "https://precision.fda.gov/uniisearch", + "mappings": { + "biocontext": "UNII", + "cheminf": "000563", + "miriam": "unii", + "n2t": "unii", + "wikidata": "P652" + }, + "name": "Unique Ingredient Identifier", + "pattern": "^[A-Z0-9]+$", + "preferred_prefix": "unii", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "UNII at U.S. Food and Drug Administration", + "homepage": "http://fdasis.nlm.nih.gov/srs/", + "name": "UNII at U.S. Food and Drug Administration", + "uri_format": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1" + } + ], + "uri_format": "https://precision.fda.gov/uniisearch/srs/unii/$1" + }, + "unimod": { + "description": "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide).", + "download_owl": "http://www.unimod.org/obo/unimod.obo", + "example": "1200", + "homepage": "http://www.unimod.org/", + "keywords": [ + "bioinformatics", + "ontology" + ], + "mappings": { + "biocontext": "UNIMOD", + "edam": "3757", + "fairsharing": "FAIRsharing.zZHCUQ", + "miriam": "unimod", + "n2t": "unimod", + "ols": "unimod" + }, + "name": "Unimod protein modification database for mass spectrometry", + "pattern": "^\\d+$", + "preferred_prefix": "unimod", + "publications": [ + { + "doi": "10.1002/pmic.200300744", + "pmc": null, + "pubmed": "15174123", + "title": "Unimod: Protein modifications for mass spectrometry.", + "year": 2004 + } + ], + "uri_format": "http://www.unimod.org/modifications_view.php?editid1=$1" + }, + "uniparc": { + "description": "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases.", + "example": "UPI000000000A", + "homepage": "https://www.ebi.ac.uk/uniparc/", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "biocontext": "UNIPARC", + "edam": "2392", + "go": "UniParc", + "miriam": "uniparc", + "n2t": "uniparc", + "prefixcommons": "uniparc", + "re3data": "r3d100011519" + }, + "name": "UniProt Archive", + "pattern": "^UPI[A-F0-9]{10}$", + "preferred_prefix": "uniparc", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "UniParc through UniProt", + "homepage": "http://www.uniprot.org/uniparc/", + "name": "UniParc through UniProt", + "uri_format": "https://www.uniprot.org/uniparc/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkh131", + "pmc": "PMC308865", + "pubmed": "14681372", + "title": "UniProt: the Universal Protein knowledgebase.", + "year": 2004 + } + ], + "uri_format": "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1" + }, + "unipathway.compound": { + "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.", + "example": "UPC04349", + "homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", + "mappings": { + "biocontext": "UNIPATHWAY.COMPOUND", + "miriam": "unipathway.compound", + "n2t": "unipathway.compound" + }, + "name": "UniPathway Compound", + "pattern": "^UPC\\d{5}$", + "preferred_prefix": "unipathway.compound", + "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1" + }, + "unipathway.reaction": { + "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.", + "example": "UCR00226", + "homepage": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", + "mappings": { + "biocontext": "UNIPATHWAY.REACTION", + "miriam": "unipathway.reaction", + "n2t": "unipathway.reaction" + }, + "name": "UniPathway Reaction", + "pattern": "^UCR\\d{5}$", + "preferred_prefix": "unipathway.reaction", + "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1" + }, + "uniprot": { + "description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.", + "example": "P0DP23", + "homepage": "http://www.uniprot.org", + "keywords": [ + "biology", + "protein" + ], + "mappings": { + "aberowl": "UP", + "biocontext": "UniProtKB", + "biolink": "UniProtKB", + "cellosaurus": "UniProtKB", + "edam": "3021", + "fairsharing": "FAIRsharing.wf28wm", + "go": "UniProtKB", + "miriam": "uniprot", + "n2t": "uniprot", + "ncbi": "UniProt", + "prefixcommons": "uniprot", + "re3data": "r3d100011521", + "wikidata": "P352" + }, + "name": "UniProt Protein", + "pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$", + "preferred_prefix": "uniprot", + "providers": [ + { + "code": "indra", + "description": "A large scale database of biomedical statements.", + "homepage": "https://db.indra.bio", + "name": "INDRA Database", + "uri_format": "https://db.indra.bio/statements/from_agents?&format=html&agent0=$1@UP" + }, + { + "code": "iptmnet", + "description": "Protein post translational modification information", + "homepage": "https://research.bioinformatics.udel.edu/iptmnet", + "name": "iPTMnet", + "uri_format": "https://research.bioinformatics.udel.edu/iptmnet/entry/$1" + }, + { + "code": "ncbi", + "description": "UniProt through NCBI", + "homepage": "https://www.ncbi.nlm.nih.gov/protein/", + "name": "UniProt through NCBI", + "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" + }, + { + "code": "oma", + "description": "The OMA project is a method and database for the inference of orthologs among complete genomes.", + "homepage": "https://omabrowser.org/oma/home/", + "name": "Orthologous Matrix Browser", + "uri_format": "http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p2=orthologs&p1=$1" + }, + { + "code": "omnipath", + "description": "Molecular interations endpoint from OmniPathDB", + "homepage": "https://omnipathdb.org/", + "name": "OmniPathDB", + "uri_format": "https://omnipathdb.org/interactions/?fields=sources,references&partners=$1" + }, + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/uniprot/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkj161", + "pmc": "PMC1347523", + "pubmed": "16381842", + "title": "The Universal Protein Resource (UniProt): an expanding universe of protein information.", + "year": 2006 + } + ], + "synonyms": [ + "SwissProt", + "UP", + "UniProt", + "UniProtKB", + "Uniprot ID", + "uniprot/swiss-prot" + ], + "uri_format": "https://purl.uniprot.org/uniprot/$1" + }, + "uniprot.arba": { + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system.", + "example": "ARBA00000001", + "github_request_issue": 620, + "homepage": "https://www.uniprot.org/arba", + "name": "Association-Rule-Based Annotator", + "pattern": "^ARBA\\d+$", + "preferred_prefix": "uniprot.arba", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "arba" + ], + "uri_format": "https://www.uniprot.org/arba/$1" + }, + "uniprot.chain": { + "description": "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein.", + "example": "PRO_0000016681", + "homepage": "https://www.uniprot.org", + "mappings": { + "miriam": "uniprot.chain" + }, + "name": "UniProt Chain", + "part_of": "uniprot", + "pattern": "^PRO_[0-9]{10}$", + "preferred_prefix": "uniprot.chain", + "synonyms": [ + "UPPRO" + ], + "uri_format": "http://purl.uniprot.org/annotation/$1" + }, + "uniprot.disease": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.", + "download_obo": "https://www.uniprot.org/diseases/?query=*&format=obo", + "example": "DI-04240", + "homepage": "https://www.uniprot.org/diseases/", + "keywords": [ + "ontology" + ], + "mappings": { + "biolink": "SPDI", + "wikidata": "P11430" + }, + "name": "UniProt Diseases", + "part_of": "uniprot", + "pattern": "^DI-\\d{5}$", + "preferred_prefix": "uniprot.disease", + "synonyms": [ + "DI", + "SP_DI" + ], + "uri_format": "https://www.uniprot.org/diseases/$1" + }, + "uniprot.isoform": { + "description": "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information.", + "example": "Q5BJF6-3", + "homepage": "http://www.uniprot.org/", + "mappings": { + "biocontext": "UNIPROT.ISOFORM", + "biolink": "UNIPROT.ISOFORM", + "miriam": "uniprot.isoform", + "n2t": "uniprot.isoform" + }, + "name": "UniProt Isoform", + "part_of": "uniprot", + "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$", + "preferred_prefix": "uniprot.isoform", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "UniProt Isoform through Universal Protein Resource using Persistent URL system", + "homepage": "http://purl.uniprot.org/", + "name": "UniProt Isoform through Universal Protein Resource using Persistent URL system", + "uri_format": "http://purl.uniprot.org/uniprot/$1" + }, + { + "code": "CURATOR_REVIEW", + "description": "UniProt Isoform through UniParc", + "homepage": "http://www.uniprot.org/uniparc/", + "name": "UniProt Isoform through UniParc", + "uri_format": "http://www.uniprot.org/uniparc/?query=$1" + }, + { + "code": "obo.1", + "description": "This incorrect encoding was found inside IDO-COVID-19", + "homepage": "http://purl.obolibrary.org", + "name": "Nonstandard OBO PURL", + "uri_format": "http://purl.obolibrary.org/obo/UniProtKB_$1" + } + ], + "synonyms": [ + "UPISO" + ], + "uri_format": "http://purl.uniprot.org/isoforms/$1" + }, + "uniprot.journal": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "identifier for a scientific journal, in the UniProt database", + "example": "3546", + "homepage": "https://www.uniprot.org/journals", + "mappings": { + "wikidata": "P4616" + }, + "name": "UniProt journal", + "pattern": "^\\d{4}$", + "preferred_prefix": "uniprot.journal", + "uri_format": "https://www.uniprot.org/journals/$1" + }, + "uniprot.keyword": { + "description": "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.", + "download_obo": "https://www.uniprot.org/keywords/?format=obo", + "example": "KW-1273", + "homepage": "http://www.uniprot.org/keywords/", + "keywords": [ + "classification", + "ontology" + ], + "mappings": { + "go": "UniProtKB-KW", + "prefixcommons": "uniprot.kw" + }, + "name": "UniProt Keywords", + "part_of": "uniprot", + "pattern": "^KW-\\d{4}$", + "preferred_prefix": "uniprot.keyword", + "synonyms": [ + "SP_KW", + "UniProtKB-KW", + "uniprot.keyword", + "uniprot.kw" + ], + "uri_format": "https://www.uniprot.org/keywords/$1" + }, + "uniprot.location": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms.", + "download_obo": "https://www.uniprot.org/locations/?query=*&format=obo", + "example": "SL-0002", + "homepage": "https://www.uniprot.org/locations/", + "keywords": [ + "ontology" + ], + "mappings": { + "go": "UniProtKB-SubCell" + }, + "name": "UniProt Subcellular Locations", + "part_of": "uniprot", + "pattern": "^SL-\\d+$", + "preferred_prefix": "uniprot.location", + "synonyms": [ + "SP_SL", + "UPLOC", + "UniProtKB-SubCell" + ], + "uri_format": "https://www.uniprot.org/locations/$1" + }, + "uniprot.proteome": { + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "UniProt provides proteome sets of proteins whose genomes have been completely sequenced.", + "example": "UP000005640", + "homepage": "https://www.uniprot.org/proteomes", + "name": "UniProt Proteomes", + "part_of": "uniprot", + "pattern": "^UP\\d{9}$", + "preferred_prefix": "uniprot.proteome", + "references": [ + "https://github.com/biopragmatics/bioregistry/pull/604" + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.uniprot.org/proteomes/$1" + }, + "uniprot.ptm": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "contributor_extras": [ + { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + } + ], + "description": "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format", + "example": "PTM-0450", + "homepage": "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist", + "keywords": [ + "biochemistry", + "post-translational modification", + "structural biology" + ], + "name": "UniProt Post-Translational Modification", + "part_of": "uniprot", + "pattern": "^PTM-\\d{4}$", + "preferred_prefix": "uniprot.ptm", + "references": [ + "https://twitter.com/cthoyt/status/1510570256619778053", + "https://www.uniprot.org/docs/ptmlist.txt" + ], + "synonyms": [ + "PTM" + ], + "uri_format": "https://biopragmatics.github.io/providers/uniprot.ptm/$1" + }, + "uniprot.resource": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources.", + "example": "DB-0174", + "homepage": "https://www.uniprot.org/database/", + "name": "UniProt Resource", + "part_of": "uniprot", + "pattern": "^DB-\\d{4}$", + "preferred_prefix": "uniprot.resource", + "synonyms": [ + "uniprot.database", + "uniprot.db" + ], + "uri_format": "https://www.uniprot.org/database/$1" + }, + "uniprot.tissue": { + "description": "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified.", + "example": "TS-0285", + "homepage": "https://www.uniprot.org/docs/tisslist.txt", + "mappings": { + "biocontext": "TISSUELIST", + "miriam": "tissuelist", + "n2t": "tissuelist" + }, + "name": "Tissue List", + "part_of": "uniprot", + "pattern": "^TS-\\d{4}$", + "preferred_prefix": "uniprot.tissue", + "uri_format": "https://www.uniprot.org/tissues/$1" + }, + "uniprot.var": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species.", + "example": "068078", + "homepage": "https://web.expasy.org/variant_pages", + "name": "UniProt Variants", + "part_of": "uniprot", + "pattern": "^\\d+$", + "preferred_prefix": "uniprot.var", + "providers": [ + { + "code": "expasy", + "description": "Expasy external page for protein variant", + "homepage": "https://web.expasy.org/variant_pages", + "name": "ExPaSy", + "uri_format": "https://web.expasy.org/variant_pages/VAR_$1.html" + } + ], + "synonyms": [ + "SP_VAR", + "UPVAR", + "UniProtKB_VAR" + ], + "uri_format": "http://purl.uniprot.org/annotation/VAR_$1" + }, + "uniref": { + "description": "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.", + "example": "UniRef90_P00750", + "homepage": "https://www.uniprot.org/", + "mappings": { + "edam": "2346", + "miriam": "uniref", + "re3data": "r3d100011518" + }, + "name": "UniRef", + "pattern": "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$", + "preferred_prefix": "uniref", + "uri_format": "https://www.uniprot.org/uniref/$1" + }, + "unirule": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites.", + "example": "UR000124451", + "homepage": "https://www.uniprot.org/unirule/", + "mappings": { + "go": "UniRule" + }, + "name": "UniRule", + "preferred_prefix": "unirule", + "uri_format": "https://www.uniprot.org/unirule/$1" + }, + "unists": { + "description": "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.", + "example": "456789", + "homepage": "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists", + "keywords": [ + "gene", + "protein" + ], + "mappings": { + "biocontext": "UNISTS", + "edam": "2389", + "miriam": "unists", + "n2t": "unists", + "ncbi": "UniSTS", + "prefixcommons": "unists" + }, + "name": "Database of Sequence Tagged Sites", + "pattern": "^\\d+$", + "preferred_prefix": "unists", + "uri_format": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1" + }, + "unite": { + "contact": { + "email": "urmas.koljalg@ut.ee", + "github": null, + "name": "Urmas Kõljalg", + "orcid": "0000-0002-5171-1668" + }, + "description": "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa.", + "example": "UDB000691", + "homepage": "http://unite.ut.ee/", + "keywords": [ + "biodiversity", + "bioinformatics", + "dna", + "ecology", + "genomics", + "metagenomics", + "taxonomy" + ], + "mappings": { + "biocontext": "UNITE", + "edam": "2390", + "fairsharing": "FAIRsharing.cnwx8c", + "miriam": "unite", + "n2t": "unite", + "ncbi": "UNITE", + "prefixcommons": "unite", + "re3data": "r3d100011316" + }, + "name": "Molecular database for the identification of fungi", + "pattern": "^UDB\\d{6}$", + "preferred_prefix": "unite", + "publications": [ + { + "doi": "10.1111/j.1469-8137.2009.03160.x", + "pmc": null, + "pubmed": "20409185", + "title": "The UNITE database for molecular identification of fungi--recent updates and future perspectives.", + "year": 2010 + } + ], + "uri_format": "http://unite.ut.ee/bl_forw.php?nimi=$1" + }, + "unpd": { + "comment": "The website is dead, there are no places to get the source information except inside https://oolonek.github.io/ISDB/.", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "homepage": "http://pkuxxj.pku.edu.cn/UNPD/", + "name": "Universal Natural Products Database", + "preferred_prefix": "unpd", + "publications": [ + { + "doi": "10.1021/acs.jnatprod.6b01093", + "pmc": null, + "pubmed": "28616931", + "title": "Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments.", + "year": 2017 + }, + { + "doi": "10.1371/journal.pone.0062839", + "pmc": "PMC3636197", + "pubmed": "23638153", + "title": "Use of natural products as chemical library for drug discovery and network pharmacology.", + "year": 2013 + } + ], + "references": [ + "http://bioinf-applied.charite.de/supernatural_new/index.php?site=vendor_info&id=Universal%20Natural%20Products%20Database", + "https://pharmacognosy.in/the-universal-natural-products-database-unpd/", + "https://oolonek.github.io/ISDB/" + ] + }, + "uo": { + "appears_in": [ + "agro", + "ms", + "rbo", + "scdo" + ], + "banana": "UO", + "contact": { + "email": "g.gkoutos@gmail.com", + "github": "gkoutos", + "name": "George Gkoutos", + "orcid": "0000-0002-2061-091X" + }, + "description": "Ontology of standardized units", + "download_obo": "http://purl.obolibrary.org/obo/uo.obo", + "download_owl": "http://purl.obolibrary.org/obo/uo.owl", + "example": "0000080", + "homepage": "https://github.com/bio-ontology-research-group/unit-ontology", + "keywords": [ + "life science", + "mathematics", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "UO", + "biocontext": "UO", + "bioportal": "UO", + "fairsharing": "FAIRsharing.mjnypw", + "miriam": "uo", + "n2t": "uo", + "obofoundry": "uo", + "ols": "uo", + "ontobee": "UO", + "prefixcommons": "uo" + }, + "name": "Units of measurement ontology", + "namespace_in_lui": true, + "pattern": "^\\d{7}$", + "preferred_prefix": "UO", + "publications": [ + { + "doi": "10.1093/database/bas033", + "pmc": "PMC3468815", + "pubmed": "23060432", + "title": "The Units Ontology: a tool for integrating units of measurement in science.", + "year": 2012 + } + ], + "repository": "https://github.com/bio-ontology-research-group/unit-ontology", + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1" + }, + "upa": { + "contact": { + "email": "Anne.Morgat@sib.swiss", + "github": "amorgat", + "name": "Anne Morgat", + "orcid": "0000-0002-1216-2969" + }, + "depends_on": [ + "ro" + ], + "deprecated": true, + "description": "A manually curated resource for the representation and annotation of metabolic pathways", + "download_obo": "https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo", + "download_owl": "http://purl.obolibrary.org/obo/upa.owl", + "example": "UCR00513", + "homepage": "https://github.com/geneontology/unipathway", + "keywords": [ + "obo", + "ontology", + "pathway" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "UPA", + "biocontext": "UNIPATHWAY", + "bioportal": "UPA", + "edam": "2645", + "go": "UniPathway", + "obofoundry": "upa", + "ols": "upa", + "ontobee": "UPA", + "prefixcommons": "unipathway" + }, + "name": "Unipathway", + "pattern": "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$", + "preferred_prefix": "UPA", + "publications": [ + { + "doi": "10.1093/nar/gkr1023", + "pmc": "PMC3245108", + "pubmed": "22102589", + "title": "UniPathway: a resource for the exploration and annotation of metabolic pathways.", + "year": 2011 + } + ], + "repository": "https://github.com/geneontology/unipathway", + "synonyms": [ + "UPa", + "unipathway", + "unipathway.pathway" + ], + "uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1", + "version": "2018-12-12" + }, + "upheno": { + "contact": { + "email": "vasilevs@ohsu.edu", + "github": "nicolevasilevsky", + "name": "Nicole Vasilevsky", + "orcid": "0000-0001-5208-3432" + }, + "description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.", + "download_json": "https://github.com/obophenotype/upheno/blob/master/upheno.json", + "download_obo": "https://github.com/obophenotype/upheno/blob/master/upheno.obo", + "download_owl": "https://github.com/obophenotype/upheno/blob/master/upheno.owl", + "homepage": "https://github.com/obophenotype/upheno", + "keywords": [ + "evolutionary biology", + "obo", + "ontology", + "phenomics" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "UPHENO", + "biocontext": "UPHENO", + "bioportal": "UPHENO", + "fairsharing": "FAIRsharing.r41qhx", + "obofoundry": "upheno", + "ols": "upheno", + "ontobee": "UPHENO" + }, + "name": "Unified Phenotype Ontology", + "no_own_terms": true, + "preferred_prefix": "UPHENO", + "repository": "https://github.com/obophenotype/upheno", + "uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", + "version": "2017-10-31" + }, + "uspto": { + "comment": "Information about the regular expression was derived from examples at https://patft.uspto.gov/netahtml/PTO/srchnum.htm. TODO, make the regular expression work for '100000000'", + "contributor_extras": [ + { + "email": null, + "github": "dhimmel", + "name": "Daniel Himmelstein", + "orcid": "0000-0002-3012-7446" + } + ], + "description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.", + "example": "4145692", + "example_extras": [ + "10,000,000", + "6923014", + "0000001", + "D000152", + "PP07514", + "RE12345", + "T855019", + "H001234", + "AI00007", + "X000001", + "RX00001" + ], + "homepage": "http://patft.uspto.gov/netahtml/PTO/index.html", + "mappings": { + "biocontext": "USPTO", + "miriam": "uspto", + "n2t": "uspto" + }, + "name": "United States Patent and Trademark Office", + "pattern": "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$", + "preferred_prefix": "uspto", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/253" + ], + "uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1" + }, + "vac": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs.", + "example": "15", + "homepage": "https://vac.niaid.nih.gov", + "keywords": [ + "biology", + "immunology", + "vaccines" + ], + "name": "Vaccine Adjuvant Compendium", + "pattern": "^\\d+$", + "preferred_prefix": "vac", + "uri_format": "https://vac.niaid.nih.gov/view?id=$1" + }, + "validatordb": { + "contact": { + "email": "david.sehnal@gmail.com", + "github": null, + "name": "David Sehnal", + "orcid": "0000-0002-0682-3089" + }, + "description": "Database of validation results for ligands and non-standard residues in the Protein Data Bank.", + "example": "2h6o", + "homepage": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/", + "keywords": [ + "life science" + ], + "mappings": { + "biocontext": "VALIDATORDB", + "fairsharing": "FAIRsharing.c9psgb", + "miriam": "validatordb", + "n2t": "validatordb" + }, + "name": "ValidatorDB", + "pattern": "^[A-Za-z0-9\\/]+$", + "preferred_prefix": "validatordb", + "provides": "pdb", + "publications": [ + { + "doi": "10.1093/nar/gku1118", + "pmc": "PMC4383933", + "pubmed": "25392418", + "title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.", + "year": 2014 + } + ], + "uri_format": "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1" + }, + "vandf": { + "contact": { + "email": "michael.lincoln@med.va.gov", + "github": null, + "name": "Michael Lincoln", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ", + "example": "4019477", + "homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF", + "keywords": [ + "biomedical science", + "ontology", + "pharmacology" + ], + "mappings": { + "aberowl": "VANDF", + "biolink": "VANDF", + "bioportal": "VANDF", + "fairsharing": "FAIRsharing.xn3pb3", + "hl7": "2.16.840.1.113883.6.229" + }, + "name": "Veterans Administration National Drug File", + "pattern": "^\\d+$", + "preferred_prefix": "vandf", + "publications": [ + { + "doi": null, + "pmc": "PMC2244318", + "pubmed": "12463886", + "title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF.", + "year": 2002 + } + ], + "uri_format": "http://purl.bioontology.org/ontology/VANDF/$1" + }, + "vann": { + "contact": { + "email": "nospam@iandavis.com", + "github": "iand", + "name": "Ian Davis", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.", + "example": "usageNote", + "homepage": "https://vocab.org/vann/", + "name": "A vocabulary for annotating vocabulary descriptions", + "preferred_prefix": "vann", + "uri_format": "https://vocab.org/vann/$1" + }, + "vario": { + "banana": "VariO", + "contact": { + "email": "mauno.vihinen@med.lu.se", + "github": "maunov", + "name": "Mauno Vihinen", + "orcid": "0000-0002-9614-7976" + }, + "deprecated": true, + "description": "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level.", + "download_obo": "http://purl.obolibrary.org/obo/vario.obo", + "download_owl": "http://purl.obolibrary.org/obo/vario.owl", + "example": "0376", + "homepage": "http://variationontology.org", + "keywords": [ + "genetics", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "VARIO", + "agroportal": "VARIO", + "biocontext": "VARIO", + "bioportal": "VARIO", + "fairsharing": "FAIRsharing.65xkbs", + "miriam": "vario", + "n2t": "vario", + "obofoundry": "vario", + "ols": "vario", + "ontobee": "VariO" + }, + "name": "Variation Ontology", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "VariO", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "VariO at Lund University", + "homepage": "http://www.variationontology.org/", + "name": "VariO at Lund University", + "uri_format": "http://www.ontobee.org/search?ontology=VariO&keywords=VariO_$1&submit=Search+terms" + } + ], + "publications": [ + { + "doi": "10.1186/s12864-018-5262-0", + "pmc": "PMC6309100", + "pubmed": "30591019", + "title": "Systematics for types and effects of DNA variations.", + "year": 2018 + }, + { + "doi": "10.1002/humu.22954", + "pmc": null, + "pubmed": "26773573", + "title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology.", + "year": 2016 + }, + { + "doi": "10.1007/s00439-015-1529-6", + "pmc": null, + "pubmed": "25616435", + "title": "Types and effects of protein variations.", + "year": 2015 + }, + { + "doi": "10.1186/2041-1480-5-9", + "pmc": "PMC3931275", + "pubmed": "24533660", + "title": "Variation ontology: annotator guide.", + "year": 2014 + }, + { + "doi": "10.1101/gr.157495.113", + "pmc": "PMC3912426", + "pubmed": "24162187", + "title": "Variation Ontology for annotation of variation effects and mechanisms.", + "year": 2013 + } + ], + "uri_format": "http://purl.obolibrary.org/obo/VARIO_$1", + "version": "2018-11-09" + }, + "vbase2": { + "contact": { + "email": "wmueller@gbf.de", + "github": null, + "name": "Werner Müller", + "orcid": "0000-0002-1297-9725" + }, + "description": "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes.", + "example": "humIGHV025", + "homepage": "http://www.vbase2.org/vbase2.php", + "keywords": [ + "gene", + "life science" + ], + "mappings": { + "biocontext": "VBASE2", + "fairsharing": "FAIRsharing.qvxhb1", + "miriam": "vbase2", + "n2t": "vbase2", + "ncbi": "VBASE2", + "prefixcommons": "vbase2" + }, + "name": "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse", + "pattern": "^\\w+$", + "preferred_prefix": "vbase2", + "publications": [ + { + "doi": "10.1093/nar/gki088", + "pmc": "PMC540042", + "pubmed": "15608286", + "title": "VBASE2, an integrative V gene database.", + "year": 2005 + } + ], + "uri_format": "http://www.vbase2.org/vgene.php?id=$1" + }, + "vbo": { + "contact": { + "email": "Sabrina@tislab.org", + "github": "sabrinatoro", + "name": "Sabrina Toro", + "orcid": "0000-0002-4142-7153" + }, + "depends_on": [ + "ncbitaxon" + ], + "description": "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names.", + "download_json": "http://purl.obolibrary.org/obo/vbo.json", + "download_obo": "http://purl.obolibrary.org/obo/vbo.obo", + "download_owl": "http://purl.obolibrary.org/obo/vbo.owl", + "example": "0000038", + "homepage": "https://github.com/monarch-initiative/vertebrate-breed-ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "VBO", + "obofoundry": "vbo", + "ols": "vbo", + "ontobee": "VBO" + }, + "name": "Vertebrate Breed Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "VBO", + "repository": "https://github.com/monarch-initiative/vertebrate-breed-ontology", + "uri_format": "http://purl.obolibrary.org/obo/VBO_$1", + "version": "2022-10-31" + }, + "vbrc": { + "description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.", + "example": "35742", + "homepage": "http://vbrc.org/", + "mappings": { + "biocontext": "VBRC", + "miriam": "vbrc", + "n2t": "vbrc", + "prefixcommons": "vbrc" + }, + "name": "Viral Bioinformatics Resource Center", + "pattern": "^\\d+$", + "preferred_prefix": "vbrc", + "uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1" + }, + "vcell": { + "description": "Models developed with the Virtual Cell (VCell) software prorgam.", + "example": "201022999", + "homepage": "https://health.uconn.edu/", + "mappings": { + "miriam": "vcell" + }, + "name": "VCell Published Models", + "pattern": "^\\d{5,}$", + "preferred_prefix": "vcell", + "uri_format": "https://vcell.org/biomodel-$1" + }, + "vectorbase": { + "description": "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis.", + "example": "ISCW007415", + "homepage": "https://www.vectorbase.org/", + "keywords": [ + "comparative genomics", + "functional genomics", + "gene", + "genome", + "genomics", + "population dynamics", + "population genetics", + "protein" + ], + "mappings": { + "biocontext": "VECTORBASE", + "fairsharing": "FAIRsharing.3etvdn", + "miriam": "vectorbase", + "n2t": "vectorbase", + "ncbi": "VectorBase", + "prefixcommons": "vectorbase", + "re3data": "r3d100010880" + }, + "name": "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens", + "pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$", + "preferred_prefix": "vectorbase", + "providers": [ + { + "code": "vectorbase.alt1", + "description": "An alternate provider based on the search functionality", + "homepage": "https://www.vectorbase.org", + "name": "Vectorbase Alt. 1", + "uri_format": "https://www.vectorbase.org/search/site/$1?&site=\"Genome\"" + }, + { + "code": "vectorbase.alt2", + "description": "An alternate provider based on the app structure", + "homepage": "https://www.vectorbase.org", + "name": "Vectorbase Alt. 2", + "uri_format": "https://vectorbase.org/vectorbase/app/record/gene/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gku1117", + "pmc": "PMC4383932", + "pubmed": "25510499", + "title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gkn857", + "pmc": "PMC2686483", + "pubmed": "19028744", + "title": "VectorBase: a data resource for invertebrate vector genomics.", + "year": 2008 + } + ], + "twitter": "VectorBase", + "uri_format": "https://vectorbase.org/gene/$1" + }, + "vega": { + "contact": { + "email": "jla1@sanger.ac.uk", + "github": null, + "name": "Jennifer L Harrow", + "orcid": "0000-0003-0338-3070" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes.", + "example": "OTTHUMG00000169812", + "homepage": "https://vega.archive.ensembl.org/index.html", + "keywords": [ + "genome", + "life science" + ], + "mappings": { + "fairsharing": "FAIRsharing.mr293q", + "prefixcommons": "vega", + "re3data": "r3d100012575" + }, + "name": "Vertebrate Genome Annotation Database", + "preferred_prefix": "vega", + "publications": [ + { + "doi": "10.1093/nar/gkt1241", + "pmc": "PMC3964964", + "pubmed": "24316575", + "title": "The Vertebrate Genome Annotation browser 10 years on.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkm987", + "pmc": "PMC2238886", + "pubmed": "18003653", + "title": "The vertebrate genome annotation (Vega) database.", + "year": 2007 + } + ], + "synonyms": [ + "VEGA" + ], + "uri_format": "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1" + }, + "vegbank": { + "description": "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. ", + "example": "VB.Ob.3736.GRSM125", + "homepage": "http://vegbank.org/", + "mappings": { + "miriam": "vegbank", + "re3data": "r3d100010153" + }, + "name": "VegBank", + "pattern": "^VB\\.[A-Za-z][A-Za-z]\\..*$", + "preferred_prefix": "vegbank", + "uri_format": "http://vegbank.org/cite/$1" + }, + "venom": { + "appears_in": [ + "vbo" + ], + "contact": { + "email": "DBrodbelt@RVC.AC.UK", + "github": null, + "name": "David Brodbelt", + "orcid": "0000-0001-5628-4194" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems.", + "example": "12969", + "homepage": "https://venomcoding.org/", + "name": "Veterinary Nomenclature", + "pattern": "^\\d+$", + "preferred_prefix": "VeNom", + "proprietary": true, + "references": [ + "https://github.com/biopragmatics/bioregistry/pull/724" + ] + }, + "vfb": { + "contact": { + "email": "r.court@ed.ac.uk", + "github": null, + "name": "Robert Court", + "orcid": "0000-0002-0173-9080" + }, + "description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.", + "example": "00000001", + "homepage": "https://VirtualFlyBrain.org", + "keywords": [ + "life science", + "neurobiology" + ], + "mappings": { + "fairsharing": "FAIRsharing.nzaz6z", + "miriam": "vfb", + "n2t": "vfb", + "re3data": "r3d100011373" + }, + "name": "Virtual Fly Brain", + "pattern": "^[0-9a-zA-Z]{8}$", + "preferred_prefix": "vfb", + "publications": [ + { + "doi": "doi:10.1186/1471-2105-13-122", + "pmc": "PMC3412715", + "pubmed": "22676296", + "title": "Web tools for large-scale 3D biological images and atlases", + "year": null + }, + { + "doi": "10.1186/1471-2105-13-122", + "pmc": "PMC3412715", + "pubmed": "22676296", + "title": "Web tools for large-scale 3D biological images and atlases.", + "year": 2012 + }, + { + "doi": "10.1093/bioinformatics/bts113", + "pmc": null, + "pubmed": "22402613", + "title": "A strategy for building neuroanatomy ontologies.", + "year": 2012 + }, + { + "doi": "10.1093/bioinformatics/btr677", + "pmc": null, + "pubmed": "22180411", + "title": "The Virtual Fly Brain browser and query interface.", + "year": 2011 + } + ], + "uri_format": "http://virtualflybrain.org/reports/$1" + }, + "vfdb.gene": { + "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.", + "example": "VFG2154", + "homepage": "http://www.mgc.ac.cn/VFs/", + "mappings": { + "biocontext": "VFDB.GENE", + "miriam": "vfdb.gene", + "n2t": "vfdb.gene" + }, + "name": "VFDB Gene", + "pattern": "^\\w+$", + "preferred_prefix": "vfdb.gene", + "uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1" + }, + "vfdb.genus": { + "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.", + "example": "Chlamydia", + "homepage": "http://www.mgc.ac.cn/VFs/", + "mappings": { + "biocontext": "VFDB.GENUS", + "miriam": "vfdb.genus", + "n2t": "vfdb.genus" + }, + "name": "VFDB Genus", + "pattern": "^\\w+$", + "preferred_prefix": "vfdb.genus", + "uri_format": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1" + }, + "vgnc": { + "description": "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee.", + "example": "3792", + "homepage": "https://vertebrate.genenames.org", + "keywords": [ + "life science" + ], + "mappings": { + "cellosaurus": "VGNC", + "fairsharing": "FAIRsharing.5NhJFK", + "miriam": "vgnc", + "ncbi": "VGNC", + "uniprot": "DB-0226" + }, + "name": "Vertebrate Gene Nomenclature Committee", + "pattern": "^\\d{1,9}$", + "preferred_prefix": "vgnc", + "publications": [ + { + "doi": "10.1093/nar/gkaa980", + "pmc": "PMC7779007", + "pubmed": "33152070", + "title": "Genenames.org: the HGNC and VGNC resources in 2021.", + "year": 2021 + } + ], + "uri_format": "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1" + }, + "vhog": { + "contact": { + "email": "bgee@isb-sib.ch", + "github": null, + "name": "Bgee team", + "orcid": null + }, + "deprecated": true, + "description": "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.", + "download_obo": "ftp://ftp.bgee.org/general/ontologies/vHOG.obo", + "download_owl": "http://purl.obolibrary.org/obo/vhog.owl", + "example": "0000411", + "homepage": "http://bgee.unil.ch", + "keywords": [ + "anatomy", + "development", + "obo", + "ontology" + ], + "mappings": { + "aberowl": "VHOG", + "biocontext": "VHOG", + "bioportal": "VHOG", + "obofoundry": "vhog", + "prefixcommons": "vhog" + }, + "name": "Vertebrate Homologous Organ Group Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "VHOG", + "synonyms": [ + "VHOG_RETIRED" + ], + "uri_format": "http://purl.obolibrary.org/obo/VHOG_$1" + }, + "viaf": { + "description": "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web.", + "example": "75121530", + "homepage": "http://viaf.org", + "mappings": { + "bartoc": "2053", + "miriam": "viaf", + "n2t": "viaf" + }, + "name": "Virtual International Authority File", + "pattern": "^\\d+$", + "preferred_prefix": "viaf", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/viaf/$1" + }, + { + "code": "viaf.https", + "description": "A duplicate endpoint over HTTPS", + "homepage": "http://viaf.org", + "name": "VIAF (https)", + "uri_format": "https://viaf.org/$1" + } + ], + "uri_format": "http://viaf.org/viaf/$1" + }, + "vido": { + "contact": { + "email": "johnbeverley2021@u.northwestern.edu", + "github": "johnbeve", + "name": "John Beverly", + "orcid": "0000-0002-1118-1738" + }, + "description": "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.", + "download_owl": "https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl", + "example": "0001114", + "homepage": "https://github.com/infectious-disease-ontology-extensions/ido-virus", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "VIDO", + "bioportal": "VIDO", + "ols": "vido", + "ontobee": "VIDO" + }, + "name": "The Virus Infectious Disease Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "vido", + "providers": [ + { + "code": "obo.1", + "description": "This incorrect encoding was found inside IDO-COVID-19", + "homepage": "http://purl.obolibrary.org", + "name": "Nonstandard OBO PURL", + "uri_format": "http://purl.obolibrary.org/VIDO_$1" + } + ], + "repository": "https://github.com/infectious-disease-ontology-extensions/ido-virus", + "uri_format": "http://purl.obolibrary.org/obo/VIDO_$1", + "version": "2020-08-25" + }, + "violinnet": { + "appears_in": [ + "oae" + ], + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "Defunct vaccine information source from the He Lab", + "example": "4140", + "name": "ViolinNet", + "pattern": "^\\d+$", + "preferred_prefix": "violinnet", + "synonyms": [ + "violinID", + "violinId" + ], + "uri_format": "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1" + }, + "viperdb": { + "description": "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.", + "example": "2c6s", + "homepage": "http://viperdb.scripps.edu/", + "keywords": [ + "small molecule", + "structure" + ], + "mappings": { + "prefixcommons": "viperdb", + "re3data": "r3d100012362" + }, + "name": "VIPERdb", + "preferred_prefix": "viperdb", + "uri_format": "http://viperdb.scripps.edu/info_page.php?VDB=$1" + }, + "vipr": { + "contact": { + "email": "rscheuermann@jcvi.org", + "github": null, + "name": "Richard Scheuermann", + "orcid": "0000-0003-1355-892X" + }, + "description": "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information.", + "example": "BeAn 70563", + "homepage": "http://www.viprbrc.org/brc/home.do?decorator=vipr", + "keywords": [ + "biomedical science", + "epidemiology", + "genomics", + "immunology", + "life science", + "proteomics", + "virology" + ], + "mappings": { + "biocontext": "VIPR", + "fairsharing": "FAIRsharing.2qx8n8", + "miriam": "vipr", + "n2t": "vipr", + "ncbi": "ViPR", + "re3data": "r3d100011931" + }, + "name": "Virus Pathogen Resource", + "pattern": "^[A-Za-z 0-9]+$", + "preferred_prefix": "vipr", + "publications": [ + { + "doi": "10.3390/v4113209", + "pmc": "PMC3509690", + "pubmed": "23202522", + "title": "Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkr859", + "pmc": "PMC3245011", + "pubmed": "22006842", + "title": "ViPR: an open bioinformatics database and analysis resource for virology research.", + "year": 2011 + }, + { + "doi": "10.1016/b978-0-12-809633-8.20995-3", + "pmc": "PMC7173540", + "pubmed": null, + "title": "Database and Analytical Resources for Viral Research Community", + "year": 2021 + }, + { + "doi": "10.1016/b978-0-12-801238-3.95728-3", + "pmc": "PMC7157461", + "pubmed": null, + "title": "Virus Databases ☆", + "year": 2017 + } + ], + "repository": "https://github.com/VirusBRC", + "uri_format": "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena" + }, + "viralzone": { + "contact": { + "email": "Philippe.Lemercier@sib.swiss", + "github": null, + "name": "Philippe Le Mercier", + "orcid": "0000-0001-8528-090X" + }, + "description": "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.", + "example": "992", + "homepage": "http://www.expasy.org/viralzone/", + "keywords": [ + "epidemiology", + "life science", + "molecular biology", + "virology", + "virus" + ], + "mappings": { + "biocontext": "VIRALZONE", + "fairsharing": "FAIRsharing.tppk10", + "go": "VZ", + "miriam": "viralzone", + "n2t": "viralzone", + "prefixcommons": "vz", + "re3data": "r3d100013314" + }, + "name": "ViralZone", + "pattern": "^\\d+$", + "preferred_prefix": "viralzone", + "providers": [ + { + "code": "viralzone.alt1", + "description": "Alternate view", + "homepage": "http://viralzone.expasy.org", + "name": "Viralzone Alt 1.", + "uri_format": "http://viralzone.expasy.org/all_by_protein/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gks1220", + "pmc": "PMC3531065", + "pubmed": "23193299", + "title": "ViralZone: recent updates to the virus knowledge resource.", + "year": 2012 + }, + { + "doi": "10.1093/nar/gkq901", + "pmc": "PMC3013774", + "pubmed": "20947564", + "title": "ViralZone: a knowledge resource to understand virus diversity.", + "year": 2010 + } + ], + "synonyms": [ + "vz" + ], + "uri_format": "https://viralzone.expasy.org/$1" + }, + "virgen": { + "description": "VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences.", + "example": "AY321118", + "homepage": "http://bioinfo.ernet.in/virgen/virgen.html", + "keywords": [ + "genome" + ], + "mappings": { + "prefixcommons": "virgen" + }, + "name": "VirGen", + "preferred_prefix": "virgen" + }, + "virmirdb": { + "description": "A database containing predicted viral miRNA candidate hairpins.", + "example": "11002", + "homepage": "http://alk.ibms.sinica.edu.tw", + "keywords": [ + "rna", + "structure" + ], + "mappings": { + "prefixcommons": "virmirdb" + }, + "name": "Vir-Mir db", + "preferred_prefix": "virmirdb", + "provides": "ncbitaxon", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1" + }, + "viroligo": { + "description": "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place.", + "example": "BM0456", + "homepage": "http://viroligo.okstate.edu", + "keywords": [ + "small molecule" + ], + "mappings": { + "prefixcommons": "viroligo" + }, + "name": "VirOligo", + "preferred_prefix": "viroligo", + "uri_format": "http://viroligo.okstate.edu/main.php?vid=$1" + }, + "virsirna": { + "description": "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region.", + "example": "virsi1909", + "homepage": "http://crdd.osdd.net/servers/virsirnadb", + "mappings": { + "biocontext": "VIRSIRNA", + "miriam": "virsirna", + "n2t": "virsirna" + }, + "name": "VIRsiRNA", + "pattern": "^virsi\\d+$", + "preferred_prefix": "virsirna", + "uri_format": "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1" + }, + "virushostdb": { + "description": "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys.", + "example": "438782", + "homepage": "https://www.genome.jp/virushostdb/", + "keywords": [ + "virus" + ], + "mappings": { + "prefixcommons": "virushostdb" + }, + "name": "Virus-HostDB", + "preferred_prefix": "virushostdb", + "provides": "ncbitaxon", + "publications": [ + { + "doi": "10.3390/v8030066", + "pmc": "PMC4810256", + "pubmed": "26938550", + "title": "Linking Virus Genomes with Host Taxonomy.", + "year": 2016 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.genome.jp/virushostdb/$1" + }, + "vita": { + "description": "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons.", + "example": "AB016785", + "homepage": "http://vita.mbc.nctu.edu.tw/", + "keywords": [ + "gene expression", + "rna", + "structure" + ], + "mappings": { + "prefixcommons": "vita" + }, + "name": "Virus' miRNA target", + "preferred_prefix": "vita", + "uri_format": "http://vita.mbc.nctu.edu.tw/search.php?acc=$1" + }, + "vmc": { + "deprecated": true, + "mappings": { + "biolink": "VMC" + }, + "name": "Variation Modelling Collaboration", + "preferred_prefix": "vmc", + "references": [ + "https://docs.google.com/document/d/12E8WbQlvfZWk5NrxwLytmympPby6vsv60RxCeD5wc1E/edit#heading=h.67hbe76b6a4z", + "https://github.com/ga4gh/vr-spec" + ] + }, + "vmhgene": { + "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", + "example": "8639.1", + "homepage": "https://www.vmh.life/", + "mappings": { + "miriam": "vmhgene" + }, + "name": "VMH Gene", + "pattern": "^[0-9]+\\.[0-9]+$", + "preferred_prefix": "vmhgene", + "uri_format": "https://www.vmh.life/#gene/$1" + }, + "vmhmetabolite": { + "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", + "example": "h2o", + "homepage": "https://www.vmh.life/", + "mappings": { + "biocontext": "VMHMETABOLITE", + "miriam": "vmhmetabolite", + "n2t": "vmhmetabolite" + }, + "name": "VMH metabolite", + "pattern": "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$", + "preferred_prefix": "vmhmetabolite", + "uri_format": "https://www.vmh.life/#metabolite/$1" + }, + "vmhreaction": { + "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", + "example": "HEX1", + "homepage": "https://www.vmh.life/", + "mappings": { + "biocontext": "VMHREACTION", + "miriam": "vmhreaction", + "n2t": "vmhreaction" + }, + "name": "VMH reaction", + "pattern": "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$", + "preferred_prefix": "vmhreaction", + "uri_format": "https://www.vmh.life/#reaction/$1" + }, + "vo": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "yongqunh@med.umich.edu", + "github": "yongqunh", + "name": "Yongqunh He", + "orcid": "0000-0001-9189-9661" + }, + "description": "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.", + "download_owl": "http://purl.obolibrary.org/obo/vo.owl", + "example": "0000093", + "homepage": "http://www.violinet.org/vaccineontology", + "keywords": [ + "biomedical science", + "immunology", + "obo", + "ontology", + "pathobiochemistry", + "small molecule", + "vaccine" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "VO", + "biocontext": "VO", + "bioportal": "VO", + "fairsharing": "FAIRsharing.zwtww5", + "obofoundry": "vo", + "ols": "vo", + "ontobee": "VO", + "prefixcommons": "vo", + "wikidata": "P1928" + }, + "name": "Vaccine Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "VO", + "publications": [ + { + "doi": "10.2174/1381612826666201125112131", + "pmc": null, + "pubmed": "33238868", + "title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development.", + "year": 2021 + }, + { + "doi": "10.1186/2041-1480-3-17", + "pmc": "PMC3639077", + "pubmed": "23256535", + "title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses.", + "year": 2012 + }, + { + "doi": "10.1186/2041-1480-2-s2-s8", + "pmc": "PMC3102897", + "pubmed": "21624163", + "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.", + "year": 2011 + }, + { + "doi": "10.1186/1745-7580-6-s1-s5", + "pmc": "PMC2946783", + "pubmed": "20875156", + "title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.", + "year": 2010 + } + ], + "repository": "https://github.com/vaccineontology/VO", + "uri_format": "http://purl.obolibrary.org/obo/VO_$1", + "version": "1.1.198" + }, + "void": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.", + "example": "feature", + "homepage": "http://vocab.deri.ie/void", + "mappings": { + "biocontext": "void" + }, + "name": "Vocabulary of Interlinked Datasets", + "preferred_prefix": "void", + "uri_format": "http://rdfs.org/ns/void#$1" + }, + "vsao": { + "contact": { + "email": "wasila.dahdul@usd.edu", + "github": null, + "name": "Wasila Dahdul", + "orcid": "0000-0003-3162-7490" + }, + "deprecated": true, + "description": "Vertebrate skeletal anatomy ontology.", + "download_obo": "http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo", + "download_owl": "http://purl.obolibrary.org/obo/vsao.owl", + "example": "VSAO_0000183", + "homepage": "https://www.nescent.org/phenoscape/Main_Page", + "keywords": [ + "anatomy", + "obo", + "ontology", + "vertebrate" + ], + "mappings": { + "aberowl": "VSAO", + "biocontext": "VSAO", + "bioportal": "VSAO", + "obofoundry": "vsao", + "prefixcommons": "vao" + }, + "name": "Vertebrate Skeletal Anatomy Ontology", + "preferred_prefix": "VSAO", + "synonyms": [ + "VSAO_RETIRED" + ], + "uri_format": "http://purl.obolibrary.org/obo/VSAO_$1" + }, + "vsdb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source.", + "example": "1868", + "homepage": "https://sitem.herts.ac.uk/aeru/vsdb", + "name": "Veterinary Substances DataBase", + "pattern": "^\\d+$", + "preferred_prefix": "vsdb", + "uri_format": "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm" + }, + "vsmo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems.", + "download_json": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.json", + "download_obo": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.obo", + "download_owl": "https://raw.githubusercontent.com/cthoyt/vsmo/main/vsmo.owl", + "example": "0000000", + "homepage": "https://code.google.com/archive/p/vector-surveillance-and-management-ontology/", + "keywords": [ + "ontology" + ], + "license": "New BSD License", + "name": "Ontology for vector surveillance and management", + "preferred_prefix": "vsmo", + "publications": [ + { + "doi": "10.1603/me12169", + "pmc": "PMC3695545", + "pubmed": "23427646", + "title": "Ontology for vector surveillance and management.", + "year": 2013 + } + ], + "uri_format": "http://purl.obolibrary.org/obo/VSMO_$1" + }, + "vso": { + "contact": { + "email": "albertgoldfain@gmail.com", + "github": null, + "name": "Albert Goldfain", + "orcid": null + }, + "description": "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ", + "download_owl": "http://aber-owl.net/media/ontologies/VSO/1/vso.owl", + "example": "0000041", + "homepage": "https://bioportal.bioontology.org/ontologies/VSO", + "keywords": [ + "biomedical science", + "health", + "health science", + "ontology", + "owl" + ], + "mappings": { + "aberowl": "VSO", + "bioportal": "VSO", + "fairsharing": "FAIRsharing.jjb2p2", + "prefixcommons": "vso" + }, + "name": "Vital Sign Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "vso", + "uri_format": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1" + }, + "vt": { + "appears_in": [ + "scdo" + ], + "contact": { + "email": "caripark@iastate.edu", + "github": "caripark", + "name": "Carissa Park", + "orcid": "0000-0002-2346-5201" + }, + "description": "An ontology of traits covering vertebrates", + "download_obo": "https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo", + "download_owl": "http://purl.obolibrary.org/obo/vt.owl", + "example": "0000685", + "homepage": "https://github.com/AnimalGenome/vertebrate-trait-ontology", + "keywords": [ + "animal physiology", + "biology", + "developmental biology", + "obo", + "ontology", + "physiology", + "trait", + "vertebrate" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "VT", + "agroportal": "VT", + "biocontext": "VT", + "bioportal": "VT", + "fairsharing": "FAIRsharing.10gr18", + "obofoundry": "vt", + "ols": "vt", + "ontobee": "VT", + "prefixcommons": "vt" + }, + "name": "Vertebrate trait ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "VT", + "publications": [ + { + "doi": "10.1186/2041-1480-4-13", + "pmc": "PMC3851175", + "pubmed": "23937709", + "title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species.", + "year": 2013 + } + ], + "repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology", + "uri_format": "http://purl.obolibrary.org/obo/VT_$1" + }, + "vto": { + "contact": { + "email": "balhoff@renci.org", + "github": "balhoff", + "name": "Jim Balhoff", + "orcid": "0000-0002-8688-6599" + }, + "description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.", + "download_obo": "http://purl.obolibrary.org/obo/vto.obo", + "download_owl": "http://purl.obolibrary.org/obo/vto.owl", + "example": "9008500", + "homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", + "keywords": [ + "obo", + "ontology", + "taxonomy" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "VTO", + "biocontext": "VTO", + "bioportal": "VTO", + "fairsharing": "FAIRsharing.akmeb9", + "obofoundry": "vto", + "ols": "vto", + "ontobee": "VTO" + }, + "name": "Vertebrate Taxonomy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "VTO", + "publications": [ + { + "doi": "10.1186/2041-1480-4-34", + "pmc": "PMC4177199", + "pubmed": "24267744", + "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.", + "year": 2013 + } + ], + "repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", + "uri_format": "http://purl.obolibrary.org/obo/VTO_$1", + "version": "2020-11-13" + }, + "vuid": { + "comment": "The example corresponds to acetaminophen", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year.", + "example": "4007166", + "homepage": "https://www.va.gov/health", + "name": "Veterans Health Administration (VHA) unique identifier", + "pattern": "^\\d+$", + "preferred_prefix": "vuid", + "references": [ + "https://academic.oup.com/jamia/article/17/4/432/866953" + ] + }, + "wb.rnai": { + "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", + "example": "WBRNAi00086878", + "homepage": "https://www.wormbase.org/", + "mappings": { + "biocontext": "WB.RNAI", + "miriam": "wb.rnai", + "n2t": "wb.rnai" + }, + "name": "WormBase RNAi", + "pattern": "^WBRNAi\\d{8}$", + "preferred_prefix": "wb.rnai", + "uri_format": "https://www.wormbase.org/species/c_elegans/rnai/$1" + }, + "wbbt": { + "contact": { + "email": "raymond@caltech.edu", + "github": "raymond91125", + "name": "Raymond Lee", + "orcid": "0000-0002-8151-7479" + }, + "description": "Ontology about the gross anatomy of the C. elegans", + "download_obo": "http://purl.obolibrary.org/obo/wbbt.obo", + "download_owl": "http://purl.obolibrary.org/obo/wbbt.owl", + "example": "0001290", + "homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology", + "worm" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "WBBT", + "biocontext": "WBbt", + "biolink": "WBbt", + "bioportal": "WB-BT", + "fairsharing": "FAIRsharing.phk7dd", + "go": "WBbt", + "obofoundry": "wbbt", + "ols": "wbbt", + "ontobee": "WBbt", + "prefixcommons": "wbbt" + }, + "name": "C. elegans Gross Anatomy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "WBbt", + "publications": [ + { + "doi": "10.1002/cfg.248", + "pmc": "PMC2447384", + "pubmed": "18629098", + "title": "Building a cell and anatomy ontology of Caenorhabditis elegans.", + "year": 2003 + } + ], + "repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", + "synonyms": [ + "WBbt" + ], + "uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", + "version": "2022-06-13" + }, + "wbls": { + "contact": { + "email": "cgrove@caltech.edu", + "github": "chris-grove", + "name": "Chris Grove", + "orcid": "0000-0001-9076-6015" + }, + "description": "Ontology about the development and life stages of the C. elegans", + "download_obo": "http://purl.obolibrary.org/obo/wbls.obo", + "download_owl": "http://purl.obolibrary.org/obo/wbls.owl", + "example": "0000690", + "homepage": "https://github.com/obophenotype/c-elegans-development-ontology", + "keywords": [ + "development", + "developmental biology", + "life science", + "obo", + "ontology", + "worm" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "WBLS", + "biocontext": "WBLS", + "biolink": "WBls", + "bioportal": "WB-LS", + "fairsharing": "FAIRsharing.sm90nh", + "go": "WBls", + "obofoundry": "wbls", + "ols": "wbls", + "ontobee": "WBls", + "prefixcommons": "wbls" + }, + "name": "C. elegans development ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "WBls", + "publications": [ + { + "doi": "10.1093/nar/gkz920", + "pmc": "PMC7145598", + "pubmed": "31642470", + "title": "WormBase: a modern Model Organism Information Resource.", + "year": 2020 + } + ], + "repository": "https://github.com/obophenotype/c-elegans-development-ontology", + "synonyms": [ + "WBls" + ], + "uri_format": "http://www.wormbase.org/get?name=$1", + "version": "2022-06-21" + }, + "wbphenotype": { + "contact": { + "email": "cgrove@caltech.edu", + "github": "chris-grove", + "name": "Chris Grove", + "orcid": "0000-0001-9076-6015" + }, + "description": "Ontology about C. elegans and other nematode phenotypes", + "download_obo": "http://purl.obolibrary.org/obo/wbphenotype.obo", + "download_owl": "http://purl.obolibrary.org/obo/wbphenotype.owl", + "example": "0000983", + "homepage": "https://github.com/obophenotype/c-elegans-phenotype-ontology", + "keywords": [ + "anatomy", + "life science", + "obo", + "ontology", + "phenotype", + "worm" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "WBPHENOTYPE", + "biocontext": "WBPhenotype", + "bioportal": "WB-PHENOTYPE", + "fairsharing": "FAIRsharing.agvc7y", + "go": "WBPhenotype", + "obofoundry": "wbphenotype", + "ols": "wbphenotype", + "ontobee": "WBPhenotype", + "prefixcommons": "wbphenotype" + }, + "name": "C. elegans phenotype", + "pattern": "^\\d{7}$", + "preferred_prefix": "WBPhenotype", + "publications": [ + { + "doi": "10.1186/1471-2105-12-32", + "pmc": "PMC3039574", + "pubmed": "21261995", + "title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.", + "year": 2011 + } + ], + "repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology", + "synonyms": [ + "WBPhenotype" + ], + "uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", + "version": "2022-06-21" + }, + "webelements": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Browser for the periodic table of the elements", + "example": "chromium", + "homepage": "https://www.webelements.com/", + "keywords": [ + "chemistry" + ], + "name": "Web Elements", + "pattern": "^\\w+$", + "preferred_prefix": "webelements", + "uri_format": "https://www.webelements.com/$1" + }, + "wgs84": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum", + "example": "latitude", + "homepage": "https://www.w3.org/2003/01/geo/wgs84_pos", + "mappings": { + "biolink": "wgs" + }, + "name": "WGS84 Geo Positioning", + "preferred_prefix": "wgs84", + "uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1" + }, + "wicell": { + "description": "Cell line collections", + "example": "ai10e-kctd13b", + "homepage": "https://www.wicell.org", + "mappings": { + "cellosaurus": "WiCell" + }, + "name": "WiCell Research Institute Cell Collection", + "preferred_prefix": "wicell", + "uri_format": "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true" + }, + "wikidata": { + "description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic.", + "example": "Q2207226", + "homepage": "https://www.wikidata.org/", + "keywords": [ + "chemistry", + "genomics", + "metabolomics", + "proteomics", + "subject agnostic" + ], + "mappings": { + "bartoc": "1940", + "biocontext": "WIKIDATA", + "biolink": "WIKIDATA", + "cellosaurus": "Wikidata", + "cheminf": "000567", + "fairsharing": "FAIRsharing.6s749p", + "miriam": "wikidata", + "n2t": "wikidata" + }, + "name": "Wikidata", + "pattern": "^(Q|P)\\d+$", + "preferred_prefix": "wikidata", + "providers": [ + { + "code": "scholia", + "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", + "homepage": "https://scholia.toolforge.org", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/$1" + } + ], + "publications": [ + { + "doi": "10.1145/2187980.2188242", + "pmc": null, + "pubmed": null, + "title": "Wikidata", + "year": 2012 + } + ], + "synonyms": [ + "WD_Entity", + "wd" + ], + "twitter": "wikidata", + "uri_format": "http://www.wikidata.org/entity/$1" + }, + "wikidata.property": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. ", + "example": "P4355", + "homepage": "https://www.wikidata.org", + "mappings": { + "biocontext": "WD_Prop", + "biolink": "WIKIDATA_PROPERTY" + }, + "name": "Wikidata Property", + "part_of": "wikidata", + "pattern": "^P\\d+$", + "preferred_prefix": "wikidata.property", + "providers": [ + { + "code": "scholia", + "description": "Scholia can generally resolve many Wikidata entries in the biomedical and bibliometric domains", + "homepage": "https://scholia.toolforge.org", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/$1" + } + ], + "uri_format": "https://www.wikidata.org/wiki/Property:$1" + }, + "wikigenes": { + "description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.", + "example": "3771877", + "homepage": "http://www.wikigenes.org/", + "mappings": { + "biocontext": "WIKIGENES", + "miriam": "wikigenes", + "n2t": "wikigenes" + }, + "name": "WikiGenes", + "pattern": "^\\d+$", + "preferred_prefix": "wikigenes", + "provides": "ncbigene", + "uri_format": "http://www.wikigenes.org/e/gene/e/$1.html" + }, + "wikipathways": { + "contact": { + "email": "egon.willighagen@gmail.com", + "github": "egonw", + "name": "Egon Willighagen", + "orcid": "0000-0001-7542-0286" + }, + "contributor_extras": [ + { + "email": "egon.willighagen@gmail.com", + "github": "egonw", + "name": "Egon Willighagen", + "orcid": "0000-0001-7542-0286" + } + ], + "description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.", + "download_owl": "http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl", + "example": "WP732", + "homepage": "http://www.wikipathways.org/", + "keywords": [ + "epidemiology", + "ontology", + "pathway", + "virology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "WIKIPATHWAYS", + "biocontext": "WIKIPATHWAYS", + "bioportal": "WIKIPATHWAYS", + "edam": "3952", + "fairsharing": "FAIRsharing.g7b4rj", + "miriam": "wikipathways", + "n2t": "wikipathways", + "prefixcommons": "wikipathways", + "re3data": "r3d100013316", + "wikidata": "P2410" + }, + "name": "WikiPathways", + "pattern": "^WP\\d{1,5}(\\_r\\d+)?$", + "preferred_prefix": "wikipathways", + "providers": [ + { + "code": "scholia", + "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.\n", + "homepage": "https://scholia.toolforge.org/", + "name": "Scholia", + "uri_format": "https://scholia.toolforge.org/wikipathways/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkaa1024", + "pmc": "PMC7779061", + "pubmed": "33211851", + "title": "WikiPathways: connecting communities.", + "year": 2021 + }, + { + "doi": "10.1093/nar/gkx1064", + "pmc": "PMC5753270", + "pubmed": "29136241", + "title": "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gkv1024", + "pmc": "PMC4702772", + "pubmed": "26481357", + "title": "WikiPathways: capturing the full diversity of pathway knowledge.", + "year": 2015 + }, + { + "doi": "10.1093/nar/gkr1074", + "pmc": "PMC3245032", + "pubmed": "22096230", + "title": "WikiPathways: building research communities on biological pathways.", + "year": 2011 + }, + { + "doi": "10.1371/journal.pbio.0060184", + "pmc": "PMC2475545", + "pubmed": "18651794", + "title": "WikiPathways: pathway editing for the people.", + "year": 2008 + } + ], + "twitter": "WikiPathways", + "uri_format": "http://www.wikipathways.org/instance/$1" + }, + "wikipedia.en": { + "description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.", + "example": "SM_UB-81", + "homepage": "http://en.wikipedia.org/wiki/Main_Page", + "mappings": { + "biocontext": "WIKIPEDIA.EN", + "go": "Wikipedia", + "miriam": "wikipedia.en", + "n2t": "wikipedia.en", + "prefixcommons": "wikipedia" + }, + "name": "Wikipedia", + "pattern": "^[A-Za-z-0-9_]+$", + "preferred_prefix": "wikipedia.en", + "providers": [ + { + "code": "CURATOR_REVIEW", + "description": "Wikipedia structured content through DBpedia", + "homepage": "http://wiki.dbpedia.org/", + "name": "Wikipedia structured content through DBpedia", + "uri_format": "http://dbpedia.org/page/$1" + }, + { + "code": "volupedia", + "description": "A mix of wikipedia and 3d", + "homepage": "http://en.volupedia.org", + "name": "Volupedia", + "uri_format": "http://en.volupedia.org/wiki/$1" + } + ], + "synonyms": [ + "wikipedia" + ], + "uri_format": "http://en.wikipedia.org/wiki/$1" + }, + "worfdb": { + "description": "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends).", + "example": "T01B6.1", + "homepage": "http://worfdb.dfci.harvard.edu/", + "keywords": [ + "dna" + ], + "mappings": { + "biocontext": "WORFDB", + "miriam": "worfdb", + "n2t": "worfdb", + "ncbi": "WorfDB", + "prefixcommons": "worfdb" + }, + "name": "C. elegans ORFeome cloning project", + "pattern": "^\\w+(\\.\\d+)$", + "preferred_prefix": "worfdb", + "uri_format": "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1" + }, + "world2dpage": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots.", + "example": "0020", + "homepage": "http://world-2dpage.expasy.org/repository/", + "keywords": [ + "2d-page", + "protein", + "structure" + ], + "mappings": { + "prefixcommons": "world2dpage", + "uniprot": "DB-0121" + }, + "name": "The World-2DPAGE database", + "preferred_prefix": "world2dpage", + "publications": [ + { + "doi": "10.1016/j.jprot.2008.02.005", + "pmc": null, + "pubmed": "18617148", + "title": "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server.", + "year": 2008 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://world-2dpage.expasy.org/repository/$1" + }, + "wormbase": { + "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.", + "example": "WBGene00000001", + "homepage": "https://www.wormbase.org/", + "keywords": [ + "anatomy", + "gene", + "genome", + "life science" + ], + "mappings": { + "biocontext": "WormBase", + "biolink": "WBVocab", + "edam": "1805", + "fairsharing": "FAIRsharing.zx1td8", + "go": "WB_REF", + "miriam": "wb", + "n2t": "wb", + "ncbi": "WormBase", + "prefixcommons": "wormbase", + "re3data": "r3d100010424", + "uniprot": "DB-0110", + "wikidata": "P3860" + }, + "name": "Wormbase Gene", + "pattern": "^WB[A-Z][a-z]+\\d+$", + "preferred_prefix": "WormBase", + "providers": [ + { + "code": "agr", + "description": "WormBase through the Alliance of Genome Resources", + "homepage": "https://www.alliancegenome.org", + "name": "WormBase through the Alliance of Genome Resources", + "uri_format": "https://www.alliancegenome.org/gene/WB:$1" + }, + { + "code": "wormbase.c_elegans", + "description": "Pages describing C. Elegans genes.", + "homepage": "http://www.wormbase.org", + "name": "WormBase C. Elegans Gene Portal", + "uri_format": "http://www.wormbase.org/species/c_elegans/gene/$1" + } + ], + "publications": [ + { + "doi": "10.1093/nar/gkz920", + "pmc": "PMC7145598", + "pubmed": "31642470", + "title": "WormBase: a modern Model Organism Information Resource.", + "year": 2020 + }, + { + "doi": "10.1093/nar/gkx998", + "pmc": "PMC5753391", + "pubmed": "29069413", + "title": "WormBase 2017: molting into a new stage.", + "year": 2018 + }, + { + "doi": "10.1186/1471-2105-12-175", + "pmc": "PMC3213741", + "pubmed": "21595960", + "title": "Toward an interactive article: integrating journals and biological databases.", + "year": 2011 + }, + { + "doi": "10.1093/nar/gkq1116", + "pmc": "PMC3013707", + "pubmed": "21071413", + "title": "The BioGRID Interaction Database: 2011 update.", + "year": 2010 + }, + { + "doi": "10.1186/1471-2105-11-550", + "pmc": "PMC2992068", + "pubmed": "21059240", + "title": "Localizing triplet periodicity in DNA and cDNA sequences.", + "year": 2010 + }, + { + "doi": "10.1002/mrd.21130", + "pmc": "PMC2830379", + "pubmed": "19921742", + "title": "Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkp1018", + "pmc": "PMC2808930", + "pubmed": "19920128", + "title": "The Gene Ontology in 2010: extensions and refinements.", + "year": 2009 + }, + { + "doi": "10.1093/nar/gkp952", + "pmc": "PMC2808986", + "pubmed": "19910365", + "title": "WormBase: a comprehensive resource for nematode research.", + "year": 2009 + }, + { + "doi": "10.1186/1471-2105-10-228", + "pmc": "PMC2719631", + "pubmed": "19622167", + "title": "Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation.", + "year": 2009 + }, + { + "doi": "10.1371/journal.pcbi.1000431", + "pmc": "PMC2699109", + "pubmed": "19578431", + "title": "The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.", + "year": 2009 + }, + { + "doi": "10.1186/1471-2105-9-549", + "pmc": "PMC2651883", + "pubmed": "19099578", + "title": "nGASP--the nematode genome annotation assessment project.", + "year": 2008 + }, + { + "doi": "10.1093/nar/29.1.82", + "pmc": "PMC29781", + "pubmed": "11125056", + "title": "WormBase: network access to the genome and biology of Caenorhabditis elegans.", + "year": 2001 + } + ], + "synonyms": [ + "WB_REF", + "wb", + "wormbase" + ], + "twitter": "wormbase", + "uri_format": "https://www.wormbase.org/get?name=$1" + }, + "wormpep": { + "description": "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.", + "example": "CE28239", + "homepage": "https://www.wormbase.org/db/seq/protein", + "keywords": [ + "protein", + "structure" + ], + "mappings": { + "biocontext": "WORMPEP", + "miriam": "wormpep", + "n2t": "wormpep", + "prefixcommons": "wormpep" + }, + "name": "Wormpep", + "pattern": "^CE\\d{5}$", + "preferred_prefix": "wormpep", + "uri_format": "https://www.wormbase.org/db/seq/protein?name=$1" + }, + "worms": { + "contact": { + "email": "leen.vandepitte@vliz.be", + "github": null, + "name": "Leen Vandepitte", + "orcid": "0000-0002-8160-7941" + }, + "contributor_extras": [ + { + "email": "meghan.balk@gmail.com", + "github": "megbalk", + "name": "Meghan Balk", + "orcid": "0000-0003-2699-3066" + } + ], + "description": "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts.", + "example": "146421", + "homepage": "http://www.marinespecies.org/", + "keywords": [ + "biodiversity", + "environmental science", + "taxonomy" + ], + "mappings": { + "bartoc": "720", + "biocontext": "WORMS", + "fairsharing": "FAIRsharing.7g1bzj", + "miriam": "worms", + "n2t": "worms", + "wikidata": "P850" + }, + "name": "WoRMS-ID for taxa", + "pattern": "^\\d+$", + "preferred_prefix": "worms", + "publications": [ + { + "doi": "10.1371/journal.pone.0194599", + "pmc": "PMC5889062", + "pubmed": "29624577", + "title": "A decade of the World Register of Marine Species - General insights and experiences from the Data Management Team: Where are we, what have we learned and how can we continue?", + "year": 2018 + } + ], + "twitter": "WRMarineSpecies", + "uri_format": "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1" + }, + "wwf.ecoregion": { + "comment": "ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658", + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.", + "example": "AT1402", + "github_request_issue": 153, + "homepage": "https://www.worldwildlife.org/biomes", + "mappings": { + "wikidata": "P1294" + }, + "name": "World Wildlife Fund Ecoregion", + "pattern": "^AT\\d+$", + "preferred_prefix": "wwf.ecoregion", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "WWF" + ], + "uri_format": "https://www.worldwildlife.org/ecoregions/$1" + }, + "xao": { + "appears_in": [ + "xpo" + ], + "contact": { + "email": "Erik.Segerdell@cchmc.org", + "github": "seger", + "name": "Erik Segerdell", + "orcid": "0000-0002-9611-1279" + }, + "description": "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis.", + "download_obo": "http://purl.obolibrary.org/obo/xao.obo", + "download_owl": "http://purl.obolibrary.org/obo/xao.owl", + "example": "0004486", + "homepage": "http://www.xenbase.org/anatomy/xao.do?method=display", + "keywords": [ + "anatomy", + "developmental biology", + "life science", + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "XAO", + "bartoc": "581", + "biocontext": "XAO", + "bioportal": "XAO", + "fairsharing": "FAIRsharing.17zapb", + "obofoundry": "xao", + "ols": "xao", + "ontobee": "XAO", + "wikidata": "P4495" + }, + "name": "Xenopus Anatomy Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "XAO", + "publications": [ + { + "doi": "10.1186/2041-1480-4-31", + "pmc": "PMC3816597", + "pubmed": "24139024", + "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.", + "year": 2013 + }, + { + "doi": "10.1186/1471-213x-8-92", + "pmc": "PMC2561031", + "pubmed": "18817563", + "title": "An ontology for Xenopus anatomy and development.", + "year": 2008 + } + ], + "repository": "https://github.com/xenopus-anatomy/xao", + "uri_format": "http://purl.obolibrary.org/obo/XAO_$1", + "version": "2021-03-04" + }, + "xco": { + "appears_in": [ + "agro", + "ecto" + ], + "contact": { + "email": "jrsmith@mcw.edu", + "github": "jrsjrs", + "name": "Jennifer Smith", + "orcid": "0000-0002-6443-9376" + }, + "description": "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.", + "download_obo": "http://purl.obolibrary.org/obo/xco.obo", + "download_owl": "http://purl.obolibrary.org/obo/xco.owl", + "example": "0000780", + "homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000", + "keywords": [ + "biomedical science", + "life science", + "measurement", + "obo", + "ontology" + ], + "license": "CC0-1.0", + "mappings": { + "aberowl": "XCO", + "biocontext": "XCO", + "bioportal": "XCO", + "fairsharing": "FAIRsharing.x39h5y", + "obofoundry": "xco", + "ols": "xco", + "ontobee": "XCO", + "prefixcommons": "xco" + }, + "name": "Experimental condition ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "XCO", + "publications": [ + { + "doi": "10.1186/2041-1480-4-26", + "pmc": "PMC3882879", + "pubmed": "24103152", + "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", + "year": 2013 + }, + { + "doi": "10.3389/fgene.2012.00087", + "pmc": "PMC3361058", + "pubmed": "22654893", + "title": "Three ontologies to define phenotype measurement data.", + "year": 2012 + } + ], + "repository": "https://github.com/rat-genome-database/XCO-experimental-condition-ontology", + "twitter": "ratgenome", + "uri_format": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1", + "version": "2019-12-18" + }, + "xenbase": { + "contact": { + "email": "troy_pells@yahoo.ca", + "github": "pellst", + "name": "Troy Pells", + "orcid": "0000-0002-2340-5356" + }, + "description": "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.", + "example": "XB-GENE-922462", + "homepage": "https://www.xenbase.org/", + "keywords": [ + "anatomy", + "cell biology", + "developmental biology", + "expression", + "functional genomics", + "genetics", + "genome", + "genomics", + "proteomics" + ], + "mappings": { + "biocontext": "Xenbase", + "biolink": "Xenbase", + "edam": "2738", + "fairsharing": "FAIRsharing.jrv6wj", + "go": "Xenbase", + "miriam": "xenbase", + "n2t": "xenbase", + "ncbi": "Xenbase", + "prefixcommons": "xenbase", + "re3data": "r3d100011331", + "uniprot": "DB-0129" + }, + "name": "Xenbase", + "pattern": "^XB\\-\\w+\\-\\d+$", + "preferred_prefix": "xenbase", + "publications": [ + { + "doi": "10.1186/s12859-022-04636-8", + "pmc": "PMC8939077", + "pubmed": "35317743", + "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.", + "year": 2022 + }, + { + "doi": "10.1093/nar/gkz933", + "pmc": "PMC7145613", + "pubmed": "31733057", + "title": "Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.", + "year": 2020 + }, + { + "doi": "doi:10.3389/fphys.2019.00154", + "pmc": "PMC6399412", + "pubmed": "30863320", + "title": "Xenbase: Facilitating the Use of Xenopus to Model Human Disease.", + "year": null + }, + { + "doi": "10.3389/fphys.2019.00154", + "pmc": "PMC6399412", + "pubmed": "30863320", + "title": "Xenbase: Facilitating the Use of", + "year": 2019 + }, + { + "doi": "doi:10.1007/978-1-4939-7737-6_10.", + "pmc": "PMC6853059", + "pubmed": "29761462", + "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.", + "year": null + }, + { + "doi": "10.1007/978-1-4939-7737-6_10", + "pmc": "PMC6853059", + "pubmed": "29761462", + "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.", + "year": 2018 + }, + { + "doi": "10.1093/nar/gkx936", + "pmc": "PMC5753396", + "pubmed": "29059324", + "title": "Xenbase: a genomic, epigenomic and transcriptomic model organism database.", + "year": 2018 + }, + { + "doi": "10.1016/j.ydbio.2016.03.030", + "pmc": "PMC5045824", + "pubmed": "27039265", + "title": "Xenopus genomic data and browser resources.", + "year": 2016 + }, + { + "doi": "10.1093/database/bau108", + "pmc": "PMC4224262", + "pubmed": "25380782", + "title": "The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.", + "year": 2014 + }, + { + "doi": "10.1093/nar/gku956", + "pmc": "PMC4384024", + "pubmed": "25313157", + "title": "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.", + "year": 2014 + }, + { + "doi": "10.1186/2041-1480-4-31", + "pmc": "PMC3816597", + "pubmed": "24139024", + "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkp953", + "pmc": "PMC2808955", + "pubmed": "19884130", + "title": "Xenbase: gene expression and improved integration.", + "year": 2009 + } + ], + "synonyms": [ + "Xenbase" + ], + "twitter": "Xenbase", + "uri_format": "https://www.xenbase.org/entry/$1" + }, + "ximbio": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Cell line collections", + "example": "151022", + "homepage": "https://ximbio.com", + "mappings": { + "cellosaurus": "Ximbio" + }, + "name": "Ximbio", + "pattern": "^\\d+$", + "preferred_prefix": "ximbio", + "uri_format": "https://ximbio.com/reagent/$1" + }, + "xl": { + "deprecated": true, + "description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.", + "download_owl": "http://purl.obolibrary.org/obo/xl.owl", + "homepage": "http://www.psidev.info/groups/controlled-vocabularies", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "XL", + "biocontext": "XL", + "ols": "xl", + "ontobee": "XL" + }, + "name": "Cross-linker reagents ontology", + "preferred_prefix": "xl", + "uri_format": "http://purl.obolibrary.org/obo/XL_$1" + }, + "xlmod": { + "contact": { + "email": "lutz.fischer@tu-berlin.de", + "github": "lutzfischer", + "name": "Lutz Fischer", + "orcid": "0000-0003-4978-0864" + }, + "description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.", + "download_obo": "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo", + "download_owl": "http://purl.obolibrary.org/obo/xlmod.owl", + "example": "00050", + "homepage": "http://www.psidev.info/groups/controlled-vocabularies", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "XLMOD", + "bioportal": "XLMOD", + "obofoundry": "xlmod", + "ols": "xlmod", + "ontobee": "XLMOD" + }, + "name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary", + "pattern": "^\\d{5}$", + "preferred_prefix": "XLMOD", + "repository": "https://github.com/HUPO-PSI/xlmod-CV", + "uri_format": "http://purl.obolibrary.org/obo/XLMOD_$1", + "version": "2019-10-28" + }, + "xmetdb": { + "banana": "XMETDB", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "Metabolites in the Xenobiotics Metabolism Database.", + "example": "171", + "homepage": "https://xmetdb.org", + "name": "Xenobiotics Metabolism Database", + "pattern": "^\\d+$", + "preferred_prefix": "xmetdb", + "uri_format": "http://www.xmetdb.org/xmetdb/protocol/$1" + }, + "xml": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML.", + "example": "lang", + "homepage": "https://www.w3.org/TR/xml/", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "biocontext": "xml", + "fairsharing": "FAIRsharing.b5cc91" + }, + "name": "Extensible Markup Language", + "preferred_prefix": "xml", + "uri_format": "http://www.w3.org/XML/1998/namespace#$1" + }, + "xpo": { + "contact": { + "email": "Erik.Segerdell@cchmc.org", + "github": "seger", + "name": "Erik Segerdell", + "orcid": "0000-0002-9611-1279" + }, + "depends_on": [ + "bfo", + "chebi", + "cl", + "go", + "iao", + "pato", + "ro", + "xao" + ], + "description": "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.", + "download_obo": "http://purl.obolibrary.org/obo/xpo.obo", + "download_owl": "http://purl.obolibrary.org/obo/xpo.owl", + "example": "0100002", + "homepage": "https://github.com/obophenotype/xenopus-phenotype-ontology", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-3.0", + "mappings": { + "aberowl": "XPO", + "biolink": "XPO", + "bioportal": "XPO", + "obofoundry": "xpo", + "ols": "xpo", + "ontobee": "XPO" + }, + "name": "Xenopus Phenotype Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "XPO", + "publications": [ + { + "doi": "10.1186/s12859-022-04636-8", + "pmc": "PMC8939077", + "pubmed": "35317743", + "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.", + "year": 2022 + } + ], + "repository": "https://github.com/obophenotype/xenopus-phenotype-ontology", + "uri_format": "http://purl.obolibrary.org/obo/XPO_$1", + "version": "2021-03-05" + }, + "xsd": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language.", + "example": "decimal", + "homepage": "http://www.w3.org/2001/XMLSchema", + "mappings": { + "biocontext": "xsd" + }, + "name": "XML Schema Definition", + "preferred_prefix": "xsd", + "uri_format": "http://www.w3.org/2001/XMLSchema#$1" + }, + "xuo": { + "appears_in": [ + "hsapdv" + ], + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "name": "XUO", + "preferred_prefix": "xuo" + }, + "ydpm": { + "description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.", + "example": "YAL001C", + "homepage": "http://www-deletion.stanford.edu/YDPM/", + "keywords": [ + "protein" + ], + "mappings": { + "biocontext": "YDPM", + "miriam": "ydpm", + "n2t": "ydpm", + "prefixcommons": "ydpm" + }, + "name": "Yeast Deletion and the Mitochondrial Proteomics Project", + "pattern": "^Y[A-Z]{2}\\d+[CW]$", + "preferred_prefix": "ydpm", + "uri_format": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1" + }, + "yeastintron": { + "description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].", + "example": "SNR17A", + "homepage": "http://intron.ucsc.edu/yeast4.3/", + "mappings": { + "biocontext": "YEASTINTRON", + "miriam": "yeastintron", + "n2t": "yeastintron" + }, + "name": "Yeast Intron Database v4.3", + "pattern": "^[A-Z0-9]+$", + "preferred_prefix": "yeastintron", + "uri_format": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1" + }, + "yeastract": { + "description": "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.", + "example": "YBR125c", + "homepage": "http://www.yeastract.com", + "keywords": [ + "dna", + "gene", + "life science", + "regulation", + "small molecule" + ], + "mappings": { + "fairsharing": "FAIRsharing.mphj4z", + "prefixcommons": "yeastract" + }, + "name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking", + "preferred_prefix": "yeastract", + "publications": [ + { + "doi": "10.1093/nar/gkt1015", + "pmc": "PMC3965121", + "pubmed": "24170807", + "title": "The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.", + "year": 2013 + }, + { + "doi": "10.1093/nar/gkq964", + "pmc": "PMC3013800", + "pubmed": "20972212", + "title": "YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.", + "year": 2010 + }, + { + "doi": "10.1093/nar/gkm976", + "pmc": "PMC2238916", + "pubmed": "18032429", + "title": "YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.", + "year": 2007 + }, + { + "doi": "10.1093/nar/gkj013", + "pmc": "PMC1347376", + "pubmed": "16381908", + "title": "The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.", + "year": 2006 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://www.yeastract.com/view.php?existing=locus&orfname=$1" + }, + "yetfasco": { + "description": "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats.", + "example": "YOR172W_571.0", + "homepage": "http://yetfasco.ccbr.utoronto.ca/", + "mappings": { + "biocontext": "YETFASCO", + "miriam": "yetfasco", + "n2t": "yetfasco" + }, + "name": "YeTFasCo", + "pattern": "^\\w+\\_\\d+(\\.\\d+)?$", + "preferred_prefix": "yetfasco", + "uri_format": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1" + }, + "ygob": { + "comment": "This resource doesn't exist on the web anymore", + "deprecated": true, + "description": "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.", + "example": "ADH1", + "homepage": "http://wolfe.gen.tcd.ie/ygob", + "keywords": [ + "gene", + "genome" + ], + "mappings": { + "prefixcommons": "ygob" + }, + "name": "Yeast Genome Order Browser", + "preferred_prefix": "ygob", + "provides": "hgnc.symbol", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1" + }, + "yid": { + "description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].", + "example": "SNR17A", + "homepage": "http://compbio.soe.ucsc.edu/yeast_introns.html", + "mappings": { + "biocontext": "YID", + "miriam": "yid", + "n2t": "yid" + }, + "name": "Yeast Intron Database v3", + "pattern": "^[A-Z0-9]+$", + "preferred_prefix": "yid", + "uri_format": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1" + }, + "ymdb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast).", + "example": "YMDB00001", + "homepage": "http://www.ymdb.ca", + "keywords": [ + "life science", + "metabolomics" + ], + "mappings": { + "fairsharing": "FAIRsharing.tawpg2", + "re3data": "r3d100012733" + }, + "name": "Yeast Metabolome Database", + "pattern": "^YMDB\\d+$", + "preferred_prefix": "ymdb", + "publications": [ + { + "doi": "10.1093/nar/gkr916", + "pmc": "PMC3245085", + "pubmed": "22064855", + "title": "YMDB: the Yeast Metabolome Database.", + "year": 2011 + } + ], + "twitter": "WishartLab", + "uri_format": "http://www.ymdb.ca/compounds/$1" + }, + "ypo": { + "contact": { + "email": "cherry@genome.stanford.edu", + "github": null, + "name": "Mike Cherry", + "orcid": "0000-0001-9163-5180" + }, + "deprecated": true, + "homepage": "http://www.yeastgenome.org/", + "keywords": [ + "obo", + "ontology" + ], + "mappings": { + "biocontext": "YPO", + "obofoundry": "ypo" + }, + "name": "Yeast Phenotype Ontology", + "preferred_prefix": "YPO", + "uri_format": "http://purl.obolibrary.org/obo/YPO_$1" + }, + "yrcpdr": { + "contact": { + "email": "mriffle@u.washington.edu", + "github": null, + "name": "Michael Riffle", + "orcid": "0000-0003-1633-8607" + }, + "description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). 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The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation.", - "created": "2019-06-11T14:17:16.858+0000", - "modified": "2019-06-11T14:17:16.858+0000", - "resources": [ - { - "id": 1218, - "mirId": "MIR:00100545", - "urlPattern": "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession={$id}", - "name": "PANTHER Pathway Component at USC (Los Angeles)", - "description": "PANTHER Pathway Component at USC (Los Angeles)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "P00266", - "resourceHomeUrl": "http://www.pantherdb.org/", - "institution": { - "id": 94, - "name": "Keck School of Medicine, University of Southern California", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "P00266", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1219, - "prefix": "gmd.profile", - "mirId": "MIR:00000423", - "name": "Golm Metabolome Database Profile", - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues.", - "created": "2019-06-11T14:17:17.038+0000", - "modified": "2019-06-11T14:17:17.038+0000", - "resources": [ - { - "id": 1220, - "mirId": "MIR:00100546", - "urlPattern": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId={$id}", - "name": "Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology", - "description": "Golm Metabolome Database (Profile) at Max Planck Institute of Molecular Plant Physiology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "10b38aaf-b977-4950-85b8-f4775f66658d", - "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", - "institution": { - "id": 806, - "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "10b38aaf-b977-4950-85b8-f4775f66658d", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1221, - "prefix": "gmd.gcms", - "mirId": "MIR:00000424", - "name": "Golm Metabolome Database GC-MS spectra", - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra.", - "created": "2019-06-11T14:17:17.255+0000", - "modified": "2019-06-11T14:17:17.255+0000", - "resources": [ - { - "id": 1222, - "mirId": "MIR:00100547", - "urlPattern": "http://gmd.mpimp-golm.mpg.de/Spectrums/{$id}", - "name": "Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology", - "description": "Golm Metabolome Database (GC-MS Spectra) at Max Planck Institute of Molecular Plant Physiology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "53d583d8-40c6-40e1-9296-23f821cd77a5", - "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", - "institution": { - "id": 806, - "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "53d583d8-40c6-40e1-9296-23f821cd77a5", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1223, - "prefix": "gmd.ref", - "mirId": "MIR:00000425", - "name": "Golm Metabolome Database Reference Substance", - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances.", - "created": "2019-06-11T14:17:17.475+0000", - "modified": "2019-06-11T14:17:17.475+0000", - "resources": [ - { - "id": 1224, - "mirId": "MIR:00100548", - "urlPattern": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/{$id}", - "name": "Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology", - "description": "Golm Metabolome Database (Reference Substance) at Max Planck Institute of Molecular Plant Physiology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "8cf84adb-b4db-4807-ac98-0004247c35df", - "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", - "institution": { - "id": 806, - "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "8cf84adb-b4db-4807-ac98-0004247c35df", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1225, - "prefix": "gmd.analyte", - "mirId": "MIR:00000426", - "name": "Golm Metabolome Database Analyte", - "pattern": "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$", - "description": "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes.", - "created": "2019-06-11T14:17:17.661+0000", - "modified": "2019-06-11T14:17:17.661+0000", - "resources": [ - { - "id": 1226, - "mirId": "MIR:00100549", - "urlPattern": "http://gmd.mpimp-golm.mpg.de/Analytes/{$id}", - "name": "Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology", - "description": "Golm Metabolome Database (Analyte) at Max Planck Institute of Molecular Plant Physiology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", - "resourceHomeUrl": "http://gmd.mpimp-golm.mpg.de/", - "institution": { - "id": 806, - "name": "Max Planck Institute of Molecular Plant Physiology, Potsdam", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1227, - "prefix": "intact.molecule", - "mirId": "MIR:00000427", - "name": "IntAct Molecule", - "pattern": "^EBI\\-[0-9]+$", - "description": "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules.", - "created": "2019-06-11T14:17:17.850+0000", - "modified": "2019-06-11T14:17:17.850+0000", - "resources": [ - { - "id": 1228, - "mirId": "MIR:00100550", - "urlPattern": "https://www.ebi.ac.uk/intact/molecule/{$id}", - "name": "IntAct Molecule at EBI", - "description": "IntAct Molecule at EBI", - "official": false, - "providerCode": "ebi", - "sampleId": "EBI-366083", - "resourceHomeUrl": "https://www.ebi.ac.uk/intact/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "EBI-366083", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1229, - "prefix": "depod", - "mirId": "MIR:00000428", - "name": "DEPOD", - "pattern": "^[A-Z0-9]+$", - "description": "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources.", - "created": "2019-06-11T14:17:18.034+0000", - "modified": "2019-06-11T14:17:18.034+0000", - "resources": [ - { - "id": 1231, - "mirId": "MIR:00100551", - "urlPattern": "http://www.depod.bioss.uni-freiburg.de/showp.php?gene={$id}", - "name": "DEPOD at EMBL", - "description": "DEPOD at EMBL", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "PTPN1", - "resourceHomeUrl": "http://www.depod.bioss.uni-freiburg.de", - "institution": { - "id": 1230, - "name": "European Molecular Biology Laboratory EMBL, Heidelberg", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "PTPN1", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1232, - "prefix": "cst", - "mirId": "MIR:00000429", - "name": "Cell Signaling Technology Pathways", - "pattern": "^[A-Za-z0-9_-]+$", - "description": "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways.", - "created": "2019-06-11T14:17:18.324+0000", - "modified": "2019-06-11T14:17:18.324+0000", - "resources": [ - { - "id": 1234, - "mirId": "MIR:00100552", - "urlPattern": "http://www.cellsignal.com/reference/pathway/{$id}.html", - "name": "CST Pathways at Cell Signaling Technology", - "description": "CST Pathways at Cell Signaling Technology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "Akt_PKB", - "resourceHomeUrl": "http://www.cellsignal.com/pathways/index.html", - "institution": { - "id": 1233, - "name": "Cell Signaling Technology, Inc., Danvers, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "Akt_PKB", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1241, - "prefix": "phytozome.locus", - "mirId": "MIR:00000432", - "name": "Phytozome Locus", - "pattern": "^[A-Za-z0-9]+$", - "description": "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information.", - "created": "2019-06-11T14:17:19.049+0000", - "modified": "2019-06-11T14:17:19.049+0000", - "resources": [ - { - "id": 1243, - "mirId": "MIR:00100556", - "urlPattern": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:{$id}", - "name": "Phytozome Locus at Joint Genome Institute", - "description": "Phytozome Locus at Joint Genome Institute", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "Glyma0021s00410", - "resourceHomeUrl": "http://www.phytozome.net/", - "institution": { - "id": 1242, - "name": "Joint Genome Institute, California, and the Center for Integrative Genomics, Lausanne", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "Glyma0021s00410", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1244, - "prefix": "subtilist", - "mirId": "MIR:00000433", - "name": "SubtiList", - "pattern": "^BG\\d+$", - "description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.", - "created": "2019-06-11T14:17:19.310+0000", - "modified": "2019-06-11T14:17:19.310+0000", - "resources": [ - { - "id": 1246, - "mirId": "MIR:00100557", - "urlPattern": "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+{$id}", - "name": "SubtiList at Pasteur Institute", - "description": "SubtiList at Pasteur Institute", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "BG11523", - "resourceHomeUrl": "http://genolist.pasteur.fr/SubtiList/", - "institution": { - "id": 1245, - "name": "Pasteur Institute, Paris", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "FR", - "countryName": "France" - } - }, - "location": { - "countryCode": "FR", - "countryName": "France" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "BG11523", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1247, - "prefix": "dailymed", - "mirId": "MIR:00000434", - "name": "DailyMed", - "pattern": "^[A-Za-z0-9-]+", - "description": "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read.", - "created": "2019-06-11T14:17:19.532+0000", - "modified": "2019-06-11T14:17:19.532+0000", - "resources": [ - { - "id": 1249, - "mirId": "MIR:00100558", - "urlPattern": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid={$id}", - "name": "DailyMed at NLM", - "description": "DailyMed at NLM", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54", - "resourceHomeUrl": "https://dailymed.nlm.nih.gov/dailymed/", - "institution": { - "id": 1248, - "name": "U.S. National Library of Medicine, Bethesda, Maryland", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "973a9333-fec7-46dd-8eb5-25738f06ee54", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1250, - "prefix": "sider.drug", - "mirId": "MIR:00000435", - "name": "SIDER Drug", - "pattern": "^\\d+$", - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER.", - "created": "2019-06-11T14:17:19.846+0000", - "modified": "2019-06-11T14:17:19.846+0000", - "resources": [ - { - "id": 1252, - "mirId": "MIR:00100559", - "urlPattern": "http://sideeffects.embl.de/drugs/{$id}/", - "name": "SIDER Drug v2 at EMBL (Heidelberg)", - "description": "SIDER Drug v2 at EMBL (Heidelberg)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "2244", - "resourceHomeUrl": "http://sideeffects.embl.de/", - "institution": { - "id": 1251, - "name": "Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "2244", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1253, - "prefix": "sider.effect", - "mirId": "MIR:00000436", - "name": "SIDER Side Effect", - "pattern": "^C\\d+$", - "description": "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER.", - "created": "2019-06-11T14:17:20.079+0000", - "modified": "2019-06-11T14:17:20.079+0000", - "resources": [ - { - "id": 1254, - "mirId": "MIR:00100560", - "urlPattern": "http://sideeffects.embl.de/se/{$id}/", - "name": "SIDER Side Effect v2 at EMBL (Heidelberg)", - "description": "SIDER Side Effect v2 at EMBL (Heidelberg)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "C0017565", - "resourceHomeUrl": "http://sideeffects.embl.de/", - "institution": { - "id": 1251, - "name": "Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "C0017565", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1255, - "prefix": "wikigenes", - "mirId": "MIR:00000437", - "name": "WikiGenes", - "pattern": "^\\d+$", - "description": "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process.", - "created": "2019-06-11T14:17:20.303+0000", - "modified": "2019-06-11T14:17:20.303+0000", - "resources": [ - { - "id": 1257, - "mirId": "MIR:00100567", - "urlPattern": "http://www.wikigenes.org/e/gene/e/{$id}.html", - "name": "WikiGenes at Massachusetts Institute of Technology", - "description": "WikiGenes at Massachusetts Institute of Technology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "3771877", - "resourceHomeUrl": "http://www.wikigenes.org/", - "institution": { - "id": 1256, - "name": "Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "3771877", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1258, - "prefix": "broad", - "mirId": "MIR:00000438", - "name": "Broad Fungal Genome Initiative", - "pattern": "^S\\d+$", - "description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. 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It stands near to the Yuanmingyuan Garden and the Summer Palace.\nPeking University is proud of its outstanding faculty, including 48 members of the Chinese Academy of Sciences (CAS), 9 members of the Chinese Academy of Engineering (CAE), and 21 members of the Third World Academy of Sciences (TWAS).", - "rorId": null, - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "AT1G01030.1", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1310, - "prefix": "iuphar.ligand", - "mirId": "MIR:00000457", - "name": "IUPHAR ligand", - "pattern": "^\\d+$", - "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands.", - "created": "2019-06-11T14:17:24.936+0000", - "modified": "2019-06-11T14:17:24.936+0000", - "resources": [ - { - "id": 1311, - "mirId": "MIR:00100592", - "urlPattern": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId={$id}", - "name": "IUPHAR ligand at University of Edinburgh", - "description": "IUPHAR ligand at University of Edinburgh", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "1755", - "resourceHomeUrl": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all", - "institution": { - "id": 827, - "name": "Centre for Cardiovascular Science, University of Edinburgh, Edinburgh", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "1755", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1312, - "prefix": "molbase", - "mirId": "MIR:00000458", - "name": "Molbase", - "pattern": "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$", - "description": "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier.", - "created": "2019-06-11T14:17:25.144+0000", - "modified": "2019-06-11T14:17:25.144+0000", - "resources": [ - { - "id": 1314, - "mirId": "MIR:00100593", - "urlPattern": "http://www.molbase.com/en/index.php?app=search&search_keyword={$id}", - "name": "Molbase at Chinese Academy of Sciences", - "description": "Molbase at Chinese Academy of Sciences", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "128796-39-4", - "resourceHomeUrl": "http://www.molbase.com/", - "institution": { - "id": 1313, - "name": "Chinese Academy of Sciences, Xuhui District Shanghai", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "128796-39-4", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1315, - "prefix": "yrcpdr", - "mirId": "MIR:00000459", - "name": "YRC PDR", - "pattern": "^\\d+$", - "description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.", - "created": "2019-06-11T14:17:25.397+0000", - "modified": "2019-06-11T14:17:25.397+0000", - "resources": [ - { - "id": 1317, - "mirId": "MIR:00100594", - "urlPattern": "http://yeastrc.org/pdr/viewProtein.do?id={$id}", - "name": "YRC PDR at University of Washington", - "description": "YRC PDR at University of Washington", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "2673500", - "resourceHomeUrl": "http://www.yeastrc.org/pdr/", - "institution": { - "id": 1316, - "name": "Department of Biochemistry, University of Washington, Seattle", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "2673500", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1318, - "prefix": "yid", - "mirId": "MIR:00000460", - "name": "Yeast Intron Database v3", - "pattern": "^[A-Z0-9]+$", - "description": "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521].", - "created": "2019-06-11T14:17:25.610+0000", - "modified": "2019-06-11T14:17:25.610+0000", - "resources": [ - { - "id": 1320, - "mirId": "MIR:00100595", - "urlPattern": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName={$id}", - "name": "Yeast Intron Database version 3 at Baskin School of Engineering", - "description": "Yeast Intron Database version 3 at Baskin School of Engineering", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "SNR17A", - "resourceHomeUrl": "http://compbio.soe.ucsc.edu/yeast_introns.html", - "institution": { - "id": 1319, - "name": "University of California, Santa Cruz", - "homeUrl": "https://www.ucsc.edu", - "description": "UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n", - "rorId": "https://ror.org/03s65by71", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "SNR17A", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1321, - "prefix": "funcbase.fly", - "mirId": "MIR:00000461", - "name": "FuncBase Fly", - "pattern": "^\\d+$", - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data.", - "created": "2019-06-11T14:17:25.854+0000", - "modified": "2019-06-11T14:17:25.854+0000", - "resources": [ - { - "id": 1323, - "mirId": "MIR:00100596", - "urlPattern": "http://func.mshri.on.ca/fly/genes/list_functional_scores/{$id}", - "name": "FuncBase Fly at Harvard Medical School", - "description": "FuncBase Fly at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "10194", - "resourceHomeUrl": "http://func.mshri.on.ca/fly", - "institution": { - "id": 1322, - "name": "Harvard Medical School, Boston, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "10194", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1324, - "prefix": "funcbase.human", - "mirId": "MIR:00000462", - "name": "FuncBase Human", - "pattern": "^\\d+$", - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. 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This collection references human data.", - "created": "2019-06-11T14:17:26.074+0000", - "modified": "2019-06-11T14:17:26.074+0000", - "resources": [ - { - "id": 1325, - "mirId": "MIR:00100597", - "urlPattern": "http://func.mshri.on.ca/human/genes/list_functional_scores/{$id}", - "name": "FuncBase Human at Harvard Medical School", - "description": "FuncBase Human at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "119514", - "resourceHomeUrl": "http://func.mshri.on.ca/human/", - "institution": { - "id": 1322, - "name": "Harvard Medical School, Boston, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "119514", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1326, - "prefix": "funcbase.mouse", - "mirId": "MIR:00000463", - "name": "FuncBase Mouse", - "pattern": "^\\d+$", - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. 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This collection references mouse.", - "created": "2019-06-11T14:17:26.285+0000", - "modified": "2019-06-11T14:17:26.285+0000", - "resources": [ - { - "id": 1327, - "mirId": "MIR:00100598", - "urlPattern": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/{$id}", - "name": "FuncBase Mouse at Harvard Medical School", - "description": "FuncBase Mouse at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "1351341", - "resourceHomeUrl": "http://func.mshri.on.ca/mouse/", - "institution": { - "id": 1322, - "name": "Harvard Medical School, Boston, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "1351341", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1881, - "prefix": "cbioportal", - "mirId": "MIR:00000679", - "name": "The cBioPortal for Cancer Genomics", - "pattern": "^[a-z0-9\\_]+$", - "description": "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.", - "created": "2019-06-11T14:18:18.874+0000", - "modified": "2019-06-11T14:18:18.874+0000", - "resources": [ - { - "id": 1883, - "mirId": "MIR:00100909", - "urlPattern": "http://www.cbioportal.org/study?id={$id}#summary", - "name": "The cBioPortal for Cancer Genomics", - "description": "The cBioPortal for Cancer Genomics", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "laml_tcga_pub", - "resourceHomeUrl": "http://www.cbioportal.org", - "institution": { - "id": 1882, - "name": "Memorial Sloan Kettering Cancer Center", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "laml_tcga_pub", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1328, - "prefix": "funcbase.yeast", - "mirId": "MIR:00000464", - "name": "FuncBase Yeast", - "pattern": "^\\d+$", - "description": "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. 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This collection references yeast.", - "created": "2019-06-11T14:17:26.470+0000", - "modified": "2019-06-11T14:17:26.470+0000", - "resources": [ - { - "id": 1329, - "mirId": "MIR:00100599", - "urlPattern": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/{$id}", - "name": "FuncBase Yeast at Harvard Medical School", - "description": "FuncBase Yeast at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "2701", - "resourceHomeUrl": "http://func.mshri.on.ca/yeast", - "institution": { - "id": 1322, - "name": "Harvard Medical School, Boston, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "2701", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1330, - "prefix": "ydpm", - "mirId": "MIR:00000465", - "name": "YDPM", - "pattern": "^Y[A-Z]{2}\\d+[CW]$", - "description": "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.", - "created": "2019-06-11T14:17:26.654+0000", - "modified": "2019-06-11T14:17:26.654+0000", - "resources": [ - { - "id": 1332, - "mirId": "MIR:00100600", - "urlPattern": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}", - "name": "YDPM at Stanford University School of Medicine", - "description": "YDPM at Stanford University School of Medicine", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "YAL001C", - "resourceHomeUrl": "http://www-deletion.stanford.edu/YDPM/", - "institution": { - "id": 1331, - "name": "Stanford University School of Medicine, Stanford, California", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "YAL001C", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1333, - "prefix": "wb.rnai", - "mirId": "MIR:00000466", - "name": "WormBase RNAi", - "pattern": "^WBRNAi\\d{8}$", - "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes.", - "created": "2019-06-11T14:17:26.886+0000", - "modified": "2019-06-11T14:17:26.886+0000", - "resources": [ - { - "id": 1334, - "mirId": "MIR:00100601", - "urlPattern": "https://www.wormbase.org/species/c_elegans/rnai/{$id}", - "name": "WormBase RNAi", - "description": "WormBase RNAi", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "WBRNAi00086878", - "resourceHomeUrl": "https://www.wormbase.org/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "WBRNAi00086878", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1335, - "prefix": "pass2", - "mirId": "MIR:00000468", - "name": "PASS2", - "pattern": "^\\d+$", - "description": "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity.", - "created": "2019-06-11T14:17:27.086+0000", - "modified": "2019-06-11T14:17:27.086+0000", - "resources": [ - { - "id": 1337, - "mirId": "MIR:00100603", - "urlPattern": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id={$id}", - "name": "PASS2 at National centre for Biological Sciences (India)", - "description": "PASS2 at National centre for Biological Sciences (India)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "46977", - "resourceHomeUrl": "http://caps.ncbs.res.in/pass2/", - "institution": { - "id": 1336, - "name": "National centre for Biological Sciences, TIFR, GKVK campus, Bangalore, Karnataka", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "IN", - "countryName": "India" - } - }, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "46977", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1338, - "prefix": "iceberg.element", - "mirId": "MIR:00000469", - "name": "ICEberg element", - "pattern": "^\\d+$", - "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements.", - "created": "2019-06-11T14:17:27.338+0000", - "modified": "2019-06-11T14:17:27.338+0000", - "resources": [ - { - "id": 1340, - "mirId": "MIR:00100604", - "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id}", - "name": "ICEberg element at Shanghai Jiaotong University", - "description": "ICEberg element at Shanghai Jiaotong University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "100", - "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", - "institution": { - "id": 1339, - "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "100", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1341, - "prefix": "iceberg.family", - "mirId": "MIR:00000470", - "name": "ICEberg family", - "pattern": "^\\d+$", - "description": "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families.", - "created": "2019-06-11T14:17:27.601+0000", - "modified": "2019-06-11T14:17:27.601+0000", - "resources": [ - { - "id": 1343, - "mirId": "MIR:00100605", - "urlPattern": "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id={$id}", - "name": "ICEberg family at Shanghai Jiaotong University", - "description": "ICEberg family at Shanghai Jiaotong University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "1", - "resourceHomeUrl": "http://db-mml.sjtu.edu.cn/ICEberg/", - "institution": { - "id": 1342, - "name": "State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp; Biotechnology, Shanghai Jiaotong University, Shanghai", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "1", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1344, - "prefix": "vfdb.genus", - "mirId": "MIR:00000471", - "name": "VFDB Genus", - "pattern": "^\\w+$", - "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus.", - "created": "2019-06-11T14:17:27.811+0000", - "modified": "2019-06-11T14:17:27.811+0000", - "resources": [ - { - "id": 1346, - "mirId": "MIR:00100606", - "urlPattern": "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus={$id}", - "name": "VFDB Genus at Institute of Pathogen Biology", - "description": "VFDB Genus at Institute of Pathogen Biology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "Chlamydia", - "resourceHomeUrl": "http://www.mgc.ac.cn/VFs/", - "institution": { - "id": 1345, - "name": "State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "Chlamydia", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1347, - "prefix": "vfdb.gene", - "mirId": "MIR:00000472", - "name": "VFDB Gene", - "pattern": "^\\w+$", - "description": "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes.", - "created": "2019-06-11T14:17:28.027+0000", - "modified": "2019-06-11T14:17:28.027+0000", - "resources": [ - { - "id": 1348, - "mirId": "MIR:00100607", - "urlPattern": "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID={$id}", - "name": "VFDB Gene at Institute of Pathogen Biology", - "description": "VFDB Gene at Institute of Pathogen Biology", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "VFG2154", - "resourceHomeUrl": "http://www.mgc.ac.cn/VFs/", - "institution": { - "id": 1345, - "name": "State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy Medical Sciences and Peking Union Medical College, Beijing", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "VFG2154", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1349, - "prefix": "mesh.2013", - "mirId": "MIR:00000473", - "name": "MeSH 2013", - "pattern": "^[A-Za-z0-9]+$", - "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013.", - "created": "2019-06-11T14:17:28.224+0000", - "modified": "2019-06-11T14:17:28.224+0000", - "resources": [ - { - "id": 1350, - "mirId": "MIR:00100608", - "urlPattern": "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index={$id}&view=expanded", - "name": "MeSH 2013 at National Library of Medicine", - "description": "MeSH 2013 at National Library of Medicine", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "17165", - "resourceHomeUrl": "http://www.nlm.nih.gov/mesh/", - "institution": { - "id": 792, - "name": "U.S. National Library of Medicine, National Institute of Health, Maryland", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "17165", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1351, - "prefix": "kegg.module", - "mirId": "MIR:00000474", - "name": "KEGG Module", - "pattern": "^([a-z]{3,5}_)?M\\d{5}$", - "description": "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules.", - "created": "2019-06-11T14:17:28.414+0000", - "modified": "2019-06-11T14:17:28.414+0000", - "resources": [ - { - "id": 1352, - "mirId": "MIR:00100609", - "urlPattern": "http://www.kegg.jp/entry/{$id}", - "name": "KEGG Module at Kyoto University Bioinformatics Center", - "description": "KEGG Module at Kyoto University Bioinformatics Center", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "M00002", - "resourceHomeUrl": "http://www.kegg.jp/kegg/module.html", - "institution": { - "id": 367, - "name": "Department of Computational Biology, University of Tokyo, Tokyo", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "M00002", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1353, - "prefix": "kegg.disease", - "mirId": "MIR:00000475", - "name": "KEGG Disease", - "pattern": "^H\\d+$", - "description": "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system.", - "created": "2019-06-11T14:17:28.601+0000", - "modified": "2019-06-11T14:17:28.601+0000", - "resources": [ - { - "id": 1354, - "mirId": "MIR:00100610", - "urlPattern": "http://www.kegg.jp/entry/{$id}", - "name": "KEGG Disease at Kyoto University Bioinformatics Center", - "description": "KEGG Disease at Kyoto University Bioinformatics Center", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "H00076", - "resourceHomeUrl": "http://www.genome.jp/kegg/disease/", - "institution": { - "id": 705, - "name": "Kyoto University Bioinformatics Center, Kyoto", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "H00076", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1355, - "prefix": "medlineplus", - "mirId": "MIR:00000476", - "name": "MedlinePlus", - "pattern": "^\\d+$", - "description": "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language.", - "created": "2019-06-11T14:17:28.795+0000", - "modified": "2019-06-11T14:17:28.795+0000", - "resources": [ - { - "id": 1356, - "mirId": "MIR:00100611", - "urlPattern": "http://www.nlm.nih.gov/medlineplus/ency/article/{$id}.htm", - "name": "MedlinePlus at NCBI", - "description": "MedlinePlus at NCBI", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "002804", - "resourceHomeUrl": "http://www.nlm.nih.gov/medlineplus/", - "institution": { - "id": 26, - "name": "National Center for Biotechnology Information", - "homeUrl": "https://www.ncbi.nlm.nih.gov/", - "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", - "rorId": "https://ror.org/02meqm098", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "002804", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1360, - "prefix": "glycoepitope", - "mirId": "MIR:00000478", - "name": "GlycoEpitope", - "pattern": "^EP\\d{4}$", - "description": "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes.", - "created": "2019-06-11T14:17:29.214+0000", - "modified": "2019-06-11T14:17:29.214+0000", - "resources": [ - { - "id": 1362, - "mirId": "MIR:00100613", - "urlPattern": "https://www.glycoepitope.jp/epitopes/{$id}", - "name": "GlycoEpitope at Ritsumeikan University", - "description": "GlycoEpitope at Ritsumeikan University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "EP0311", - "resourceHomeUrl": "https://www.glycoepitope.jp/epitopes/", - "institution": { - "id": 1361, - "name": "Kawasaki laboratory, Research Center for Glycobiotechnology, Ritsumeikan University", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "EP0311", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1363, - "prefix": "jcggdb", - "mirId": "MIR:00000479", - "name": "JCGGDB", - "pattern": "^JCGG-STR\\d{6}$", - "description": "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc.", - "created": "2019-06-11T14:17:29.437+0000", - "modified": "2019-06-11T14:17:29.437+0000", - "resources": [ - { - "id": 1365, - "mirId": "MIR:00100614", - "urlPattern": "http://jcggdb.jp/idb/jcggdb/{$id}", - "name": "JCGGDB at Advanced Science Institute (Japan)", - "description": "JCGGDB at Advanced Science Institute (Japan)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "JCGG-STR008690", - "resourceHomeUrl": "http://jcggdb.jp/index_en.html", - "institution": { - "id": 1364, - "name": "RIKEN Advanced Science Institute", - "homeUrl": "http://www.riken.jp/en/about/reports/evaluation/asi/", - "description": "Established by RIKEN in April 2008, based on the DRI (Discovery Research Institute) and the FRS (Frontier Research System). ASI is unique since it is structured as comprehensive system supporting the full range of scientific fields including high energy/nuclear/astro-physics, condensed matter physics, chemistry, electronic engineering, biology and medicine.", - "rorId": "https://ror.org/030vbmf58", - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "JCGG-STR008690", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1366, - "prefix": "noncodev4.gene", - "mirId": "MIR:00000480", - "name": "NONCODE v4 Gene", - "pattern": "^NONHSAG\\d{5}$", - "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions.", - "created": "2019-06-11T14:17:29.649+0000", - "modified": "2019-06-11T14:17:29.649+0000", - "resources": [ - { - "id": 1367, - "mirId": "MIR:00100616", - "urlPattern": "http://www.bioinfo.org/NONCODEv4/show_gene.php?id={$id}", - "name": "NONCODE v4 Gene at Chinese Academy of Sciences", - "description": "NONCODE v4 Gene at Chinese Academy of Sciences", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "NONHSAG00001", - "resourceHomeUrl": "http://www.bioinfo.org/NONCODEv4/", - "institution": { - "id": 737, - "name": "Chinese Academy of Sciences", - "homeUrl": "http://english.cas.cn/", - "description": "The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches.", - "rorId": "https://ror.org/034t30j35", - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "NONHSAG00001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1884, - "prefix": "vfb", - "mirId": "MIR:00000680", - "name": "Virtual Fly Brain", - "pattern": "^[0-9a-zA-Z]{8}$", - "description": "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster.", - "created": "2019-06-11T14:18:19.150+0000", - "modified": "2019-06-11T14:18:19.150+0000", - "resources": [ - { - "id": 1886, - "mirId": "MIR:00100911", - "urlPattern": "http://virtualflybrain.org/reports/{$id}", - "name": "Virtual Fly Brain", - "description": "Virtual Fly Brain", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "00000001", - "resourceHomeUrl": "https://VirtualFlyBrain.org", - "institution": { - "id": 1885, - "name": "The University of Cambridge", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "00000001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1368, - "prefix": "noncodev4.rna", - "mirId": "MIR:00000481", - "name": "NONCODE v4 Transcript", - "pattern": "^NONHSAT\\d{6}$", - "description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts.", - "created": "2019-06-11T14:17:29.833+0000", - "modified": "2019-06-11T14:17:29.833+0000", - "resources": [ - { - "id": 1369, - "mirId": "MIR:00100617", - "urlPattern": "http://www.bioinfo.org/NONCODEv4/show_rna.php?id={$id}", - "name": "NONCODE v4 Transcript at Chinese Academy of Sciences", - "description": "NONCODE v4 Transcript at Chinese Academy of Sciences", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "NONHSAT000001", - "resourceHomeUrl": "http://www.bioinfo.org/NONCODEv4/", - "institution": { - "id": 737, - "name": "Chinese Academy of Sciences", - "homeUrl": "http://english.cas.cn/", - "description": "The Chinese Academy of Sciences is the linchpin of China’s drive to explore and harness high technology and the natural sciences for the benefit of China and the world. CAS brings together scientists and engineers from China and around the world to address both theoretical and applied problems using world-class scientific and management approaches.", - "rorId": "https://ror.org/034t30j35", - "location": { - "countryCode": "CN", - "countryName": "China" - } - }, - "location": { - "countryCode": "CN", - "countryName": "China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "NONHSAT000001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1370, - "prefix": "oryzabase.gene", - "mirId": "MIR:00000482", - "name": "Oryzabase Gene", - "pattern": "^\\d+$", - "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information.", - "created": "2019-06-11T14:17:30.027+0000", - "modified": "2019-06-11T14:17:30.027+0000", - "resources": [ - { - "id": 1372, - "mirId": "MIR:00100618", - "urlPattern": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/{$id}", - "name": "Oryzabase v4 Gene at National Institute of Genetics (Japan)", - "description": "Oryzabase v4 Gene at National Institute of Genetics (Japan)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "117", - "resourceHomeUrl": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", - "institution": { - "id": 1371, - "name": "Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "117", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1373, - "prefix": "oryzabase.mutant", - "mirId": "MIR:00000483", - "name": "Oryzabase Mutant", - "pattern": "^\\d+$", - "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information.", - "created": "2019-06-11T14:17:30.248+0000", - "modified": "2019-06-11T14:17:30.248+0000", - "resources": [ - { - "id": 1374, - "mirId": "MIR:00100619", - "urlPattern": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/{$id}", - "name": "Oryzabase v4 Mutant at National Institute of Genetics (Japan)", - "description": "Oryzabase v4 Mutant at National Institute of Genetics (Japan)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "21393", - "resourceHomeUrl": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", - "institution": { - "id": 1371, - "name": "Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "21393", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1375, - "prefix": "oryzabase.strain", - "mirId": "MIR:00000484", - "name": "Oryzabase Strain", - "pattern": "^\\d+$", - "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. 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This collection references wild strain information.", - "created": "2019-06-11T14:17:30.425+0000", - "modified": "2019-06-11T14:17:30.425+0000", - "resources": [ - { - "id": 1376, - "mirId": "MIR:00100620", - "urlPattern": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/{$id}", - "name": "Oryzabase v4 Strain at National Institute of Genetics (Japan)", - "description": "Oryzabase v4 Strain at National Institute of Genetics (Japan)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "1", - "resourceHomeUrl": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", - "institution": { - "id": 1371, - "name": "Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "1", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1377, - "prefix": "oryzabase.stage", - "mirId": "MIR:00000485", - "name": "Oryzabase Stage", - "pattern": "^\\d+$", - "description": "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. 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This collection references development stage information.", - "created": "2019-06-11T14:17:30.616+0000", - "modified": "2019-06-11T14:17:30.616+0000", - "resources": [ - { - "id": 1378, - "mirId": "MIR:00100621", - "urlPattern": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/{$id}", - "name": "Oryzabase v4 Stage at National Institute of Genetics (Japan)", - "description": "Oryzabase v4 Stage at National Institute of Genetics (Japan)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "34", - "resourceHomeUrl": "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/", - "institution": { - "id": 1371, - "name": "Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "34", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1379, - "prefix": "otl", - "mirId": "MIR:00000486", - "name": "Oryza Tag Line", - "pattern": "^A[A-Z]+\\d+$", - "description": "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. 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It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information.", - "created": "2019-06-11T14:17:30.833+0000", - "modified": "2019-06-11T14:17:30.833+0000", - "resources": [ - { - "id": 1381, - "mirId": "MIR:00100622", - "urlPattern": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line={$id}", - "name": "Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI", - "description": "Oryza Tag Line at CIRAD-INRA-SUPAGRO-UMI", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "AADB12", - "resourceHomeUrl": "http://oryzatagline.cirad.fr/", - "institution": { - "id": 1380, - "name": "CIRAD-INRA-SUPAGRO-UMII, Biological Systems Department, Montpellier", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "FR", - "countryName": "France" - } - }, - "location": { - "countryCode": "FR", - "countryName": "France" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "AADB12", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1382, - "prefix": "genewiki", - "mirId": "MIR:00000487", - "name": "Gene Wiki", - "pattern": "^\\d+$", - "description": "The Gene Wiki is project which seeks to provide detailed information on human genes. 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This collection references protein abundance information by species.", - "created": "2019-06-11T14:17:31.315+0000", - "modified": "2019-06-11T14:17:31.315+0000", - "resources": [ - { - "id": 1386, - "mirId": "MIR:00100624", - "urlPattern": "http://pax-db.org/#!species/{$id}", - "name": "PaxDb v3 at University of Zurich", - "description": "PaxDb v3 at University of Zurich", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "9606", - "resourceHomeUrl": "http://pax-db.org/", - "institution": { - "id": 1385, - "name": "Institute of Molecular Life Sciences, University of Zurich, Zurich", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "9606", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1387, - "prefix": "paxdb.protein", - "mirId": "MIR:00000489", - "name": "PaxDb Protein", - "pattern": "^\\d+$", - "description": "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. 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This collection references G-protein coupled receptors.", - "created": "2019-06-11T14:17:32.633+0000", - "modified": "2019-06-11T14:17:32.633+0000", - "resources": [ - { - "id": 1400, - "mirId": "MIR:00100634", - "urlPattern": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id={$id}", - "name": "GLIDA GPCR at Kyoto University", - "description": "GLIDA GPCR at Kyoto University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "ACM1_HUMAN", - "resourceHomeUrl": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", - "institution": { - "id": 1399, - "name": "Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "ACM1_HUMAN", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1401, - "prefix": "glida.ligand", - "mirId": "MIR:00000494", - "name": "GLIDA Ligand", - "pattern": "^L\\d+$", - "description": "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. 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This collection references ligands.", - "created": "2019-06-11T14:17:32.872+0000", - "modified": "2019-06-11T14:17:32.872+0000", - "resources": [ - { - "id": 1402, - "mirId": "MIR:00100635", - "urlPattern": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id={$id}", - "name": "GLIDA Ligand at Kyoto University", - "description": "GLIDA Ligand at Kyoto University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "L000001", - "resourceHomeUrl": "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/", - "institution": { - "id": 1399, - "name": "Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "L000001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1403, - "prefix": "grsdb", - "mirId": "MIR:00000495", - "name": "GRSDB", - "pattern": "^\\d+$", - "description": "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). 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This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.", - "created": "2019-06-11T14:17:36.823+0000", - "modified": "2019-06-11T14:17:36.823+0000", - "resources": [ - { - "id": 1442, - "mirId": "MIR:00100657", - "urlPattern": "https://www.ebi.ac.uk/ega/studies/{$id}", - "name": "EGA Study at European Bioinformatics Institute", - "description": "EGA Study at European Bioinformatics Institute", - "official": true, - "providerCode": "ebi", - "sampleId": "EGAS00000000001", - "resourceHomeUrl": "https://www.ebi.ac.uk/ega/studies", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1443, - "mirId": "MIR:00100851", - "urlPattern": "https://www.omicsdi.org/dataset/ega/{$id}", - "name": "EGA Study through OmicsDI", - "description": "EGA Study through OmicsDI", - "official": false, - "providerCode": "omicsdi", - "sampleId": "EGAS00000000001", - "resourceHomeUrl": "https://www.omicsdi.org/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "EGAS00000000001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1444, - "prefix": "ega.dataset", - "mirId": "MIR:00000512", - "name": "European Genome-phenome Archive Dataset", - "pattern": "^EGAD\\d{11}$", - "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", - "created": "2019-06-11T14:17:37.233+0000", - "modified": "2019-06-11T14:17:37.233+0000", - "resources": [ - { - "id": 1445, - "mirId": "MIR:00100658", - "urlPattern": "https://www.ebi.ac.uk/ega/datasets/{$id}", - "name": "EGA Dataset at European Bioinformatics Institute", - "description": "EGA Dataset at European Bioinformatics Institute", - "official": true, - "providerCode": "ebi", - "sampleId": "EGAD00000000001", - "resourceHomeUrl": "https://www.ebi.ac.uk/ega/dataset", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1446, - "mirId": "MIR:00100852", - "urlPattern": "https://www.omicsdi.org/dataset/ega/{$id}", - "name": "EGA Dataset through OmicsDI", - "description": "EGA Dataset through OmicsDI", - "official": false, - "providerCode": "omicsdi", - "sampleId": "EGAD00000000001", - "resourceHomeUrl": "https://www.omicsdi.org/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "EGAD00000000001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1453, - "prefix": "pride.project", - "mirId": "MIR:00000515", - "name": "PRIDE Project", - "pattern": "^P(X|R)D\\d{6}$", - "description": "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.", - "created": "2019-06-11T14:17:38.030+0000", - "modified": "2019-06-11T14:17:38.030+0000", - "resources": [ - { - "id": 1454, - "mirId": "MIR:00100662", - "urlPattern": "https://www.ebi.ac.uk/pride/archive/projects/{$id}", - "name": "PRIDE Project at EBI", - "description": "PRIDE Project at EBI", - "official": true, - "providerCode": "ebi", - "sampleId": "PXD000440", - "resourceHomeUrl": "https://www.ebi.ac.uk/pride/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1455, - "mirId": "MIR:00100858", - "urlPattern": "https://www.omicsdi.org/dataset/pride/{$id}", - "name": "PRIDE Project through OmicsDI", - "description": "PRIDE Project through OmicsDI", - "official": false, - "providerCode": "omicsdi", - "sampleId": "PXD000440", - "resourceHomeUrl": "https://www.omicsdi.org/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "PXD000440", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1456, - "prefix": "antibodyregistry", - "mirId": "MIR:00000516", - "name": "Antibody Registry", - "pattern": "^\\d{6}$", - "description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.", - "created": "2019-06-11T14:17:38.379+0000", - "modified": "2019-06-11T14:17:38.379+0000", - "resources": [ - { - "id": 1458, - "mirId": "MIR:00100664", - "urlPattern": "http://antibodyregistry.org/AB_{$id}", - "name": "Antibody Registry at University of California", - "description": "Antibody Registry at University of California", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "493771", - "resourceHomeUrl": "http://antibodyregistry.org/", - "institution": { - "id": 1457, - "name": "Neuroscience Information Framework, University of California, San Diego, California", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "493771", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1459, - "prefix": "mamo", - "mirId": "MIR:00000517", - "name": "Mathematical Modelling Ontology", - "pattern": "^MAMO_\\d{7}$", - "description": "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.", - "created": "2019-06-11T14:17:38.625+0000", - "modified": "2019-06-11T14:17:38.625+0000", - "resources": [ - { - "id": 1460, - "mirId": "MIR:00100665", - "urlPattern": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id}", - "name": "MAMO through BioPortal", - "description": "MAMO through BioPortal", - "official": false, - "providerCode": "bptl", - "sampleId": "MAMO_0000026", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/MAMO", - "institution": { - "id": 5, - "name": "National Center for Biomedical Ontology, Stanford", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1461, - "mirId": "MIR:00100758", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form={$id}", - "name": "MaMO through OLS", - "description": "MaMO through OLS", - "official": false, - "providerCode": "ols", - "sampleId": "MAMO_0000026", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/mamo", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "MAMO_0000026", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1462, - "prefix": "eo", - "mirId": "MIR:00000518", - "name": "Plant Environment Ontology", - "pattern": "^(P)?EO\\:\\d{7}$", - "description": "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.", - "created": "2019-06-11T14:17:38.985+0000", - "modified": "2019-06-11T14:17:38.985+0000", - "resources": [ - { - "id": 1463, - "mirId": "MIR:00100667", - "urlPattern": "http://archive.gramene.org/db/ontology/search?query=EO:{$id}", - "name": "Plant Environment Ontology through Gramene", - "description": "Plant Environment Ontology through Gramene", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "0007404", - "resourceHomeUrl": "http://archive.gramene.org/db/ontology/search_term?id=EO:0007359", - "institution": { - "id": 556, - "name": "Cold Spring Harbor Laboratory, New York", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1464, - "mirId": "MIR:00100668", - "urlPattern": "http://purl.bioontology.org/ontology/PECO/EO:{$id}", - "name": "Plant Environment Ontology through BioPortal", - "description": "Plant Environment Ontology through BioPortal", - "official": false, - "providerCode": "bptl", - "sampleId": "0007404", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/PECO", - "institution": { - "id": 5, - "name": "National Center for Biomedical Ontology, Stanford", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1465, - "mirId": "MIR:00100669", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=EO:{$id}", - "name": "Plant Environment Ontology through OLS", - "description": "Plant Environment Ontology through OLS", - "official": false, - "providerCode": "ols", - "sampleId": "0007404", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/eo", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "0007404", - "namespaceEmbeddedInLui": true, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1466, - "prefix": "idot", - "mirId": "MIR:00000519", - "name": "Identifiers.org Terms", - "pattern": "^[A-Za-z]+$", - "description": "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.", - "created": "2019-06-11T14:17:39.487+0000", - "modified": "2019-06-11T14:17:39.487+0000", - "resources": [ - { - "id": 1467, - "mirId": "MIR:00100670", - "urlPattern": "https://biomodels.net/vocab/idot.rdf#{$id}", - "name": "IdoT via biomodels.net", - "description": "IdoT via biomodels.net", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "identifierPattern", - "resourceHomeUrl": "https://identifiers.org/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "identifierPattern", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1470, - "prefix": "yeastintron", - "mirId": "MIR:00000521", - "name": "Yeast Intron Database v4.3", - "pattern": "^[A-Z0-9]+$", - "description": "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].", - "created": "2019-06-11T14:17:39.906+0000", - "modified": "2019-06-11T14:17:39.906+0000", - "resources": [ - { - "id": 1471, - "mirId": "MIR:00100673", - "urlPattern": "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id}", - "name": "Yeast Intron Database version 4.3 at Baskin School of Engineering", - "description": "Yeast Intron Database version 4.3 at Baskin School of Engineering", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "SNR17A", - "resourceHomeUrl": "http://intron.ucsc.edu/yeast4.3/", - "institution": { - "id": 1319, - "name": "University of California, Santa Cruz", - "homeUrl": "https://www.ucsc.edu", - "description": "UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n", - "rorId": "https://ror.org/03s65by71", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "SNR17A", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1472, - "prefix": "ardb", - "mirId": "MIR:00000522", - "name": "Antibiotic Resistance Genes Database", - "pattern": "^[A-Z_]{3}[0-9]{4,}$", - "description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", - "created": "2019-06-11T14:17:40.104+0000", - "modified": "2019-06-11T14:17:40.104+0000", - "resources": [ - { - "id": 1474, - "mirId": "MIR:00100678", - "urlPattern": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term={$id}", - "name": "ARDB at University of Maryland", - "description": "ARDB at University of Maryland", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "CAE46076", - "resourceHomeUrl": "http://ardb.cbcb.umd.edu/", - "institution": { - "id": 1473, - "name": "Center for Bioinformatics and Computational Biology, University of Maryland, Maryland", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "CAE46076", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1475, - "prefix": "proteomicsdb.protein", - "mirId": "MIR:00000524", - "name": "ProteomicsDB Protein", - "pattern": "^\\d+$", - "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.", - "created": "2019-06-11T14:17:40.344+0000", - "modified": "2019-06-11T14:17:40.344+0000", - "resources": [ - { - "id": 1477, - "mirId": "MIR:00100680", - "urlPattern": "https://www.proteomicsdb.org/#human/proteinDetails/{$id}/summary", - "name": "Proteomics DB Protein at Center for Integrated Protein Science", - "description": "Proteomics DB Protein at Center for Integrated Protein Science", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "53504", - "resourceHomeUrl": "https://www.proteomicsdb.org/#human", - "institution": { - "id": 1476, - "name": "Center for Integrated Protein Science, Munich,", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "53504", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1478, - "prefix": "proteomicsdb.peptide", - "mirId": "MIR:00000525", - "name": "ProteomicsDB Peptide", - "pattern": "^\\d+$", - "description": "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.", - "created": "2019-06-11T14:17:40.583+0000", - "modified": "2019-06-11T14:17:40.583+0000", - "resources": [ - { - "id": 1480, - "mirId": "MIR:00100681", - "urlPattern": "https://www.proteomicsdb.org/#human/proteinDetails/{$id}/peptides/", - "name": "Proteomics DB Peptide at Center for Integrated Protein Science", - "description": "Proteomics DB Peptide at Center for Integrated Protein Science", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "53504", - "resourceHomeUrl": "https://www.proteomicsdb.org/#peptideSearch", - "institution": { - "id": 1479, - "name": "Center for Integrated Protein Science, Munich", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "53504", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1481, - "prefix": "hpm.protein", - "mirId": "MIR:00000526", - "name": "Human Proteome Map Protein", - "pattern": "^\\d+$", - "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.", - "created": "2019-06-11T14:17:40.825+0000", - "modified": "2019-06-11T14:17:40.825+0000", - "resources": [ - { - "id": 1482, - "mirId": "MIR:00100682", - "urlPattern": "http://www.humanproteomemap.org/protein.php?hpm_id={$id}", - "name": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)", - "description": "Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "1968", - "resourceHomeUrl": "http://www.humanproteomemap.org/index.php", - "institution": { - "id": 1087, - "name": "Institute of Bioinformatics, International Tech Park, Bangalore", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "IN", - "countryName": "India" - } - }, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "1968", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1483, - "prefix": "hpm.peptide", - "mirId": "MIR:00000527", - "name": "Human Proteome Map Peptide", - "pattern": "^\\d+$", - "description": "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra.", - "created": "2019-06-11T14:17:41.032+0000", - "modified": "2019-06-11T14:17:41.032+0000", - "resources": [ - { - "id": 1484, - "mirId": "MIR:00100683", - "urlPattern": "http://www.humanproteomemap.org/spectrum.php?pep_id={$id}", - "name": "Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)", - "description": "Human Proteome Map Peptide at Institute of Bioinformatics (Bangalore)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "9606117", - "resourceHomeUrl": "http://www.humanproteomemap.org/index.php", - "institution": { - "id": 1087, - "name": "Institute of Bioinformatics, International Tech Park, Bangalore", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "IN", - "countryName": "India" - } - }, - "location": { - "countryCode": "IN", - "countryName": "India" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "9606117", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1485, - "prefix": "drugbankv4.target", - "mirId": "MIR:00000528", - "name": "DrugBank Target v4", - "pattern": "^BE\\d{7}$", - "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.", - "created": "2019-06-11T14:17:41.273+0000", - "modified": "2019-06-11T14:17:41.273+0000", - "resources": [ - { - "id": 1487, - "mirId": "MIR:00100687", - "urlPattern": "http://www.drugbank.ca/biodb/bio_entities/{$id}", - "name": "DrugBank Target information version 4", - "description": "DrugBank Target information version 4", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "BE0000048", - "resourceHomeUrl": "http://www.drugbank.ca/targets", - "institution": { - "id": 1486, - "name": "Departments of Computing Science, Biological Sciences, University of Alberta", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CA", - "countryName": "Canada" - } - }, - "location": { - "countryCode": "CA", - "countryName": "Canada" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "BE0000048", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1488, - "prefix": "zinc", - "mirId": "MIR:00000529", - "name": "ZINC", - "pattern": "^(ZINC)?\\d+$", - "description": "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number.", - "created": "2019-06-11T14:17:41.559+0000", - "modified": "2019-06-11T14:17:41.559+0000", - "resources": [ - { - "id": 1490, - "mirId": "MIR:00100688", - "urlPattern": "http://zinc15.docking.org/substances/{$id}", - "name": "ZINC at University of California (San Francisco)", - "description": "ZINC at University of California (San Francisco)", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "ZINC1084", - "resourceHomeUrl": "http://zinc15.docking.org/", - "institution": { - "id": 1489, - "name": "Shoichet Laboratory, Department of Pharmaceutical Chemistry, University of California, San Francisco", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "ZINC1084", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1491, - "prefix": "foodb.compound", - "mirId": "MIR:00000530", - "name": "FooDB Compound", - "pattern": "^FDB\\d+$", - "description": "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds.", - "created": "2019-06-11T14:17:41.796+0000", - "modified": "2019-06-11T14:17:41.796+0000", - "resources": [ - { - "id": 1492, - "mirId": "MIR:00100689", - "urlPattern": "http://foodb.ca/compounds/{$id}", - "name": "FooDB database of food additives at University of Alberta", - "description": "FooDB database of food additives at University of Alberta", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "FDB002100", - "resourceHomeUrl": "http://foodb.ca/foods", - "institution": { - "id": 334, - "name": "University of Alberta", - "homeUrl": "https://www.ualberta.ca", - "description": "The University of Alberta in Edmonton is one of Canada's top teaching and research universities, with an international reputation for excellence across the humanities, sciences, creative arts, business, engineering and health sciences.", - "rorId": "https://ror.org/0160cpw27", - "location": { - "countryCode": "CA", - "countryName": "Canada" - } - }, - "location": { - "countryCode": "CA", - "countryName": "Canada" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "FDB002100", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1493, - "prefix": "unii", - "mirId": "MIR:00000531", - "name": "UNII", - "pattern": "^[A-Z0-9]+$", - "description": "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information.", - "created": "2019-06-11T14:17:41.988+0000", - "modified": "2019-06-11T14:17:41.988+0000", - "resources": [ - { - "id": 1494, - "mirId": "MIR:00100690", - "urlPattern": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno={$id}", - "name": "UNII at U.S. Food and Drug Administration", - "description": "UNII at U.S. Food and Drug Administration", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "3G6A5W338E", - "resourceHomeUrl": "http://fdasis.nlm.nih.gov/srs/", - "institution": { - "id": 1238, - "name": "U.S. Food and Drug Administration, Maryland", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "3G6A5W338E", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1495, - "prefix": "orphanet.ordo", - "mirId": "MIR:00000532", - "name": "Orphanet Rare Disease Ontology", - "pattern": "^Orphanet(_|:)C?\\d+$", - "description": "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10).", - "created": "2019-06-11T14:17:42.194+0000", - "modified": "2019-06-11T14:17:42.194+0000", - "resources": [ - { - "id": 1496, - "mirId": "MIR:00100705", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/ordo/terms?short_form={$id}", - "name": "ORDO via OLS", - "description": "ORDO via OLS", - "official": true, - "providerCode": "ols", - "sampleId": "Orphanet_C023", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/ordo", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "Orphanet_C023", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1497, - "prefix": "psipar", - "mirId": "MIR:00000533", - "name": "Protein Affinity Reagents", - "pattern": "^PAR:\\d+$", - "description": "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms.", - "created": "2019-06-11T14:17:42.461+0000", - "modified": "2019-06-11T14:17:42.461+0000", - "resources": [ - { - "id": 1498, - "mirId": "MIR:00100709", - "urlPattern": "https://www.ebi.ac.uk/ontology-lookup/?termId={$id}", - "name": "Protein Affinity Reagents through OLS", - "description": "Protein Affinity Reagents through OLS", - "official": false, - "providerCode": "ols", - "sampleId": "PAR:0116", - "resourceHomeUrl": "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "PAR:0116", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1499, - "prefix": "clinvar.record", - "mirId": "MIR:00000534", - "name": "ClinVar Record", - "pattern": "^RCV\\d+(\\.\\d+)?$", - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession.", - "created": "2019-06-11T14:17:42.685+0000", - "modified": "2019-06-11T14:17:42.685+0000", - "resources": [ - { - "id": 1501, - "mirId": "MIR:00100710", - "urlPattern": "http://www.ncbi.nlm.nih.gov/clinvar/{$id}/", - "name": "ClinVar Record at NCBI", - "description": "ClinVar Record at NCBI", - "official": false, - "providerCode": "ncbi", - "sampleId": "RCV000033555.3", - "resourceHomeUrl": "http://www.ncbi.nlm.nih.gov/clinvar/", - "institution": { - "id": 26, - "name": "National Center for Biotechnology Information", - "homeUrl": "https://www.ncbi.nlm.nih.gov/", - "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", - "rorId": "https://ror.org/02meqm098", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "RCV000033555.3", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1502, - "prefix": "mgnify.proj", - "mirId": "MIR:00000535", - "name": "MGnify Project", - "pattern": "^[A-Z]+[0-9]+$", - "description": "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.", - "created": "2019-06-11T14:17:42.938+0000", - "modified": "2019-06-11T14:17:42.938+0000", - "resources": [ - { - "id": 1503, - "mirId": "MIR:00100711", - "urlPattern": "https://www.ebi.ac.uk/metagenomics/projects/{$id}", - "name": "MGnify Project", - "description": "MGnify Project", - "official": false, - "providerCode": "ebi", - "sampleId": "ERP004492", - "resourceHomeUrl": "https://www.ebi.ac.uk/metagenomics", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "ERP004492", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1504, - "prefix": "euclinicaltrials", - "mirId": "MIR:00000536", - "name": "EU Clinical Trials", - "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", - "description": "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.", - "created": "2019-06-11T14:17:43.129+0000", - "modified": "2019-06-11T14:17:43.129+0000", - "resources": [ - { - "id": 1506, - "mirId": "MIR:00100712", - "urlPattern": "https://www.clinicaltrialsregister.eu/ctr-search/search?query={$id}", - "name": "EU Clinical Trials at European Medicines Agency", - "description": "EU Clinical Trials at European Medicines Agency", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "2008-005144-16", - "resourceHomeUrl": "https://www.clinicaltrialsregister.eu/", - "institution": { - "id": 1505, - "name": "European Medicines Agency, London", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "2008-005144-16", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1507, - "prefix": "google.patent", - "mirId": "MIR:00000537", - "name": "Google Patents", - "pattern": "^[A-Z]{2}\\d+([A-Z])?$", - "description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.", - "created": "2019-06-11T14:17:43.371+0000", - "modified": "2019-06-11T14:17:43.371+0000", - "resources": [ - { - "id": 1509, - "mirId": "MIR:00100714", - "urlPattern": "https://www.google.com/patents/{$id}", - "name": "Google Patents at Google", - "description": "Google Patents at Google", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "US4145692", - "resourceHomeUrl": "https://www.google.com/patents/", - "institution": { - "id": 1508, - "name": "Google Incorporated", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "US4145692", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1510, - "prefix": "uspto", - "mirId": "MIR:00000538", - "name": "USPTO", - "pattern": "^(D|PP|R|T|H|X|AI)?\\d+$", - "description": "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement.", - "created": "2019-06-11T14:17:43.583+0000", - "modified": "2019-06-11T14:17:43.583+0000", - "resources": [ - { - "id": 1512, - "mirId": "MIR:00100715", - "urlPattern": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/{$id}", - "name": "USPTO patents at USPTO", - "description": "USPTO patents at USPTO", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "4145692", - "resourceHomeUrl": "http://patft.uspto.gov/netahtml/PTO/index.html", - "institution": { - "id": 1511, - "name": "United States Patent and Trademark Office", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "4145692", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1513, - "prefix": "cpc", - "mirId": "MIR:00000539", - "name": "Cooperative Patent Classification", - "pattern": "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$", - "description": "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.", - "created": "2019-06-11T14:17:43.853+0000", - "modified": "2019-06-11T14:17:43.853+0000", - "resources": [ - { - "id": 1515, - "mirId": "MIR:00100716", - "urlPattern": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC={$id}", - "name": "Cooperative Patent Classification at Espace", - "description": "Cooperative Patent Classification at Espace", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "A01M1/026", - "resourceHomeUrl": "https://worldwide.espacenet.com/classification", - "institution": { - "id": 1514, - "name": "Espace, European Patent Office", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "A01M1/026", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1516, - "prefix": "gwascentral.study", - "mirId": "MIR:00000540", - "name": "GWAS Central Study", - "pattern": "^HGVST\\d+$", - "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study.", - "created": "2019-06-11T14:17:44.062+0000", - "modified": "2019-06-11T14:17:44.062+0000", - "resources": [ - { - "id": 1517, - "mirId": "MIR:00100717", - "urlPattern": "https://www.gwascentral.org/study/{$id}", - "name": "GWAS Central Study at University of Leicester", - "description": "GWAS Central Study at University of Leicester", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "HGVST1828", - "resourceHomeUrl": "https://www.gwascentral.org/studies", - "institution": { - "id": 1079, - "name": "Department of Genetics, University of Leicester, Leicester", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "HGVST1828", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1518, - "prefix": "exac.variant", - "mirId": "MIR:00000541", - "name": "ExAC Variant", - "pattern": "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$", - "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.", - "created": "2019-06-11T14:17:44.275+0000", - "modified": "2019-06-11T14:17:44.275+0000", - "resources": [ - { - "id": 1520, - "mirId": "MIR:00100718", - "urlPattern": "http://exac.broadinstitute.org/variant/{$id}", - "name": "ExAC Variant at Exome Aggregation Consortium", - "description": "ExAC Variant at Exome Aggregation Consortium", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "22-46615880-T-C", - "resourceHomeUrl": "http://exac.broadinstitute.org/", - "institution": { - "id": 1519, - "name": "Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "22-46615880-T-C", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1521, - "prefix": "gwascentral.marker", - "mirId": "MIR:00000542", - "name": "GWAS Central Marker", - "pattern": "^HGVM\\d+$", - "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker.", - "created": "2019-06-11T14:17:44.511+0000", - "modified": "2019-06-11T14:17:44.511+0000", - "resources": [ - { - "id": 1522, - "mirId": "MIR:00100719", - "urlPattern": "https://www.gwascentral.org/marker/{$id}", - "name": "GWAS Central Marker at University of Leicester", - "description": "GWAS Central Marker at University of Leicester", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "HGVM15354", - "resourceHomeUrl": "https://www.gwascentral.org/markers/", - "institution": { - "id": 1079, - "name": "Department of Genetics, University of Leicester, Leicester", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "HGVM15354", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1555, - "prefix": "bigg.metabolite", - "mirId": "MIR:00000556", - "name": "BiGG Metabolite", - "pattern": "^[a-z_A-Z0-9]+$", - "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references individual metabolotes.", - "created": "2019-06-11T14:17:47.850+0000", - "modified": "2019-06-11T14:17:47.850+0000", - "resources": [ - { - "id": 1556, - "mirId": "MIR:00100733", - "urlPattern": "http://bigg.ucsd.edu/models/universal/metabolites/{$id}", - "name": "BiGG Metabolite at University of Cakifornia", - "description": "BiGG Metabolite at University of Cakifornia", - "official": false, - "providerCode": "ucsd", - "sampleId": "12dgr161", - "resourceHomeUrl": "http://bigg.ucsd.edu/universal/metabolites", - "institution": { - "id": 190, - "name": "University of California, San Diego", - "homeUrl": "https://ucsd.edu/", - "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", - "rorId": "https://ror.org/0168r3w48", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "12dgr161", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1525, - "prefix": "lincs.cell", - "mirId": "MIR:00000544", - "name": "LINCS Cell", - "pattern": "(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)", - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.", - "created": "2019-06-11T14:17:44.903+0000", - "modified": "2019-06-11T14:17:44.903+0000", - "resources": [ - { - "id": 1527, - "mirId": "MIR:00100721", - "urlPattern": "http://lincsportal.ccs.miami.edu/cells/#/view/{$id}", - "name": "LINCS Portal", - "description": "LINCS Portal", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "LCL-2085", - "resourceHomeUrl": "http://lincsportal.ccs.miami.edu/cells/", - "institution": { - "id": 1526, - "name": "University of Miami, BD2K-LINCS DCIC", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "LCL-2085", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1528, - "prefix": "lincs.protein", - "mirId": "MIR:00000545", - "name": "LINCS Protein", - "pattern": "^\\d+$", - "description": "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins.", - "created": "2019-06-11T14:17:45.145+0000", - "modified": "2019-06-11T14:17:45.145+0000", - "resources": [ - { - "id": 1529, - "mirId": "MIR:00100722", - "urlPattern": "http://lincs.hms.harvard.edu/db/proteins/{$id}/", - "name": "LINCS Protein at Harvard Medical School", - "description": "LINCS Protein at Harvard Medical School", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "200282", - "resourceHomeUrl": "http://lincs.hms.harvard.edu/db/proteins/", - "institution": { - "id": 1322, - "name": "Harvard Medical School, Boston, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "200282", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1530, - "prefix": "lincs.smallmolecule", - "mirId": "MIR:00000546", - "name": "LINCS Small Molecule", - "pattern": "^LSM-\\d+$", - "description": "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC).", - "created": "2019-06-11T14:17:45.396+0000", - "modified": "2019-06-11T14:17:45.396+0000", - "resources": [ - { - "id": 1532, - "mirId": "MIR:00100723", - "urlPattern": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/{$id}", - "name": "LINCS Portal", - "description": "LINCS Portal", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "LSM-6306", - "resourceHomeUrl": "http://lincsportal.ccs.miami.edu/SmallMolecules/", - "institution": { - "id": 1531, - "name": "University of Miami, BD2K-LINCS DCIC, USA", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "LSM-6306", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1533, - "prefix": "exac.transcript", - "mirId": "MIR:00000547", - "name": "ExAC Transcript", - "pattern": "^ENST\\d{11}$", - "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. 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This collection references transcript information.", - "created": "2019-06-11T14:17:45.691+0000", - "modified": "2019-06-11T14:17:45.691+0000", - "resources": [ - { - "id": 1534, - "mirId": "MIR:00100724", - "urlPattern": "http://exac.broadinstitute.org/transcript/{$id}", - "name": "ExAC Transcript at Exome Aggregation Consortium", - "description": "ExAC Transcript at Exome Aggregation Consortium", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "ENST00000407236", - "resourceHomeUrl": "http://exac.broadinstitute.org/", - "institution": { - "id": 1519, - "name": "Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "ENST00000407236", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1535, - "prefix": "exac.gene", - "mirId": "MIR:00000548", - "name": "ExAC Gene", - "pattern": "^ENSG\\d{11}$", - "description": "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. 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This collection references gene information.", - "created": "2019-06-11T14:17:45.890+0000", - "modified": "2019-06-11T14:17:45.890+0000", - "resources": [ - { - "id": 1536, - "mirId": "MIR:00100725", - "urlPattern": "http://exac.broadinstitute.org/gene/{$id}", - "name": "ExAC Gene at Exome Aggregation Consortium", - "description": "ExAC Gene at Exome Aggregation Consortium", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "ENSG00000169174", - "resourceHomeUrl": "http://exac.broadinstitute.org/", - "institution": { - "id": 1519, - "name": "Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "ENSG00000169174", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1542, - "prefix": "unipathway.compound", - "mirId": "MIR:00000551", - "name": "UniPathway Compound", - "pattern": "^UPC\\d{5}$", - "description": "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds.", - "created": "2019-06-11T14:17:46.612+0000", - "modified": "2019-06-11T14:17:46.612+0000", - "resources": [ - { - "id": 1544, - "mirId": "MIR:00100728", - "urlPattern": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid={$id}", - "name": "UniPathway Compound at Swiss Institute of Bioinformatics (SIB)", - "description": "UniPathway Compound at Swiss Institute of Bioinformatics (SIB)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "UPC04349", - "resourceHomeUrl": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", - "institution": { - "id": 1730, - "name": "SIB Swiss Institute of Bioinformatics", - "homeUrl": "https://www.sib.swiss", - "description": "SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide.", - "rorId": "https://ror.org/002n09z45", - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": true, - "deprecationDate": "2019-10-01T12:10:54.792+0000" - } - ], - "sampleId": "UPC04349", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1545, - "prefix": "seed", - "mirId": "MIR:00000552", - "name": "SEED Subsystem", - "pattern": "^\\w+$", - "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems.", - "created": "2019-06-11T14:17:46.875+0000", - "modified": "2019-06-11T14:17:46.875+0000", - "resources": [ - { - "id": 1547, - "mirId": "MIR:00100729", - "urlPattern": "https://registry.identifiers.org/deprecation/resources/MIR:00100729/{$id}", - "name": "SEED Subsystem at Argonne National Laboratory", - "description": "SEED Subsystem at Argonne National Laboratory", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "Biotin_biosynthesis", - "resourceHomeUrl": "http://seed-viewer.theseed.org/seedviewer.cgi", - "institution": { - "id": 1546, - "name": "Argonne National Laboratory", - "homeUrl": "https://www.anl.gov", - "description": "Argonne is a multidisciplinary science and engineering research center, where talented scientists and engineers work together to answer the biggest questions facing humanity, from how to obtain affordable clean energy to protecting ourselves and our environment.", - "rorId": "https://ror.org/05gvnxz63", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": true, - "deprecationDate": "2019-10-08T08:49:23.021+0000" - } - ], - "sampleId": "Biotin_biosynthesis", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1548, - "prefix": "seed.compound", - "mirId": "MIR:00000553", - "name": "SEED Compound", - "pattern": "^cpd\\d+$", - "description": "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. 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This collection references subsystems.", - "created": "2019-06-11T14:17:47.133+0000", - "modified": "2019-06-11T14:17:47.133+0000", - "resources": [ - { - "id": 1549, - "mirId": "MIR:00100730", - "urlPattern": "http://modelseed.org/biochem/compounds/{$id}", - "name": "SEED Compound at Argonne National Laboratory", - "description": "SEED Compound at Argonne National Laboratory", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "cpd15380", - "resourceHomeUrl": "http://modelseed.org/", - "institution": { - "id": 1546, - "name": "Argonne National Laboratory", - "homeUrl": "https://www.anl.gov", - "description": "Argonne is a multidisciplinary science and engineering research center, where talented scientists and engineers work together to answer the biggest questions facing humanity, from how to obtain affordable clean energy to protecting ourselves and our environment.", - "rorId": "https://ror.org/05gvnxz63", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "cpd15380", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1550, - "prefix": "bigg.model", - "mirId": "MIR:00000554", - "name": "BiGG Model", - "pattern": "^[a-z_A-Z0-9]+$", - "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models.", - "created": "2019-06-11T14:17:47.362+0000", - "modified": "2019-06-11T14:17:47.362+0000", - "resources": [ - { - "id": 1552, - "mirId": "MIR:00100731", - "urlPattern": "http://bigg.ucsd.edu/models/{$id}", - "name": "BiGG Model at University of California", - "description": "BiGG Model at University of California", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "iECABU_c1320", - "resourceHomeUrl": "http://bigg.ucsd.edu/models", - "institution": { - "id": 190, - "name": "University of California, San Diego", - "homeUrl": "https://ucsd.edu/", - "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", - "rorId": "https://ror.org/0168r3w48", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "iECABU_c1320", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1553, - "prefix": "bigg.compartment", - "mirId": "MIR:00000555", - "name": "BiGG Compartment", - "pattern": "^[a-z_A-Z]+$", - "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references model compartments.", - "created": "2019-06-11T14:17:47.621+0000", - "modified": "2019-06-11T14:17:47.621+0000", - "resources": [ - { - "id": 1554, - "mirId": "MIR:00100732", - "urlPattern": "http://bigg.ucsd.edu/compartments/{$id}", - "name": "BiGG Compartment at University of California", - "description": "BiGG Compartment at University of California", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "c", - "resourceHomeUrl": "http://bigg.ucsd.edu/compartments/", - "institution": { - "id": 190, - "name": "University of California, San Diego", - "homeUrl": "https://ucsd.edu/", - "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", - "rorId": "https://ror.org/0168r3w48", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "c", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1537, - "prefix": "wikidata", - "mirId": "MIR:00000549", - "name": "Wikidata", - "pattern": "^(Q|P)\\d+$", - "description": "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. 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Items represent topics, for which basic information is stored that identifies each topic.", - "created": "2019-06-11T14:17:46.087+0000", - "modified": "2020-11-30T14:15:44.647+0000", - "resources": [ - { - "id": 1538, - "mirId": "MIR:00100726", - "urlPattern": "http://www.wikidata.org/entity/{$id}", - "name": "Wikidata at Wikimedia Foundation", - "description": "Wikidata at Wikimedia Foundation", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "Q2207226", - "resourceHomeUrl": "https://www.wikidata.org/", - "institution": { - "id": 1111, - "name": "Wikimedia Foundation, San Francisco, California", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "Q2207226", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1557, - "prefix": "bigg.reaction", - "mirId": "MIR:00000557", - "name": "BiGG Reaction", - "pattern": "^[a-z_A-Z0-9]+$", - "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references reactions.", - "created": "2019-06-11T14:17:48.059+0000", - "modified": "2019-06-11T14:17:48.059+0000", - "resources": [ - { - "id": 1558, - "mirId": "MIR:00100734", - "urlPattern": "http://bigg.ucsd.edu/models/universal/reactions/{$id}", - "name": "BiGG Reaction at University of California", - "description": "BiGG Reaction at University of California", - "official": false, - "providerCode": "ucsd", - "sampleId": "13GS", - "resourceHomeUrl": "http://bigg.ucsd.edu/universal/reactions", - "institution": { - "id": 190, - "name": "University of California, San Diego", - "homeUrl": "https://ucsd.edu/", - "description": "is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.", - "rorId": "https://ror.org/0168r3w48", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "13GS", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1561, - "prefix": "umls", - "mirId": "MIR:00000559", - "name": "UMLS", - "pattern": "^C\\d+$", - "description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.", - "created": "2019-06-11T14:17:48.502+0000", - "modified": "2019-06-11T14:17:48.502+0000", - "resources": [ - { - "id": 1562, - "mirId": "MIR:00100736", - "urlPattern": "http://linkedlifedata.com/resource/umls/id/{$id}", - "name": "Unified Medical Language System at LinkedLifeData", - "description": "Unified Medical Language System at LinkedLifeData", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "C0021390", - "resourceHomeUrl": "http://linkedlifedata.com/", - "institution": { - "id": 63, - "name": "Linkedlifedata, Ontotext, Sofia", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "BG", - "countryName": "Bulgaria" - } - }, - "location": { - "countryCode": "BG", - "countryName": "Bulgaria" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "C0021390", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1565, - "prefix": "emdb", - "mirId": "MIR:00000561", - "name": "Electron Microscopy Data Bank", - "pattern": "^EMD-\\d{4}$", - "description": "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community.", - "created": "2019-06-11T14:17:48.947+0000", - "modified": "2019-06-11T14:17:48.947+0000", - "resources": [ - { - "id": 1566, - "mirId": "MIR:00100738", - "urlPattern": "https://www.ebi.ac.uk/pdbe/entry/emdb/{$id}", - "name": "EMDB at Protein Data Bank in Europe", - "description": "EMDB at Protein Data Bank in Europe", - "official": false, - "providerCode": "ebi", - "sampleId": "EMD-1001", - "resourceHomeUrl": "https://www.ebi.ac.uk/pdbe/emdb/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "EMD-1001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1567, - "prefix": "mirtarbase", - "mirId": "MIR:00000562", - "name": "miRTarBase", - "pattern": "^MIRT\\d{6}$", - "description": "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments.", - "created": "2019-06-11T14:17:49.171+0000", - "modified": "2019-06-11T14:17:49.171+0000", - "resources": [ - { - "id": 1569, - "mirId": "MIR:00100739", - "urlPattern": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid={$id}", - "name": "miRTarBase at National Chiao Tung University", - "description": "miRTarBase at National Chiao Tung University", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "MIRT000002", - "resourceHomeUrl": "http://mirtarbase.mbc.nctu.edu.tw/", - "institution": { - "id": 1568, - "name": "Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "TW", - "countryName": "Taiwan, Province of China" - } - }, - "location": { - "countryCode": "TW", - "countryName": "Taiwan, Province of China" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "MIRT000002", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1570, - "prefix": "meddra", - "mirId": "MIR:00000563", - "name": "MedDRA", - "pattern": "^\\d+$", - "description": "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).", - "created": "2019-06-11T14:17:49.428+0000", - "modified": "2019-06-11T14:17:49.428+0000", - "resources": [ - { - "id": 1571, - "mirId": "MIR:00100740", - "urlPattern": "http://purl.bioontology.org/ontology/MEDDRA/{$id}", - "name": "MedDRA through BioPortal", - "description": "MedDRA through BioPortal", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "10015919", - "resourceHomeUrl": "http://bioportal.bioontology.org/ontologies/MEDDRA", - "institution": { - "id": 5, - "name": "National Center for Biomedical Ontology, Stanford", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "10015919", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1572, - "prefix": "dashr", - "mirId": "MIR:00000564", - "name": "DASHR", - "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", - "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records.", - "created": "2019-06-11T14:17:49.634+0000", - "modified": "2019-06-11T14:17:49.634+0000", - "resources": [ - { - "id": 1574, - "mirId": "MIR:00100741", - "urlPattern": "http://lisanwanglab.org/DASHR/entry/{$id}", - "name": "DASHR at University of Pennsylvania", - "description": "DASHR at University of Pennsylvania", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "hsa-mir-200a", - "resourceHomeUrl": "http://lisanwanglab.org/DASHR/", - "institution": { - "id": 1573, - "name": "Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "hsa-mir-200a", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1575, - "prefix": "dashr.expression", - "mirId": "MIR:00000565", - "name": "DASHR expression", - "pattern": "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$", - "description": "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression.", - "created": "2019-06-11T14:17:49.866+0000", - "modified": "2019-06-11T14:17:49.866+0000", - "resources": [ - { - "id": 1576, - "mirId": "MIR:00100742", - "urlPattern": "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#{$id}#exprPerTissueTable", - "name": "DASHR expression at University of Pennsylvania", - "description": "DASHR expression at University of Pennsylvania", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "hsa-mir-200a", - "resourceHomeUrl": "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0", - "institution": { - "id": 1573, - "name": "Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "hsa-mir-200a", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1577, - "prefix": "splash", - "mirId": "MIR:00000566", - "name": "SPLASH", - "pattern": "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$", - "description": "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance.", - "created": "2019-06-11T14:17:50.083+0000", - "modified": "2019-06-11T14:17:50.083+0000", - "resources": [ - { - "id": 1579, - "mirId": "MIR:00100746", - "urlPattern": "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/{$id}", - "name": "Mass Bank of North America (MoNA)", - "description": "Mass Bank of North America (MoNA)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "splash10-0zq2000000-77302b0326a418630a84", - "resourceHomeUrl": "http://mona.fiehnlab.ucdavis.edu/", - "institution": { - "id": 1578, - "name": "University of Californai, Davis, California", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "splash10-0zq2000000-77302b0326a418630a84", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1563, - "prefix": "mesh", - "mirId": "MIR:00000560", - "name": "MeSH", - "pattern": "^(C|D)\\d{6,9}$", - "description": "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc.", - "created": "2019-06-11T14:17:48.752+0000", - "modified": "2020-04-21T17:40:51.334+0000", - "resources": [ - { - "id": 1564, - "mirId": "MIR:00100737", - "urlPattern": "http://id.nlm.nih.gov/mesh/{$id}", - "name": "MeSH Linked Data at National Library of Medicine", - "description": "MeSH Linked Data at National Library of Medicine", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "C000100", - "resourceHomeUrl": "http://id.nlm.nih.gov/mesh/", - "institution": { - "id": 792, - "name": "U.S. National Library of Medicine, National Institute of Health, Maryland", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "C000100", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1580, - "prefix": "metanetx.chemical", - "mirId": "MIR:00000567", - "name": "MetaNetX chemical", - "pattern": "^(MNXM\\d+|BIOMASS|WATER)$", - "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components.", - "created": "2019-06-11T14:17:50.332+0000", - "modified": "2021-02-26T09:36:59.253+0000", - "resources": [ - { - "id": 1582, - "mirId": "MIR:00100748", - "urlPattern": "https://www.metanetx.org/chem_info/{$id}", - "name": "MetaNetX chemical at SIB Swiss Institute of Bioinformatics", - "description": "MetaNetX chemical at SIB Swiss Institute of Bioinformatics", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "MNXM1723", - "resourceHomeUrl": "https://www.metanetx.org/", - "institution": { - "id": 1581, - "name": "Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "MNXM1723", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1583, - "prefix": "metanetx.reaction", - "mirId": "MIR:00000568", - "name": "MetaNetX reaction", - "pattern": "^(MNXR\\d+|EMPTY)$", - "description": "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. 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It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions.", - "created": "2019-06-11T14:17:51.017+0000", - "modified": "2019-06-11T14:17:51.017+0000", - "resources": [ - { - "id": 1588, - "mirId": "MIR:00100752", - "urlPattern": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid={$id}", - "name": "UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)", - "description": "UniPathway Reaction at Swiss Institute of Bioinformatics (SIB)", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "UCR00226", - "resourceHomeUrl": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway", - "institution": { - "id": 1730, - "name": "SIB Swiss Institute of Bioinformatics", - "homeUrl": "https://www.sib.swiss", - "description": "SIB provides bioinformatics services and resources for scientists and clinicians from academia and industry in Switzerland and worldwide.", - "rorId": "https://ror.org/002n09z45", - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": true, - "deprecationDate": "2019-10-01T12:11:20.049+0000" - } - ], - "sampleId": "UCR00226", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1589, - "prefix": "hp", - "mirId": "MIR:00000571", - "name": "Human Phenotype Ontology", - "pattern": "^HP:\\d{7}$", - "description": "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM.", - "created": "2019-06-11T14:17:51.237+0000", - "modified": "2019-06-11T14:17:51.237+0000", - "resources": [ - { - "id": 1592, - "mirId": "MIR:00100754", - "urlPattern": "https://www.ebi.ac.uk/ols/ontologies/hp/terms?obo_id=HP:{$id}", - "name": "Human Phenotype Ontology through OLS", - "description": "Human Phenotype Ontology through OLS", - "official": false, - "providerCode": "ols", - "sampleId": "0000118", - "resourceHomeUrl": "https://www.ebi.ac.uk/ols/ontologies/hp", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1591, - "mirId": "MIR:00100753", - "urlPattern": "https://hpo.jax.org/app/browse/term/HP:{$id}", - "name": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics", - "description": "Human Phenotype Ontology at Institute for Medical Genetics and Human Genetics", - "official": true, - "providerCode": "CURATOR_REVIEW", - "sampleId": "0000118", - "resourceHomeUrl": "http://human-phenotype-ontology.github.io/", - "institution": { - "id": 1590, - "name": "Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "DE", - "countryName": "Germany" - } - }, - "location": { - "countryCode": "DE", - "countryName": "Germany" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "0000118", - "namespaceEmbeddedInLui": true, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1593, - "prefix": "sasbdb", - "mirId": "MIR:00000572", - "name": "SASBDB", - "pattern": "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$", - "description": "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. 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A large focus of the ontology is its consideration of LGBTQIA+ terminology.", - "created": "2020-11-05T10:42:17.722+0000", - "modified": "2020-11-05T10:59:53.808+0000", - "resources": [ - { - "id": 2424, - "mirId": "MIR:00000758", - "urlPattern": "http://purl.obolibrary.org/obo/GSSO_{$id}", - "name": "National Center for Biomedical Ontology (NCBO) BioPortal", - "description": "One of the National Centers for Biomedical Computing, and is funded by the NIH. 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Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.", - "created": "2019-06-11T14:17:28.979+0000", - "modified": "2020-11-20T10:55:30.526+0000", - "resources": [ - { - "id": 1359, - "mirId": "MIR:00100612", - "urlPattern": "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id={$id}", - "name": "LigandBox at N2PC", - "description": "LigandBox at N2PC", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "D00001", - "resourceHomeUrl": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en", - "institution": { - "id": 1358, - "name": "Next generation Natural Products Chemistry", - "homeUrl": "https://www.natprodchem.jp/", - "description": "https://www.natprodchem.jp/files/english.pdf", - "rorId": null, - "location": { - "countryCode": "JP", - "countryName": "Japan" - } - }, - "location": { - "countryCode": "JP", - "countryName": "Japan" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "D00001", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1666, - "prefix": "pgx", - "mirId": "MIR:00000600", - "name": "Progenetix", - "pattern": "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$", - "description": "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs.", - "created": "2019-06-11T14:17:59.445+0000", - "modified": "2020-11-25T15:01:33.103+0000", - "resources": [ - { - "id": 1668, - "mirId": "MIR:00100801", - "urlPattern": "https://progenetix.org/services/ids/{$id}", - "name": "Progenetix", - "description": "Progenetix", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "pgxbs-kftva5zv", - "resourceHomeUrl": "https://progenetix.org/", - "institution": { - "id": 1667, - "name": "University of Zurich", - "homeUrl": "https://www.uzh.ch/en.html", - "description": "No description available", - "rorId": "https://ror.org/02crff812", - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "pgxbs-kftva5zv", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2477, - "prefix": "covid19", - "mirId": "MIR:00000789", - "name": "SARS-CoV-2", - "pattern": "^\\w+_COVID19_[-\\w]+$", - "description": "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease.", - "created": "2020-12-14T12:49:56.333+0000", - "modified": "2020-12-14T12:49:56.333+0000", - "resources": [ - { - "id": 2478, - "mirId": "MIR:00000787", - "urlPattern": "https://covid19.sfb.uit.no/api/records/{$id}", - "name": "Elixir@UiT", - "description": "Elixir@UiT is the local branch of ELIXIR-NO node based at UiT.", - "official": true, - "providerCode": "sfb", - "sampleId": "SFB_COVID19_MW286762", - "resourceHomeUrl": "https://covid19.sfb.uit.no", - "institution": { - "id": 2476, - "name": "University of Tromsø - The Arctic University of Norway", - "homeUrl": "https://uit.no/startsida", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/00wge5k78' with Wikidata IDs [Q279724], and ISNI IDs [0000000122595234]", - "rorId": null, - "location": { - "countryCode": "NO", - "countryName": "Norway" - } - }, - "location": { - "countryCode": "NO", - "countryName": "Norway" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "SFB_COVID19_MW286762", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2484, - "prefix": "oma.hog", - "mirId": "MIR:00000785", - "name": "OMA HOGs", - "pattern": "^HOG:[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", - "description": "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. 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", - "created": "2020-12-14T12:57:54.560+0000", - "modified": "2020-12-14T12:57:54.560+0000", - "resources": [ - { - "id": 2485, - "mirId": "MIR:00000761", - "urlPattern": "https://omabrowser.org/oma/hog/resolve/HOG:{$id}/", - "name": "ETH Zurich", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05a28rw58' with Wikidata IDs [Q11942], and ISNI IDs [0000 0001 2156 2780]", - "official": true, - "providerCode": "oma", - "sampleId": "HOG:0459895", - "resourceHomeUrl": "https://omabrowser.org", - "institution": { - "id": 2483, - "name": "ETH Zurich", - "homeUrl": "https://ethz.ch/en.html", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05a28rw58' with Wikidata IDs [Q11942], and ISNI IDs [0000 0001 2156 2780]", - "rorId": null, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "HOG:0459895", - "namespaceEmbeddedInLui": true, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2497, - "prefix": "vmhgene", - "mirId": "MIR:00000774", - "name": "VMH Gene", - "pattern": "^[0-9]+\\.[0-9]+", - "description": "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease.", - "created": "2021-02-01T15:47:59.756+0000", - "modified": "2021-02-01T15:47:59.756+0000", - "resources": [ - { - "id": 2498, - "mirId": "MIR:00000794", - "urlPattern": "https://www.vmh.life/#gene/{$id}", - "name": "VMH Gene", - "description": "VMH Gene, provided by Thiele Group, NUI Galway. \nThe VMH database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data.", - "official": true, - "providerCode": "NUI", - "sampleId": "8639.1", - "resourceHomeUrl": "https://www.vmh.life/", - "institution": { - "id": 2496, - "name": "National University of Ireland, Galway", - "homeUrl": "http://www.nuigalway.ie/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03bea9k73' with Wikidata IDs [Q644478], and ISNI IDs [0000 0004 0488 0789]", - "rorId": null, - "location": { - "countryCode": "IE", - "countryName": "Ireland" - } - }, - "location": { - "countryCode": "IE", - "countryName": "Ireland" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "8639.1", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 1523, - "prefix": "gwascentral.phenotype", - "mirId": "MIR:00000543", - "name": "GWAS Central Phenotype", - "pattern": "^HGVPM\\d+$", - "description": "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype.", - "created": "2019-06-11T14:17:44.698+0000", - "modified": "2021-02-01T16:43:30.697+0000", - "resources": [ - { - "id": 1524, - "mirId": "MIR:00100720", - "urlPattern": "https://www.gwascentral.org/phenotype/{$id}", - "name": "GWAS Central Phenotype at University of Leicester", - "description": "GWAS Central Phenotype at University of Leicester", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "HGVPM623", - "resourceHomeUrl": "https://www.gwascentral.org/phenotypes", - "institution": { - "id": 1079, - "name": "Department of Genetics, University of Leicester, Leicester", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "HGVPM623", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2518, - "prefix": "clinvar.submitter", - "mirId": "MIR:00000769", - "name": "ClinVar Submitter", - "pattern": "^\\d+$", - "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. 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This collection references submitters (submitter ids) that submit the submissions (SCVs).", - "created": "2021-02-17T17:56:14.329+0000", - "modified": "2021-02-17T17:56:14.329+0000", - "resources": [ - { - "id": 2519, - "mirId": "MIR:00000783", - "urlPattern": "https://www.ncbi.nlm.nih.gov/clinvar/submitters/{$id}", - "name": "ClinVar Submitter at NCBI", - "description": "ClinVar Submitter ids are assigned by NCBI for all authorized submitters of clinvar submissions (SCVs)", - "official": true, - "providerCode": "ncbi", - "sampleId": "26957", - "resourceHomeUrl": "https://www.ncbi.nlm.nih.gov/clinvar/", - "institution": { - "id": 26, - "name": "National Center for Biotechnology Information", - "homeUrl": "https://www.ncbi.nlm.nih.gov/", - "description": "The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.", - "rorId": "https://ror.org/02meqm098", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "26957", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2521, - "prefix": "ped", - "mirId": "MIR:00000777", - "name": "Protein Ensemble Database", - "pattern": "^PED\\d{5}$", - "description": "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.", - "created": "2021-02-17T18:02:05.160+0000", - "modified": "2021-02-17T18:02:05.160+0000", - "resources": [ - { - "id": 2522, - "mirId": "MIR:00000784", - "urlPattern": "https://proteinensemble.org/{$id}", - "name": "PED - Protein Ensemble Database", - "description": "The Protein Ensemble Database (PED) is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.", - "official": true, - "providerCode": "ped", - "sampleId": "PED00037", - "resourceHomeUrl": "https://proteinensemble.org/", - "institution": { - "id": 1769, - "name": "University of Padua", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "IT", - "countryName": "Italy" - } - }, - "location": { - "countryCode": "IT", - "countryName": "Italy" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "PED00037", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2532, - "prefix": "repeatsdb.protein", - "mirId": "MIR:00000792", - "name": "RepeatsDB Protein", - "pattern": "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$", - "description": "RepeatsDB is a database of annotated tandem repeat protein structures. 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This collection references cellular compartments.", - "created": "2019-06-11T14:17:50.805+0000", - "modified": "2021-02-26T09:49:03.051+0000", - "resources": [ - { - "id": 1586, - "mirId": "MIR:00100750", - "urlPattern": "https://www.metanetx.org/comp_info/{$id}", - "name": "MetaNetX compartment at SIB Swiss Institute of Bioinformatics", - "description": "MetaNetX compartment at SIB Swiss Institute of Bioinformatics", - "official": false, - "providerCode": "CURATOR_REVIEW", - "sampleId": "MNXC15", - "resourceHomeUrl": "https://www.metanetx.org/", - "institution": { - "id": 1581, - "name": "Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - } - }, - "location": { - "countryCode": "CH", - "countryName": "Switzerland" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "MNXC15", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2559, - "prefix": "qtldb", - "mirId": "MIR:00000798", - "name": "Animal Genome QTL", - "pattern": "^\\d+$", - "description": "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. 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", - "official": true, - "providerCode": "ps", - "sampleId": "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a", - "resourceHomeUrl": "https://discover.pennsieve.io", - "institution": { - "id": 1674, - "name": "University of Pennsylvania", - "homeUrl": "CURATOR_REVIEW", - "description": "CURATOR_REVIEW", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 2638, - "prefix": "icdc", - "mirId": "MIR:00000812", - "name": "Integrated Canine Data Commons", - "pattern": "^\\d{6}$", - "description": "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer.", - "created": "2021-05-10T19:40:34.200+0000", - "modified": "2022-03-31T16:55:06.915+0000", - "resources": [ - { - "id": 2639, - "mirId": "MIR:00000811", - "urlPattern": "https://caninecommons.cancer.gov/#/study/{$id}", - "name": "Integrated Canine Data Commons", - "description": "Integrated Canine Data Commons at National Cancer Institute (USA)", - "official": true, - "providerCode": "icdc", - "sampleId": "000009", - "resourceHomeUrl": "https://caninecommons.cancer.gov/#/", - "institution": { - "id": 2637, - "name": "National Cancer Institute", - "homeUrl": "https://www.cancer.gov/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/040gcmg81' with Wikidata IDs [Q664846], and ISNI IDs [0000 0004 1936 8075]", - "rorId": "https://ror.org/040gcmg81", - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "000009", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 361, - "prefix": "pdb-ccd", - "mirId": "MIR:00000113", - "name": "Chemical Component Dictionary", - "pattern": "^\\w{1,3}$", - "description": "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.", - "created": "2019-06-11T14:16:03.054+0000", - "modified": "2022-05-18T15:48:21.884+0000", - "resources": [ - { - "id": 362, - "mirId": "MIR:00100146", - "urlPattern": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/{$id}", - "name": "Protein Data Bank Chemical Component Dictionary at EBI", - "description": "Protein Data Bank Chemical Component Dictionary at EBI", - "official": false, - "providerCode": "ebi", - "sampleId": "AB0", - "resourceHomeUrl": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/", - "institution": { - "id": 2, - "name": "European Bioinformatics Institute", - "homeUrl": "https://www.ebi.ac.uk", - "description": "At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.", - "rorId": "https://ror.org/02catss52", - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - } - }, - "location": { - "countryCode": "GB", - "countryName": "United Kingdom" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "AB0", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3252, - "prefix": "civic.sid", - "mirId": "MIR:00000953", - "name": "CIViC Source", - "pattern": "^[0-9]+$", - "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). 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The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.", - "created": "2022-08-08T18:33:25.710+0000", - "modified": "2022-08-08T18:33:25.710+0000", - "resources": [ - { - "id": 3256, - "mirId": "MIR:00000954", - "urlPattern": "https://civicdb.org/links/drugs/{$id}", - "name": "Clinical Interpretation of Variants in Cancer (CIViC)", - "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.", - "official": true, - "providerCode": "civicdb", - "sampleId": "14", - "resourceHomeUrl": "https://civicdb.org/", - "institution": { - "id": 2750, - "name": "Washington University in St. Louis", - "homeUrl": "https://wustl.edu/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "14", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3258, - "prefix": "civic.did", - "mirId": "MIR:00000957", - "name": "CIViC Disease", - "pattern": "^[0-9]+$", - "description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.", - "created": "2022-08-08T18:34:15.882+0000", - "modified": "2022-08-08T18:34:15.882+0000", - "resources": [ - { - "id": 3259, - "mirId": "MIR:00000956", - "urlPattern": "https://civicdb.org/links/diseases/{$id}", - "name": "Clinical Interpretation of Variants in Cancer (CIViC)", - "description": "CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.https://civicdb.org/\n", - "official": true, - "providerCode": "civicdb", - "sampleId": "46", - "resourceHomeUrl": "https://civicdb.org/", - "institution": { - "id": 2750, - "name": "Washington University in St. Louis", - "homeUrl": "https://wustl.edu/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/01yc7t268' with Wikidata IDs [Q777403], and ISNI IDs [0000 0001 2355 7002]", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "46", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3263, - "prefix": "metatlas", - "mirId": "MIR:00000959", - "name": "Metabolic Atlas", - "pattern": "^MA[MR]\\d{5}[a-z]?$", - "description": "Metabolic Atlas facilitates metabolic modelling by presenting open source genome-scale metabolic models for easy browsing and analysis.", - "created": "2022-08-08T18:36:40.981+0000", - "modified": "2022-08-08T18:36:40.981+0000", - "resources": [ - { - "id": 3264, - "mirId": "MIR:00000958", - "urlPattern": "https://metabolicatlas.org/identifier/MetabolicAtlas/{$id}", - "name": "Metabolic Atlas", - "description": "Metabolic Atlas is a web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. The goal is to collect curated GEMs, and to bring these models closer to FAIR principles. The website provides visualisations and comparisons of the GEMs, and links to resources, algorithms, other databases, and more general software applications.", - "official": true, - "providerCode": "metatlas", - "sampleId": "MAR01234", - "resourceHomeUrl": "https://metabolicatlas.org", - "institution": { - "id": 3262, - "name": "National Bioinformatics Infrastructure Sweden", - "homeUrl": "https://nbis.se", - "description": "NBIS (National Bioinformatics Infrastructure Sweden) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities and the Knut and Alice Wallenberg Foundation, providing state-of-the-art bioinformatics to the Swedish life science researchers community. NBIS is also the Swedish contact point to the European infrastructure for biological information ELIXIR.\n\nPresent NBIS staff has expertise in protein bioinformatics, mass spectrometry (MS), next generation sequencing (NGS), large-scale data handling and integration, metagenomics, systems biology, biostatistics and RNAseq.\n\nNBIS is predominantly offering bioinformatics support in various projects, depending on the user needs. In the projects, the NBIS persons are working close to the research group, and they spend part of their time to teach the users in order to propagate the bioinformatics knowledge. Furthermore, NBIS provides infrastructure and tools for bioinformatics analyses in order to facilitate these analyses for the users.\n\nNBIS forms the bioinformatics platform at the Science for Life Laboratory.", - "rorId": null, - "location": { - "countryCode": "SE", - "countryName": "Sweden" - } - }, - "location": { - "countryCode": "SE", - "countryName": "Sweden" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "MAR01234", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3271, - "prefix": "ror", - "mirId": "MIR:00000961", - "name": "ROR", - "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", - "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", - "created": "2022-08-15T19:28:35.707+0000", - "modified": "2022-08-18T13:14:34.725+0000", - "resources": [ - { - "id": 3272, - "mirId": "MIR:00001056", - "urlPattern": "https://ror.org/{$id}", - "name": "ROR", - "description": "ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ", - "official": true, - "providerCode": "ror", - "sampleId": "03yrm5c26", - "resourceHomeUrl": "https://ror.org", - "institution": { - "id": 3270, - "name": "California Digital Library", - "homeUrl": "https://www.cdlib.org/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03yrm5c26' with Wikidata IDs [Q5020447], and ISNI IDs [0000 0001 1957 5136]", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "03yrm5c26", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3292, - "prefix": "clb", - "mirId": "MIR:00000964", - "name": "ChecklistBank", - "pattern": "^[0-9]+(LR)?$", - "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", - "created": "2022-11-03T14:17:05.019+0000", - "modified": "2022-11-03T14:17:05.019+0000", - "resources": [ - { - "id": 3293, - "mirId": "MIR:00000963", - "urlPattern": "https://www.checklistbank.org/dataset/{$id}", - "name": "ChecklistBank", - "description": "ChecklistBank at GBIF. Codeveloped with the Catalogue of Life", - "official": true, - "providerCode": "clb", - "sampleId": "1010", - "resourceHomeUrl": "https://www.checklistbank.org", - "institution": { - "id": 3291, - "name": "Global Biodiversity Information Facility", - "homeUrl": "https://www.gbif.org/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", - "rorId": null, - "location": { - "countryCode": "DK", - "countryName": "Denmark" - } - }, - "location": { - "countryCode": "DK", - "countryName": "Denmark" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "1010", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3298, - "prefix": "drugcentral", - "mirId": "MIR:00000966", - "name": "DrugCentral", - "pattern": "^[0-9]+$", - "description": "DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.", - "created": "2022-11-04T09:54:32.976+0000", - "modified": "2022-11-04T09:54:32.976+0000", - "resources": [ - { - "id": 3299, - "mirId": "MIR:00000965", - "urlPattern": "https://drugcentral.org/drugcard/{$id}", - "name": "University of New Mexico", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", - "official": true, - "providerCode": "drugcentral", - "sampleId": "257", - "resourceHomeUrl": "http://www.unm.edu/", - "institution": { - "id": 3297, - "name": "University of New Mexico", - "homeUrl": "http://www.unm.edu/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fs6jp91' with Wikidata IDs [Q1190812], and ISNI IDs [0000 0001 2188 8502]", - "rorId": null, - "location": { - "countryCode": "US", - "countryName": "United States" - } - }, - "location": { - "countryCode": "US", - "countryName": "United States" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "257", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3307, - "prefix": "skm", - "mirId": "MIR:00000968", - "name": "Stress Knowledge Map", - "pattern": "^rx[0-9]{5}$", - "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", - "created": "2022-11-04T12:17:30.200+0000", - "modified": "2022-11-04T12:17:30.200+0000", - "resources": [ - { - "id": 3308, - "mirId": "MIR:00000967", - "urlPattern": "https://skm.nib.si/api/pss/reactions?reaction_id={$id}&return_field=summary", - "name": "National Institute of Biology", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03s5t0r17' with no Wikidata information, and ISNI IDs [0000 0004 0637 0790]", - "official": true, - "providerCode": "skm", - "sampleId": "rx00408", - "resourceHomeUrl": "http://www.nib.si/eng/", - "institution": { - "id": 3306, - "name": "National Institute of Biology", - "homeUrl": "http://www.nib.si/eng/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/03s5t0r17' with no Wikidata information, and ISNI IDs [0000 0004 0637 0790]", - "rorId": null, - "location": { - "countryCode": "SI", - "countryName": "Slovenia" - } - }, - "location": { - "countryCode": "SI", - "countryName": "Slovenia" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "rx00408", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3311, - "prefix": "col", - "mirId": "MIR:00000969", - "name": "Catalogue of Life", - "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", - "description": "Identifier of a taxon or synonym in the Catalogue of Life", - "created": "2022-11-04T13:50:22.141+0000", - "modified": "2022-11-04T13:50:22.141+0000", - "resources": [ - { - "id": 3312, - "mirId": "MIR:00000970", - "urlPattern": "https://www.checklistbank.org/dataset/3LR/taxon/{$id}", - "name": "ChecklistBank", - "description": "ChecklistBank, an index and repository for taxonomic data, hosted at GBIF\n", - "official": true, - "providerCode": "clb", - "sampleId": "4QHKG", - "resourceHomeUrl": "https://www.checklistbank.org", - "institution": { - "id": 3291, - "name": "Global Biodiversity Information Facility", - "homeUrl": "https://www.gbif.org/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", - "rorId": null, - "location": { - "countryCode": "DK", - "countryName": "Denmark" - } - }, - "location": { - "countryCode": "DK", - "countryName": "Denmark" - }, - "deprecated": false, - "deprecationDate": null - }, - { - "id": 3328, - "mirId": "MIR:00000971", - "urlPattern": "https://www.catalogueoflife.org/data/taxon/{$id}", - "name": "Catalogue of Life (COL)", - "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", - "official": false, - "providerCode": "col", - "sampleId": "4QHKG", - "resourceHomeUrl": "https://www.catalogueoflife.org", - "institution": { - "id": 3291, - "name": "Global Biodiversity Information Facility", - "homeUrl": "https://www.gbif.org/", - "description": "Organization information obtained from ROR API using ROR ID 'https://ror.org/05fjyn938' with Wikidata IDs [Q1531570], and no ISNI information", - "rorId": null, - "location": { - "countryCode": "DK", - "countryName": "Denmark" - } - }, - "location": { - "countryCode": "DK", - "countryName": "Denmark" - }, - "deprecated": false, - "deprecationDate": null - } - ], - "sampleId": "4QHKG", - "namespaceEmbeddedInLui": false, - "deprecated": false, - "deprecationDate": null - } - ] - } -} \ No newline at end of file diff --git a/normalizer/src/test/java/org/biopax/paxtools/normalizer/MiriamLinkTest.java b/normalizer/src/test/java/org/biopax/paxtools/normalizer/MiriamLinkTest.java deleted file mode 100644 index f8915d399..000000000 --- a/normalizer/src/test/java/org/biopax/paxtools/normalizer/MiriamLinkTest.java +++ /dev/null @@ -1,186 +0,0 @@ -package org.biopax.paxtools.normalizer; - -import static org.junit.Assert.*; - -import java.util.*; - -import net.biomodels.miriam.Resource; -import net.biomodels.miriam.Miriam.Datatype; - -import org.junit.Before; -import org.junit.Test; - -public class MiriamLinkTest { - - static final String MIURN = "urn:miriam:psimi"; - static final String MIPAGE = "http://www.ebi.ac.uk/ontology-lookup/"; - static final String MIETRY_PREFIX = "http://www.ebi.ac.uk/ontology-lookup/?termId="; - static final String MI = "Molecular Interactions Ontology"; - static final String MISYN = "mi"; - static final String MIRESID = "MIR:00100142"; - static final String MIID = "MIR:00000109"; - - - @Before - public void setUp() throws Exception { - } - - @Test - public final void testGetServicesVersion() { - String version = MiriamLink.getServicesVersion(); - assertNotNull(version); - } - - @Test - public final void testGetDataTypeURI() { - assertEquals(MIURN, MiriamLink.getDataTypeURI(MI)); - assertEquals(MIURN, MiriamLink.getDataTypeURI(MISYN)); - assertEquals(MIURN, MiriamLink.getDataTypeURI(MIURN)); - } - - @Test - public final void testGetDataTypeURIs() { - String[] uris = MiriamLink.getDataTypeURIs(MI); -// System.out.println(Arrays.toString(uris)); - assertTrue(uris.length > 0); - assertTrue(Arrays.toString(uris).contains(MIURN)); - } - - @Test - public final void testGetResourceLocation() { - assertEquals("UK", - MiriamLink.getResourceLocation(MIRESID)); - } - - @Test - public final void testGetResourceInstitution() { - assertEquals("European Bioinformatics Institute, Hinxton, Cambridge", - MiriamLink.getResourceInstitution(MIRESID)); - } - - @Test - public final void testGetURI() { - assertEquals("urn:miriam:psimi:MI%3A0000", MiriamLink.getURI(MISYN, "MI:0000")); - - try{ - MiriamLink.getURI(MISYN, "MI_0000"); - fail("must throw IllegalArgumentException (wrong ID format)"); - } catch (IllegalArgumentException e) { - } - } - - @Test - public final void testGetDataTypeDef() { - String def = MiriamLink.getDataTypeDef(MISYN); - assertNotNull(def); - assertTrue(def.contains("MI is developed by")); - } - - @Test - public final void testGetLocations() { - String[] locs = MiriamLink.getLocations(MI, "MI:0000"); - assertTrue(locs.length>0); - assertTrue(Arrays.asList(locs).contains("https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI%3A0000")); - } - - @Test - public final void testGetDataResources() { - String[] drs = MiriamLink.getDataResources(MI); - assertEquals(2, drs.length); - assertTrue(Arrays.asList(drs).contains("https://www.ebi.ac.uk/ols/ontologies/mi")); - } - - @Test - public final void testIsDeprecated() { - assertFalse(MiriamLink.isDeprecated("urn:miriam:hmdb")); - assertTrue(MiriamLink.isDeprecated("http://www.hmdb.ca/")); - } - - @Test - public final void testGetDataTypePattern() { - assertEquals("^MI:\\d{4}$", MiriamLink.getDataTypePattern(MI)); - } - - - @Test - public final void testGetName() { - assertEquals(MI, MiriamLink.getName(MIURN)); - } - - - @Test - public final void testGetNames() { - String[] names = MiriamLink.getNames(MIURN); - assertTrue(names.length==2); - String s = names[0] + names[1]; - assertTrue(s.contains("MI")); - assertTrue(s.contains(MI)); - } - - @Test - public final void testGetNames2() { - String[] names = MiriamLink.getNames("nci_nature"); - assertTrue(names.length > 1); - assertTrue(Arrays.toString(names).contains("PID")); - } - - - @Test - public final void testGetDataTypesName() { - String[] dts = MiriamLink.getDataTypesName(); - List names = Arrays.asList(dts); - assertFalse(names.contains("MI")); - assertTrue(names.contains(MI)); - assertTrue(names.contains("CluSTr")); - } - - @Test - public final void testGetDataTypesId() { - String[] dts = MiriamLink.getDataTypesId(); - List names = Arrays.asList(dts); - assertTrue(names.contains(MIID)); - assertTrue(names.contains("MIR:00000021")); - } - - @Test - public final void testCheckRegExp() { - assertTrue(MiriamLink.checkRegExp("MI:0000", MI)); - assertFalse(MiriamLink.checkRegExp("0000", MI)); - } - - @Test - public final void testGetOfficialDataTypeURIDatatype() { - Datatype dt = MiriamLink.getDatatype(MI); - assertNotNull(dt); - assertEquals(MIID, dt.getId()); - String urn = MiriamLink.getOfficialDataTypeURI(dt); - assertEquals(MIURN, urn); - } - - @Test - public final void testGetResourcesId() { - String[] rs = MiriamLink.getResourcesId(); - List names = Arrays.asList(rs); - assertTrue(names.contains(MIRESID)); - assertTrue(names.contains("MIR:00100096")); - } - - @Test - public final void testGetResource() { - Resource resource = MiriamLink.getResource("MIR:00100008"); - assertNotNull(resource); - assertEquals("Canada", resource.getDataLocation()); - } - - @Test - public final void testConvertUrn() { - assertEquals("http://identifiers.org/obo.go/GO:0045202", MiriamLink.convertUrn("urn:miriam:obo.go:GO%3A0045202")); - } - - @Test - public final void testGetIdentifiersOrgURI() { - assertEquals("http://identifiers.org/go/GO:0045202", MiriamLink.getIdentifiersOrgURI("urn:miriam:obo.go", "GO:0045202")); - assertEquals("http://identifiers.org/go/GO:0045202", MiriamLink.getIdentifiersOrgURI("go", "GO:0045202")); - } - -} diff --git a/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java b/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java index 056713840..f0f030f2b 100644 --- a/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java +++ b/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java @@ -8,9 +8,6 @@ import org.biopax.paxtools.model.level3.*; import org.junit.Test; -//import java.io.ByteArrayOutputStream; -import java.io.UnsupportedEncodingException; - import static org.junit.Assert.*; /** @@ -27,112 +24,114 @@ public class NormalizerTest { @Test public final void testUri() { - // using null or non-standard db - assertEquals(Normalizer.uri("test/", "foo", "bar", UnificationXref.class), Normalizer.uri("test/", "FOo", "bar", UnificationXref.class)); - //'pubchem' is a ambigous synonym (correct ones are: pubchem-substance, pubchem-compound, etc.) - assertEquals(Normalizer.uri("", "pubchem", "bar", UnificationXref.class), Normalizer.uri("", "PubChem", "bar", UnificationXref.class)); - assertEquals(Normalizer.uri("", null, "bar", UnificationXref.class), Normalizer.uri(null, null, "bar", UnificationXref.class)); - assertFalse(Normalizer.uri(null, "foo", "bar", UnificationXref.class).equals(Normalizer.uri(null, "foo", "BAR", UnificationXref.class))); - assertFalse(Normalizer.uri(null, "foo", "bar", UnificationXref.class).equals(Normalizer.uri(null, "foo", "bar", PublicationXref.class))); - - // using standard db names (Miriam is used to normalize name and/or get identifiers.org URI) - - assertEquals(Normalizer.uri("test/", "pubmed", "12345", PublicationXref.class), Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class)); - assertEquals("http://identifiers.org/pubmed/12345", Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class)); - assertFalse("http://identifiers.org/pubmed/12345".equals(Normalizer.uri(null, "PubMED", "12345", RelationshipXref.class))); //- not PublicationXref - - assertEquals("http://identifiers.org/chebi/CHEBI:12345",Normalizer.uri("", "chebi", "CHEBI:12345", SmallMoleculeReference.class)); - assertEquals("http://identifiers.org/pubchem.substance/12345",Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class)); - - System.setProperty("biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_SIMPLE); - assertEquals("SequenceModificationVocabulary_protein_modification_ontology_MOD_12345",Normalizer.uri("", "PSI-mod", "MOD:12345", SequenceModificationVocabulary.class)); - assertEquals("ControlledVocabulary_protein_modification_ontology_MOD_12345",Normalizer.uri("", "MOD", "MOD:12345", ControlledVocabulary.class)); - System.setProperty("biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_MD5); - //wrong id (case-sens.) - assertFalse("http://identifiers.org/chebi/CHEBI:12345".equals(Normalizer.uri("", "chebi", "chebi:12345", SmallMoleculeReference.class))); - //no 'pubchem' namespace there - assertFalse("http://identifiers.org/pubchem/12345".equals(Normalizer.uri("", "pubchem-substance", "12345", UnificationXref.class))); - - //when there're special symbols, spaces in the 'id' part - assertEquals("UnificationXref_foo_bar", Normalizer.uri(null, null, "foo bar", UnificationXref.class)); - - assertEquals("http://identifiers.org/taxonomy/9606", Normalizer.uri(null, "taxonomy", "9606", BioSource.class)); - assertEquals("http://identifiers.org/taxonomy/9606", Normalizer.uri(null, "NCBI Taxonomy", "9606", BioSource.class)); - assertEquals("http://identifiers.org/taxonomy/9606", Normalizer.uri(null, "NEWT", "9606", BioSource.class)); + // using null or non-standard db + assertEquals(Normalizer.uri("test/", "foo", "bar", UnificationXref.class), Normalizer.uri("test/", "FOo", "bar", UnificationXref.class)); + //'pubchem' is a ambigous synonym (correct ones are: pubchem-substance, pubchem-compound, etc.) + assertEquals(Normalizer.uri("", "pubchem", "bar", UnificationXref.class), Normalizer.uri("", "PubChem", "bar", UnificationXref.class)); + assertEquals(Normalizer.uri("", null, "bar", UnificationXref.class), Normalizer.uri(null, null, "bar", UnificationXref.class)); + assertFalse(Normalizer.uri(null, "foo", "bar", UnificationXref.class).equals(Normalizer.uri(null, "foo", "BAR", UnificationXref.class))); + assertFalse(Normalizer.uri(null, "foo", "bar", UnificationXref.class).equals(Normalizer.uri(null, "foo", "bar", PublicationXref.class))); + + // using standard db names (MIRIAM) + assertEquals(Normalizer.uri("test/", "pubmed", "12345", PublicationXref.class), Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class)); + assertEquals("pubmed:12345", Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class)); + assertFalse("pubmed:12345".equals(Normalizer.uri(null, "PubMED", "12345", RelationshipXref.class))); //not PublicationXref + + assertEquals("bioregistry.io/chebi:12345",Normalizer.uri("", "chebi", "CHEBI:12345", SmallMoleculeReference.class)); + assertEquals("bioregistry.io/pubchem.substance:12345",Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class)); + + System.setProperty("biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_SIMPLE); + assertEquals("SMV_mod_MOD_12345",Normalizer.uri("", "mod", "MOD:12345", SequenceModificationVocabulary.class)); + assertEquals("V_mod_MOD_12345",Normalizer.uri("", "MOD", "MOD:12345", ControlledVocabulary.class)); + System.setProperty("biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_MD5); + //wrong id (case-sens.) + assertFalse("bioregistry.io/chebi:12345".equals(Normalizer.uri("", "chebi", "chebi:12345", SmallMoleculeReference.class))); + + //no 'pubchem' namespace + assertFalse("bioregistry.io/pubchem:12345".equals(Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class))); + //dbName:"pubchem-substance" is mapped to the namespace prefix "pubchem.substance" + assertEquals("bioregistry.io/pubchem.substance:12345", Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class)); + + //when special symbols or spaces in the 'id' part + assertEquals("UX_foo_bar", Normalizer.uri(null, null, "foo bar", UnificationXref.class)); + + assertEquals("bioregistry.io/ncbitaxon:9606", Normalizer.uri(null, "taxonomy", "9606", BioSource.class)); + assertEquals("bioregistry.io/ncbitaxon:9606", Normalizer.uri(null, "NCBI Taxonomy", "9606", BioSource.class)); + assertEquals("bioregistry.io/ncbitaxon:9606", Normalizer.uri(null, "NEWT", "9606", BioSource.class)); //when organism's id is not taxID (e.g., if the BioSource has tissue, cellType CVs...) - assertNotSame("http://identifiers.org/taxonomy/9606",Normalizer.uri(null, "taxonomy", "9606_blah_blah", BioSource.class)); + assertNotSame("bioregistry.io/ncbitaxon:9606",Normalizer.uri(null, "taxonomy", "9606_blah_blah", BioSource.class)); String uri = Normalizer.uri("", "UniProt", "W0C7J9", UnificationXref.class); - assertEquals("UnificationXref_uniprot_knowledgebase_W0C7J9", uri); + assertEquals("uniprot:W0C7J9", uri); } @Test - public final void testNormalize() throws UnsupportedEncodingException { + public final void testNormalize() { // Note: a UniProt AC version (e.g. P68250.1 .. P68250.94) is not the same thing as isoform ID! - Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); - Xref ref = model.addNew(UnificationXref.class, "Xref1"); - ref.setDb("uniprotkb"); - ref.setId("P68250"); - ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1"); - pr.setDisplayName("ProteinReference1"); - pr.addXref(ref); - ref = model.addNew(RelationshipXref.class, "Xref2"); - ref.setDb("refseq"); - ref.setId("NP_001734"); - ref.setIdVersion("1"); // this xref won't be removed by norm. (version matters in xrefs comparing!) + Xref ref = model.addNew(UnificationXref.class, "Xref1"); + ref.setDb("uniprotkb"); + ref.setId("P68250"); + ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1"); + pr.setDisplayName("ProteinReference1"); + pr.addXref(ref); + ref = model.addNew(RelationshipXref.class, "Xref2"); + ref.setDb("refseq"); + ref.setId("NP_001734"); + ref.setIdVersion("1"); // this xref won't be removed by norm. (version matters in xrefs comparing!) pr.addXref(ref); - ref = model.addNew(UnificationXref.class, "Xref3"); - ref.setDb("uniprotkb"); // will be converted to 'uniprot knowledgebase' - /* The following ID is the secondary accession of P68250, - * but Normalizer won't complain (it's Validator's and - later - Merger's job)! - * However, if it were P68250, the normalize(model) would throw exception - * (because ProteinReference1 becomes ProteinReference2, both get RDFId= urn:miriam:uniprot:P68250!) - */ - ref.setId("Q0VCL1"); - Xref uniprotX = ref; - - pr = model.addNew(ProteinReference.class, "ProteinReference2"); - pr.setDisplayName("ProteinReference2"); - pr.addXref(uniprotX); - ref = model.addNew(RelationshipXref.class, "Xref4"); - ref.setDb("refseq"); - ref.setId("NP_001734"); + + ref = model.addNew(UnificationXref.class, "Xref3"); + ref.setDb("uniprotkb"); // will be converted to 'uniprot' + /* Q0VCL1 is the secondary accession for P68250, but Normalizer won't mind nor merge these. + * If it were P68250 here, normalize(model) would throw exception because ProteinReference1 + * becomes ProteinReference2, both getting the same uniprot:P68250 unification xref. + */ + ref.setId("Q0VCL1"); + Xref uniprotX = ref; + + pr = model.addNew(ProteinReference.class, "ProteinReference2"); + pr.setDisplayName("ProteinReference2"); + pr.addXref(uniprotX); + ref = model.addNew(RelationshipXref.class, "Xref4"); + ref.setDb("refseq"); + ref.setId("NP_001734"); pr.addXref(ref); - + // this ER is duplicate (same uniprot xref as ProteinReference2's) and must be removed by normalizer - pr = model.addNew(ProteinReference.class, "ProteinReference3"); - pr.setDisplayName("ProteinReference3"); - pr.addXref(uniprotX); - ref = model.addNew(RelationshipXref.class, "Xref5"); - ref.setDb("refseq"); - ref.setId("NP_001734"); + pr = model.addNew(ProteinReference.class, "ProteinReference3"); + pr.setDisplayName("ProteinReference3"); + pr.addXref(uniprotX); + ref = model.addNew(RelationshipXref.class, "Xref5"); + ref.setDb("refseq"); + ref.setId("NP_001734"); pr.addXref(ref); - + // normalizer won't merge diff. types of xref with the same db:id - ref = model.addNew(PublicationXref.class, "Xref6"); - ref.setDb("pubmed"); - ref.setId("2549346"); // the same id - pr.addXref(ref); - ref = model.addNew(RelationshipXref.class,"Xref7"); - ref.setDb("pubmed"); - ref.setId("2549346"); // the same id - pr.addXref(ref); + ref = model.addNew(PublicationXref.class, "Xref6"); + ref.setDb("pubmed"); + ref.setId("2549346"); // the same id + pr.addXref(ref); + ref = model.addNew(RelationshipXref.class,"Xref7"); + ref.setDb("pubmed"); + ref.setId("2549346"); // the same id + pr.addXref(ref); // add biosource - ref = model.addNew(UnificationXref.class, "Xref8"); - ref.setDb("taxonomy"); - ref.setId("10090"); // the same id + ref = model.addNew(UnificationXref.class, "Xref8"); + ref.setDb("taxonomy"); + ref.setId("10090"); // the same id BioSource bioSource = model.addNew(BioSource.class, "BioSource_Mouse_Tissue"); - bioSource.addXref((UnificationXref)ref); + bioSource.addXref(ref); // Provenance (must set ID and standard names from a name) Provenance pro1 = model.addNew(Provenance.class, "pid"); - pro1.addName("nci_nature"); // must be case insensitive (recognized) + pro1.addName("nci_nature"); // must be case-insensitive (recognized) pro1.setStandardName("foo"); // must be replaced // Provenance (must create names from urn) - Provenance pro2 = model.addNew(Provenance.class, "http://identifiers.org/signaling-gateway/"); - + Provenance pro2 = model.addNew(Provenance.class, "bioregistry.io/signaling-gateway/"); + // add some entities with props Pathway pw1 = model.addNew(Pathway.class, "pathway"); pw1.addDataSource(pro1); @@ -141,44 +140,44 @@ public final void testNormalize() throws UnsupportedEncodingException { pw2.setStandardName("Sub-Pathway"); pw2.addDataSource(pro2); pw1.addPathwayComponent(pw2); - + // add data to test uniprot isoform xref and PR normalization - ref = model.addNew(UnificationXref.class, "Xref9"); - ref.setDb("UniProt"); // normalizer will change it to "uniprot isoform" - ref.setId("P68250-2"); - pr = model.addNew(ProteinReference.class, "ProteinReference4"); - pr.setDisplayName("ProteinReference1isoformA"); - pr.addXref(ref); - - // next ones are to test normalizer can auto-fix 'uniprot' to 'uniprot isoform' xref, - // and also merge xrefs #9,#10 and PRs #4,#5 into one PR with one xref - //below, uniprot xref's idVersion='2' will be moved back to the id value, and db set to "UniProt Isoform" - - ref = model.addNew(UnificationXref.class, "Xref10"); - ref.setDb("UniProtKb"); // NOT to be replaced with "UniProt Isoform" (version and isoform # are not the same thing) - ref.setId("P68250"); - ref.setIdVersion("2"); //may be lost after merging with two other P68250 xrefs + ref = model.addNew(UnificationXref.class, "Xref9"); + ref.setDb("UniProt"); // normalizer will change it to "uniprot isoform" + ref.setId("P68250-2"); + pr = model.addNew(ProteinReference.class, "ProteinReference4"); + pr.setDisplayName("ProteinReference1isoformA"); + pr.addXref(ref); + + // next ones are to test normalizer can auto-fix 'uniprot' to 'uniprot isoform' xref, + // and also merge xrefs #9,#10 and PRs #4,#5 into one PR with one xref + //below, uniprot xref's idVersion='2' will be moved back to the id value, and db set to "UniProt Isoform" - + ref = model.addNew(UnificationXref.class, "Xref10"); + ref.setDb("UniProtKb"); // NOT to be replaced with "UniProt Isoform" (version and isoform # are not the same thing) + ref.setId("P68250"); + ref.setIdVersion("2"); //may be lost after merging with two other P68250 xrefs // (version is not the same as isoform, unless db name is 'uniprot isoform') - pr = model.addNew(ProteinReference.class, "ProteinReference5"); - pr.setDisplayName("ProteinReference1isoformB"); - pr.addXref(ref); - + pr = model.addNew(ProteinReference.class, "ProteinReference5"); + pr.setDisplayName("ProteinReference1isoformB"); + pr.addXref(ref); + // Following three Xrefs and PRs will be normalized to uniprot.isoform:P68250-1 and merged into one - ref = model.addNew(UnificationXref.class, "Xref11"); - ref.setDb("UniProtKb"); // will be replaced with "uniprot isoform" - ref.setId("P68250-1"); - pr = model.addNew(ProteinReference.class, "ProteinReference6"); - pr.addXref(ref); - ref = model.addNew(UnificationXref.class, "Xref12"); - ref.setDb("UniProt Isoform"); // because this is standard (isoform) db name (special case) -> - ref.setId("P68250"); //- this id will set to "P68250-1", - ref.setIdVersion("1"); //- and idVersion will be cleared! - pr = model.addNew(ProteinReference.class, "ProteinReference7"); - pr.addXref(ref); - ref = model.addNew(UnificationXref.class, "Xref13"); - ref.setDb("UniProt Isoform"); - ref.setId("P68250-1"); - pr = model.addNew(ProteinReference.class, "ProteinReference8"); - pr.addXref(ref); + ref = model.addNew(UnificationXref.class, "Xref11"); + ref.setDb("UniProtKb"); // will be replaced with "uniprot isoform" + ref.setId("P68250-1"); + pr = model.addNew(ProteinReference.class, "ProteinReference6"); + pr.addXref(ref); + ref = model.addNew(UnificationXref.class, "Xref12"); + ref.setDb("UniProt Isoform"); // because this is standard (isoform) db name (special case) -> + ref.setId("P68250"); //- this id will set to "P68250-1", + ref.setIdVersion("1"); //- and idVersion will be cleared! + pr = model.addNew(ProteinReference.class, "ProteinReference7"); + pr.addXref(ref); + ref = model.addNew(UnificationXref.class, "Xref13"); + ref.setDb("UniProt Isoform"); + ref.setId("P68250-1"); + pr = model.addNew(ProteinReference.class, "ProteinReference8"); + pr.addXref(ref); //special dangling UXs to test/catch a weird bug that accidentally makes db='uniprot isoform'... UnificationXref ux = model.addNew(UnificationXref.class, "UniprotUX1"); @@ -197,34 +196,27 @@ public final void testNormalize() throws UnsupportedEncodingException { ux = model.addNew(UnificationXref.class, "UniprotUX5"); ux.setDb("uniprot"); //will be changed to 'uniprot isoform' ux.setId("P68250-3"); - + // go normalize! Normalizer normalizer = new Normalizer(); - normalizer.normalize(model); - -// //tmp test print -// ByteArrayOutputStream out = new ByteArrayOutputStream(); -// simpleIO.convertToOWL(model, out); -// System.out.println(out.toString()); + normalizer.normalize(model); // test for a bug that causes db='uniprot' become 'uniprot isoform' (the id matches both patterns) - assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9")); - assertFalse(model.containsID("UnificationXref_uniprot_isoform_W0C7J9")); - assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9_1")); - assertTrue(model.containsID("UnificationXref_uniprot_isoform_W0C7J9-1")); - assertTrue(model.containsID("UnificationXref_uniprot_isoform_P68250-3")); - assertTrue(model.containsID("UnificationXref_uniprot_knowledgebase_W0C7J9")); + assertTrue(model.containsID("uniprot:W0C7J9")); + assertFalse(model.containsID("uniprot.isoform:W0C7J9")); //it's auto fixed/replaced with uniprot:W0C7J9 + assertTrue(model.containsID("uniprot.isoform:W0C7J9-1")); + assertTrue(model.containsID("uniprot.isoform:P68250-3")); // check Xref String normUri = Normalizer.uri(model.getXmlBase(), "uniprot", "P68250", UnificationXref.class); BioPAXElement bpe = model.getByID(normUri); assertTrue(bpe instanceof UnificationXref); - + // check PR - bpe = model.getByID("http://identifiers.org/uniprot/Q0VCL1"); + bpe = model.getByID("bioregistry.io/uniprot:Q0VCL1"); assertTrue(bpe instanceof ProteinReference); - assertTrue(model.containsID("Xref7")); //RX is not normalized unless (by mistake) it has identifiers.org uri - + assertFalse(model.containsID("Xref7")); //RXs are now all normalized as well + //test BioSource assertFalse(model.containsID("BioSource_Mouse_Tissue")); bpe = model.getByID(Normalizer.uri(model.getXmlBase(), "taxonomy", "10090", BioSource.class)); //"taxonomy" - capitalization can be any @@ -232,19 +224,18 @@ public final void testNormalize() throws UnsupportedEncodingException { normUri = Normalizer.uri(model.getXmlBase(), "taxonomy", "10090", UnificationXref.class); bpe = model.getByID(normUri); assertTrue(bpe instanceof UnificationXref); - + // test that one of each pair ProteinReference, 2nd,3rd and 4th,5th is removed/merged: assertEquals(4, model.getObjects(ProteinReference.class).size()); - // Provenance is no more normalized (Miriam is not enough for this task)! assertEquals(2, model.getObjects(Provenance.class).size()); - + // dataSource property is not inferred/inherited from pw1 anymore (prop. inference feature was removed) pw2 = (Pathway) model.getByID("sub_pathway"); assertEquals(1, pw2.getDataSource().size()); pw1 = (Pathway) model.getByID("pathway"); assertEquals(1, pw1.getDataSource().size()); - + //test uniprot isoform xrefs are detected and normalized the same way // get the expected xref URI first normUri = Normalizer.uri(model.getXmlBase(), "uniprot isoform", "P68250-2", UnificationXref.class); @@ -257,12 +248,11 @@ public final void testNormalize() throws UnsupportedEncodingException { @Test public final void testAutoName() { Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); - Provenance pro = model.addNew(Provenance.class, "http://identifiers.org/pid.pathway/"); + Provenance pro = model.addNew(Provenance.class, "bioregistry.io/pid.pathway/"); pro.setStandardName("foo"); Normalizer.autoName(pro); assertNotNull(pro.getStandardName()); - assertTrue(pro.getName().contains("PID")); - assertTrue(pro.getName().contains("NCI_Nature curated")); + assertTrue(pro.getName().contains("pid.pathway")); assertFalse(pro.getStandardName().equals("foo")); } @@ -271,99 +261,85 @@ public final void testAutoName() { public final void testNormalize2() { Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); Xref ref = model.addNew(UnificationXref.class, "Xref1"); - ref.setDb("uniprotkb"); // will be converted to 'uniprot' - ref.setId("Q0VCL1"); - Xref uniprotX = ref; - ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference"); - pr.setDisplayName("ProteinReference"); - pr.addXref(uniprotX); - ref = model.addNew(RelationshipXref.class, "Xref2"); - ref.setDb("refseq"); - ref.setId("NP_001734"); + ref.setDb("uniprot"); + ref.setId("Q0VCL1"); + Xref uniprotX = ref; + ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference"); + pr.setDisplayName("ProteinReference"); + pr.addXref(uniprotX); + ref = model.addNew(RelationshipXref.class, "Xref2"); + ref.setDb("refseq"); + ref.setId("NP_001734"); pr.addXref(ref); // normalizer won't merge diff. types of xref with the same db:id - ref = model.addNew(PublicationXref.class, "Xref3"); - ref.setDb("pubmed"); - ref.setId("2549346"); // the same id - pr.addXref(ref); - ref = model.addNew(RelationshipXref.class,"Xref4"); - ref.setDb("pubmed"); - ref.setId("2549346"); // the same id - pr.addXref(ref); - + ref = model.addNew(PublicationXref.class, "Xref3"); + ref.setDb("pubmed"); + ref.setId("2549346"); // the same id + pr.addXref(ref); + ref = model.addNew(RelationshipXref.class,"Xref4"); + ref.setDb("pubmed"); + ref.setId("2549346"); // the same id + pr.addXref(ref); + Normalizer normalizer = new Normalizer(); normalizer.normalize(model); - - ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1"); + + ProteinReference e = (ProteinReference) model.getByID("bioregistry.io/uniprot:Q0VCL1"); assertNotNull(e); - assertEquals(4, e.getXref().size()); -// print(e, model); } @Test public final void testNormalize3() { Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); Xref ref = model.addNew(UnificationXref.class, "Xref1"); - ref.setDb("uniprotkb"); // will be converted to 'uniprot' - ref.setId("Q0VCL1"); - ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1"); - pr.setDisplayName("A ProteinReference"); - pr.addXref(ref); - assertEquals(1, ref.getXrefOf().size()); - -// System.out.println("Before the model is normalized - "); -// print(pr, model); - - // go normalize! + ref.setDb("uniprot"); // will be converted to 'uniprot' + ref.setId("Q0VCL1"); + ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1"); + pr.setDisplayName("A ProteinReference"); + pr.addXref(ref); + assertEquals(1, ref.getXrefOf().size()); + + // go normalize! Normalizer normalizer = new Normalizer(); normalizer.normalize(model); - -// System.out.println("After the model is normalized - "); -// print(pr, model); - + assertFalse(model.contains(pr)); // replaced by new norm. PR in the model assertFalse(model.contains(ref)); // replaced by new norm. xref in the model //now xrefOf is consistent with xref for all objects inn the model (since after some paxtools 4.1.3 snapshot) assertEquals(0, pr.getXref().size()); // old PR has xref removed! assertEquals(0, ref.getXrefOf().size()); // because the old xref was replaced in all parent elements! - - ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1"); - assertNotNull(e); + + ProteinReference e = (ProteinReference) model.getByID("bioregistry.io/uniprot:Q0VCL1"); + assertNotNull(e); assertEquals(1, e.getXref().size()); - + String normUri = Normalizer.uri(model.getXmlBase(), "UNIPROT", "Q0VCL1", UnificationXref.class); ref = (UnificationXref) model.getByID(normUri); assertNotNull(ref); assertEquals(1, ref.getXrefOf().size()); - -// print(e, model); } @Test public final void testNormalizeInoh() { - //there're two Protein objects that have entityReference - //rdf:ID="IMR_0100366_G_alpha_s_Canonical" (in fact a generic ProteinReference inproperly defined); - //and that PR has two UniProt UnificationXref: P63092 (human), P63095 (rat). - //Identifiers.org URI for the PR should NOT be generated. - // + //There are two Proteins that have entityReference rdf:ID="IMR_0100366_G_alpha_s_Canonical", + //and that PR has two uniprot unification xrefs: P63092 (human) and P63095 (rat). + //Therefore, the URI of this PR should NOT be normalized. //Also, there was a bug when replacing the PR's URI (warning: IllegalBioPAXArgumentException: Incompatible type!..) - //The cause is that there was a (weird, invalid) PublicationXref having db:id as UniProt:P63092 that gets the same URI! - //To avoid such issues altogether (despite illegal pub. xrefs), the Normalizer won't use Identifiers.org for PublicationXrefs anymore. - + //as the invalid PublicationXref UniProt:P63092 was getting the same normalized URI... + //To avoid all such issues (despite illegal pub. xrefs), the Normalizer won't make + //canonical URI for a PublicationXref anymore, unless xref.db is pubmed. Model model = simpleIO.convertFromOWL(getClass().getResourceAsStream("/test-inoh.owl")); Normalizer normalizer = new Normalizer(); normalizer.setXmlBase(""); normalizer.normalize(model); - //A weird PublicationXref that uses a UniProt ID won't be normalized: assertFalse(model.containsID("http://identifiers.org/uniprot/P63092")); - + assertFalse(model.containsID("identifiers.org/uniprot/P63092")); + assertFalse(model.containsID("bioregistry.io/uniprot:P63092")); //A PR with two UniProt IDs/unif.xrefs - human, rat - won't be normalized! - assertTrue(model.containsID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical")); - assertEquals("ProteinReference", model.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical") - .getModelInterface().getSimpleName()); + assertTrue(model.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical") instanceof ProteinReference); } private void print(XReferrable xr, Model m) { diff --git a/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java b/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java new file mode 100644 index 000000000..4a77694ff --- /dev/null +++ b/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java @@ -0,0 +1,50 @@ +package org.biopax.paxtools.normalizer; + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class ResolverTest { + static final String MI = "Molecular Interactions Controlled Vocabulary"; //name corresponds to "mi" record in bioregistry.io + + @Test + public final void getNamespace() { + assertNotNull(Resolver.getNamespace("obo.mi"));//auto-detected as "mi" + assertEquals(MI, Resolver.getNamespace("urn:miriam:mi").getName()); + assertNotNull(Resolver.getNamespace("psi-mi"));//becomes "mi" + assertNotNull(Resolver.getNamespace("MolecularInteractions Ontology", true));//misspelling variant (allowed by default) + assertNull(Resolver.getNamespace("MolecularInteractions Ontology", false));//null when spelling variants not allowed + assertNotNull(Resolver.getNamespace("http://bioregistry.io/chebi")); + assertNotNull(Resolver.getNamespace("bioregistry.io/uniprot")); + assertNotNull(Resolver.getNamespace("https://identifiers.org/psi-mi")); //matches "mi" registry prefix/namespace + } + + @Test + public final void getPattern() { + assertEquals("^\\d{4}$", Resolver.getNamespace(MI).getPattern()); + } + + + @Test + public final void checkRegExp() { + assertTrue(Resolver.checkRegExp("MI:0000", MI)); //auto-ignores "MI:" + assertTrue(Resolver.checkRegExp("0000", MI)); + } + + @Test + public final void getURI() { + //standard prefix and id with "banana" prefix + assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("chebi", "CHEBI:36927")); + //old ns prefix (should auto-fix as "chebi") and id without "CHEBI:" banana... + assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("identifiers.org/chebi/", "36927")); + //similar, but using bioregistry.io/ base, with ending slash, and with banana... + assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("bioregistry.io/chebi", "CHEBI:36927")); + } + + @Test + public final void getCURIE() { + assertEquals("uniprot:P12345", Resolver.getCURIE("uniprot", "P12345")); + assertEquals("go:0045202", Resolver.getCURIE("go", "GO:0045202")); + } + +} diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java index 7a58deaf9..021ec30ac 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/CommonIDFetcher.java @@ -3,9 +3,7 @@ import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.pattern.util.HGNC; -import org.biopax.paxtools.util.IllegalBioPAXArgumentException; -import java.util.Comparator; import java.util.HashSet; import java.util.Set; import java.util.TreeSet; @@ -36,7 +34,7 @@ public Set fetchID(BioPAXElement ele) else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { - Set names = new TreeSet(); + Set names = new TreeSet<>(); for(String name : e.getName()) { if(!name.contains("...")) names.add(name); @@ -44,7 +42,8 @@ else if (!e.getName().isEmpty()) { set.add(names.toString()); } } - else if (useUniprotIDs && ele.getUri().startsWith("http://identifiers.org/uniprot/")) + else if (useUniprotIDs && + (ele.getUri().contains("identifiers.org/uniprot") || ele.getUri().contains("bioregistry.io/uniprot"))) { set.add(ele.getUri().substring(ele.getUri().lastIndexOf("/") + 1)); } @@ -60,7 +59,7 @@ else if (ele instanceof XReferrable) if (db != null && id != null && !id.isEmpty()) { db = db.toLowerCase(); - if (!useUniprotIDs && db.startsWith("hgnc")) + if (!useUniprotIDs && db.startsWith("hgnc")) //"hgnc.symbol" or "hgnc gene symbol" { //valid id is either a HGNC:1234 ID or Symbol (gene name) String symbol = HGNC.getSymbol(id); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java index 2955000a8..0795ba916 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ConfigurableIDFetcher.java @@ -71,7 +71,7 @@ public List getChemDbStartsWithOrEquals() { /** * Set the flag to use the entity reference's names * when no desired ID type can be found (none of xref.db - * matched before, or there're no xrefs at all). + * matched before, or there were no xrefs at all). * * @param useNameWhenNoDbMatch true/false (default is 'true' - when this method's never been called) * @return this id-fetcher instance @@ -92,20 +92,18 @@ public Set fetchID(BioPAXElement ele) ? chemDbStartsWithOrEquals : seqDbStartsWithOrEquals; for (String dbStartsWith : dbStartsWithOrEquals) { - //a shortcut for URI like "http://identifiers.org/uniprot/", "http://identifiers.org/chebi/"; //this prevents collecting lots of secondary IDs of the same type - if(ele.getUri().startsWith("http://identifiers.org/"+dbStartsWith)) { + if(ele.getUri().contains("identifiers.org/"+dbStartsWith) + || ele.getUri().contains("bioregistry.io/"+dbStartsWith) ) { set.add(ele.getUri().substring(ele.getUri().lastIndexOf("/") + 1)); - } - else - { - for (UnificationXref x : new ClassFilterSet(((XReferrable) ele).getXref(), + } else { + for (UnificationXref x : new ClassFilterSet<>(((XReferrable) ele).getXref(), UnificationXref.class)) { collectXrefIdIfDbLike(x, dbStartsWith, set); } //if none was found in unif. xrefs, try rel, xrefs if (set.isEmpty()) { - for (RelationshipXref x : new ClassFilterSet(((XReferrable) ele).getXref(), + for (RelationshipXref x : new ClassFilterSet<>(((XReferrable) ele).getXref(), RelationshipXref.class)) { collectXrefIdIfDbLike(x, dbStartsWith, set); } @@ -127,7 +125,7 @@ public Set fetchID(BioPAXElement ele) else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { - Set names = new TreeSet(); + Set names = new TreeSet<>(); for(String name : e.getName()) { if(!name.contains("...")) names.add(name); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java index 8b0c6770d..a704dda02 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/ExtendedSIFWriter.java @@ -12,7 +12,7 @@ /** * This class is used for writing the binary interactions to a text output stream in the - * so called Pathway Commons EXTENDED_BINARY_SIF format. + * so-called Pathway Commons EXTENDED_BINARY_SIF format. * * @author Ozgun Babur */ diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFToText.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFToText.java index 20f793b71..f6ac5613a 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFToText.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/SIFToText.java @@ -12,5 +12,5 @@ public interface SIFToText * @param inter the interaction * @return text data */ - public String convert(SIFInteraction inter); + String convert(SIFInteraction inter); } diff --git a/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java b/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java index 387460800..b3a6e2eb9 100644 --- a/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java +++ b/pattern/src/temp/java/org/biopax/paxtools/pattern/TempTests.java @@ -194,7 +194,7 @@ private void debugPattern() throws Throwable Pattern p = PatternBox.controlsExpressionWithTemplateReac(); Match m = new Match(p.size()); - ProteinReference er = (ProteinReference) model.getByID("http://identifiers.org/uniprot/P42229"); + ProteinReference er = (ProteinReference) model.getByID("identifiers.org/uniprot/P42229"); PhysicalEntity pe = (PhysicalEntity) model.getByID("http://pid.nci.nih.gov/biopaxpid_10369"); m.set(er, 0); m.set(pe, 1); diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java index 88d75f2ba..691bdaf86 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java @@ -161,7 +161,7 @@ public void generateSomeSIFGraph() throws IOException public Pattern constructPattern() { Pattern pattern = super.constructPattern(); - pattern.add(new IDConstraint(Collections.singleton("http://identifiers.org/uniprot/Q9NVZ3")), "upper controller ER"); + pattern.add(new IDConstraint(Collections.singleton("identifiers.org/uniprot/Q9NVZ3")), "upper controller ER"); return pattern; } }; diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java index 95a7c9aa2..bf4990ae6 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java @@ -691,15 +691,16 @@ private static void summarizeHgncIds(Model model, PrintStream out) { PathAccessor pa = new PathAccessor("EntityReference/entityReferenceOf/dataSource", model.getLevel()); Set problemErs = new TreeSet<>(); for(EntityReference ser : model.getObjects(EntityReference.class)) { - //skip if it's a SMR or generic + //skip if it's SMR or generic if(ser instanceof SmallMoleculeReference || !ser.getMemberEntityReference().isEmpty()) continue; Set hgncSymbols = new HashSet<>(); Set hgncIds = new HashSet<>(); + final String uri = ser.getUri(); - if(ser.getUri().startsWith("http://identifiers.org/hgnc")) { - String s = ser.getUri().substring(ser.getUri().lastIndexOf("/")+1); + if(uri.startsWith("identifiers.org/hgnc") || uri.startsWith("bioregistry.io/hgnc")) { + String s = uri.substring(uri.lastIndexOf("/")+1); if(s.startsWith("HGNC:")) { hgncIds.add(s); } else { @@ -708,14 +709,15 @@ private static void summarizeHgncIds(Model model, PrintStream out) { } for(Xref x : ser.getXref()) { - if(x instanceof PublicationXref || x.getDb()==null || x.getId()==null) { - continue; //skip + if(x instanceof PublicationXref || StringUtils.isBlank(x.getDb()) || StringUtils.isBlank(x.getId())) { + continue; //skip PX, or when db or id is undefined/blank } - if(x.getDb().toLowerCase().startsWith("hgnc") && !x.getId().toLowerCase().startsWith("hgnc:")) { - hgncSymbols.add(x.getId().toLowerCase()); - } - else if(x.getDb().toLowerCase().startsWith("hgnc") && x.getId().toLowerCase().startsWith("hgnc:")) { - hgncIds.add(x.getId().toLowerCase()); + if(x.getDb().toLowerCase().startsWith("hgnc")) { + String id = x.getId().toLowerCase(); + if(StringUtils.startsWithIgnoreCase(id,"hgnc:") || StringUtils.isNumeric(id)) + hgncIds.add(id); + else + hgncSymbols.add(id); } } @@ -727,7 +729,7 @@ else if(x.getDb().toLowerCase().startsWith("hgnc") && x.getId().toLowerCase().st for(Object provenance : pa.getValueFromBean(ser)) { if (hgncSymbols.isEmpty() && hgncIds.isEmpty()) { problemErs.add(String.format("%s\t%s\t%s", - ((Provenance)provenance).getDisplayName(), ser.getDisplayName(), ser.getUri())); + ((Provenance)provenance).getDisplayName(), ser.getDisplayName(), uri)); MutableInt n = numProblematicErs.get(provenance); if (n == null) { numProblematicErs.put((Provenance) provenance, new MutableInt(1)); @@ -768,7 +770,7 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { Map numErs = new HashMap<>(); Map numProblematicErs = new HashMap<>(); PathAccessor pa = new PathAccessor("EntityReference/entityReferenceOf:Protein/dataSource", model.getLevel()); - Set problemErs = new TreeSet(); + Set problemErs = new TreeSet<>(); for(ProteinReference pr : model.getObjects(ProteinReference.class)) { //skip a generic one if(!pr.getMemberEntityReference().isEmpty()) { @@ -776,10 +778,14 @@ private static void summarizeUniprotIds(Model model, PrintStream out) { } for(Object provenance : pa.getValueFromBean(pr)) { - if(!pr.getUri().startsWith("http://identifiers.org/uniprot") - && !pr.getXref().toString().toLowerCase().contains("uniprot")) { + String uri = pr.getUri(); + //when the protein reference does not have any uniprot AC/ID - + if(!uri.startsWith("identifiers.org/uniprot") + && !uri.startsWith("bioregistry.io/uniprot") + && !pr.getXref().toString().toLowerCase().contains("uniprot")) + { problemErs.add(String.format("%s\t%s\t%s", - ((Provenance) provenance).getDisplayName(), pr.getDisplayName(), pr.getUri())); + ((Provenance) provenance).getDisplayName(), pr.getDisplayName(), uri)); MutableInt n = numProblematicErs.get(provenance); if (n == null) { numProblematicErs.put((Provenance) provenance, new MutableInt(1)); @@ -827,8 +833,9 @@ private static void summarizeChebiIds(Model model, PrintStream out) { continue; } for(Object provenance : pa.getValueFromBean(smr)) { - if(!smr.getUri().startsWith("http://identifiers.org/chebi/CHEBI:") - && !smr.getXref().toString().contains("CHEBI:")) { + if(!StringUtils.startsWithIgnoreCase(smr.getUri(), "identifiers.org/chebi") + && !StringUtils.startsWithIgnoreCase(smr.getUri(),"bioregistry.io/chebi") + && !StringUtils.containsIgnoreCase(smr.getXref().toString(),"chebi:")) { problemErs.add(String.format("%s\t%s\t%s", ((Provenance) provenance).getDisplayName(), smr.getDisplayName(), smr.getUri())); MutableInt n = numProblematicErs.get(provenance); @@ -1062,18 +1069,6 @@ else if(bpe instanceof SequenceEntityReference && ((SequenceEntityReference)bpe) ); } - static void toSer(String[] argv) throws IOException { - String in = argv[1]; - String out = argv[2]; - log.info("Loading BioPAX data from " + in); - long start = System.currentTimeMillis(); - Model model = io.convertFromOWL(getInputStream(in)); - log.info("Writing Paxtools Model to (binary file) " + out); - ModelUtils.serialize(model, new FileOutputStream(out)); - long stop = System.currentTimeMillis(); - log.info(String.format("Done (in %d sec)", TimeUnit.MILLISECONDS.toSeconds(stop-start))); - } - private static List> sortToName( Set> classes) { List> list = new ArrayList<>(classes); diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java index e52b26a3c..ce51395c0 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Main.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Main.java @@ -1,6 +1,4 @@ package org.biopax.paxtools; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import java.io.*; @@ -10,10 +8,7 @@ * Paxtools console application (useful BioPAX tools). */ public final class Main { - final static Logger log = LoggerFactory.getLogger(Main.class); - - public static void main(String[] argv) throws Exception - { + public static void main(String[] argv) throws Exception { if (argv.length == 0) { help(); } else { @@ -21,80 +16,80 @@ public static void main(String[] argv) throws Exception Command.valueOf(command).run(argv); } } - - enum Command { - merge(" \n" + - "\t- merges file2 into file1 and writes it into output") - {public void run(String[] argv) throws IOException{merge(argv);} }, - toSIF(" [-extended] [-andSif] [\"include=SIFType,..\"] [\"exclude=SIFType,..\"]" + - " [\"seqDb=db,..\"] [\"chemDb=db,..\"] [-dontMergeInteractions] [-useNameIfNoId] [ ...]\n" + - "\t- converts a BioPAX model to SIF (default) or custom SIF-like text format;\n" + - "\t will use blacklist.txt (recommended) file in the current directory, if present.\n" + - "\t- Include or exclude to/from the analysis one or more relationship types by \n" + - "\t using 'include=' and/or 'exclude=', respectively, e.g., exclude=NEIGHBOR_OF,INTERACTS_WITH\n" + - "\t (mind using underscore instead of minus sign in the SIF type names; the default is to use all types).\n" + - "\t- With 'seqDb=' and 'chemDb=', you can specify standard sequence/gene/chemical ID type(s)\n" + - "\t (can be just a unique prefix) to match actual xref.db values in the BioPAX model,\n" + - "\t e.g., \"seqDb=uniprot,hgnc,refseq\", and in that order, means: if a UniProt entity ID is found,\n" + - "\t other ID types ain't used; otherwise, if an 'hgnc' ID/Symbol is found... and so on;\n" + - "\t when not specified, then 'hgnc' (in fact, 'HGNC Symbol') for bio-polymers - \n" + - "\t and ChEBI IDs or name (if '-useNameIfNoId' is set) for chemicals - are selected.\n" + - "\t- With '-extended' flag, the output will be the Pathway Commons TXT (Extended SIF) format:\n" + - "\t two sections separated with one blank line - first come inferred SIF interactions -\n" + - "\t 'A\trelationship-type\tB' plus RESOURCE, PUBMED, PATHWAY, MEDIATOR extra columns, \n" + - "\t followed by interaction participants description section).\n" + - "\t- If '-andSif' flag is present (only makes sense together with '-extended'), then the \n" + - "\t classic SIF output file is also created (will have '.sif' extension).\n" + - "\t- Finally, ... list is to specify 4th, 5th etc. custom output columns;\n" + - "\t use pre-defined column names (accessors): \n" + - "\t\tMEDIATOR,\n" + - "\t\tPUBMED,\n" + - "\t\tPMC,\n" + - "\t\tCOMMENTS,\n" + - "\t\tPATHWAY,\n" + - "\t\tPATHWAY_URI,\n" + - "\t\tRESOURCE,\n" + - "\t\tSOURCE_LOC,\n" + - "\t\tTARGET_LOC\n" + - "\t or custom biopax property path accessors (XPath-like expressions to apply to each mediator entity; \n" + - "\t see https://github.com/BioPAX/Paxtools/wiki/PatternBinaryInteractionFramework)") - {public void run(String[] argv) throws IOException{toSifnx(argv);} }, - toSBGN(" [-nolayout]\n" + - "\t- converts model to the SBGN format and applies COSE layout unless optional -nolayout flag is set.") - {public void run(String[] argv) throws IOException { toSbgn(argv); } }, - validate(" [xml|html|biopax] [auto-fix] [only-errors] [maxerrors=n] [notstrict]\n" + - "\t- validate BioPAX file/directory (up to ~25MB in total size, -\n" + - "\totherwise download and run the stand-alone validator)\n" + - "\tin the directory using the online validator service\n" + - "\t(generates html or xml report, or gets the processed biopax\n" + - "\t(cannot be perfect though) see http://www.biopax.org/validator)") - {public void run(String[] argv) throws IOException{validate(argv);} }, - integrate(" \n" + - "\t- integrates file2 into file1 and writes it into output (experimental)") - {public void run(String[] argv) throws IOException{integrate(argv);} }, - toLevel3(" [-psimiToComplexes]\n" + - "\t- converts BioPAX level 1 or 2, PSI-MI 2.5 and PSI-MITAB to the level 3 file;\n" + - "\t-psimiToComplexes forces PSI-MI Interactions become BioPAX Complexes instead MolecularInteractions.") - {public void run(String[] argv) throws IOException{toLevel3(argv);} }, - toGSEA(" [-crossSpecies] [-subPathways] [-notPathway] [organisms=9606,human,rat,..]\n" + - "\t- converts BioPAX data to the GSEA software format (GMT); options/flags:\n" - + "\t - gene/protein ID type; values: uniprot, hgnc, refseq, etc. (a name or prefix to match\n" + + enum Command { + merge(" \n" + + "\t- merges file2 into file1 and writes it into output") + {public void run(String[] argv) throws IOException{merge(argv);} }, + toSIF(" [-extended] [-andSif] [\"include=SIFType,..\"] [\"exclude=SIFType,..\"]" + + " [\"seqDb=db,..\"] [\"chemDb=db,..\"] [-dontMergeInteractions] [-useNameIfNoId] [ ...]\n" + + "\t- converts a BioPAX model to SIF (default) or custom SIF-like text format;\n" + + "\t will use blacklist.txt (recommended) file in the current directory, if present.\n" + + "\t- Include or exclude to/from the analysis one or more relationship types by \n" + + "\t using 'include=' and/or 'exclude=', respectively, e.g., exclude=NEIGHBOR_OF,INTERACTS_WITH\n" + + "\t (mind using underscore instead of minus sign in the SIF type names; the default is to use all types).\n" + + "\t- With 'seqDb=' and 'chemDb=', you can specify standard sequence/gene/chemical ID type(s)\n" + + "\t (can be just a unique prefix) to match actual xref.db values in the BioPAX model,\n" + + "\t e.g., \"seqDb=uniprot,hgnc,refseq\", and in that order, means: if a UniProt entity ID is found,\n" + + "\t other ID types ain't used; otherwise, if an 'hgnc' ID/Symbol is found... and so on;\n" + + "\t when not specified, then 'hgnc' (in fact, 'HGNC Symbol') for bio-polymers - \n" + + "\t and ChEBI IDs or name (if '-useNameIfNoId' is set) for chemicals - are selected.\n" + + "\t- With '-extended' flag, the output will be the Pathway Commons TXT (Extended SIF) format:\n" + + "\t two sections separated with one blank line - first come inferred SIF interactions -\n" + + "\t 'A\trelationship-type\tB' plus RESOURCE, PUBMED, PATHWAY, MEDIATOR extra columns, \n" + + "\t followed by interaction participants description section).\n" + + "\t- If '-andSif' flag is present (only makes sense together with '-extended'), then the \n" + + "\t classic SIF output file is also created (will have '.sif' extension).\n" + + "\t- Finally, ... list is to specify 4th, 5th etc. custom output columns;\n" + + "\t use pre-defined column names (accessors): \n" + + "\t\tMEDIATOR,\n" + + "\t\tPUBMED,\n" + + "\t\tPMC,\n" + + "\t\tCOMMENTS,\n" + + "\t\tPATHWAY,\n" + + "\t\tPATHWAY_URI,\n" + + "\t\tRESOURCE,\n" + + "\t\tSOURCE_LOC,\n" + + "\t\tTARGET_LOC\n" + + "\t or custom biopax property path accessors (XPath-like expressions to apply to each mediator entity; \n" + + "\t see https://github.com/BioPAX/Paxtools/wiki/PatternBinaryInteractionFramework)") + {public void run(String[] argv) throws IOException{toSifnx(argv);} }, + toSBGN(" [-nolayout]\n" + + "\t- converts model to the SBGN format and applies COSE layout unless optional -nolayout flag is set.") + {public void run(String[] argv) throws IOException { toSbgn(argv); } }, + validate(" [xml|html|biopax] [auto-fix] [only-errors] [maxerrors=n] [notstrict]\n" + + "\t- validate BioPAX file/directory (up to ~25MB in total size, -\n" + + "\totherwise download and run the stand-alone validator)\n" + + "\tin the directory using the online validator service\n" + + "\t(generates html or xml report, or gets the processed biopax\n" + + "\t(cannot be perfect though) see http://www.biopax.org/validator)") + {public void run(String[] argv) throws IOException{validate(argv);} }, + integrate(" \n" + + "\t- integrates file2 into file1 and writes it into output (experimental)") + {public void run(String[] argv) throws IOException{integrate(argv);} }, + toLevel3(" [-psimiToComplexes]\n" + + "\t- converts BioPAX level 1 or 2, PSI-MI 2.5 and PSI-MITAB to the level 3 file;\n" + + "\t-psimiToComplexes forces PSI-MI Interactions become BioPAX Complexes instead MolecularInteractions.") + {public void run(String[] argv) throws IOException{toLevel3(argv);} }, + toGSEA(" [-crossSpecies] [-subPathways] [-notPathway] [organisms=9606,human,rat,..]\n" + + "\t- converts BioPAX data to the GSEA software format (GMT); options/flags:\n" + + "\t - gene/protein ID type; values: uniprot, hgnc, refseq, etc. (a name or prefix to match\n" + "\t ProteinReference/xref/db property values in the input BioPAX model).\n" - + "\t-crossSpecies - allows printing on the same line gene/protein IDs from different species;\n" + + "\t-crossSpecies - allows printing on the same line gene/protein IDs from different species;\n" + "\t-subPathways - traverse into sub-pathways to collect all protein IDs for a pathway.\n" + "\t-notPathway - also list those protein/gene IDs that cannot be reached from pathways.\n" + "\torganisms - optional filter; a comma-separated list of taxonomy IDs and/or names\n") - {public void run(String[] argv) throws IOException{toGSEA(argv);} }, - fetch(" [uris=URI1,..] [-absolute] \n" + - "\t- extracts a self-integral BioPAX sub-model from file1 and writes to the output; options:\n" + + {public void run(String[] argv) throws IOException{toGSEA(argv);} }, + fetch(" [uris=URI1,..] [-absolute] \n" + + "\t- extracts a self-integral BioPAX sub-model from file1 and writes to the output; options:\n" + "\turi=... - an optional list of existing in the model BioPAX elements' full URIs;\n" + "\t-absolute - set this flag to write full/absolute URIs to the output (i.e., 'rdf:about' instead 'rdf:ID').") - {public void run(String[] argv) throws IOException{fetch(argv);} }, - getNeighbors(" \n" + - "\t- nearest neighborhood graph query (id1,id2 - of Entity sub-class only)") - {public void run(String[] argv) throws IOException{getNeighbors(argv);} }, - summarize(" [--model] [--pathways] [--hgnc-ids] [--uniprot-ids] [--chebi-ids]\n" + - "\t- (experimental) summary of the input BioPAX model;\n " + + {public void run(String[] argv) throws IOException{fetch(argv);} }, + getNeighbors(" \n" + + "\t- nearest neighborhood graph query (id1,id2 - of Entity sub-class only)") + {public void run(String[] argv) throws IOException{getNeighbors(argv);} }, + summarize(" [--model] [--pathways] [--hgnc-ids] [--uniprot-ids] [--chebi-ids]\n" + + "\t- (experimental) summary of the input BioPAX model;\n " + "\truns one or several analyses and writes to the output file;\n " + "\t'--model' - (default) BioPAX classes, properties and values summary;\n " + "\t'--pathways' - pathways and sub-pathways hierarchy;\n " + @@ -103,33 +98,34 @@ enum Command { "\t'--chebi-ids' - ChEBI IDs in small molecule references;\n " + "\t'--uri-ids' - URI,type,name(s) and standard identifiers (in JSON format) for each physical entity;\n " + "\tthe options' order defines the results output order.") - {public void run(String[] argv) throws IOException{summarize(argv);} }, + {public void run(String[] argv) throws IOException{summarize(argv);} }, blacklist(" \n" + - "\t- creates a blacklist of ubiquitous small molecules, like ATP, \n" - + "\tfrom the BioPAX model and writes it to the output file. The blacklist can be used with\n " - + "\tpaxtools graph queries or when converting from the SAME BioPAX data to the SIF formats.") + "\t- creates a blacklist of ubiquitous small molecules, like ATP, \n" + + "\tfrom the BioPAX model and writes it to the output file. The blacklist can be used with\n " + + "\tpaxtools graph queries or when converting from the SAME BioPAX data to the SIF formats.") {public void run(String[] argv) throws IOException{blacklist(argv);} }, pattern("\n\t- BioPAX pattern search tool (opens a new dialog window)") {public void run(String[] argv){pattern(argv);} }, - toSer(" \n" + - "\t- converts BioPAX data to serialized Model (bytes); for very large models requires more stack size, JVM option: -Xss256g or more") - {public void run(String[] argv) throws IOException { toSer(argv); } }, - help("\n\t- prints this screen and exits\n") + help("\n\t- prints this screen and exits\n") {public void run(String[] argv){ help();} }; - String description; + private final String description_; - Command(String description) { - this.description = description; - } + public String getDescription() { + return description_; + } - public abstract void run(String[] argv) throws IOException; - } + Command(String description) { + description_ = description; + } + + public abstract void run(String[] argv) throws IOException; + } private static void help() { System.out.println("Available commands:"); for (Command cmd : Command.values()) { - System.out.println(cmd.name() + " " + cmd.description); + System.out.println(cmd.name() + " " + cmd.getDescription()); } System.out.println("Commands can also use compressed input files (only '.gz')."); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java index bfdd2bb6b..6d6a7acc5 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/IdFetcher.java @@ -90,20 +90,18 @@ public Set fetchID(BioPAXElement ele) ? chemDbStartsWithOrEquals : seqDbStartsWithOrEquals; for (String dbStartsWith : dbStartsWithOrEquals) { - //a shortcut for URI like "http://identifiers.org/uniprot/", "http://identifiers.org/chebi/"; - //this prevents collecting lots of secondary IDs of the same type - if(ele.getUri().startsWith("http://identifiers.org/"+dbStartsWith)) { + //a shortcut for normalized URIs; prevents collecting lots of secondary IDs of the same type + if(ele.getUri().startsWith("(?i)identifiers.org/"+dbStartsWith) + || ele.getUri().startsWith("(?i)bioregistry.io/"+dbStartsWith)) { set.add(ele.getUri().substring(ele.getUri().lastIndexOf("/") + 1)); - } - else - { - for (UnificationXref x : new ClassFilterSet(((XReferrable) ele).getXref(), + } else { + for (UnificationXref x : new ClassFilterSet<>(((XReferrable) ele).getXref(), UnificationXref.class)) { collectXrefIdIfDbLike(x, dbStartsWith, set); } //if none was found in unif. xrefs, try rel, xrefs if (set.isEmpty()) { - for (RelationshipXref x : new ClassFilterSet(((XReferrable) ele).getXref(), + for (RelationshipXref x : new ClassFilterSet<>(((XReferrable) ele).getXref(), RelationshipXref.class)) { collectXrefIdIfDbLike(x, dbStartsWith, set); } @@ -125,7 +123,7 @@ public Set fetchID(BioPAXElement ele) else if (e.getStandardName() != null && !e.getStandardName().contains("...")) set.add(e.getStandardName()); else if (!e.getName().isEmpty()) { - Set names = new TreeSet(); + Set names = new TreeSet<>(); for(String name : e.getName()) { if(!name.contains("...")) names.add(name); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java index 0746322b9..168292159 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java @@ -90,6 +90,10 @@ public final class ModelUtils */ public static void replace(Model model, final Map subs) { + if(subs == null || subs.isEmpty()) { + return; + } + // update properties Visitor visitor = (domain, range, bpModel, propertyEditor) -> { if (propertyEditor instanceof ObjectPropertyEditor && range != null && subs.containsKey(range)) @@ -1176,10 +1180,8 @@ public static void mergeEquivalentInteractions(Model model) * * @param model to edit/update */ - public static void mergeEquivalentPhysicalEntities(Model model) - { - HashMap subs = new HashMap(); - + public static void mergeEquivalentPhysicalEntities(Model model) { + HashMap subs = new HashMap<>(); EquivalenceGrouper groups = new EquivalenceGrouper(model.getObjects(PhysicalEntity.class)); for (List group : groups.getBuckets()) { if (group.size() > 1) { @@ -1325,53 +1327,4 @@ public static boolean isGeneric(BioPAXElement e) { ); //false when e==null } - - /** - * Serialize a not too large object (mainly for testing). - * @param o - * @return - * @throws IOException - */ - public static byte[] serialize(Object o) throws IOException { - ByteArrayOutputStream baos = new ByteArrayOutputStream(); - serialize(o, baos); - return baos.toByteArray(); - } - - /** - * Deserialize a not too large object (mainly for testing). - * @param bytes - * @return object - * @throws IOException - * @throws ClassNotFoundException - */ - public static Object deserialize(byte[] bytes) throws IOException, ClassNotFoundException { - return deserialize(new ByteArrayInputStream(bytes)); - } - - /** - * Serialize. - * @param o - * @param os - * @throws IOException - */ - public static void serialize(Object o, OutputStream os) throws IOException { - ObjectOutputStream oos = new ObjectOutputStream(os); - oos.writeObject(o); - oos.close(); - } - - /** - * Deserialize. - * @param is - * @return object - * @throws IOException - * @throws ClassNotFoundException - */ - public static Object deserialize(InputStream is) throws IOException, ClassNotFoundException { - ObjectInputStream ois = new ObjectInputStream(is); - Object o = ois.readObject(); - ois.close(); - return o; - } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java index 61c44ef89..f91bbb904 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/BioPAXElementImpl.java @@ -1,5 +1,6 @@ package org.biopax.paxtools.impl; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.builder.EqualsBuilder; import org.apache.commons.lang3.builder.HashCodeBuilder; import org.biopax.paxtools.model.BioPAXElement; @@ -47,13 +48,14 @@ public String getUri() * what you're doing (and can use Java Reflection). * * @param uri new absolute URI + * @throws IllegalArgumentException when uri is null/blank */ @SuppressWarnings("unused") private void setUri(String uri) { - if(uri == null) - throw new IllegalArgumentException(); - + if(StringUtils.isBlank(uri)) { + throw new IllegalArgumentException("Blank or null URI is not allowed"); + } this.uri = uri; } @@ -67,7 +69,7 @@ public String toString() public Map getAnnotations() { synchronized (annotations) { if(annotations.isEmpty()) { - annotations = new HashMap<>(); + annotations = new HashMap<>(2); } return annotations; } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java index 46da19787..020e5be70 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/MockFactory.java @@ -73,8 +73,7 @@ private void populateMock(BioPAXElement bpe) if (propertyEditor instanceof StringPropertyEditor) { value = getStrings(bpe, multiple); - } else - { + } else { Class range = propertyEditor.getRange(); if (propertyEditor instanceof PrimitivePropertyEditor) { diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java index 2afe5826b..19fc6afa2 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/ModelImpl.java @@ -18,28 +18,22 @@ */ public class ModelImpl implements Model { -// ------------------------------ FIELDS ------------------------------ - private static final long serialVersionUID = -2087521863213381434L; protected final Map idMap; private final Map nameSpacePrefixMap; private BioPAXLevel level; private transient BioPAXFactory factory; + private final transient Set exposedObjectSet; private boolean addDependencies = false; private String xmlBase; private String uri; private String name; -// --------------------------- CONSTRUCTORS --------------------------- protected ModelImpl() { - idMap = BPCollections.I.createMap(100); - nameSpacePrefixMap = new HashMap<>(5); - } - - protected ModelImpl(int initialCapacity) { - idMap = BPCollections.I.createMap(initialCapacity); + idMap = BPCollections.I.createMap(); nameSpacePrefixMap = new HashMap<>(5); + exposedObjectSet = new UnmodifiableImplicitSet(idMap.values()); //a wrapper, no copying to save memory } protected ModelImpl(BioPAXLevel level) @@ -53,13 +47,6 @@ public ModelImpl(BioPAXFactory factory) { this.level = factory.getLevel(); } - public ModelImpl(BioPAXFactory factory, int initialCapacity) { - this(initialCapacity); - this.factory = factory; - this.level = factory.getLevel(); - } - -// --------------------- GETTER / SETTER METHODS --------------------- public synchronized boolean containsID(String id) { return this.idMap.containsKey(id); @@ -96,23 +83,18 @@ public void setFactory(BioPAXFactory factory) this.level = factory.getLevel(); } -// ------------------------ INTERFACE METHODS ------------------------ - -// --------------------- Interface Model --------------------- - -// --------------------- ACCESSORS and MUTATORS--------------------- - public synchronized Collection getObjects() + public synchronized Set getObjects() { - return new UnmodifiableImplicitSet(idMap.values()); + return exposedObjectSet; } - public synchronized Collection getObjects(Class filterBy) + public synchronized Set getObjects(Class filterBy) { - return new ClassFilterSet<>(getObjects(), filterBy); + return new ClassFilterSet<>(exposedObjectSet, filterBy); } - //a setter for persistence, serialize or tests + //a setter for persistence, serialize, tests synchronized void setObjects(Collection objects) { idMap.clear(); for(BioPAXElement bpe : objects) { @@ -121,7 +103,9 @@ synchronized void setObjects(Collection objects) { } public synchronized void remove(BioPAXElement aBioPAXElement) { - idMap.remove(aBioPAXElement.getUri()); + if(contains(aBioPAXElement)) { + idMap.remove(aBioPAXElement.getUri()); + } } public synchronized T addNew(Class c, String id) @@ -148,7 +132,6 @@ public synchronized boolean contains(BioPAXElement aBioPAXElement) return idMap.get(aBioPAXElement.getUri()) == aBioPAXElement; } -// -------------------------- OTHER METHODS -------------------------- public String getUri() { return uri; @@ -168,21 +151,17 @@ public void setName(String modelName) { public synchronized void add(BioPAXElement aBioPAXElement) { + if(!level.hasElement(aBioPAXElement)) { + throw new IllegalBioPAXArgumentException("Given object is of wrong level"); + } String uri = aBioPAXElement.getUri(); if (uri == null) { - throw new IllegalBioPAXArgumentException( - "BioPAX object URI is null: " + aBioPAXElement); - } - else if(!level.hasElement(aBioPAXElement)) { - throw new IllegalBioPAXArgumentException( - "Given object is of wrong level"); - } - else if (idMap.containsKey(uri)) { - throw new IllegalBioPAXArgumentException( - "I already have an object with the same ID: " + uri + - ". Try removing it first"); - } - else { + throw new IllegalBioPAXArgumentException("URI is null, element: " + aBioPAXElement); + } else if (contains(aBioPAXElement)) { + throw new IllegalBioPAXArgumentException("Duplicate element: " + aBioPAXElement); + } else if (idMap.containsKey(uri)) { + throw new IllegalBioPAXArgumentException("URI already exists: " + uri); + } else { idMap.put(uri, aBioPAXElement); } } @@ -207,14 +186,13 @@ public boolean isAddDependencies() { return addDependencies; } - private class UnmodifiableImplicitSet implements Set { - + private class UnmodifiableImplicitSet implements Set + { private final Collection elements; public UnmodifiableImplicitSet( Collection elements) { - this.elements = elements; } @@ -245,7 +223,7 @@ public Object[] toArray() public T[] toArray(T[] a) { - return elements.toArray(a); + return elements.toArray(a); } public boolean add(BioPAXElement bioPAXElement) @@ -296,8 +274,9 @@ public synchronized void replace(final BioPAXElement existing, final BioPAXEleme { ModelUtils.replace(this, Collections.singletonMap(existing, replacement)); remove(existing); - if(replacement != null) + if(replacement != null) { add(replacement); + } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ScoreImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ScoreImpl.java index e4b1c7489..17320aa39 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ScoreImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/ScoreImpl.java @@ -4,50 +4,41 @@ import org.biopax.paxtools.model.level3.Score; -public class ScoreImpl extends XReferrableImpl implements Score -{ - - private String value; - private Provenance scoreSource; - - public ScoreImpl() { - } - - // - // BioPAXElement interface implementation - // - //////////////////////////////////////////////////////////////////////////// - - public Class getModelInterface() - { - return Score.class; - } - - - - // - // confidence interface implementation - // - //////////////////////////////////////////////////////////////////////////// - - public String getValue() - { - return value; - } - - public void setValue(String value) - { - this.value = value; - } - - public Provenance getScoreSource() - { - return scoreSource; - } - - public void setScoreSource(Provenance scoreSource) - { - this.scoreSource = scoreSource; - } +public class ScoreImpl extends XReferrableImpl implements Score { + + private String value; + private Provenance scoreSource; + + public ScoreImpl() { + } + + // + // BioPAXElement interface implementation + // + + public Class getModelInterface() { + return Score.class; + } + + + // + // confidence interface implementation + // + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public Provenance getScoreSource() { + return scoreSource; + } + + public void setScoreSource(Provenance scoreSource) { + this.scoreSource = scoreSource; + } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java index 665c06173..a3f15473a 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/SimplePhysicalEntityImpl.java @@ -60,9 +60,8 @@ public void setEntityReference(EntityReference entityReference) @Override - public int equivalenceCode() - { - return this.entityReference==null? hashCode():31 * super.locationAndFeatureCode() + + public int equivalenceCode() { + return this.entityReference==null ? hashCode() : 31 * super.locationAndFeatureCode() + entityReference.equivalenceCode(); } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TransportImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TransportImpl.java index d4b0799d3..9f32446d8 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TransportImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/TransportImpl.java @@ -10,7 +10,7 @@ public TransportImpl() { // --------------------- Interface BioPAXElement --------------------- - public Class getModelInterface() + public Class getModelInterface() { return Transport.class; } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/XrefImpl.java b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/XrefImpl.java index 75cc3cbd1..3f7c70e48 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/XrefImpl.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/impl/level3/XrefImpl.java @@ -8,109 +8,96 @@ import java.util.Set; -public abstract class XrefImpl extends L3ElementImpl implements Xref -{ - private String db; - private String dbVersion; - private String idVersion; - private String refId; - private Set xrefOf; - - /** - * Constructor. - */ - public XrefImpl() - { - this.xrefOf = BPCollections.I.createSafeSet(); - } - - @Override - protected boolean semanticallyEquivalent(BioPAXElement other) - { - if(!(other instanceof Xref)) return false; - - final Xref anXref = (Xref) other; - - return - (db != null ? - db.equalsIgnoreCase(anXref.getDb()) : - anXref.getDb() == null) - && - (refId != null ? - refId.equals(anXref.getId()) : - anXref.getId() == null) - && - (dbVersion != null ? - dbVersion.equalsIgnoreCase(anXref.getDbVersion()) : - anXref.getDbVersion() == null) - && - (idVersion != null ? - idVersion.equals(anXref.getIdVersion()) : - anXref.getIdVersion() == null); - } - - @Override - public int equivalenceCode() - { - int result = 29 + (db != null ? db.hashCode() : 0); - result = 29 * result + (dbVersion != null ? dbVersion.hashCode() : 0); - result = 29 * result + (idVersion != null ? idVersion.hashCode() : 0); - result = 29 * result + (refId != null ? refId.hashCode() : 0); - return result; - } - - public String getDb() - { - return db; - } - - public void setDb(String db) - { - this.db = db; - } - - public String getDbVersion() - { - return dbVersion; - } - - public void setDbVersion(String dbVersion) - { - this.dbVersion = dbVersion; - } - - public String getIdVersion() - { - return idVersion; - } - - public void setIdVersion(String idVersion) - { - this.idVersion = idVersion; - } - - - public String getId() - { - return refId; - } - - public void setId(String id) - { - this.refId = id; - } - - public Set getXrefOf() - { - return xrefOf; - } - - @Override - public String toString() { - return getDb() + - ((getDbVersion()==null)? "" : "." + getDbVersion()) - + ":" + getId() + - ((getIdVersion()==null)? "" : "." + getIdVersion()); - } - +public abstract class XrefImpl extends L3ElementImpl implements Xref { + private String db; + private String dbVersion; + private String idVersion; + private String refId; + private Set xrefOf; + + /** + * Constructor. + */ + public XrefImpl() { + this.xrefOf = BPCollections.I.createSafeSet(); + } + + @Override + protected boolean semanticallyEquivalent(BioPAXElement other) { + if (!(other instanceof Xref)) return false; + + final Xref anXref = (Xref) other; + + return + (db != null ? + db.equalsIgnoreCase(anXref.getDb()) : + anXref.getDb() == null) + && + (refId != null ? + refId.equals(anXref.getId()) : + anXref.getId() == null) + && + (dbVersion != null ? + dbVersion.equalsIgnoreCase(anXref.getDbVersion()) : + anXref.getDbVersion() == null) + && + (idVersion != null ? + idVersion.equals(anXref.getIdVersion()) : + anXref.getIdVersion() == null); + } + + @Override + public int equivalenceCode() { + int result = 29 + (db != null ? db.hashCode() : 0); + result = 29 * result + (dbVersion != null ? dbVersion.hashCode() : 0); + result = 29 * result + (idVersion != null ? idVersion.hashCode() : 0); + result = 29 * result + (refId != null ? refId.hashCode() : 0); + return result; + } + + public String getDb() { + return db; + } + + public void setDb(String db) { + this.db = db; + } + + public String getDbVersion() { + return dbVersion; + } + + public void setDbVersion(String dbVersion) { + this.dbVersion = dbVersion; + } + + public String getIdVersion() { + return idVersion; + } + + public void setIdVersion(String idVersion) { + this.idVersion = idVersion; + } + + + public String getId() { + return refId; + } + + public void setId(String id) { + this.refId = id; + } + + public Set getXrefOf() { + return xrefOf; + } + + @Override + public String toString() { + return getDb() + + ((getDbVersion() == null) ? "" : "." + getDbVersion()) + + ":" + getId() + + ((getIdVersion() == null) ? "" : "." + getIdVersion()); + } + } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java b/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java index da8f89a30..a018eb239 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/io/SimpleIOHandler.java @@ -157,8 +157,7 @@ public String getXmlStreamInfo() r = xmlf.createXMLStreamReader(in); triples = new LinkedList<>(); } catch (XMLStreamException e) { - //e.printStackTrace(); - throw new BioPaxIOException(e.getClass().getSimpleName() + " " + e.getMessage() + "; " + e.getLocation()); + throw new BioPaxIOException(e.getClass().getSimpleName() + " " + e.getMessage() + "; " + e.getLocation(), e); } } @@ -855,5 +854,33 @@ public boolean isMergeDuplicates() return this.mergeDuplicates; } + /** + * Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string. + * (This is used in e.g. BioPAX Validator web app.) + * + * @param model a BioPAX object model to convert to the RDF/XML format + * @return the BioPAX data in the RDF/XML format + * @throws IllegalArgumentException if model is null + * @throws OutOfMemoryError when it cannot be stored in a byte array (max 2Gb). + */ + public static String convertToOwl(Model model) + { + if (model == null) throw new IllegalArgumentException(); + + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + + (new SimpleIOHandler(model.getLevel())).convertToOWL(model, outputStream); + + try + { + return outputStream.toString("UTF-8"); + } + catch (UnsupportedEncodingException e) + { + log.error("convertToOwl, outputStream.toString failed", e); + return outputStream.toString(); + } + } + } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXFactory.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXFactory.java index 3e303afe3..5d23bfd46 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXFactory.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/BioPAXFactory.java @@ -59,12 +59,6 @@ public BioPAXElement create(String localName, String uri) */ public T create(Class aClass, String uri) { -// //could use the following shortcut, but it might hurt performance of creating/reading large valid models -// if(!canInstantiate(aClass)) { -// log.error("Non-instantiable: cannot create BioPAX object, uri:"+uri+", with abstract type: " + aClass); -// return null; -// } - T bpe = null; // create a new instance of the BioPAX type diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java index 99b2490fd..33b80894c 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/Model.java @@ -1,8 +1,9 @@ package org.biopax.paxtools.model; + import java.io.Serializable; -import java.util.Collection; import java.util.Map; +import java.util.Set; /** * A model acts as a container for BioPAX elements. @@ -73,7 +74,7 @@ public interface Model extends Serializable * @see #containsID(String) * * @param aBioPAXElement to be checked - * @return true if the parameter is in the model (objects) + * @return true if the parameter is in the model */ boolean contains(BioPAXElement aBioPAXElement); @@ -105,21 +106,20 @@ public interface Model extends Serializable // --------------------- ACCESSORS and MUTATORS--------------------- /** - * This method returns the objects in the model - * (This collection should not be modified.) - * @return objects (the collection should not be modified). + * This method returns all the objects in the model. + * + * @return objects (unmodifiable set). */ - Collection getObjects(); + Set getObjects(); /** - * This method returns the objects of the given class in the model - * (The collection should not be modified.) + * This method returns the objects of the given class in the model. * - * @param a BioPAX type + * @param a BioPAX type * @param filterBy class to be used as a filter. - * @return objects of the given class. + * @return objects of the given class (unmodifiable set). */ - Collection getObjects(Class filterBy); + Set getObjects(Class filterBy); /** * This method removes the given BioPAX Element from the model. @@ -213,7 +213,7 @@ public interface Model extends Serializable * Note: it's not required that all the BioPAX objects * in the model have the same URI prefix/namespace; * e.g., there are can be (and perfectly legal) objects - * that use other URI bases, such as http://identifiers.org/, + * that use other URI bases, such as identifiers.org/, bioregistry.io/, * http://purl.org/, etc. (- usually these are well-known * standard xml bases, or these result from merging several BioPAX * models of different data providers into one model.) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/BioSource.java b/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/BioSource.java index badf175a4..f620fd0fd 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/BioSource.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/model/level3/BioSource.java @@ -4,7 +4,7 @@ /** * Definition: The biological source of an entity (e.g. protein, RNA or DNA). Some entities are * considered source-neutral (e.g. small molecules), and the biological source of others can be - * deduced from their constituentss (e.g. complex, pathway). Examples: HeLa cells, human, and mouse + * deduced from their constituents (e.g. complex, pathway). Examples: HeLa cells, human, and mouse * liver tissue. */ public interface BioSource extends UtilityClass, Named diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java index e62f3fa28..1593922a1 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/AbstractFilterSet.java @@ -58,7 +58,6 @@ public int size() return new FilterIterator(baseSet.iterator()); } - private class FilterIterator implements Iterator { E next = null; diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java index 38d6b1e75..95da6d18f 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java @@ -1,14 +1,13 @@ package org.biopax.paxtools.util; +import org.apache.commons.lang3.StringUtils; import org.biopax.paxtools.model.BioPAXElement; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import java.util.*; - -public enum BPCollections -{ +public enum BPCollections { I; // singleton /** @@ -16,71 +15,54 @@ public enum BPCollections * and initialize and load factor for all sets and maps * used in all model objects for performance purposes. */ - public interface CollectionProvider - { + public interface CollectionProvider { Set createSet(); Map createMap(); - Map createMap(int initSz); + Collection createCollection(int initSz); + } + + //Default CollectionProvider implementation (HashMap, HashSet, ArrayList) + public static class DefaultCollectionProvider implements CollectionProvider { + public Set createSet() { + return new HashSet<>(); + } - Collection createCollection(); + public Map createMap() { + return new HashMap<>(); + } - Collection createCollection(int initSz); + public Collection createCollection(int initSz) { + return new ArrayList<>(initSz); + } } private CollectionProvider cProvider; - + private String safeSetOpt_; private final Logger log = LoggerFactory.getLogger(BPCollections.class); - - BPCollections() - { + BPCollections() { + //if a custom collection provider was specified, try to use that String prop = System.getProperty("paxtools.CollectionProvider"); - log.info("System property: paxtools.CollectionProvider=" + prop); - if (prop != null) - { - try - { - Class cProviderClass = - (Class) Class.forName(prop); + log.info("System property: paxtools.CollectionProvider=" + prop); + if (StringUtils.isNotBlank(prop)) { + try { + Class cProviderClass = (Class) Class.forName(prop); cProvider = cProviderClass.getDeclaredConstructor().newInstance(); - log.info("CollectionProvider " + prop + " was successfully activated."); - } - catch (Exception e) - { - log.warn("Could not initialize the specified collector provider:" + prop + - " . Falling back to default " + - "Hash based implementation. Underlying exception is " + e); - + log.info("Custom CollectionProvider " + prop + " was successfully activated."); + } catch (Exception e) { + log.warn("Could not initialize the specified collection provider: " + prop + + "; will use the default implementation; error: " + e); } } - - if (cProvider == null) { - //Use the default CollectionProvider implementation (HashMap, HashSet, ArrayList) - cProvider = new CollectionProvider() { - public Set createSet() { - return new HashSet<>(); - } - - public Map createMap() { - return new HashMap<>(); - } - - public Map createMap(int initSz) { - return new HashMap<>(initSz); - } - - public Collection createCollection(int initSz) { - return new ArrayList<>(initSz); - } - - public Collection createCollection() { - return new ArrayList<>(); - } - }; + if(cProvider == null) { + cProvider = new DefaultCollectionProvider(); log.info("Using the default CollectionProvider."); } + + safeSetOpt_ = System.getProperty("paxtools.model.safeset","map"); + log.info("System property: paxtools.model.safeset=" + safeSetOpt_); } @@ -106,9 +88,14 @@ public Set createSet() return cProvider.createSet(); } - public Set createSafeSet() - { - return new BiopaxSafeSet(); + public Set createSafeSet() { + switch (safeSetOpt_) { + case "list": + return new BiopaxElements<>();//Set based on Map (faster, more memory, for building/merging Models) + case "map": + default: + return new BiopaxSafeSet<>();//Set based on List (slower, less memory, for read-only analyses, queries) + } } public Map createMap() @@ -116,29 +103,8 @@ public Map createMap() return cProvider.createMap(); } - public Map createMap(int initSize) - { - return cProvider.createMap(initSize); - } - - public Collection createCollection() - { - return cProvider.createCollection(); - } - public Collection createCollection(int initSize) { return cProvider.createCollection(initSize); } - - public Collection createSafeCollection() - { - return new BiopaxSafeCollection<>(); - } - - public Collection createSafeCollection(int initSz) - { - return new BiopaxSafeCollection<>(initSz); - } - } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxElements.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxElements.java new file mode 100644 index 000000000..ce01fbc1e --- /dev/null +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxElements.java @@ -0,0 +1,98 @@ +package org.biopax.paxtools.util; + +import org.biopax.paxtools.model.BioPAXElement; + +import java.io.Serializable; +import java.util.*; + +/** + * Another thread-safe Set of BioPAX objects that prevents adding several elements with the same URI. + * This is backed by an internal List (less memory but slower ~O(N) add/contains/remove operations). + */ +public class BiopaxElements extends AbstractSet implements Serializable +{ + //initial map is to be reset to a modifiable instance on first write + private final static Collection empty = Collections.emptyList(); + private Collection c_; //list + private int l_; //initial size + + public BiopaxElements() { + c_ = empty; + l_ = 2; //instead of the default 10 + } + + public BiopaxElements(int initialCapacity) { + c_ = empty; + l_ = initialCapacity; + } + + public synchronized Iterator iterator() { + return c_.iterator(); + } + + public synchronized int size() { + return (c_ == empty) ? 0 : c_.size(); + } + + /** + * Adds a new element to the collection unless it is null or URI is blank, + * or already contains an (equal) element with the same URI and model interface. + * #{@inheritDoc} + * @param bpe + * @return true when the element was actually added to the set + * @throws NullPointerException when bpe or uri is null + */ + @Override + public synchronized boolean add(E bpe) { + if (c_ == empty) { //replace the unmodifiable empty list + c_ = BPCollections.I.createCollection(l_); + return c_.add(bpe); + } + else if(!containsUri(bpe.getUri())) { //no duplicates (this is a Set backed by internal List) + return c_.add(bpe); + } + else { + return false; + } + } + + private synchronized boolean containsUri(String uri) { + if (c_ != empty) { + Iterator it = iterator(); + while (it.hasNext()) + if (uri.equals(it.next().getUri())) + return true; + } + return false; + } + + @Override + public synchronized boolean contains(Object o) { + if (c_ != empty) { + Iterator it = iterator(); + while (it.hasNext()) + if (o == it.next()) + return true; + } + return false; + } + + /** + * #{@inheritDoc} + * @throws NullPointerException when o or o.uri is null + * @throws ClassCastException when the o is not a BioPAX element + */ + @Override + public synchronized boolean remove(Object o) { + if (c_ != empty) { + Iterator it = iterator(); + while (it.hasNext()) + if (o == it.next()) { + it.remove(); + return true; + } + } + return false; + } + +} diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java deleted file mode 100644 index b72fa60c6..000000000 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeCollection.java +++ /dev/null @@ -1,74 +0,0 @@ -package org.biopax.paxtools.util; - -import org.biopax.paxtools.model.BioPAXElement; - -import java.util.*; - -/** - * A thread-safe, not necessarily ordered, collection of unique BioPAX elements - * to be used mostly with add and iterator methods, - * rarely - remove or clear, and never insert or get. - */ -public class BiopaxSafeCollection extends AbstractCollection -{ - //initial map is to be reset to a modifiable instance on first write - private final static Collection empty = Collections.emptyList(); - - private Collection c_; - private int l_; - - public BiopaxSafeCollection() { - c_ = empty; - l_ = 10; - } - - @Override - public Iterator iterator() { - return c_.iterator(); - } - - public BiopaxSafeCollection(int initialCapacity) { - c_ = empty; - l_ = initialCapacity; - } - - public int size() { - synchronized (c_) { - return c_.size(); - } - } - - @Override - public boolean add(E bpe) - { - if(bpe == null) { - return false; - } - - synchronized (c_) { - if(c_ == empty) { //replace the unmodifiable empty list - this.c_ = BPCollections.I.createCollection(l_); - } - } - - synchronized (c_) { - if(!c_.contains(bpe)) { - c_.add(bpe); - return true; - } - return false; - } - } - - @Override - public boolean contains(Object o) { - if (c_ == empty || !(o instanceof BioPAXElement) || ((E)o).getUri() == null) { - return false; - } - - synchronized (c_) { - return super.contains(o); //~O(N); uses iterator() and E.equals() (compares BioPAX URI and interface) - } - } - -} diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java index 5da993dc8..d6e30d1da 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BiopaxSafeSet.java @@ -7,22 +7,16 @@ /** - * A thread-safe set of BioPAX objects that also prevents adding several elements - * having the same URI. It also allows to quickly get a BioPAX - * object by URI. This set is used internally by all multiple cardinality - * BioPAX object property and inverse property implementations (since v4.2, 2013). - * - * @author rodche + * A thread-safe Set of BioPAX objects that also prevents adding several elements having the same URI. + * This is backed by an internal Map (more memory but faster ~O(1) add/contains/remove operations). */ public class BiopaxSafeSet extends AbstractSet implements Serializable { //initial map is to be reset to a modifiable instance on first write private final static Map empty = Collections.emptyMap(); - private Map map; - public BiopaxSafeSet() - { + public BiopaxSafeSet() { map = empty; } @@ -32,55 +26,81 @@ public Iterator iterator() { } } - public int size() - { + public int size() { synchronized (map) { - return map.size(); + return (map == empty) ? 0 : map.size(); } } - /** - * Adds a new element to the collection unless it is null, or URI is null, - * or already contains an element with the same URI. - * @param bpe - * @return + * Adds a new element to the collection unless it is null, wrong type, or URI is blank, + * or already contains an element with the same URI and model interface. + * #{@inheritDoc} + * @param bpe biopax object + * @return true when the element was actually added to the set + * @throws NullPointerException when bpe or uri is null */ @Override public boolean add(E bpe) { - if(bpe == null || bpe.getUri() == null) { - return false; - } - + String uri = bpe.getUri(); synchronized (map) { - if(map.isEmpty()) - { //new real map instead of initial fake (empty) one - this.map = BPCollections.I.createMap(); + if(map == empty) {//modifiable map instead of initial empty stub + map = BPCollections.I.createMap(); + map.put(uri, bpe); + return true; } - } - - String uri = bpe.getUri(); - synchronized (map) { //sync on the new map instance - if (!map.containsKey(uri)) { //prevent replacing existing objects with the same URI + else if (!map.containsKey(uri)) { //prevent replacing existing objects with the same URI map.put(uri, bpe); return true; - } else { - // do not throw an ex., because duplicate attempts may occur naturally - return false; + } + else { + return false; //ignored the duplicate uri el. } } } - + /** + * #{@inheritDoc} + * @throws NullPointerException when o or o.uri is null + * @throws ClassCastException when the o is not a BioPAX element + */ @Override public boolean contains(Object o) { - if(map == empty || !(o instanceof BioPAXElement) || ((E)o).getUri() == null) { + if(o == null || !(o instanceof BioPAXElement) || ((E)o).getUri() == null) { return false; } - synchronized (map) { - return map.get(((E)o).getUri()) == o; + return (map == empty) ? false : map.get(((E) o).getUri()) == o; // ~O(1) + } + } + + /** + * #{@inheritDoc} + * @throws NullPointerException when o or o.uri is null + * @throws ClassCastException when the o is not a BioPAX element + */ + @Override + public boolean remove(Object o) { // ~O(1) + synchronized (map) { + if (contains(o)) { + return map.remove(((E) o).getUri()) != null; + } + } + return false; + } + + /** + * Gets a BioPAX element by URI. + * + * @param uri absolute URI of a BioPAX individual + * @return BioPAX object or null + */ + public E get(String uri) { + if(map==empty) + return null; + synchronized (map) { + return map.get(uri); } } } diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java index 32d5edd93..aabe86553 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/EquivalenceGrouper.java @@ -100,14 +100,11 @@ public void add(T bpe) // AND if that something is a bucket contains something that is equivalent to bpe // AND if that something is not a bucket, and it is equivalent to bpe EquivalanceBucket bucket = access(bpe); - if (bucket == null) - { + if (bucket == null) { bucket = new EquivalanceBucket(bpe); this.buckets.add(bucket); - } else - { - for (T t : bucket) - { + } else { + for (T t : bucket) { if(t==bpe) return; } bucket.add(bpe); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java index b5aab71e8..46abca45a 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/SetEquivalenceChecker.java @@ -4,7 +4,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Collection; import java.util.HashSet; import java.util.List; import java.util.Set; @@ -13,7 +12,6 @@ * This class performs set operations based on equivalence. */ public class SetEquivalenceChecker { - private static final Logger LOG = LoggerFactory.getLogger(SetEquivalenceChecker.class); /** @@ -22,7 +20,7 @@ public class SetEquivalenceChecker { * @param Both sets should be of type that extends from T. * @return true iff both sets are of equal size and all objects in set1 has an equivalent object in set2. */ - public static boolean isEquivalent(Collection set1, Collection set2) + public static boolean isEquivalent(Set set1, Set set2) { if (set1 != null && !set1.isEmpty() && set2 != null && !set2.isEmpty()) { @@ -46,7 +44,6 @@ public static boolean isEquivalent(Collection boolean isEquivalent(Collection set, BioPAXElement query) + public static boolean containsEquivalent(Set set, BioPAXElement query) { if (set != null && query != null) { @@ -76,12 +73,9 @@ public static boolean containsEquivalent(Collection set * @param Both sets should be of type that extends from T. * @return elements of set1 that has an equivalent element in set2 */ - public static Set findEquivalentIntersection(Collection set1, - Collection set2) - { - + public static Set findEquivalentIntersection(Set set1, + Set set2) { Set value = new HashSet<>(); - if (set1 != null && !set1.isEmpty() && set2 != null && !set2.isEmpty()) { EquivalenceGrouper grouper = new EquivalenceGrouper(); @@ -114,8 +108,8 @@ public static Set findEquivalentIntersection(Collec * @param Both sets should be of type that extends from T. * @return true iff there are at least one equivalent element between set1 and set2, or both sets are empty. */ - public static boolean hasEquivalentIntersection(Collection set1, - Collection set2) + public static boolean hasEquivalentIntersection(Set set1, + Set set2) { if (!set1.isEmpty() && !set2.isEmpty()) { EquivalenceGrouper grouper1 = new EquivalenceGrouper<>(set1); @@ -138,5 +132,4 @@ public static boolean hasEquivalentIntersection(Collec return true; } } - } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java index 383ba8272..687efb5f6 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java @@ -9,7 +9,6 @@ import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.util.IllegalBioPAXArgumentException; -import org.biopax.paxtools.util.SetEquivalenceChecker; import org.junit.Assert; import org.junit.Test; @@ -18,7 +17,6 @@ import java.util.Arrays; import java.util.Map; -import static org.hamcrest.core.Is.is; import static org.junit.Assert.*; public class ModelUtilsTest { @@ -186,22 +184,20 @@ public final void testRemoveObjectsIfDangling() { } @Test - public void testGenericNormalization() - { + public void testGenericNormalization() { MockFactory mock = new MockFactory(BioPAXLevel.L3); Model model = mock.createModel(); Protein[] p = mock.create(model, Protein.class, 3); ProteinReference[] pr = mock.create(model, ProteinReference.class, 2); mock.bindArrays("entityReference", Arrays.copyOfRange(p, 0, 2), pr); - mock.bindInPairs("memberPhysicalEntity", p[2],p[0], p[2],p[1]); ModelUtils.normalizeGenerics(model); - assertThat(true, is(p[2].getEntityReference()!=null)); - assertThat(true, is(p[2].getEntityReference().getMemberEntityReference().contains(pr[0]))); - assertThat(true, is(p[2].getEntityReference().getMemberEntityReference().contains(pr[1]))); + assertTrue(p[2].getEntityReference()!=null); + assertTrue(p[2].getEntityReference().getMemberEntityReference().contains(pr[0])); + assertTrue(p[2].getEntityReference().getMemberEntityReference().contains(pr[1])); } @Test @@ -310,19 +306,4 @@ public void testBase62() { String shortUri = ModelUtils.shortenUri("http://www.ctdbase.org/", longUri); Assert.assertEquals("http://www.ctdbase.org/k9viXaDIiOW", shortUri); } - - @Test - public final void testSerializeDeserializeModel() throws Exception { - SimpleIOHandler io = new SimpleIOHandler(); - Model m1 = io.convertFromOWL(SimpleIOHandlerTest.class.getClassLoader() - .getResourceAsStream("L3" + File.separator + "biopax3-short-metabolic-pathway.owl")); - byte[] s1 = ModelUtils.serialize(m1); - Model m2 = (Model) ModelUtils.deserialize(s1); - - assertEquals(m1.size(), m2.size()); - assertTrue(SetEquivalenceChecker.isEquivalent(m1.getObjects(), m2.getObjects())); - - //REM: if we'd write/read m1,m2 to/from string/bytes and then compare, - //it would not match as the elements processing order is not guaranteed ;) - } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java index 90b4be5f8..4a30688cf 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java @@ -1,65 +1,57 @@ -/** - * - */ package org.biopax.paxtools.controller; -import org.biopax.paxtools.io.*; import org.biopax.paxtools.model.*; import org.biopax.paxtools.model.level3.*; -import org.biopax.paxtools.util.Filter; -import org.junit.Before; import org.junit.Test; -import java.io.ByteArrayOutputStream; import static org.junit.Assert.*; /** * @author rodche - * */ public class SimpleMergerTest { - @Test - public final void testMergeModel() { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - Model model = factory.createModel(); - Xref ref = model.addNew(UnificationXref.class, "Xref1"); - ref.setDb("uniprotkb"); // will be converted to 'uniprot' - ref.setId("Q0VCL1"); - Xref uniprotX = ref; - ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference"); - pr.setDisplayName("ProteinReference"); - pr.addXref(uniprotX); - ref = model.addNew(RelationshipXref.class, "Xref2"); - ref.setDb("refseq"); - ref.setId("NP_001734"); - pr.addXref(ref); - // normalizer won't merge diff. types of xref with the same db:id - ref = model.addNew(PublicationXref.class, "Xref3"); - ref.setDb("pubmed"); - ref.setId("2549346"); // the same id - pr.addXref(ref); - ref = model.addNew(RelationshipXref.class,"Xref4"); - ref.setDb("pubmed"); - ref.setId("2549346"); // the same id - pr.addXref(ref); - - // create the following, add as value to corr. properties, - // but not add to the model explicitely (merger should find and add them!) - BioSource bs = factory.create(BioSource.class, "Mouse"); - ref = factory.create(UnificationXref.class, "Xref5"); - ref.setDb("taxonomy"); - ref.setId("10090"); // the same id - bs.addXref(ref); - pr.setOrganism(bs); - - assertEquals(5, model.getObjects().size()); - - // do merge - SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); - merger.merge(model, model); // to itself - // - can use model.merge(model) or model.repair() instead + @Test + public final void testMergeModel() { + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + Model model = factory.createModel(); + Xref ref = model.addNew(UnificationXref.class, "Xref1"); + ref.setDb("uniprotkb"); // will be converted to 'uniprot' + ref.setId("Q0VCL1"); + Xref uniprotX = ref; + ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference"); + pr.setDisplayName("ProteinReference"); + pr.addXref(uniprotX); + ref = model.addNew(RelationshipXref.class, "Xref2"); + ref.setDb("refseq"); + ref.setId("NP_001734"); + pr.addXref(ref); + // normalizer won't merge diff. types of xref with the same db:id + ref = model.addNew(PublicationXref.class, "Xref3"); + ref.setDb("pubmed"); + ref.setId("2549346"); // the same id + pr.addXref(ref); + ref = model.addNew(RelationshipXref.class, "Xref4"); + ref.setDb("pubmed"); + ref.setId("2549346"); // the same id + pr.addXref(ref); + + // create the following, add as value to corr. properties, + // but not add to the model explicitely (merger should find and add them!) + BioSource bs = factory.create(BioSource.class, "Mouse"); + ref = factory.create(UnificationXref.class, "Xref5"); + ref.setDb("taxonomy"); + ref.setId("10090"); // the same id + bs.addXref(ref); + pr.setOrganism(bs); + + assertEquals(5, model.getObjects().size()); + + // do merge + SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); + merger.merge(model, model); // to itself + // - can use model.merge(model) or model.repair() instead /* try { ByteArrayOutputStream out = new ByteArrayOutputStream(); @@ -68,280 +60,276 @@ public final void testMergeModel() { } catch (Exception e) { fail(e.toString()); }*/ - - bs = (BioSource) model.getByID("Mouse"); - assertEquals(1, bs.getXref().size()); - pr = (ProteinReference) model.getByID("ProteinReference"); - assertEquals(4, pr.getXref().size()); - assertEquals(7, model.getObjects().size()); // Bug fixed: SimpleMerger adds BioSource to the model but not its children (xref)! - } - - @Test - public final void testMergeObject() { - SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - Model model = factory.createModel(); - - Xref ref = factory.create(UnificationXref.class, "9606"); - ref.setDb("Taxonomy"); - ref.setId("9606"); - BioSource bs = factory.create(BioSource.class, "Human"); - bs.addXref(ref); - - merger.merge(model, ref); - assertEquals(1, model.getObjects().size()); - //merge the other object, having child xref (same as already merged) - merger.merge(model, bs); - assertEquals(2, model.getObjects().size()); - - //merge into an empty target - model = factory.createModel(); - merger.merge(model, bs); - assertEquals(2, model.getObjects().size()); //has bs, ref - } - - @Test - public final void testMergeToInconsistentModel() { - // Let's merge an object having one xref into a model that - // implicitly "contains" a different xref with the same URI; - // merged model will explicitly contain only the xref - // of the just merged object (not the original, implicit one; - // and therefore the model is still not self-integral; - // let's begin... - - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - Model model = factory.createModel(); //target model - - //create an xref outside the model, - Xref mref =factory.create(UnificationXref.class, "10090"); - mref.setDb("Taxonomy"); - mref.setId("10090"); - //and a BioSource - in the model - BioSource mouse = model.addNew(BioSource.class, "mouse"); - mouse.addXref(mref); - //mref is owned by the mouse but is not in the model explicitly - assertEquals(1, model.getObjects().size()); - - //Create two more objects outside the model, one owns the other - - Xref href = factory.create(UnificationXref.class, "9606"); - href.setDb("Taxonomy"); - href.setId("9606"); - BioSource human = factory.create(BioSource.class, "human"); - human.addXref(href); - - //do merge - SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); - merger.merge(model, human); - - assertEquals(3, model.getObjects().size()); //there's no mref - Xref 10090! - assertNull(model.getByID("10090")); - - - // now, if both xrefs had the same URI, such as 'ref', - // then 'human' would become pointing to the mouse taxID, - // or vice versa, depending on whether the initial model - // was self-integral or not. - - model = factory.createModel(); //fresh target model - - //create an xref outside the model, - mref = factory.create(UnificationXref.class, "ref"); - mref.setDb("Taxonomy"); - mref.setId("10090"); - mouse = model.addNew(BioSource.class, "mouse"); - mouse.addXref(mref); - - //Create two more objects outside the model, one owns the other - - href = factory.create(UnificationXref.class, "ref"); //on purpose - same URI, different xref! - href.setDb("Taxonomy"); - href.setId("9606"); - human = factory.create(BioSource.class, "human"); - human.addXref(href); - - merger.merge(model, human); - - assertEquals(3, model.getObjects().size()); // - there's no Xref 10090 - Xref x = (UnificationXref)model.getByID("ref"); - assertNotNull(x); - assertEquals("9606", x.getId()); - BioSource bs = (BioSource) model.getByID("mouse"); - assertNotNull(bs); - assertEquals("10090", bs.getXref().iterator().next().getId()); //but that xref is not in the model - assertEquals("9606", human.getXref().iterator().next().getId()); - - //But. - //If the initial target model contained both the mouse and mref, - model = factory.createModel(); //fresh target model - mref = model.addNew(UnificationXref.class, "ref"); - mref.setDb("Taxonomy"); - mref.setId("10090"); - mouse = model.addNew(BioSource.class, "mouse"); - mouse.addXref(mref); - //then - merger.merge(model, human); - //makes the human have mouse xref - - assertEquals(3, model.getObjects().size()); - x = (UnificationXref)model.getByID("ref"); - assertNotNull(x); - assertEquals("10090", x.getId()); //aha - bs = (BioSource) model.getByID("mouse"); - assertNotNull(bs); - assertEquals("10090", bs.getXref().iterator().next().getId()); //ok - assertNotNull(model.getByID("human")); - assertEquals("10090", human.getXref().iterator().next().getId()); - //- 'human' (as well as 'mouse') BioSource now points to mouse's taxID xref! - - //PS: - //in order to make a model self-integral, one can try merging it to itself, - //which make all implicit objects become explicit members of the model, or fails, - //if there are different objects using same URIs somewhere... - } - - @Test - public final void testMergeWithoutFilter() { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - Model model = factory.createModel(); - //create a PR, BS, etc., in the (target) model - BioSource human = model.addNew(BioSource.class, "human"); - human.setStandardName("Homo sapiens"); //no displayName, no other names - UnificationXref uxHuman = model.addNew(UnificationXref.class, "9606"); - human.addXref(uxHuman); - ProteinReference pr = model.addNew(ProteinReference.class, "pr"); - pr.setDisplayName("one"); - pr.setOrganism(human); - - //another PR with the SAME URI to be merged into the target model - ProteinReference pr1 = factory.create(ProteinReference.class, "pr"); - Xref ux = factory.create(UnificationXref.class, "ux"); - ux.setDb("UniProt"); - ux.setId("P12345"); - pr1.addName("one"); - pr1.addName("two"); - pr1.addXref(ux); - UnificationXref uxHuman1 = factory.create(UnificationXref.class, "9606"); //also, the same URI as for uxHuman above - BioSource human1 = factory.create(BioSource.class, "human"); //same URI as for the other BioSource above - human1.addXref(uxHuman1); - human1.setDisplayName("human"); //but - no standardName nor other names are set - pr1.setOrganism(human1); - PublicationXref px = factory.create(PublicationXref.class, "publication"); - human1.addXref(px); - - //merge NOT using any filters (in the Constructor) - SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); - merger.merge(model, pr1); - - assertEquals(5, model.getObjects().size()); - ProteinReference mergedPr = (ProteinReference) model.getByID("pr"); - assertTrue(mergedPr.getXref().isEmpty()); //xref wasn't copied - assertEquals("one", mergedPr.getDisplayName()); - assertEquals(1, mergedPr.getName().size()); //name "two" wasn't copied (when no Filter used) - assertEquals("Homo sapiens", mergedPr.getOrganism().getStandardName()); - assertNull(mergedPr.getOrganism().getDisplayName()); - assertEquals(1, mergedPr.getOrganism().getName().size()); //there's only displayName ('name' is a sub-prop. of that) - assertNotNull(model.getByID("publication")); //the pub.xref was merged - // but it's dangling, because - assertEquals(1, mergedPr.getOrganism().getXref().size()); - assertEquals(uxHuman, mergedPr.getOrganism().getXref().iterator().next()); - } - - - @Test - public final void testMergeWithFilter() { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - Model model = factory.createModel(); - //create a PR, BS, etc., in the (target) model - BioSource human = model.addNew(BioSource.class, "human"); - human.setStandardName("Homo sapiens"); //no displayName, no other names - UnificationXref uxHuman = model.addNew(UnificationXref.class, "9606"); - uxHuman.setDb("taxonomy"); - uxHuman.setId("9606"); - human.addXref(uxHuman); - ProteinReference pr = model.addNew(ProteinReference.class, "pr"); - pr.setDisplayName("one"); - pr.setOrganism(human); - - //another PR with the same URI to be merged into the target model - ProteinReference pr1 = factory.create(ProteinReference.class, "pr"); - Xref ux = factory.create(UnificationXref.class, "ux"); - ux.setDb("UniProt"); - ux.setId("P12345"); - pr1.addName("one"); - pr1.addName("two"); - pr1.addXref(ux); - UnificationXref uxHuman1 = factory.create(UnificationXref.class, "9606"); //use the same URI as for uxHuman above - uxHuman1.setDb("Taxonomy"); //Capitalized, unlike the uxHuman above - uxHuman1.setId("9606"); - BioSource human1 = factory.create(BioSource.class, "human"); //same URI as for the other BioSource above - human1.addXref(uxHuman1); - human1.setDisplayName("human"); //but - no standardName nor other names are set - pr1.setOrganism(human1); - PublicationXref px = factory.create(PublicationXref.class, "publication"); - px.setId("00000"); - px.setDb("PubMed"); - human1.addXref(px); - - // Merge using a Filter, which - // enables copying mul. card. property values of same-URI source EntityReference objects - // (for all other types, if the target model has a same-type object with the same URI as in the sources - // , incl. nested objects, then ) - SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3, new Filter() { - public boolean filter(BioPAXElement object) { - return object instanceof EntityReference; - } - }); - merger.merge(model, pr1); - - assertEquals(5, model.getObjects().size()); - ProteinReference mergedPr = (ProteinReference) model.getByID("pr"); - assertFalse(mergedPr.getXref().isEmpty()); - assertEquals("one", mergedPr.getDisplayName()); - assertEquals(2, mergedPr.getName().size()); - - assertEquals("Homo sapiens", mergedPr.getOrganism().getStandardName()); - assertNull(mergedPr.getOrganism().getDisplayName()); - //and, because BioSource is not considered in the Filter (see SimpleMerger's constructor parameter), - // the 'human' name and publication xref px were not copied from source (human1) to the target (human) BioSource: - assertEquals(1, mergedPr.getOrganism().getName().size()); - assertEquals(1, mergedPr.getOrganism().getXref().size()); - px = (PublicationXref)model.getByID("publication"); - assertNotNull(px); //the pub.xref was merged to the target model, - // but it's dangling, because - - for(XReferrable xReferrable : px.getXrefOf()) - assertFalse(model.contains(xReferrable)); - - // Well. - // Next, merge using another Filter (adding BioSource type there) - merger = new SimpleMerger(SimpleEditorMap.L3, new Filter() { - public boolean filter(BioPAXElement object) { - return object instanceof EntityReference - || object instanceof BioSource; //i.e., enable copying BioSource's props too - } - }); - model = factory.createModel(); //a fresh empty model - model.add(pr); - model.add(human); - model.add(uxHuman); - - merger.merge(model, pr1); - - assertEquals(5, model.getObjects().size()); - mergedPr = (ProteinReference) model.getByID("pr"); - assertFalse(mergedPr.getXref().isEmpty()); - assertEquals("one", mergedPr.getDisplayName()); - assertEquals(2, mergedPr.getName().size()); - assertEquals("Homo sapiens", mergedPr.getOrganism().getStandardName()); //it's the BioSource from orig. 'pr' - assertNull(mergedPr.getOrganism().getDisplayName()); //single-cardinality prop. were not touched - //and, because BioSource is now part of the Filter, - //the 'human' (name) and publication xref px are copied from human1 to human BioSource: - assertEquals(2, mergedPr.getOrganism().getName().size()); - assertTrue(mergedPr.getOrganism().getName().contains("human")); //originally, it wasn't there - assertEquals(2, mergedPr.getOrganism().getXref().size()); //both xrefs - px = (PublicationXref)model.getByID("publication"); - assertNotNull(px); //the pub.xref was copied; it's NOT dangling - - assertTrue(mergedPr.getOrganism().getXref().contains(px)); - //the same URI uni.xref did actually not overwrite the original uxHuman (having lowercase "taxonomy" as its db) - assertTrue(mergedPr.getOrganism().getXref().contains(uxHuman)); - assertFalse(mergedPr.getOrganism().getXref().contains(uxHuman1)); - } + + bs = (BioSource) model.getByID("Mouse"); + assertEquals(1, bs.getXref().size()); + pr = (ProteinReference) model.getByID("ProteinReference"); + assertEquals(4, pr.getXref().size()); + assertEquals(7, model.getObjects().size()); // Bug fixed: SimpleMerger adds BioSource to the model but not its children (xref)! + } + + @Test + public final void testMergeObject() { + SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + Model model = factory.createModel(); + + Xref ref = factory.create(UnificationXref.class, "9606"); + ref.setDb("Taxonomy"); + ref.setId("9606"); + BioSource bs = factory.create(BioSource.class, "Human"); + bs.addXref(ref); + + merger.merge(model, ref); + assertEquals(1, model.getObjects().size()); + //merge the other object, having child xref (same as already merged) + merger.merge(model, bs); + assertEquals(2, model.getObjects().size()); + + //merge into an empty target + model = factory.createModel(); + merger.merge(model, bs); + assertEquals(2, model.getObjects().size()); //has bs, ref + } + + @Test + public final void testMergeToInconsistentModel() { + // Let's merge an object having one xref into a model that + // implicitly "contains" a different xref with the same URI; + // merged model will explicitly contain only the xref + // of the just merged object (not the original, implicit one; + // and therefore the model is still not self-integral; + // let's begin... + + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + Model model = factory.createModel(); //target model + + //create an xref outside the model, + Xref mref = factory.create(UnificationXref.class, "10090"); + mref.setDb("Taxonomy"); + mref.setId("10090"); + //and a BioSource - in the model + BioSource mouse = model.addNew(BioSource.class, "mouse"); + mouse.addXref(mref); + //mref is owned by the mouse but is not in the model explicitly + assertEquals(1, model.getObjects().size()); + + //Create two more objects outside the model, one owns the other - + Xref href = factory.create(UnificationXref.class, "9606"); + href.setDb("Taxonomy"); + href.setId("9606"); + BioSource human = factory.create(BioSource.class, "human"); + human.addXref(href); + + //do merge + SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); + merger.merge(model, human); + + assertEquals(3, model.getObjects().size()); //there's no mref - Xref 10090! + assertNull(model.getByID("10090")); + + + // now, if both xrefs had the same URI, such as 'ref', + // then 'human' would become pointing to the mouse taxID, + // or vice versa, depending on whether the initial model + // was self-integral or not. + + model = factory.createModel(); //fresh target model + + //create an xref outside the model, + mref = factory.create(UnificationXref.class, "ref"); + mref.setDb("Taxonomy"); + mref.setId("10090"); + mouse = model.addNew(BioSource.class, "mouse"); + mouse.addXref(mref); + + //Create two more objects outside the model, one owns the other - + href = factory.create(UnificationXref.class, "ref"); //on purpose - same URI, different xref! + href.setDb("Taxonomy"); + href.setId("9606"); + human = factory.create(BioSource.class, "human"); + human.addXref(href); + + merger.merge(model, human); + + assertEquals(3, model.getObjects().size()); // - there's no Xref 10090 + Xref x = (UnificationXref) model.getByID("ref"); + assertNotNull(x); + assertEquals("9606", x.getId()); + BioSource bs = (BioSource) model.getByID("mouse"); + assertNotNull(bs); + assertEquals("10090", bs.getXref().iterator().next().getId()); //but that xref is not in the model + assertEquals("9606", human.getXref().iterator().next().getId()); + + //But. + //If the initial target model contained both the mouse and mref, + model = factory.createModel(); //fresh target model + mref = model.addNew(UnificationXref.class, "ref"); + mref.setDb("Taxonomy"); + mref.setId("10090"); + mouse = model.addNew(BioSource.class, "mouse"); + mouse.addXref(mref); + //then + merger.merge(model, human); + //makes the human have mouse xref - + assertEquals(3, model.getObjects().size()); + x = (UnificationXref) model.getByID("ref"); + assertNotNull(x); + assertEquals("10090", x.getId()); //aha + bs = (BioSource) model.getByID("mouse"); + assertNotNull(bs); + assertEquals("10090", bs.getXref().iterator().next().getId()); //ok + assertNotNull(model.getByID("human")); + assertEquals("10090", human.getXref().iterator().next().getId()); + //- 'human' (as well as 'mouse') BioSource now points to mouse's taxID xref! + + //PS: + //in order to make a model self-integral, one can try merging it to itself, + //which make all implicit objects become explicit members of the model, or fails, + //if there are different objects using same URIs somewhere... + } + + @Test + public final void testMergeWithoutFilter() { + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + Model model = factory.createModel(); + //create a PR, BS, etc., in the (target) model + BioSource human = model.addNew(BioSource.class, "human"); + human.setStandardName("Homo sapiens"); //no displayName, no other names + UnificationXref uxHuman = model.addNew(UnificationXref.class, "9606"); + human.addXref(uxHuman); + ProteinReference pr = model.addNew(ProteinReference.class, "pr"); + pr.setDisplayName("one"); + pr.setOrganism(human); + + //another PR with the SAME URI to be merged into the target model + ProteinReference pr1 = factory.create(ProteinReference.class, "pr"); + Xref ux = factory.create(UnificationXref.class, "ux"); + ux.setDb("UniProt"); + ux.setId("P12345"); + pr1.addName("one"); + pr1.addName("two"); + pr1.addXref(ux); + UnificationXref uxHuman1 = factory.create(UnificationXref.class, "9606"); //also, the same URI as for uxHuman above + BioSource human1 = factory.create(BioSource.class, "human"); //same URI as for the other BioSource above + human1.addXref(uxHuman1); + human1.setDisplayName("human"); //but - no standardName nor other names are set + pr1.setOrganism(human1); + PublicationXref px = factory.create(PublicationXref.class, "publication"); + human1.addXref(px); + + //merge NOT using any filters (in the Constructor) + SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); + merger.merge(model, pr1); + + assertEquals(5, model.getObjects().size()); + ProteinReference mergedPr = (ProteinReference) model.getByID("pr"); + assertTrue(mergedPr.getXref().isEmpty()); //xref wasn't copied + assertEquals("one", mergedPr.getDisplayName()); + assertEquals(1, mergedPr.getName().size()); //name "two" wasn't copied (when no Filter used) + assertEquals("Homo sapiens", mergedPr.getOrganism().getStandardName()); + assertNull(mergedPr.getOrganism().getDisplayName()); + assertEquals(1, mergedPr.getOrganism().getName().size()); //there's only displayName ('name' is a sub-prop. of that) + assertNotNull(model.getByID("publication")); //the pub.xref was merged + // but it's dangling, because + assertEquals(1, mergedPr.getOrganism().getXref().size()); + assertEquals(uxHuman, mergedPr.getOrganism().getXref().iterator().next()); + } + + + @Test + public final void testMergeWithFilter() { + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + Model model = factory.createModel(); + //create a PR, BS, etc., in the (target) model + BioSource human = model.addNew(BioSource.class, "human"); + human.setStandardName("Homo sapiens"); //no displayName, no other names + UnificationXref uxHuman = model.addNew(UnificationXref.class, "9606"); + uxHuman.setDb("taxonomy"); + uxHuman.setId("9606"); + human.addXref(uxHuman); + ProteinReference pr = model.addNew(ProteinReference.class, "pr"); + pr.setDisplayName("one"); + pr.setOrganism(human); + + //another PR with the same URI to be merged into the target model + ProteinReference pr1 = factory.create(ProteinReference.class, "pr"); + Xref ux = factory.create(UnificationXref.class, "ux"); + ux.setDb("UniProt"); + ux.setId("P12345"); + pr1.addName("one"); + pr1.addName("two"); + pr1.addXref(ux); + UnificationXref uxHuman1 = factory.create(UnificationXref.class, "9606"); //use the same URI as for uxHuman above + uxHuman1.setDb("Taxonomy"); //Capitalized, unlike the uxHuman above + uxHuman1.setId("9606"); + BioSource human1 = factory.create(BioSource.class, "human"); //same URI as for the other BioSource above + human1.addXref(uxHuman1); + human1.setDisplayName("human"); //but - no standardName nor other names are set + pr1.setOrganism(human1); + PublicationXref px = factory.create(PublicationXref.class, "publication"); + px.setId("00000"); + px.setDb("PubMed"); + human1.addXref(px); + + // Merge using a Filter, which + // enables copying mul. card. property values of same-URI source EntityReference objects + // (for all other types, if the target model has a same-type object with the same URI as in the sources + // , incl. nested objects, then ) + SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3, object -> object instanceof EntityReference); + merger.merge(model, pr1); + + assertEquals(5, model.getObjects().size()); + ProteinReference mergedPr = (ProteinReference) model.getByID("pr"); + assertFalse(mergedPr.getXref().isEmpty()); + assertEquals("one", mergedPr.getDisplayName()); + assertEquals(2, mergedPr.getName().size()); + + assertEquals("Homo sapiens", mergedPr.getOrganism().getStandardName()); + assertNull(mergedPr.getOrganism().getDisplayName()); + //and, because BioSource is not considered in the Filter (see SimpleMerger's constructor parameter), + // the 'human' name and publication xref px were not copied from source (human1) to the target (human) BioSource: + assertEquals(1, mergedPr.getOrganism().getName().size()); + assertEquals(1, mergedPr.getOrganism().getXref().size()); + px = (PublicationXref) model.getByID("publication"); + assertNotNull(px); //the pub.xref was merged to the target model, + // but it's dangling, because - + for (XReferrable xReferrable : px.getXrefOf()) { + assertFalse(model.contains(xReferrable)); + } + + // Well. + // Next, merge using another Filter (adding BioSource type there) + merger = new SimpleMerger(SimpleEditorMap.L3, object -> { + return object instanceof EntityReference + || object instanceof BioSource; //i.e., enable copying BioSource's props too + }); + model = factory.createModel(); //a fresh empty model + model.add(pr); + model.add(human); + model.add(uxHuman); + + merger.merge(model, pr1); + + assertEquals(5, model.getObjects().size()); + mergedPr = (ProteinReference) model.getByID("pr"); + assertFalse(mergedPr.getXref().isEmpty()); + assertEquals("one", mergedPr.getDisplayName()); + assertEquals(2, mergedPr.getName().size()); + assertEquals("Homo sapiens", mergedPr.getOrganism().getStandardName()); //it's the BioSource from orig. 'pr' + assertNull(mergedPr.getOrganism().getDisplayName()); //single-cardinality prop. were not touched + //and, because BioSource is now part of the Filter, + //the 'human' (name) and publication xref px are copied from human1 to human BioSource: + assertEquals(2, mergedPr.getOrganism().getName().size()); + assertTrue(mergedPr.getOrganism().getName().contains("human")); //originally, it wasn't there + assertEquals(2, mergedPr.getOrganism().getXref().size()); //both xrefs + px = (PublicationXref) model.getByID("publication"); + assertNotNull(px); //the pub.xref was copied; it's NOT dangling - + assertTrue(mergedPr.getOrganism().getXref().contains(px)); + //the same URI uni.xref did actually not overwrite the original uxHuman (having lowercase "taxonomy" as its db) + assertTrue(mergedPr.getOrganism().getXref().contains(uxHuman)); + assertEquals(uxHuman, uxHuman1); //two xrefs have same type and URI are equal, + assertFalse(mergedPr.getOrganism().getXref().contains(uxHuman1)); //different object but same URI + } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java index d56e311b2..49de4db0c 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java @@ -4,10 +4,12 @@ import java.util.Set; import org.biopax.paxtools.model.*; +import org.biopax.paxtools.model.level3.Provenance; import org.biopax.paxtools.model.level3.RelationshipXref; import org.biopax.paxtools.model.level3.UnificationXref; import org.biopax.paxtools.model.level3.Xref; +import org.biopax.paxtools.util.BiopaxElements; import org.biopax.paxtools.util.BiopaxSafeSet; import org.junit.Test; @@ -15,10 +17,10 @@ public class EqualsEtcTest { - @Test - public final void testEquals() { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + static final BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + @Test + public final void equals() { // a BioPAX object (e.g., xref) UnificationXref x1 = factory.create(UnificationXref.class, "x1"); x1.setDb("MI"); @@ -58,13 +60,8 @@ public final void testEquals() { assertTrue(x1.isEquivalent(x5)); // x5 has different rdfId but same db/id } - - // we override 'equals' and 'hashCode' methods in BioPAXElementImpl (base class); - // the must PASS @Test - public final void testCollectionOfBiopaxElementsCustom() { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - + public final void hashSetOfBpe() { UnificationXref x1 = factory.create(UnificationXref.class, "x1"); x1.setDb("foo"); x1.setId("foo"); @@ -76,7 +73,7 @@ public final void testCollectionOfBiopaxElementsCustom() { col.add(x1); assertTrue(col.contains(x1)); assertTrue(col.contains(x2)); // different xref, same URI and type! - col.add(x2); //silently ignored + col.add(x2); // - silently ignored (due to x1.equals(x2) returns true)! assertTrue(col.size() == 1); col.remove(x2); //actually removes x1 (equal object) @@ -96,9 +93,7 @@ public final void testCollectionOfBiopaxElementsCustom() { @Test - public final void testBiopaxSafeSet() { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - + public final void biopaxSafeSet() { UnificationXref x1 = factory.create(UnificationXref.class, "x1"); x1.setDb("foo"); x1.setId("foo"); @@ -112,10 +107,10 @@ public final void testBiopaxSafeSet() { col.add(x1); assertTrue(col.contains(x1)); - assertFalse(col.contains(x2)); + assertFalse(col.contains(x2)); //not the same thing despite same uri and type col.add(x2); //duplicate URI object is ignored - assertFalse(col.contains(x2)); + assertTrue(col.size() == 1); //did not add the second one x2 = factory.create(UnificationXref.class, "x2"); x2.setDb("bar"); @@ -123,7 +118,7 @@ public final void testBiopaxSafeSet() { col.add(x2); assertTrue(col.size() == 2); - Set col1 = new BiopaxSafeSet(); + Set col1 = new BiopaxSafeSet<>(); col1.addAll(col); assertTrue(col1.size() == 2); assertTrue(col1.contains(x1)); @@ -133,5 +128,32 @@ public final void testBiopaxSafeSet() { assertTrue(col1.size() == 1); assertTrue(col1.contains(x1)); assertFalse(col1.contains(x2)); + + assertFalse(col.contains("foo")); + assertFalse(col.remove("foo")); + assertFalse(col.contains(null)); + assertFalse(col.remove(null)); + } + + @Test + public final void biopaxElements() { + Set xrefs = new BiopaxElements<>(); + UnificationXref ux1 = factory.create(UnificationXref.class, "ux1"); + RelationshipXref rx1 = factory.create(RelationshipXref.class, "rx1"); + Provenance pro = factory.create(Provenance.class, "pro"); + xrefs.add(ux1); + xrefs.add(rx1); + assertEquals(2, xrefs.size()); + assertFalse(xrefs.remove(pro)); + Xref x2 = factory.create(RelationshipXref.class, "rx1"); //already used uri + assertFalse(xrefs.contains(x2)); + assertTrue(xrefs.contains(rx1)); + assertFalse(xrefs.add(x2)); //ignored + assertTrue(xrefs.remove(rx1)); + assertEquals(1, xrefs.size()); + assertFalse(xrefs.contains("foo")); + assertFalse(xrefs.contains(null)); + assertFalse(xrefs.remove("foo")); + assertFalse(xrefs.remove(null)); } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java index f9d41c0eb..b3b3767ac 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java @@ -25,8 +25,8 @@ public final void testSemanticallyEquivalent() { EvidenceCodeVocabulary ecv = m.addNew(EvidenceCodeVocabulary.class, "EvidenceCodeVocab_1"); ecv.addTerm("in vitro"); ecv.addXref(x); - Evidence inVitro = m.addNew(Evidence.class, "Evidence_InVitro"); - inVitro.addEvidenceCode(ecv); + Evidence inVitro = m.addNew(Evidence.class, "Evidence_InVitro"); + inVitro.addEvidenceCode(ecv); x = m.addNew(UnificationXref.class, "ExpType_MI_0493"); x.setDb("MI"); @@ -36,7 +36,7 @@ public final void testSemanticallyEquivalent() { ecv.addXref(x); Evidence inVivo = m.addNew(Evidence.class, "Evidence_InVivo"); - assertFalse(inVitro.isEquivalent(inVivo)); + assertFalse(inVitro.isEquivalent(inVivo)); } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java index 06c1d98cf..ae91228d3 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java @@ -7,20 +7,14 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.junit.Test; -import java.lang.reflect.InvocationTargetException; - import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; -/** - */ public class ModelCoverageTest { @Test - public void testCreationMethods() throws InvocationTargetException, IllegalAccessException - { + public void testCreationMethods() { MockFactory factory = new MockFactory(BioPAXLevel.L3); - //test reflectively create EditorMap map = SimpleEditorMap.L3; int i = 0; diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java index 45b786910..57727bb5a 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java @@ -12,19 +12,18 @@ import static org.junit.Assert.*; -public class SimpleIOHandlerTest -{ - +public class SimpleIOHandlerTest { + private void outputModel(Model m, OutputStream out) { (new SimpleIOHandler()).convertToOWL(m, out); } - + @Test public final void testExportL2() throws FileNotFoundException { Model model = BioPAXLevel.L2.getDefaultFactory().createModel(); FileOutputStream out = new FileOutputStream( getClass().getResource("").getFile() - + File.separator + "simple.owl" + + File.separator + "simple.owl" ); outputModel(model, out); } @@ -39,20 +38,17 @@ public final void testReadWriteL2() throws IOException assertFalse(model.getObjects().isEmpty()); System.out.println("Model has " + model.getObjects().size() + " objects)"); FileOutputStream out = - new FileOutputStream( - getClass().getResource("").getFile() - + File.separator + "simpleReadWrite.owl" - ); + new FileOutputStream( + getClass().getResource("").getFile() + + File.separator + "simpleReadWrite.owl" + ); io.convertToOWL(model, out); } public static Model getL2Model(BioPAXIOHandler io) { - String s = "L2" + File.separator - + "biopax_id_557861_mTor_signaling.owl"; - + String s = "L2" + File.separator + "biopax_id_557861_mTor_signaling.owl"; System.out.println("file = " + s); - System.out.println("starting " + s); InputStream in = SimpleIOHandlerTest.class.getClassLoader().getResourceAsStream(s); assertNotNull(in); @@ -66,9 +62,7 @@ public final void testReadWriteL3() throws IOException Model model = getL3Model(io); assertNotNull(model); assertFalse(model.getObjects().isEmpty()); - System.out.println("Model has " + model.getObjects().size() - + " objects)"); - + System.out.println("Model has " + model.getObjects().size() + " objects)"); FileOutputStream out = new FileOutputStream(getClass().getResource("") .getFile() + File.separator + "simpleReadWrite.owl"); io.convertToOWL(model, out); @@ -78,7 +72,6 @@ public static Model getL3Model(BioPAXIOHandler io) { String s = "L3" + File.separator + "biopax3-short-metabolic-pathway.owl"; InputStream in = SimpleIOHandlerTest.class.getClassLoader().getResourceAsStream(s); - return io.convertFromOWL(in); } @@ -96,15 +89,15 @@ public final void testDuplicateNamesByExporter() throws IOException FileOutputStream out = new FileOutputStream( // to the target test dir getClass().getResource("").getFile() - + File.separator + "testDuplicateNamesByExporter.xml" + + File.separator + "testDuplicateNamesByExporter.xml" ); - + outputModel(m, out); // read BufferedReader in = new BufferedReader( new FileReader(getClass().getResource("").getFile() - + File.separator + "testDuplicateNamesByExporter.xml")); + + File.separator + "testDuplicateNamesByExporter.xml")); char[] buf = new char[1000]; in.read(buf); String xml = new String(buf); @@ -114,8 +107,8 @@ public final void testDuplicateNamesByExporter() throws IOException } } - - + + @Test public final void testDuplicateConversionInBiochemicalPathwayStepByExporter() throws IOException { @@ -127,25 +120,25 @@ public final void testDuplicateConversionInBiochemicalPathwayStepByExporter() th Model m = factory.createModel(); m.add(bps); m.add(reaction); - + FileOutputStream out = new FileOutputStream( // to the target test dir getClass().getResource("").getFile() - + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml" + + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml" ); - + outputModel(m, out); // read back BufferedReader in = new BufferedReader( - new FileReader(getClass().getResource("").getFile() - + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml")); + new FileReader(getClass().getResource("").getFile() + + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml")); char[] buf = new char[3000]; in.read(buf); String xml = new String(buf); - + assertTrue(xml.contains(" & % : + && #"; - System.out.println(s); - pr[0].getName().clear(); - pr[0].addName(s); - - // Write - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - io.convertToOWL(model, outputStream); - outputStream.flush(); - - // Read - ByteArrayInputStream inputStream = new ByteArrayInputStream(outputStream.toByteArray()); - outputStream.close(); - Model newModel = io.convertFromOWL(inputStream); - - Protein prot = (Protein) newModel.getObjects().iterator().next(); - assertTrue(prot.getName().iterator().next().equals(s)); - } + @Test + public final void testXMLEscapes() throws IOException { + BioPAXIOHandler io = new SimpleIOHandler(); //auto-detects level + MockFactory mock = new MockFactory(BioPAXLevel.L3); + final Model model = mock.createModel(); + Protein[] pr = mock.create(model, Protein.class, 1); + + String s = "\" \' < > & % : + && #"; + System.out.println(s); + pr[0].getName().clear(); + pr[0].addName(s); + + // Write + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + io.convertToOWL(model, outputStream); + outputStream.flush(); + + // Read + ByteArrayInputStream inputStream = new ByteArrayInputStream(outputStream.toByteArray()); + outputStream.close(); + Model newModel = io.convertFromOWL(inputStream); + + Protein prot = (Protein) newModel.getObjects().iterator().next(); + assertTrue(prot.getName().iterator().next().equals(s)); + } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java index bd4d4e76b..64f4b1129 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java @@ -16,14 +16,20 @@ public class BioPAXFactoryTest { @Test public void create() throws Exception { SequenceSite ss = factory.create(SequenceSite.class,"ss"); + assertNotNull(ss); } @Test - public void canInstantiate() throws Exception { + public void canInstantiate() { assertTrue(factory.canInstantiate(SequenceSite.class)); assertFalse(factory.canInstantiate(Process.class)); assertFalse(factory.canInstantiate(EntityReference.class)); assertFalse(factory.canInstantiate(SimplePhysicalEntity.class)); assertTrue(factory.canInstantiate(Interaction.class)); + assertTrue(factory.canInstantiate(Control.class)); + assertFalse(factory.canInstantiate(XReferrable.class)); + assertFalse(factory.canInstantiate(Observable.class)); + assertFalse(factory.canInstantiate(Xref.class)); + assertFalse(factory.canInstantiate(Controller.class)); } } \ No newline at end of file diff --git a/paxtools-search/pom.xml b/paxtools-search/pom.xml index 2ac50b627..e69de29bb 100644 --- a/paxtools-search/pom.xml +++ b/paxtools-search/pom.xml @@ -1,74 +0,0 @@ - - - 4.0.0 - - - paxtools - org.biopax.paxtools - 6.0.0-SNAPSHOT - - - paxtools-search - BioPAX Full-text Search - BioPAX full-text indexing and searching (Lucene based) - - https://biopax.github.io/Paxtools - - https://github.com/BioPAX/Paxtools - HEAD - - - - 7.5.0 - - - - - org.biopax.paxtools - paxtools-core - ${project.version} - - - org.apache.lucene - lucene-core - - - org.apache.lucene - lucene-highlighter - - - org.apache.lucene - lucene-analyzers-common - - - org.apache.lucene - lucene-queryparser - - - - - - - org.apache.lucene - lucene-core - ${lucene.version} - - - org.apache.lucene - lucene-highlighter - ${lucene.version} - - - org.apache.lucene - lucene-analyzers-common - ${lucene.version} - - - org.apache.lucene - lucene-queryparser - ${lucene.version} - - - - - diff --git a/paxtools-search/src/main/java/org/biopax/paxtools/search/Indexer.java b/paxtools-search/src/main/java/org/biopax/paxtools/search/Indexer.java deleted file mode 100644 index 4a9f97f3e..000000000 --- a/paxtools-search/src/main/java/org/biopax/paxtools/search/Indexer.java +++ /dev/null @@ -1,5 +0,0 @@ -package org.biopax.paxtools.search; - -public interface Indexer { - void index(); -} diff --git a/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java b/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java deleted file mode 100644 index 5c74195eb..000000000 --- a/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchEngine.java +++ /dev/null @@ -1,766 +0,0 @@ -package org.biopax.paxtools.search; - -import java.io.IOException; -import java.io.StringReader; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.*; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.TimeUnit; -import java.util.concurrent.atomic.AtomicInteger; -import java.util.regex.Pattern; - -import org.apache.commons.lang3.StringUtils; -import org.apache.lucene.analysis.Analyzer; -import org.apache.lucene.analysis.TokenStream; -import org.apache.lucene.analysis.core.KeywordAnalyzer; -import org.apache.lucene.analysis.miscellaneous.PerFieldAnalyzerWrapper; -import org.apache.lucene.analysis.standard.StandardAnalyzer; -import org.apache.lucene.analysis.tokenattributes.CharTermAttribute; -import org.apache.lucene.document.Document; -import org.apache.lucene.document.Field; -import org.apache.lucene.document.StoredField; -import org.apache.lucene.document.StringField; -import org.apache.lucene.document.TextField; -import org.apache.lucene.index.IndexWriter; -import org.apache.lucene.index.IndexWriterConfig; -import org.apache.lucene.index.Term; -import org.apache.lucene.queryparser.classic.MultiFieldQueryParser; -import org.apache.lucene.queryparser.classic.ParseException; -import org.apache.lucene.queryparser.classic.QueryParser; -import org.apache.lucene.search.BooleanQuery; -import org.apache.lucene.search.IndexSearcher; -import org.apache.lucene.search.Query; -import org.apache.lucene.search.ScoreDoc; -import org.apache.lucene.search.SearcherFactory; -import org.apache.lucene.search.SearcherManager; -import org.apache.lucene.search.TermQuery; -import org.apache.lucene.search.TopDocs; -import org.apache.lucene.search.TopScoreDocCollector; -import org.apache.lucene.search.BooleanClause.Occur; -import org.apache.lucene.search.highlight.Highlighter; -import org.apache.lucene.search.highlight.QueryScorer; -import org.apache.lucene.search.highlight.SimpleHTMLFormatter; -import org.apache.lucene.search.highlight.SimpleSpanFragmenter; -import org.apache.lucene.store.FSDirectory; -import org.apache.lucene.store.MMapDirectory; -import org.biopax.paxtools.controller.DataPropertyEditor; -import org.biopax.paxtools.controller.Fetcher; -import org.biopax.paxtools.controller.ModelUtils; -import org.biopax.paxtools.controller.SimpleEditorMap; -import org.biopax.paxtools.model.BioPAXElement; -import org.biopax.paxtools.model.Model; -import org.biopax.paxtools.model.level3.*; -import org.biopax.paxtools.model.level3.Process; -import org.biopax.paxtools.util.ClassFilterSet; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - - -/** - * A full-text searcher/indexer for BioPAX L3 models. - * - * @author rodche - */ -public class SearchEngine implements Indexer, Searcher { - private static final Logger LOG = LoggerFactory.getLogger(SearchEngine.class); - - // search fields - public static final String FIELD_URI = "uri"; - public static final String FIELD_KEYWORD = "keyword"; //anything, e.g., names, terms, comments, incl. - from child elements - public static final String FIELD_NAME = "name"; - public static final String FIELD_XREFID = "xrefid"; //xref.id - public static final String FIELD_PATHWAY = "pathway"; //parent/owner pathways; to be inferred from the whole biopax model - public static final String FIELD_N_PARTICIPANTS = "participants"; // num. of PEs or Genes in a process or Complex - public static final String FIELD_N_PROCESSES = "processes"; // is same as 'size' used to be before cPath2 v7 - // Full-text search/filter fields (case sensitive) - - //index organism names, cell/tissue type (term), taxonomy id, but only store BioSource URIs - public static final String FIELD_ORGANISM = "organism"; - //index data source names, but only URIs are stored in the index - public static final String FIELD_DATASOURCE = "datasource"; - public static final String FIELD_TYPE = "type"; - - //Default fields to use with the MultiFieldQueryParser; - //one can still search in other fields directly, e.g., - //pathway:some_keywords datasource:"pid", etc. - public final static String[] DEFAULT_FIELDS = - { - FIELD_KEYWORD, //includes all data type properties (names, terms, comments), - // also from child elements up to given depth (3), also includes pathway names (inferred) - FIELD_NAME, // standardName, displayName, other names - FIELD_XREFID, //xref.id (also direct child's xref.id, i.e., can find both xref and its owners using a xrefid: query string) - }; - - /** - * A Key for the value in a - * BioPAX element's annotations map - * where additional information about - * corresponding search hit will be stored. - */ - public enum HitAnnotation - { - HIT_EXCERPT, - HIT_PROCESSES, - HIT_PARTICIPANTS, - HIT_ORGANISM, - HIT_DATASOURCE, - HIT_PATHWAY, - } - - private final Model model; - private int maxHitsPerPage; - private final Analyzer analyzer; - private final Path indexFile; - private SearcherManager searcherManager; - - public final static int DEFAULT_MAX_HITS_PER_PAGE = 100; - - - /** - * Constructor. - * - * @param model the BioPAX Model to index or search - * @param indexLocation index directory location - */ - public SearchEngine(Model model, String indexLocation) { - this.model = model; - this.indexFile = Paths.get(indexLocation); - initSearcherManager(); - this.maxHitsPerPage = DEFAULT_MAX_HITS_PER_PAGE; - Map analyzersPerField = new HashMap<>(); - analyzersPerField.put(FIELD_NAME, new KeywordAnalyzer()); - analyzersPerField.put(FIELD_XREFID, new KeywordAnalyzer()); - analyzersPerField.put(FIELD_URI, new KeywordAnalyzer()); - analyzersPerField.put(FIELD_PATHWAY, new KeywordAnalyzer()); - this.analyzer = new PerFieldAnalyzerWrapper(new StandardAnalyzer(), analyzersPerField); - } - - private void initSearcherManager() { - try { - if(Files.exists(indexFile)) - this.searcherManager = - new SearcherManager(MMapDirectory.open(indexFile), new SearcherFactory()); - else - LOG.info(indexFile + " does not exist."); - } catch (IOException e) { - LOG.warn("Could not create a searcher: " + e); - } - } - - /** - * Sets the maximum no. hits per search results page (pagination). - * - * @param maxHitsPerPage positive int value; otherwise - unlimited - */ - public void setMaxHitsPerPage(int maxHitsPerPage) { - this.maxHitsPerPage = maxHitsPerPage; - } - - /** - * Gets the maximum no. hits per search results page (pagination parameter). - * @return int value - */ - public int getMaxHitsPerPage() { - return maxHitsPerPage; - } - - public SearchResult search(String query, int page, - Class filterByType, String[] datasources, - String[] organisms) - { - SearchResult response; - - LOG.debug("search: " + query + ", page: " + page - + ", filterBy: " + filterByType - + "; extra filters: ds in (" + Arrays.toString(datasources) - + "), org. in (" + Arrays.toString(organisms) + ")"); - - IndexSearcher searcher = null; - - try { - QueryParser queryParser = new MultiFieldQueryParser(DEFAULT_FIELDS, analyzer); - queryParser.setAllowLeadingWildcard(true);//TODO do we really want leading wildcards (e.g. *sulin)? - searcher = searcherManager.acquire(); - - //find and transform top docs to search hits (beans), considering pagination... - if(!query.trim().equals("*")) { //if not "*" query, which is not supported out-of-the-box, then - //create the lucene query - Query q = queryParser.parse(query); - LOG.debug("parsed lucene query is " + q.getClass().getSimpleName()); - - //create filter: type AND (d OR d...) AND (o OR o...) - Query filter = createFilter(filterByType, datasources, organisms); - - //final query with filter - q = (filter != null) - ? new BooleanQuery.Builder().add(q,Occur.MUST).add(filter,Occur.FILTER).build() - : q; - - //get the first page of top hits - TopDocs topDocs = searcher.search(q, maxHitsPerPage); - - //get the required hits page if page>0 - if(page>0) { - TopScoreDocCollector collector = TopScoreDocCollector.create(maxHitsPerPage*(page+1)); - searcher.search(q, collector); - topDocs = collector.topDocs(page * maxHitsPerPage, maxHitsPerPage); - } - - //transform docs to hits, use a highlighter to get excerpts - response = transform(q, searcher, true, topDocs); - - } else { - //find ALL objects of a particular BioPAX class (+ filters by organism, datasource) - if(filterByType==null) { - filterByType = Level3Element.class; - } - - //replace q="*" with a search for the class or its sub-class name in the TYPE field - BooleanQuery.Builder b = new BooleanQuery.Builder(); - for(Class subType : SimpleEditorMap.L3.getKnownSubClassesOf(filterByType)) { - b.add(new TermQuery(new Term(FIELD_TYPE, subType.getSimpleName().toLowerCase())), Occur.SHOULD); - } - - Query filter = createFilter(null, datasources, organisms); - - //combine star and filter queries into one special boolean - Query q = (filter != null) - ? new BooleanQuery.Builder().add(b.build(),Occur.MUST).add(filter,Occur.FILTER).build() - : b.build(); - - //get the first page of top hits - TopDocs topDocs = searcher.search(q, maxHitsPerPage); - - //get the required hits page if page>0 - if(page>0) { - TopScoreDocCollector collector = TopScoreDocCollector.create(maxHitsPerPage*(page+1)); - searcher.search(q, collector); - topDocs = collector.topDocs(page * maxHitsPerPage, maxHitsPerPage); - } - - //convert - response = transform(q, searcher, false, topDocs); - } - } catch (ParseException e) { - throw new RuntimeException("getTopDocs: failed to parse the query string.", e); - } catch (IOException e) { - throw new RuntimeException("getTopDocs: failed.", e); - } finally { - try { - if(searcher != null) { - searcherManager.release(searcher); - } - } catch (IOException e) {} - } - - response.setPage(page); - return response; - } - - - /** - * Returns a SearchResult - * that contains a List, - * some parameters, totals, etc. - */ - private SearchResult transform(Query query, IndexSearcher searcher, boolean highlight, TopDocs topDocs) - throws IOException - { - final SearchResult response = new SearchResult(); - final List hits = new ArrayList<>(); - - response.setMaxHitsPerPage(maxHitsPerPage); - response.setHits(hits); - - for(ScoreDoc scoreDoc : topDocs.scoreDocs) { - Document doc = searcher.doc(scoreDoc.doc); - String uri = doc.get(FIELD_URI); - BioPAXElement bpe = model.getByID(uri); - Map annotations = bpe.getAnnotations(); - LOG.debug("transform: doc:" + scoreDoc.doc + ", uri:" + uri); - - // use the highlighter (get matching fragments) - // for this to work, all keywords were stored in the index field - if (highlight && doc.get(FIELD_KEYWORD) != null) { - // use a Highlighter (store.YES must be enabled for 'keyword' field) - QueryScorer scorer = new QueryScorer(query, FIELD_KEYWORD); - //this fixes scoring/highlighting for all-field wildcard queries like q=insulin* - //but not for term/prefix queries, i.e, q=name:insulin*, q=pathway:brca2. TODO - scorer.setExpandMultiTermQuery(true); - - //TODO try PostingsHighlighter once it's stable... - // (see http://lucene.apache.org/core/4_10_0/highlighter/org/apache/lucene/search/postingshighlight/PostingsHighlighter.html) - SimpleHTMLFormatter formatter = new SimpleHTMLFormatter("", ""); - Highlighter highlighter = new Highlighter(formatter, scorer); - highlighter.setTextFragmenter(new SimpleSpanFragmenter(scorer, 80)); - - final String text = StringUtils.join(doc.getValues(FIELD_KEYWORD), " "); - try { - TokenStream tokenStream = analyzer.tokenStream("", new StringReader(text)); - String res = highlighter.getBestFragments(tokenStream, text, 7, "..."); - - if(res != null && !res.isEmpty()) { - annotations.put(HitAnnotation.HIT_EXCERPT.name(), res); - } - - } catch (Exception e) {throw new RuntimeException(e);} - - } else if(highlight) { - LOG.warn("Highlighter skipped, because KEYWORD field was null; hit: " - + uri + ", " + bpe.getModelInterface().getSimpleName()); - } - - // extract organisms (URI only) if not done before - if(doc.get(FIELD_ORGANISM) != null && !annotations.containsKey(HitAnnotation.HIT_ORGANISM.name())) { - Set uniqueVals = new TreeSet<>(); - for(String o : doc.getValues(FIELD_ORGANISM)) { - //note: only URIS are stored in the index - uniqueVals.add(o); - } - annotations.put(HitAnnotation.HIT_ORGANISM.name(), uniqueVals); - } - - // extract values form the index if not previously done - if(doc.get(FIELD_DATASOURCE) != null && !annotations.containsKey(HitAnnotation.HIT_DATASOURCE.name())) { - Set uniqueVals = new TreeSet(); - for(String d : doc.getValues(FIELD_DATASOURCE)) { - //note: only URIS are stored in the index - uniqueVals.add(d); - } - annotations.put(HitAnnotation.HIT_DATASOURCE.name(), uniqueVals); - } - - // extract only pathway URIs if not previously done - //(because names and IDs used to be stored in the index field as well) - if(doc.get(FIELD_PATHWAY) != null && !annotations.containsKey(HitAnnotation.HIT_PATHWAY.name())) { - Set uniqueVals = new TreeSet(); - for(String d : doc.getValues(FIELD_PATHWAY)) { - //only URIs were stored (though all names/ids were indexed/analyzed) - if(!d.equals(uri)) //exclude itself - uniqueVals.add(d); - } - annotations.put(HitAnnotation.HIT_PATHWAY.name(), uniqueVals); - } - - //store the no. processes in the sub-network if not previously done - if(doc.get(FIELD_N_PARTICIPANTS)!=null && !annotations.containsKey(HitAnnotation.HIT_PARTICIPANTS.name())) - annotations.put(HitAnnotation.HIT_PARTICIPANTS.name(), Integer.valueOf(doc.get(FIELD_N_PARTICIPANTS))); - if(doc.get(FIELD_N_PROCESSES)!=null && !annotations.containsKey(HitAnnotation.HIT_PROCESSES.name())) - annotations.put(HitAnnotation.HIT_PROCESSES.name(), Integer.valueOf(doc.get(FIELD_N_PROCESSES))); - - //store the Lucene's score and explanation. - String excerpt = (String) annotations.get(HitAnnotation.HIT_EXCERPT.name()); - if(excerpt == null) excerpt = ""; - excerpt += " -SCORE- " + scoreDoc.score + " -EXPLANATION- " + searcher.explain(query, scoreDoc.doc); - annotations.put(HitAnnotation.HIT_EXCERPT.name(), excerpt); - - hits.add(bpe); - } - - //set total no. hits - response.setTotalHits(topDocs.totalHits); - - return response; - } - - - public void index() { - final int numObjects = model.getObjects().size(); - LOG.info("index(), there are " + numObjects + " BioPAX objects to be (re-)indexed."); - IndexWriter iw; - try { - //close the searcher manager if the old index exists - if(searcherManager != null) { - searcherManager.close(); - searcherManager = null; - } - IndexWriterConfig conf = new IndexWriterConfig(analyzer); - iw = new IndexWriter(FSDirectory.open(indexFile), conf); - //cleanup - iw.deleteAll(); - iw.commit(); - } catch (IOException e) { - throw new RuntimeException("Failed to create a new IndexWriter.", e); - } - final IndexWriter indexWriter = iw; - - ExecutorService exec = Executors.newFixedThreadPool(30); - - final AtomicInteger numLeft = new AtomicInteger(numObjects); - - final org.biopax.paxtools.util.Filter dataPropertiesToConsider = editor -> { - final String prop = editor.getProperty(); - //to include in the index, as keywords, only the following properties - // (basically, to exclude float type properties, embedded xml, db names, etc.): - return (prop.equalsIgnoreCase("author") || prop.equalsIgnoreCase("availability") - || prop.equalsIgnoreCase("chemicalFormula") || prop.equalsIgnoreCase("comment") - || prop.equalsIgnoreCase("controlType") || prop.equalsIgnoreCase("conversionDirection") - || prop.equalsIgnoreCase("eCNumber") || prop.equalsIgnoreCase("id") - || prop.equalsIgnoreCase("name") || prop.equalsIgnoreCase("displayName") - || prop.equalsIgnoreCase("standardName") || prop.equalsIgnoreCase("sequence") - || prop.equalsIgnoreCase("source") || prop.equalsIgnoreCase("year") - || prop.equalsIgnoreCase("term") || prop.equalsIgnoreCase("stepDirection") - || prop.equalsIgnoreCase("structureData") || prop.equalsIgnoreCase("templateDirection") - || prop.equalsIgnoreCase("title") || prop.equalsIgnoreCase("url") - ); - }; - - final Fetcher fetcher = new Fetcher(SimpleEditorMap.L3, Fetcher.nextStepFilter); - fetcher.setSkipSubPathways(true); - - for(final BioPAXElement bpe : model.getObjects()) { - // prepare & index each element in a separate thread - exec.execute(() -> { - // get or infer some important values if possible from this, child or parent objects: - Set keywords = ModelUtils.getKeywords(bpe, 3, dataPropertiesToConsider); - // a hack to remove special (debugging) biopax comments - for(String s : new HashSet<>(keywords)) { - //exclude additional comments generated by normalizer, merger, etc. - if(s.startsWith("REPLACED ") || s.contains("ADDED")) - keywords.remove(s); - } - - Map annotations = bpe.getAnnotations(); - annotations.put(FIELD_KEYWORD, keywords); - annotations.put(FIELD_DATASOURCE, ModelUtils.getDatasources(bpe)); - annotations.put(FIELD_ORGANISM, ModelUtils.getOrganisms(bpe)); - annotations.put(FIELD_PATHWAY, ModelUtils.getParentPathways(bpe)); - //- includes itself if bpe is a pathway - - //set (PEs/Genes), (interactions/pathways) index fields: - if(bpe instanceof Process) { - int numProc = fetcher.fetch(bpe, Process.class).size(); //except itself - int numPeAndG = fetcher.fetch(bpe, PhysicalEntity.class).size() - + fetcher.fetch(bpe, Gene.class).size(); - annotations.put(FIELD_N_PARTICIPANTS, Integer.toString(numPeAndG)); - annotations.put(FIELD_N_PROCESSES, Integer.toString(numProc)); - } else if(bpe instanceof Complex) { - int numPEs = fetcher.fetch(bpe, PhysicalEntity.class).size(); - annotations.put(FIELD_N_PARTICIPANTS, Integer.toString(numPEs)); - } - - //add IDs of uni. and rel. xrefs of this element and its children - if(bpe instanceof Entity || bpe instanceof EntityReference) - { - final Set ids = new HashSet<>(); - - //fetch all children of (implicit) type XReferrable, which means - either - //BioSource or ControlledVocabulary or Evidence or Provenance or Entity or EntityReference - //(we actually want only the latter two types and their sub-types; will skip the rest later on): - Set children = fetcher.fetch(bpe, XReferrable.class); - //include itself (- for fetcher only gets child elements) - children.add((XReferrable) bpe); - for(XReferrable child : children) { - //skip IDs of Evidence,CV,Provenance (included into 'keyword' field anyway) - if(!(child instanceof Entity || child instanceof EntityReference)) - continue; - // collect standard bio IDs (skip publications); try/use id-mapping to associate more IDs: - for(Xref x : child.getXref()) { - if (!(x instanceof PublicationXref) && x.getId()!=null && x.getDb()!=null) { - ids.add(x.getId()); - } - } - } - if(!ids.isEmpty()) { - annotations.put(SearchEngine.FIELD_XREFID, ids); - } - } - - index(bpe, indexWriter); - - //count, log a progress message - int left = numLeft.decrementAndGet(); - if(left % 10000 == 0) - LOG.info("index(), biopax objects left to index: " + left); - }); - } - - exec.shutdown(); //stop accepting new tasks - try { //wait - exec.awaitTermination(Long.MAX_VALUE, TimeUnit.SECONDS); - } catch (InterruptedException e) { - throw new RuntimeException("Interrupted!", e); - } - - try { - indexWriter.close(); //wait for pending op., auto-commit, close. - } catch (IOException e) { - throw new RuntimeException("Failed to close IndexWriter.", e); - } - - //finally, create a new searcher manager - initSearcherManager(); - } - - - // internal methods - - /** - * Creates a new Lucene Document that corresponds to a BioPAX object. - * It does not check whether the document exists (should not be there, - * because the {@link #index()} method cleans up the index) - * - * Some fields also include biopax data type property values not only from - * the biopax object but also from its child elements, up to some depth - * (using key-value pairs in the pre-computed bpe.annotations map): - * - * 'uri' - biopax object's absolute URI, analyze=no, store=yes; - * - * 'name' - names, analyze=yes, store=yes; boosted; - * - * 'keyword' - infer from this bpe and its child objects' data properties, - * such as Score.value, structureData, structureFormat, chemicalFormula, - * availability, term, comment, patoData, author, source, title, url, published, - * up to given depth/level; and also all 'pathway' field values are included here; - * analyze=yes, store=yes; - * - * 'datasource', 'organism' and 'pathway' - infer from this bpe and its child objects - * up to given depth/level, analyze=no, store=yes; - * - * 'size' - number of child processes, an integer as string; analyze=no, store=yes - * - * @param bpe BioPAX object - * @param indexWriter index writer - */ - void index(BioPAXElement bpe, IndexWriter indexWriter) { - // create a new document - final Document doc = new Document(); - - // save URI (not indexed field) - Field field = new StoredField(FIELD_URI, bpe.getUri()); - doc.add(field); - - // index and store but not analyze/tokenize the biopax class name: - field = new StringField(FIELD_TYPE, bpe.getModelInterface().getSimpleName().toLowerCase(), Field.Store.YES); - doc.add(field); - - // make index fields from the annotations map (of pre-calculated/inferred values) - Map annotations = bpe.getAnnotations(); - if(!annotations.isEmpty()) { - if(annotations.containsKey(FIELD_PATHWAY)) { - addPathways((Set)annotations.get(FIELD_PATHWAY), doc); - } - if(annotations.containsKey(FIELD_ORGANISM)) { - addOrganisms((Set)annotations.get(FIELD_ORGANISM), doc); - } - if(annotations.containsKey(FIELD_DATASOURCE)) { - addDatasources((Set)annotations.get(FIELD_DATASOURCE), doc); - } - if(annotations.containsKey(FIELD_KEYWORD)) { - addKeywords((Set)annotations.get(FIELD_KEYWORD), doc); - } - if(annotations.containsKey(FIELD_N_PARTICIPANTS)) { - field = new StoredField(FIELD_N_PARTICIPANTS, - Integer.parseInt((String)annotations.get(FIELD_N_PARTICIPANTS))); - doc.add(field); - } - if(annotations.containsKey(FIELD_N_PROCESSES)) { - doc.add(new StoredField(FIELD_N_PROCESSES, - Integer.parseInt((String)annotations.get(FIELD_N_PROCESSES)))); - } - if(annotations.containsKey(FIELD_XREFID)) { - //index biological IDs as keywords - addKeywords((Set)annotations.get(FIELD_XREFID), doc); - - //index all IDs using "xrefid" fields - for (String id : (Set)annotations.get(FIELD_XREFID)) { - Field f = new StringField(FIELD_XREFID, id.toLowerCase(), Field.Store.NO); - doc.add(f); - } - } - } - - //cleanup the biopax object from temporary annotations (saves memory) - annotations.remove(FIELD_KEYWORD); - annotations.remove(FIELD_DATASOURCE); - annotations.remove(FIELD_ORGANISM); - annotations.remove(FIELD_PATHWAY); - annotations.remove(FIELD_N_PARTICIPANTS); - annotations.remove(FIELD_N_PROCESSES); - annotations.remove(FIELD_XREFID); - - // name (we store both original and lowercased names due to use of StringField and KeywordAnalyser) - if(bpe instanceof Named) { - Named named = (Named) bpe; - if(named.getStandardName() != null) { - String stdName = named.getStandardName().trim(); - doc.add(new StringField(FIELD_NAME, stdName.toLowerCase(), Field.Store.NO)); - doc.add(new StringField(FIELD_NAME, stdName, Field.Store.NO)); - } - if(named.getDisplayName() != null && !named.getDisplayName().equalsIgnoreCase(named.getStandardName())) { - String dspName = named.getDisplayName().trim(); - doc.add(new StringField(FIELD_NAME, dspName.toLowerCase(), Field.Store.NO)); - doc.add(new StringField(FIELD_NAME, dspName, Field.Store.NO)); - } - for(String name : named.getName()) { - if(!name.equalsIgnoreCase(named.getDisplayName()) && !name.equalsIgnoreCase(named.getStandardName())) { - name = name.trim(); - doc.add(new StringField(FIELD_NAME, name.toLowerCase(), Field.Store.NO)); - doc.add(new StringField(FIELD_NAME, name, Field.Store.NO)); - } - doc.add(new TextField(FIELD_KEYWORD, name.toLowerCase(), Field.Store.NO)); - } - } - - // write - try { - indexWriter.addDocument(doc); - } catch (IOException e) { - throw new RuntimeException("Failed to index; " + bpe.getUri(), e); - } - } - - private void addKeywords(Set keywords, Document doc) { - for (String keyword : keywords) { - Field f = new TextField(FIELD_KEYWORD, keyword.toLowerCase(), Field.Store.YES); - doc.add(f); - } - } - - private void addDatasources(Set set, Document doc) { - for (Provenance p : set) { - // Index and store URI (untokinized) - - // required to accurately calculate no. entities or to filter by data source (diff. datasources may share same names) - doc.add(new StringField(FIELD_DATASOURCE, p.getUri(), Field.Store.YES)); - // index names as well - for (String s : p.getName()) - doc.add(new TextField(FIELD_DATASOURCE, s.toLowerCase(), Field.Store.NO)); - } - } - - private void addOrganisms(Set set, Document doc) { - for(BioSource bs : set) { - // store URI as is (not indexed, untokinized) - doc.add(new StoredField(FIELD_ORGANISM, bs.getUri())); - - // add organism names - for(String s : bs.getName()) { - doc.add(new TextField(FIELD_ORGANISM, s.toLowerCase(), Field.Store.NO)); - } - // add taxonomy - for(UnificationXref x : new ClassFilterSet<>(bs.getXref(), UnificationXref.class)) { - if(x.getId() != null) - doc.add(new TextField(FIELD_ORGANISM, x.getId().toLowerCase(), Field.Store.NO)); - } - // include tissue type terms - if (bs.getTissue() != null) { - for (String s : bs.getTissue().getTerm()) - doc.add(new TextField(FIELD_ORGANISM, s.toLowerCase(), Field.Store.NO)); - } - // include cell type terms - if (bs.getCellType() != null) { - for (String s : bs.getCellType().getTerm()) { - doc.add(new TextField(FIELD_ORGANISM, s.toLowerCase(), Field.Store.NO)); - } - } - } - } - - private void addPathways(Set set, Document doc) { - for(Pathway pw : set) { - //add URI as is (do not lowercase; do not index; store=yes - required to report hits, e.g., as xml) - doc.add(new StoredField(FIELD_PATHWAY, pw.getUri())); - - // add names to the 'pathway' (don't store) and 'keywords' (store, don't index) fields - for (String s : pw.getName()) { - doc.add(new TextField(FIELD_PATHWAY, s.toLowerCase(), Field.Store.NO)); - doc.add(new StoredField(FIELD_KEYWORD, s.toLowerCase()));//for highlighting only, not indexed - } - - // add unification xref IDs too - for (UnificationXref x : new ClassFilterSet( - pw.getXref(), UnificationXref.class)) { - if (x.getId() != null) { - // index in both 'pathway' (don't store) and 'keywords' (store, don't index) - doc.add(new TextField(FIELD_PATHWAY, x.getId().toLowerCase(), Field.Store.NO)); - doc.add(new StoredField(FIELD_KEYWORD, x.getId().toLowerCase()));//for highlighting only, not indexed - } - } - } - } - - /* - * Creates a search filter like - * type AND (datasource OR datasource...) - * AND (organism OR organism OR...) - * - * Both names (partial or full) and URIs should work as filter values. - */ - private Query createFilter(Class type, String[] datasources, String[] organisms) - { - BooleanQuery.Builder builder = new BooleanQuery.Builder(); - - //AND datasources - if (datasources != null && datasources.length > 0) { - builder.add(subQuery(datasources, FIELD_DATASOURCE), Occur.MUST); - } - //AND organisms - if (organisms != null && organisms.length > 0) { - builder.add(subQuery(organisms, FIELD_ORGANISM), Occur.MUST); - } - //AND type - if(type != null) { //add biopax class filter - BooleanQuery.Builder query = new BooleanQuery.Builder(). - add(new TermQuery(new Term(FIELD_TYPE, type.getSimpleName().toLowerCase())), Occur.SHOULD);//OR - //for each biopax subclass (interface), add the name to the filter query - for(Class subType : SimpleEditorMap.L3.getKnownSubClassesOf(type)) { - query.add(new TermQuery(new Term(FIELD_TYPE, subType.getSimpleName().toLowerCase())), Occur.SHOULD);//OR - } - builder.add(query.build(), Occur.MUST); - } - - BooleanQuery filter = builder.build(); - //TODO: use LRUQueryCache with the filter somewhere, e.g.: - // Query q = queryCache.doCache(filter, defaultCachingPolicy); - - if(!filter.clauses().isEmpty()) { - return filter; - } else - return null; - } - - - /* - * Values are joint with OR, but if a value - * has whitespace symbols, it also makes a sub-query, - * in which terms are joint with AND. This is to filter - * by datasource/organism's full name, partial name, uri, - * using multiple datasources/organisms. - */ - private Query subQuery(String[] filterValues, String filterField) - { - BooleanQuery.Builder query = new BooleanQuery.Builder(); - final Pattern pattern = Pattern.compile("\\s"); - for(String v : filterValues) { - //if v has whitespace chars (several words), make a "word1 AND word2 AND..." subquery - if(pattern.matcher(v).find()) { - BooleanQuery.Builder bq = new BooleanQuery.Builder(); - try { - //use the same analyser as when indexing - TokenStream tokenStream = analyzer.tokenStream(filterField, new StringReader(v)); - CharTermAttribute chattr = tokenStream.addAttribute(CharTermAttribute.class); - tokenStream.reset(); - while(tokenStream.incrementToken()) { - //'of', 'and', 'for',.. never occur as tokens (this is how the analyzer works) - String token = chattr.toString(); - bq.add(new TermQuery(new Term(filterField, token)), Occur.MUST); - } - tokenStream.end(); - tokenStream.close(); - } catch (IOException e) { - //should never happen as we use StringReader - throw new RuntimeException("Failed to open a token stream; " - + "field:" + filterField + ", value:" + v,e); - } - query.add(bq.build(), Occur.SHOULD); - } else { - query.add(new TermQuery(new Term(filterField, v.toLowerCase())), Occur.SHOULD); - } - } - - return query.build(); - } - -} diff --git a/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchResult.java b/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchResult.java deleted file mode 100644 index c69f75241..000000000 --- a/paxtools-search/src/main/java/org/biopax/paxtools/search/SearchResult.java +++ /dev/null @@ -1,58 +0,0 @@ -package org.biopax.paxtools.search; - -import java.util.List; - -import org.biopax.paxtools.model.BioPAXElement; - - -public class SearchResult { - - private List hits; - private long totalHits; - private long maxHitsPerPage = 100; - private int page = 0; - - public SearchResult() { - } - - - public List getHits() { - return hits; - } - - - public void setHits(List hits) { - this.hits = hits; - } - - - public long getTotalHits() { - return totalHits; - } - - - public void setTotalHits(long totalHits) { - this.totalHits = totalHits; - } - - - public long getMaxHitsPerPage() { - return maxHitsPerPage; - } - - - public void setMaxHitsPerPage(long maxHitsPerPage) { - this.maxHitsPerPage = maxHitsPerPage; - } - - - public int getPage() { - return page; - } - - - public void setPage(int page) { - this.page = page; - } - -} diff --git a/paxtools-search/src/main/java/org/biopax/paxtools/search/Searcher.java b/paxtools-search/src/main/java/org/biopax/paxtools/search/Searcher.java deleted file mode 100644 index 5b28f39ed..000000000 --- a/paxtools-search/src/main/java/org/biopax/paxtools/search/Searcher.java +++ /dev/null @@ -1,20 +0,0 @@ -package org.biopax.paxtools.search; - - -import org.biopax.paxtools.model.BioPAXElement; - -public interface Searcher { - /** - * Full-text search for BioPAX elements. - * - * @param query String (keywords or Lucene query string) - * @param page hits page number (when the number of hits exceeds a threshold) - * @param filterByType - class filter - * @param datasources - filter by datasource - * @param organisms - filter by organism - * @return a bean that contains the list of BioPAX objects (hits) and annotations. - */ - SearchResult search(String query, int page, - Class filterByType, String[] datasources, String[] organisms); - -} diff --git a/paxtools-search/src/main/java/org/biopax/paxtools/search/package-info.java b/paxtools-search/src/main/java/org/biopax/paxtools/search/package-info.java deleted file mode 100644 index 89674574c..000000000 --- a/paxtools-search/src/main/java/org/biopax/paxtools/search/package-info.java +++ /dev/null @@ -1,8 +0,0 @@ -/** - * Public interfaces and classes (API) - * for indexing and full-text searching - * BioPAX models. - * - * @author rodche - */ -package org.biopax.paxtools.search; \ No newline at end of file diff --git a/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java b/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java deleted file mode 100644 index 5a17150a9..000000000 --- a/paxtools-search/src/test/java/org/biopax/paxtools/search/SearchEngineTest.java +++ /dev/null @@ -1,191 +0,0 @@ -package org.biopax.paxtools.search; - -import static org.junit.Assert.*; - -import java.io.File; -import java.io.IOException; -import java.util.Map; -import java.util.zip.GZIPInputStream; - -import org.biopax.paxtools.io.SimpleIOHandler; -import org.biopax.paxtools.model.BioPAXElement; -import org.biopax.paxtools.model.Model; -import org.biopax.paxtools.model.level3.Interaction; -import org.biopax.paxtools.model.level3.Pathway; -import org.biopax.paxtools.model.level3.PhysicalEntity; -import org.biopax.paxtools.model.level3.Provenance; -import org.biopax.paxtools.model.level3.SmallMoleculeReference; -import org.biopax.paxtools.search.SearchEngine.HitAnnotation; -import org.junit.Test; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - - -public class SearchEngineTest { - final String indexLocation = System.getProperty("java.io.tmpdir") + File.separator; - final static Logger log = LoggerFactory.getLogger(SearchEngineTest.class); - - @Test - public final void testSearch() { - SimpleIOHandler reader = new SimpleIOHandler(); - Model model = reader.convertFromOWL(getClass().getResourceAsStream("/pathwaydata1.owl")); - SearchEngine searchEngine = new SearchEngine(model, indexLocation + "index1"); - searchEngine.index(); - assertTrue(new File(indexLocation + "index1").exists()); - - SearchResult response = searchEngine.search("ATP", 0, null, null, null); - assertNotNull(response); - assertFalse(response.getHits().isEmpty()); - assertEquals(7, response.getHits().size()); - assertEquals(7, response.getTotalHits()); - - response = searchEngine.search("ATP", 0, Interaction.class, null, null); - assertNotNull(response); - assertEquals(2, response.getHits().size()); - - response = searchEngine.search("ATP", 0, Pathway.class, null, null); - assertNotNull(response); - assertEquals(1, response.getHits().size()); - - BioPAXElement hit = response.getHits().get(0); - assertEquals(4, hit.getAnnotations().get(HitAnnotation.HIT_PROCESSES.name())); - assertEquals(7, hit.getAnnotations().get(HitAnnotation.HIT_PARTICIPANTS.name())); - assertTrue(hit instanceof Pathway); - assertEquals(6, hit.getAnnotations().keySet().size()); - - //test a special implementation for wildcard queries - response = searchEngine.search("*", 0, Pathway.class, null, null); - assertNotNull(response); - assertEquals(1, response.getHits().size()); - - //find all objects (this here works with page=0 as long as the - //total no. objects in the test model < max hits per page) - response = searchEngine.search("*", 0, null, null, null); - assertEquals(50, response.getHits().size()); - - response = searchEngine.search("*", 0, PhysicalEntity.class, null, null); - assertEquals(8, response.getHits().size()); - - response = searchEngine.search("*", 0, PhysicalEntity.class, null, new String[] {"562"}); - assertEquals(2, response.getHits().size()); - - response = searchEngine.search("*", 0, PhysicalEntity.class, null, new String[] {"Escherichia"}); - assertEquals(2, response.getHits().size()); - - response = searchEngine.search("*", 0, PhysicalEntity.class, null, new String[] {"Escherichia coliü"}); - assertEquals(2, response.getHits().size()); - - response = searchEngine.search("*", 0, Provenance.class, null, null); - assertEquals(2, response.getHits().size()); - - response = searchEngine.search("*", 0, Provenance.class, new String[] {"kegg"}, null); - assertEquals(1, response.getHits().size()); - - //now - same but using the long name (with 'of' an 'and') as filter value: - response = searchEngine.search("*", 0, Provenance.class, new String[] {"Kyoto Encyclopedia of Genes and Genomes"}, null); - assertEquals(1, response.getHits().size()); - - //filter by data source (Provenance) URI - to tell Provenance objects having same name (but perhaps different organism or version) - // from each other if necessary - - response = searchEngine.search("*", 0, Pathway.class, new String[] {"http://identifiers.org/kegg.pathway/"}, null); - assertEquals(1, response.getHits().size()); - - response = searchEngine.search("glycolysis", 0, SmallMoleculeReference.class, null, null); - assertTrue(response.getHits().isEmpty()); //parent pathway names are searched for in the keywords, names, etc. default fields - - response = searchEngine.search("pathway:glycolysis", 0, SmallMoleculeReference.class, null, null); - assertEquals(5, response.getHits().size()); - - //test search with pagination - searchEngine.setMaxHitsPerPage(10); - response = searchEngine.search("*", 0, null, null, null); - assertEquals(50, response.getTotalHits()); - assertEquals(10, response.getHits().size()); - response = searchEngine.search("*", 1, null, null, null); - assertEquals(10, response.getHits().size()); - - } - - @Test - public final void testHitsOrder() throws IOException { - SimpleIOHandler reader = new SimpleIOHandler(); - Model model = reader.convertFromOWL(new GZIPInputStream( - getClass().getResourceAsStream("/three-bmp-pathways.owl.gz"))); - - //there are three BMP pathways (one is an empty pathway), and a trivial sub-pathway (not bmp): - //"http://purl.org/pc2/7/Pathway_3f75176b9a6272a62f9257f0540dc63b" ("bmppathway", "BMP receptor signaling") - //"http://purl.org/pc2/7/Pathway_b8fa8401d3053b57a10d4c29a3211258" ("BMP signaling pathway") - //"http://identifiers.org/reactome/REACT_12034.3" ("Signaling by BMP" - the one we want...) - //"http://purl.org/pc2/7/Pathway_aaa00bbf872fc777ce1e5eafc108752b" ("proteasomal ubiquitin-dependent protein catabolic process", a black-box) - - SearchEngine searchEngine = new SearchEngine(model, indexLocation + "index2"); - searchEngine.index(); - assertTrue(new File(indexLocation + "index2").exists()); - - // A wide search in the default fields - - SearchResult response = searchEngine.search("signaling by bmp", 0, Pathway.class, null, null); - assertNotNull(response); - assertFalse(response.getHits().isEmpty()); - int i=0; - for(BioPAXElement bpe : response.getHits()) { - Map ann = bpe.getAnnotations(); - log.debug(String.format("Hit %d: %s; participants: %s; processes: %s; excerpt: %s", - ++i, bpe.getUri(), ann.get(HitAnnotation.HIT_PARTICIPANTS.name()), - ann.get(HitAnnotation.HIT_PROCESSES.name()), - ann.get(HitAnnotation.HIT_EXCERPT.name()))); - } - assertEquals(3, response.getHits().size()); - assertEquals(3, response.getTotalHits()); - assertEquals("http://identifiers.org/reactome/REACT_12034.3", response.getHits().get(0).getUri()); - - // more accurate search in all the default fields using quotation marks around - - response = searchEngine.search("\"signaling by bmp\"", 0, Pathway.class, null, null); - assertNotNull(response); - assertFalse(response.getHits().isEmpty()); - assertEquals(1, response.getTotalHits()); - assertEquals("http://identifiers.org/reactome/REACT_12034.3", response.getHits().get(0).getUri()); - - //Next, narrow search in 'name' field only using quoted string - response = searchEngine.search("name:\"Signaling by BMP\"", 0, Pathway.class, null, null); - assertNotNull(response); - assertFalse(response.getHits().isEmpty()); -// for(BioPAXElement bpe : response.getHits()) { -// log.debug(String.format("Hit: %s; size: %s; excerpt: %s", bpe.getUri(), -// bpe.getAnnotation(HitAnnotation.HIT_SIZE.name()) -// , bpe.getAnnotation(HitAnnotation.HIT_EXCERPT.name()))); -// } - //there are three BMP pathways (one is an empty pathway), and a sub-pathway (should not match) - - assertEquals(1, response.getHits().size()); - assertEquals(1, response.getTotalHits()); - assertEquals("http://identifiers.org/reactome/REACT_12034.3", response.getHits().get(0).getUri()); - - - //Next, search in 'pathway' field only, using quoted string - response = searchEngine.search("pathway:\"signaling by bmp\"", 0, Pathway.class, null, null); - assertNotNull(response); - assertFalse(response.getHits().isEmpty()); -// for(BioPAXElement bpe : response.getHits()) { -// log.debug(String.format("Hit: %s; size: %s; excerpt: %s", bpe.getUri(), -// bpe.getAnnotation(HitAnnotation.HIT_SIZE.name()) -// , bpe.getAnnotation(HitAnnotation.HIT_EXCERPT.name()))); -// } - //there is one pathway, and no sub-pathways of it - assertEquals(1, response.getHits().size()); - assertEquals(1, response.getTotalHits()); - assertEquals("http://identifiers.org/reactome/REACT_12034.3", response.getHits().get(0).getUri()); - - response = searchEngine.search("pathway:\"bmp receptor signaling\"", 0, Pathway.class, null, null); - assertNotNull(response); - assertFalse(response.getHits().isEmpty()); -// for(BioPAXElement bpe : response.getHits()) { -// log.debug(String.format("Hit: %s; size: %s; excerpt: %s", bpe.getUri(), -// bpe.getAnnotation(HitAnnotation.HIT_SIZE.name()) -// , bpe.getAnnotation(HitAnnotation.HIT_EXCERPT.name()))); -// } - assertEquals(2, response.getTotalHits()); - // - the second pathway is a trivial one, member of Pathway_3f75176b9a6272a62f9257f0540dc63b and of many other parent pathways. - - //check the top pathway is the main one (parent) - assertEquals("http://purl.org/pc2/7/Pathway_3f75176b9a6272a62f9257f0540dc63b", response.getHits().get(0).getUri()); - } -} diff --git a/paxtools-search/src/test/resources/logback-test.xml b/paxtools-search/src/test/resources/logback-test.xml deleted file mode 100644 index 4a310942d..000000000 --- a/paxtools-search/src/test/resources/logback-test.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - - true - - - - - - - - - %d %-5level [%thread] %logger{25} - %msg%n - true - - - - - - - - - - \ No newline at end of file diff --git a/paxtools-search/src/test/resources/pathwaydata1.owl b/paxtools-search/src/test/resources/pathwaydata1.owl deleted file mode 100644 index 8225d49c9..000000000 --- a/paxtools-search/src/test/resources/pathwaydata1.owl +++ /dev/null @@ -1,504 +0,0 @@ - - - - - - - - Escherichia coliü - - - - - - [CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O) - - SMILES - - ATP - - - - C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO) - - SMILES - - beta-fructose-6-phosphate - - - - - KEGG Pathway - KEGG - Kyoto Encyclopedia of Genes and Genomes - - - - cytoplasm - - This example is meant to provide - an illustration of how various BioPAX slots should be filled; it is - not intended to provide useful (or even accurate) biological - information - - - - UniProt - P27797 - PMID: 15608167 - - - - chebi - CHEBI:422 - PMID: 9847135 - - - - kegg reaction - R02740 - PMID: 9847135 - - - - Reactome - Reactome - - - - beta-D-glucose 6-phosphate - - - b-D-glu-6-p - - - 260.14 - - C6H13O9P - - - - - - true - b-D-glu => - b-D-glu-6-p - 2.7.1.1 - 2.7.1.2 - - - glucose ATP phosphotransferase - ATP:D-glucose 6-phosphotransferase - - REVERSIBLE - - - - beta-D-glu + ATP => - beta-D-glu-6-p + ADP - - - - - - beta-D-glucose - - - b-D-glu - - - 180.16 - - C6H12O6 - - - - - beta-D-fructose - 6-phosphate - - b-D-fru-6-p - - - 260.14 - - C6H13O9P - - - - - glucokinase - - GLK - - glucose kinase - MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSGAHLRQTLGHIL - - - - - - chebi - CHEBI:28 - PMID: 9847135 - - - - chebi - CHEBI:20 - PMID: 9847135 - - - - - - b-D-fru-6-p - - <FONT - FACE="Symbol">b</FONT>-D-fructose-6-phosphate - - beta-D-fructose - 6-phosphate - - - - - - Adenosine - 5'-diphosphate - - ADP - - adenosine diphosphate - 427.2 - - C10H15N5O10P2 - - - - - Adenosine - 5'-triphosphate - - ATP - - adenosine triphosphate - 507.18 - - C10H16N5O13P3 - - - - - - - LEFT_TO_RIGHT - - GLK -> (a-D-glu - <=> a-D-glu-6-p) - - ACTIVATION - - The source of this data did not - store catalyses of reactions as separate objects, so there are no - unification x-refs pointing to the source of these BioPAX instances. - - catalysis of (alpha-D-glu - <=> alpha-D-glu-6-p) - - - - - - - b-D-glu-6-p <=> - b-D-fru-6-p - 5.3.1.9 - - beta-D-Glucose 6-phosphate - ketol-isomerase - beta-D-Glucose 6-phosphate => - beta-D-Fructose 6-phosphate - REVERSIBLE - - - - beta-D-glu-6-p <=> - beta-D-fru-6-p - - - - - - kegg reaction - R01786 - PMID: 9847135 - - - - - - ADP - adenosine diphosphate - Adenosine - 5'-diphosphate - - - - - - - - GLK - GLK_ECOLI - glucokinase - - - - - - 0.4 - - - - - - PGI - GPI - phosphohexose isomerase - PHI - glucose-6-phosphate isomerase - phosphoglucose isomerase - - - - - - - - - - Embden-Meyerhof pathway - glucose degradation - see - http://www.amaze.ulb.ac.be/ - All data within the - pathway has the same availability - - - - - This example is meant to provide - an illustration of how various BioPAX slots should be filled; it is - not intended to provide useful (or even accurate) biological - information - Glycolysis Pathway - - glycolysis - - - - - - - - H2a/x - Histone H2A.x - - - Reactome DB_ID: 56151 - - - - - - H2AX - - - UniProt - P16104 - - - Reactome - REACT_3939 - 1 - - - - Taxonomy - 562 - - - - phosphoglucose isomerase - - PGI - - GPI - phosphohexose isomerase - PHI - glucose-6-phosphate isomerase - KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT - - This example is meant to provide - an illustration of how various BioPAX slots should be filled; it is - not intended to provide useful (or even accurate) biological - information - - - - - - - ATP - adenosine triphosphate - Adenosine - 5'-triphosphate - - - - - - - PubChem - 14438 - PMID: 9847135 - - - - - LEFT_TO_RIGHT - - PGI -> (b-d-glu-6-p - <=> b-D-fru-6p) - - ACTIVATION - - The source of this data did not - store catalyses of reactions as separate objects, so there are no - unification x-refs pointing to the source of these BioPAX instances. - - catalysis of - (beta-D-glu-6-p <=> beta-D-fruc-6-p) - - - - - - PUBCHEM-substance - 14439 - PMID: 9847135 - - - - - - a-D-glu-6-p - - D-glucose-6-P - glucose-6-P - beeta-D-glucose-6-p - b-D-glucose-6-phoshate - beta-D-glucose 6-phosphate - - - - - - - LEFT_TO_RIGHT - - - - - - - - - b-D-glu - - <FONT - FACE="Symbol">a</FONT>-D-glucose - beta-D-glucose - - - - - - - Gene Ontology - GO:0005737 - PMID: 11483584 - - - - PubMed - 2549346 - - - - LEFT_TO_RIGHT - - - - - - - - C1(C(O)C(O)C(O)C(O1)CO)(O) - - SMILES - - alpha-D-glucose - - - - C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1) - - SMILES - - beta-glucose-6-phosphate - - - - - c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O)) - - SMILES - - ADP - - - - UniProt - Q16602 - PMID: 15608167 - - - - - MOD:00046 - Protein Modification Ontology - - - - O-phospho-L-serine - - - - - - - - - diff --git a/paxtools-search/src/test/resources/three-bmp-pathways.owl.gz b/paxtools-search/src/test/resources/three-bmp-pathways.owl.gz deleted file mode 100644 index 277b92ed9ba163a090487251edb04d1b367539fd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 386188 zcmV(%K;pk2iwFp!9gkE119WI|Wo0d5ZE!7cVRUGBVR>^dZ+C0}>|JY98%MMLo?oHD zmGdP5=6>PCc?*oNiMbhY;+!vAb2WM+w7k+{oAc{WuXZIZvH*bwBkYq(Qj~W0*_oc6 zzD;-UZ~yvo-fevf{Xr-1y9@X*8^_x_KegcY z-eBX)z`tBMD~gMa_4Uu6Kd*hJYkB|UIzb4pf7stUacAM&yjU6Co`3G%a64H?avd&D 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-374,11 +373,6 @@ commons-lang3 3.8.1 - - org.codehaus.jackson - jackson-mapper-asl - 1.9.12 - com.hp.hpl.jena jena @@ -429,6 +423,21 @@ 2.3.0 runtime + + com.fasterxml.jackson.core + jackson-core + 2.14.2 + + + com.fasterxml.jackson.core + jackson-databind + 2.14.2 + + + org.projectlombok + lombok + 1.18.24 + diff --git a/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java b/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java index a10cd59aa..175f4300e 100644 --- a/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java +++ b/psimi-converter/src/main/java/org/biopax/paxtools/converter/psi/EntryMapper.java @@ -236,7 +236,7 @@ private Provenance createProvenance(Source source) { private Entity processInteraction(Interaction interaction, Set avail, Provenance pro, boolean isComplex) { - Entity bpInteraction = null; //interaction or complex + Entity bpInteraction; //interaction or complex boolean isGeneticInteraction = false; // get interaction name/short name @@ -587,7 +587,7 @@ private Entity findEquivalentEntity(final Entity entity) { /* * Converts a PSIMI participant to BioPAX physical entity or gene. * It can be then used either as a participant of an interaction - * or exp. form entity of a exp. form of a participant's evidence, + * or exp. form entity of an exp. form of a participant's evidence, * depending on the caller method and the map provided. * The result entity is not added to the model yet (but its entity reference, * if applicable, Xrefs, CVs are added to the model). @@ -677,19 +677,16 @@ private Entity createParticipant(Participant participant, Interactor interactor, entityReferenceClass = null; } else if ("interaction".equals(entityType)) { -// entityClass = null; -// entityReferenceClass = null; LOG.warn("EntryMapper.createParticipant(): skip for interactor: " + interactor.getId() + " that has type: " + entityType + ", participant:" + participant.getId() + ")."); return null; } - //else - peptide, biopolymer, molecule set, unknown, etc. - consider this is a Protein. } //make consistent biopax URI (for the entity ref., if applies, or phys. entity) - String entityUri = ""; + String entityUri; String baseUri = ""; final RelationshipXref x = getInteractorPrimaryRef(interactor.getXref()); @@ -939,8 +936,8 @@ private BioSource getBioSource(Interactor interactor) { } } - String uri = xmlBase + "BioSource_" + - "taxonomy_" + ncbiId; //tissue and cell type terms can be added below + String uri = xmlBase + "BIO_" + + "ncbitaxon_" + ncbiId; //tissue and cell type terms can be added below if(tissue!=null && !tissue.getTerm().isEmpty()) uri += "_" + encode(tissue.getTerm().iterator().next()); if(cellType!=null && !cellType.getTerm().isEmpty()) @@ -953,22 +950,22 @@ private BioSource getBioSource(Interactor interactor) { toReturn = bpModel.addNew(BioSource.class, uri); - String taxonXrefUri = xmlBase + "UnificationXref_taxonomy_" + ncbiId; + String taxonXrefUri = xmlBase + "UX_ncbitaxon_" + ncbiId; UnificationXref taxonXref = (UnificationXref) bpModel.getByID(taxonXrefUri); if(taxonXref == null) { taxonXref = bpModel.addNew(UnificationXref.class, taxonXrefUri); taxonXref.setDb("Taxonomy"); taxonXref.setId(ncbiId); } - toReturn.addXref((Xref)taxonXref); + toReturn.addXref(taxonXref); if (cellType != null) { - toReturn.setCellType((CellVocabulary) cellType); + toReturn.setCellType(cellType); } if (tissue != null) { - toReturn.setTissue((TissueVocabulary) tissue); + toReturn.setTissue(tissue); } if (name != null) { toReturn.setStandardName(name); @@ -1067,24 +1064,24 @@ private void xref(DbReference psiref, Set bpXrefs) { // process ref type String refType = (psiref.hasRefType()) ? psiref.getRefType() : null; String refTypeAc = (psiref.hasRefTypeAc()) ? psiref.getRefTypeAc() : null; - String psiDBRefId = psiref.getId(); - String psiDBRefDb = psiref.getDb(); - // If multiple ids given with comma separated values, then split them. - for (String dbRefId : psiDBRefId.split(",")) { - Xref bpXref = null; + String psiDBRefId = psiref.getId(); + String psiDBRefDb = psiref.getDb(); + // If multiple ids given with comma separated values, then split them. + for (String dbRefId : psiDBRefId.split(",")) { + Xref bpXref; // Let's not make UnificationXrefs. RelationshipXref is more safe. // Often, a gene or omim ID (can be another species') is a protein's xref id with 'identity' type... - if(!"pubmed".equalsIgnoreCase(psiDBRefDb)) { + if(!"pubmed".equalsIgnoreCase(psiDBRefDb)) { bpXref = relationshipXref(psiDBRefDb, dbRefId, refType, refTypeAc); - } - else { - //TODO shall we skip PublicationXref here (IntAct puts the same PSIMI paper pmid everywhere...)? + } + else { + //TODO shall we skip PublicationXref here (IntAct puts the same PSIMI paper pmid everywhere...)? bpXref = publicationXref(psiDBRefDb, dbRefId); - } + } - if (bpXref != null) - bpXrefs.add(bpXref); - } + if (bpXref != null) + bpXrefs.add(bpXref); + } } @@ -1097,7 +1094,7 @@ private String dbQuickFix(String db) { || "geneid".equalsIgnoreCase(db) || "gene id".equalsIgnoreCase(db) || "ncbigene".equalsIgnoreCase(db)) - db = "NCBI Gene"; + db = "Entrez Gene"; return db; } @@ -1152,7 +1149,7 @@ private UnificationXref unificationXref(String db, String id) { } id = id.trim(); - String xuri = xmlBase + "UnificationXref_" + encode(db.toLowerCase() + "_" + id); + String xuri = xmlBase + "UX_" + encode(db.toLowerCase() + "_" + id); UnificationXref x = (UnificationXref) bpModel.getByID(xuri); if(x==null) { x= bpModel.addNew(UnificationXref.class, xuri); @@ -1183,7 +1180,7 @@ private PublicationXref publicationXref(String db, String id) { return null; } - String xuri = xmlBase + "PublicationXref_" + encode(db.toLowerCase() + "_" + id); + String xuri = xmlBase + "PX_" + encode(db.toLowerCase() + "_" + id); PublicationXref x = (PublicationXref) bpModel.getByID(xuri); if(x==null) { x= bpModel.addNew(PublicationXref.class, xuri); @@ -1380,53 +1377,52 @@ else if (name.hasFullName()) { private RelationshipXref relationshipXref(String db, String id, String refType, String refTypeAc) - { + { if(db == null || db.trim().isEmpty()) { LOG.warn("relationshipXref(), db is null, id=" + id); return null; } - + db = dbQuickFix(db); - + if(id == null || id.trim().isEmpty() || BAD_ID_VALS.contains(id.trim().toUpperCase())) { LOG.warn("relationshipXref(), illegal id=" + id); return null; } - + id = id.trim(); - + //generate URI - String uri = xmlBase + "RelationshipXref_"; + String uri = xmlBase + "RX_"; if(refType!=null && !refType.isEmpty()) uri += encode(db.toLowerCase()+"_"+id+"_"+refType); else - uri += encode(db.toLowerCase()+"_"+id); - - RelationshipXref x = (RelationshipXref) bpModel.getByID(uri); - - if (x == null) { //create/add a new RX - x = bpModel.addNew(RelationshipXref.class, uri); - x.setDb(db); - x.setId(id); - if (refType != null) //use the standard CV term and accession - { - String cvUri = (refTypeAc!=null) ? "http://identifiers.org/psimi/" + refTypeAc - : xmlBase + "RTV_" + encode(refType);//the latter should not happen often (ever, in a valid PSI-MI XML) - RelationshipTypeVocabulary rtv = (RelationshipTypeVocabulary) bpModel.getByID(cvUri); - if(rtv == null) { - rtv = bpModel.addNew(RelationshipTypeVocabulary.class, cvUri); - rtv.addTerm(refType); - if(refTypeAc != null && !refTypeAc.isEmpty()) {//null happens, e.g., for 'uniprot-removed-ac' terms... - UnificationXref cvx = bpModel.addNew(UnificationXref.class, genUri(UnificationXref.class)); - cvx.setDb("PSI-MI"); - cvx.setId(refTypeAc); - rtv.addXref(cvx); - } - } - x.setRelationshipType(rtv); - } - } - + uri += encode(db.toLowerCase()+"_"+id); + + RelationshipXref x = (RelationshipXref) bpModel.getByID(uri); + if (x == null) { //create/add a new RX + x = bpModel.addNew(RelationshipXref.class, uri); + x.setDb(db); + x.setId(id); + if (refType != null) //use the standard CV term and accession + { + String cvUri = (refTypeAc!=null) ? "mi/" + refTypeAc + : xmlBase + "RTV_" + encode(refType);//the latter should not happen often (ever, in a valid PSI-MI XML) + RelationshipTypeVocabulary rtv = (RelationshipTypeVocabulary) bpModel.getByID(cvUri); + if(rtv == null) { + rtv = bpModel.addNew(RelationshipTypeVocabulary.class, cvUri); + rtv.addTerm(refType); + if(refTypeAc != null && !refTypeAc.isEmpty()) {//null happens, e.g., for 'uniprot-removed-ac' terms... + UnificationXref cvx = bpModel.addNew(UnificationXref.class, genUri(UnificationXref.class)); + cvx.setDb("MI"); + cvx.setId(refTypeAc); + rtv.addXref(cvx); + } + } + x.setRelationshipType(rtv); + } + } + return x; } @@ -1580,7 +1576,7 @@ private SequenceInterval getSequenceLocation(long beginSequenceInterval, private boolean isGeneticInteraction(Set bpEvidence) { if (bpEvidence != null && !bpEvidence.isEmpty()) { - for (Evidence e : (Set) bpEvidence) { + for (Evidence e : bpEvidence) { Set evidenceCodes = e.getEvidenceCode(); if (evidenceCodes != null) { for (EvidenceCodeVocabulary cv : evidenceCodes) { @@ -1603,7 +1599,7 @@ private boolean isGeneticInteraction(Set bpEvidence) * original xml ids (optional, for debugging), * BioPAX model interface name and some unique number. * The idea is virtually never ever return the same URI here (taking into account - * that there are multiple threads converting different PSI-MI Entries, one per thread, + * that there are multiple threads converting different MI Entries, one per thread, * simultaneously) */ private String genUri(Class type, Object... psimiIds) { diff --git a/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java b/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java index eb457ecea..d35e3e04f 100644 --- a/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java +++ b/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java @@ -49,16 +49,15 @@ import java.io.IOException; import java.io.InputStream; import java.util.Collection; -import java.util.Set; import java.util.zip.GZIPInputStream; /** * * This test depends upon a particular random number generator * with a particular seed. - * + * * TODO more tests - * + * * @author rodche (Igor Rodchenkov) */ public class TestMapping { @@ -67,110 +66,110 @@ public class TestMapping { * psi-mi test file */ private static final String PSI_MI_TEST_FILE = "10523676-compact.xml.gz"; - + /** * psi-mitab test file */ private static final String PSI_MITAB_TEST_FILE = "12167173.txt"; - + /** * A test data excerpt from BIND PSI-MI XML */ private static final String BIND_TEST_FILE = "bind-test.psimi.xml"; - + private static final String INTACT_TEST_FILE = "human_31.xml.gz"; - @Test - public void testApi() throws Exception { - - // unmarshall the data, close the stream - PsimiXmlReader reader = new PsimiXmlReader(); - InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(PSI_MI_TEST_FILE)); - EntrySet es = reader.read(is); - is.close(); - Collection entries = es.getEntries(); - // we should only have 1 entry - assertEquals(1, entries.size()); - // get entry - Entry entry = (Entry)entries.iterator().next(); - - assertTrue(entry.hasExperiments()); - assertEquals(4, entry.getExperiments().size()); - assertEquals(10, entry.getInteractions().size()); - - Interaction interaction = null; - for(Interaction it : entry.getInteractions()) { - if(it.getId()==1) { - interaction = it; - break; - } - } - - //despite there is instead of items - - assertFalse(interaction.hasExperimentRefs()); - assertEquals(0, interaction.getExperimentRefs().size()); - //(- weird, but this is how PSIMI API works!) - //at the same time the following is set correctly: - assertTrue(interaction.hasExperiments()); - assertEquals(1, interaction.getExperiments().size()); - - assertFalse(interaction.getParticipants().isEmpty()); - Participant participant = interaction.getParticipants().iterator().next(); - //despite there was interactorRef, - assertFalse(participant.hasInteractorRef()); - assertNull(participant.getInteractorRef()); - //at the same time, the following is set: - assertTrue(participant.hasInteractor()); - assertNotNull(participant.getInteractor()); - - assertFalse(participant.hasInteractionRef()); - assertFalse(participant.hasInteraction()); - - - //TODO assert experimentalRole.hasExperiments()==true always (if there're experiments); experimentalRole.hasExperimentRefs()==false - } - - - /** - * Tests that a PSI document (level 2.5) is correctly mapped into a biopax model. + @Test + public void testApi() throws Exception { + + // unmarshall the data, close the stream + PsimiXmlReader reader = new PsimiXmlReader(); + InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(PSI_MI_TEST_FILE)); + EntrySet es = reader.read(is); + is.close(); + Collection entries = es.getEntries(); + // we should only have 1 entry + assertEquals(1, entries.size()); + // get entry + Entry entry = (Entry)entries.iterator().next(); + + assertTrue(entry.hasExperiments()); + assertEquals(4, entry.getExperiments().size()); + assertEquals(10, entry.getInteractions().size()); + + Interaction interaction = null; + for(Interaction it : entry.getInteractions()) { + if(it.getId()==1) { + interaction = it; + break; + } + } + + //despite there is instead of items - + assertFalse(interaction.hasExperimentRefs()); + assertEquals(0, interaction.getExperimentRefs().size()); + //(- weird, but this is how PSIMI API works!) + //at the same time the following is set correctly: + assertTrue(interaction.hasExperiments()); + assertEquals(1, interaction.getExperiments().size()); + + assertFalse(interaction.getParticipants().isEmpty()); + Participant participant = interaction.getParticipants().iterator().next(); + //despite there was interactorRef, + assertFalse(participant.hasInteractorRef()); + assertNull(participant.getInteractorRef()); + //at the same time, the following is set: + assertTrue(participant.hasInteractor()); + assertNotNull(participant.getInteractor()); + + assertFalse(participant.hasInteractionRef()); + assertFalse(participant.hasInteraction()); + + + //TODO assert experimentalRole.hasExperiments()==true always (if there're experiments); experimentalRole.hasExperimentRefs()==false + } + + + /** + * Tests that a PSI document (level 2.5) is correctly mapped into a biopax model. */ - @Test - public void testMapping() { + @Test + public void testMapping() { Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); - + // open file try { // unmarshall the data, close the stream PsimiXmlReader reader = new PsimiXmlReader(); - InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(PSI_MI_TEST_FILE)); + InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(PSI_MI_TEST_FILE)); EntrySet es = reader.read(is); is.close(); Collection entries = es.getEntries(); - + // we should only have 1 entry - assertEquals(1, entries.size()); + assertEquals(1, entries.size()); // get entry - Entry entry = (Entry)entries.iterator().next(); + Entry entry = entries.iterator().next(); EntryMapper mapper = new EntryMapper(bpModel, false); mapper.run(entry); } catch (Exception e) { e.printStackTrace(); } - + assertNotNull(bpModel); assertFalse(bpModel.getObjects().isEmpty()); - + //EFs are generated assertFalse(bpModel.getObjects(ExperimentalForm.class).isEmpty()); - + //TODO add more assertions } - + @Test public void testMitabToMi() throws Exception { PsimiTabReader reader = new PsimiTabReader(); @@ -183,70 +182,69 @@ public void testMitabToMi() throws Exception { EntrySet es = (new Tab2Xml()).convert(its); Collection entries = es.getEntries(); - + //only one entry - multiple interactions assertEquals(1, entries.size()); assertEquals(11, entries.iterator().next().getInteractions().size()); } - - @Test - public void testParticipantsAreNotDuplicated() throws IOException { + + @Test + public void testParticipantsAreNotDuplicated() throws IOException { Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); // open file try { // unmarshall the data, close the stream PsimiXmlReader reader = new PsimiXmlReader(); - InputStream is = getClass().getClassLoader().getResourceAsStream(BIND_TEST_FILE); + InputStream is = getClass().getClassLoader().getResourceAsStream(BIND_TEST_FILE); EntrySet es = reader.read(is); is.close(); Collection entries = es.getEntries(); - assertEquals(1, entries.size()); - Entry entry = (Entry)entries.iterator().next(); + assertEquals(1, entries.size()); + Entry entry = entries.iterator().next(); EntryMapper mapper = new EntryMapper(bpModel, false); mapper.run(entry); } catch (Exception e) { e.printStackTrace(); } - + assertNotNull(bpModel); assertFalse(bpModel.getObjects().isEmpty()); - + assertEquals(3, bpModel.getObjects(MolecularInteraction.class).size()); - - save(bpModel, getClass().getClassLoader().getResource("").getPath() - + File.separator + "testConvertBindPsimi.owl"); - + + save(bpModel, getClass().getClassLoader().getResource("").getPath() + + File.separator + "testConvertBindPsimi.owl"); + // there are 6 PSI-MI participants that refer to: 6 interactors and 3 experimental interactors // (but these refer to only 5 unique primary xref IDs - 4 of protein and 1 of dna type) // 4 "Max"/"GST-Max" and "Myc-associated factor X" interactors that have same ID makes only one PR // 2 HMBS promoter dnas make one DnaReference assertEquals(4, bpModel.getObjects(ProteinReference.class).size()); - // 2 dna type interactors ans experimental inter. merge into one + // 2 dna type interactors and experimental inter. merge into one assertEquals(1, bpModel.getObjects(DnaReference.class).size()); // 9 original physical entities, some were merged (e.g., two gst-max...) assertEquals(8, bpModel.getObjects(SimplePhysicalEntity.class).size()); - + ProteinReference pr = (ProteinReference) bpModel.getByID("ProteinReference_refseq_NP_002373_identity"); assertNotNull(pr); assertEquals(2, pr.getName().size()); assertTrue(pr.getName().contains("Max")); assertTrue(pr.getName().contains("Myc-associated factor X")); - } - - @Test - public void testMappingIntAct() { - Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); + + @Test + public void testMappingIntAct() { + Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); try { PsimiXmlReader reader = new PsimiXmlReader(); - InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(INTACT_TEST_FILE)); + InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(INTACT_TEST_FILE)); EntrySet es = reader.read(is); is.close(); - Collection entries = es.getEntries(); + Collection entries = es.getEntries(); // we should only have 1 entry - assertEquals(11, entries.size()); + assertEquals(11, entries.size()); Entry entry = (Entry)entries.iterator().next(); EntryMapper mapper = new EntryMapper(bpModel, false); mapper.run(entry); @@ -254,7 +252,7 @@ public void testMappingIntAct() { } catch (Exception e) { e.printStackTrace(); - } + } assertNotNull(bpModel); assertFalse(bpModel.getObjects().isEmpty()); Collection evs = bpModel.getObjects(Evidence.class); @@ -269,8 +267,8 @@ public void testMappingIntAct() { assertNotNull(interaction); assertTrue(interaction.getComment().contains(EntryMapper.FIGURE_LEGEND_CODE+ ":1C")); } - - private void save(Model model, String file) throws IOException { - new SimpleIOHandler(BioPAXLevel.L3).convertToOWL(model, new FileOutputStream(file)); - } + + private void save(Model model, String file) throws IOException { + new SimpleIOHandler(BioPAXLevel.L3).convertToOWL(model, new FileOutputStream(file)); + } } diff --git a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/idmapping/EntrezGene.java b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/idmapping/EntrezGene.java index c9a2b63e7..34cee78c4 100644 --- a/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/idmapping/EntrezGene.java +++ b/sbgn-converter/src/main/java/org/biopax/paxtools/io/sbgn/idmapping/EntrezGene.java @@ -52,7 +52,7 @@ public static boolean containsSymbol(String symbol) { try { - sym2id = new HashMap(); + sym2id = new HashMap<>(); BufferedReader reader = new BufferedReader(new InputStreamReader( HGNC.class.getResourceAsStream("EntrezGene.txt"))); for (String line = reader.readLine(); line != null; line = reader.readLine()) @@ -67,7 +67,7 @@ public static boolean containsSymbol(String symbol) } reader.close(); - id2sym = new HashMap(); + id2sym = new HashMap<>(); for (String key : sym2id.keySet()) { id2sym.put(sym2id.get(key), key); From d911b803f4b8bade4f54ddc5b84f16df504d46ae Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 24 Jun 2023 16:52:27 -0400 Subject: [PATCH 08/20] Paxtools-6: several changes - added Resolver.synonymap setter/getter (for Validator project) - improved normalizer (better URI for CV, BioSource) - deleted paxtools-archetype module (old, does not worth upgrading) - migrated to JUnit5 completely --- .../paxtools/io/gsea/GSEAConverterTest.java | 41 +- .../io/jsonld/JsonldBiopaxConverterTest.java | 4 +- .../paxtools/normalizer/Normalizer.java | 18 +- .../biopax/paxtools/normalizer/Resolver.java | 46 +- .../paxtools/normalizer/NormalizerTest.java | 179 +- .../paxtools/normalizer/ResolverTest.java | 53 +- .../biopax/paxtools/pattern/DBParsers.java | 20 +- .../paxtools/pattern/PatternBoxTest.java | 37 +- .../pattern/constraint/ConBoxTest.java | 103 +- .../pattern/constraint/ConstraintTest.java | 73 +- .../pattern/constraint/TestParent.java | 6 +- .../paxtools/pattern/miner/MinerTest.java | 4 +- .../pattern/miner/SIFSearcherTest.java | 80 +- paxtools-archetype/README.md | 8 - paxtools-archetype/pom.xml | 42 - .../META-INF/maven/archetype-metadata.xml | 19 - .../resources/archetype-resources/pom.xml | 101 - .../src/main/java/com/example/Example.java | 84 - .../biopax3-short-metabolic-pathway.owl | 574 - .../src/main/resources/circadian_clock.owl | 63790 ---------------- .../src/main/resources/dna_replication.owl | 37107 --------- .../raf_map_kinase_cascade_reactome.owl | 4386 -- .../projects/basic/archetype.properties | 5 - .../test/resources/projects/basic/goal.txt | 0 .../paxtools/examples/ProteinNameLister.java | 16 +- .../controller/CommandManagerTest.java | 4 +- .../controller/CompleterClonerTest.java | 26 +- .../controller/EditorMapImplTest.java | 10 +- .../paxtools/controller/FetcherTest.java | 17 +- .../paxtools/controller/ModelUtilsTest.java | 23 +- .../paxtools/controller/PathAccessorTest.java | 9 +- .../paxtools/controller/ShallowCopyTest.java | 10 +- .../controller/SimpleEditorMapTest.java | 12 +- .../paxtools/controller/SimpleMergerTest.java | 14 +- .../controller/TransitiveAccessorTest.java | 25 +- .../controller/UnionPropertyAccessorTest.java | 12 +- .../paxtools/converter/LevelUpgraderTest.java | 36 +- .../paxtools/impl/level3/EqualsEtcTest.java | 4 +- .../impl/level3/EquivalenceImplTest.java | 8 +- .../impl/level3/ModelCoverageTest.java | 9 +- .../paxtools/io/SimpleIOHandlerTest.java | 628 +- .../paxtools/model/BioPAXFactoryTest.java | 4 +- .../org/biopax/paxtools/query/QueryTest.java | 17 +- pom.xml | 39 +- .../paxtools/converter/psi/TestMapping.java | 17 +- .../paxtools/io/sbgn/SBGNConverterTest.java | 34 +- 46 files changed, 820 insertions(+), 106934 deletions(-) delete mode 100644 paxtools-archetype/README.md delete mode 100644 paxtools-archetype/pom.xml delete mode 100755 paxtools-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml delete mode 100755 paxtools-archetype/src/main/resources/archetype-resources/pom.xml delete mode 100755 paxtools-archetype/src/main/resources/archetype-resources/src/main/java/com/example/Example.java delete mode 100755 paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/biopax3-short-metabolic-pathway.owl delete mode 100755 paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/circadian_clock.owl delete mode 100755 paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/dna_replication.owl delete mode 100755 paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/raf_map_kinase_cascade_reactome.owl delete mode 100644 paxtools-archetype/src/test/resources/projects/basic/archetype.properties delete mode 100644 paxtools-archetype/src/test/resources/projects/basic/goal.txt diff --git a/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java b/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java index e67e4b722..36f788b8b 100644 --- a/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java +++ b/gsea-converter/src/test/java/org/biopax/paxtools/io/gsea/GSEAConverterTest.java @@ -3,13 +3,12 @@ import org.biopax.paxtools.io.BioPAXIOHandler; import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.Model; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; import java.io.*; import java.util.Collection; -import static org.junit.Assert.*; - /** * GSEA (GMT) conversion test. */ @@ -18,7 +17,7 @@ public class GSEAConverterTest { static BioPAXIOHandler handler = new SimpleIOHandler(); @Test - public void testWriteL2GSEA() throws Exception { + public void writeL2GSEA() throws Exception { // write the output InputStream in = getClass().getResourceAsStream("/L2/biopax_id_557861_mTor_signaling.owl"); Model level2 = handler.convertFromOWL(in); @@ -26,15 +25,15 @@ public void testWriteL2GSEA() throws Exception { Collection entries = gseaConverter.convert(level2); // assert some things //for(GMTEntry gseaEntry : entries) System.out.println("gsea: " + gseaEntry.toString()); - assertEquals(1, entries.size()); + Assertions.assertEquals(1, entries.size()); GMTEntry entry = entries.iterator().next(); //CPATH-557861 - assertEquals("http://cbio.mskcc.org/cpathCPATH-557861", entry.name()); - assertTrue(entry.description().contains("mTOR signaling pathway")); - assertTrue(entry.description().contains("nci-nature")); - assertEquals("9606", entry.taxID()); - assertEquals("GENE_SYMBOL", entry.idType()); - assertEquals(27, entry.identifiers().size()); + Assertions.assertEquals("http://cbio.mskcc.org/cpathCPATH-557861", entry.name()); + Assertions.assertTrue(entry.description().contains("mTOR signaling pathway")); + Assertions.assertTrue(entry.description().contains("nci-nature")); + Assertions.assertEquals("9606", entry.taxID()); + Assertions.assertEquals("GENE_SYMBOL", entry.idType()); + Assertions.assertEquals(27, entry.identifiers().size()); // dump the output (new GSEAConverter("GENE_SYMBOL", true)).writeToGSEA(level2, System.out); @@ -42,27 +41,27 @@ public void testWriteL2GSEA() throws Exception { gseaConverter = new GSEAConverter("NP", true); entries.clear(); entries = gseaConverter.convert(level2); - assertEquals(1, entries.size()); + Assertions.assertEquals(1, entries.size()); entry = entries.iterator().next(); - assertEquals("http://cbio.mskcc.org/cpathCPATH-557861", entry.name()); - assertTrue(entry.identifiers().isEmpty()); + Assertions.assertEquals("http://cbio.mskcc.org/cpathCPATH-557861", entry.name()); + Assertions.assertTrue(entry.identifiers().isEmpty()); gseaConverter = new GSEAConverter("ref_seq", true); //test data has this non-standard name (instead RefSeq) entries.clear(); entries = gseaConverter.convert(level2); // assert some things - assertEquals(1, entries.size()); + Assertions.assertEquals(1, entries.size()); entry = entries.iterator().next(); - assertEquals("http://cbio.mskcc.org/cpathCPATH-557861", entry.name()); - assertTrue(entry.description().contains("nci-nature")); - assertEquals("9606", entry.taxID()); - assertEquals("ref_seq", entry.idType()); - assertEquals(33, entry.identifiers().size()); + Assertions.assertEquals("http://cbio.mskcc.org/cpathCPATH-557861", entry.name()); + Assertions.assertTrue(entry.description().contains("nci-nature")); + Assertions.assertEquals("9606", entry.taxID()); + Assertions.assertEquals("ref_seq", entry.idType()); + Assertions.assertEquals(33, entry.identifiers().size()); (new GSEAConverter("NP", true)).writeToGSEA(level2, System.out); } @Test - public void testWriteL3GSEA() throws Exception { + public void writeL3GSEA() throws Exception { InputStream in = getClass().getResourceAsStream("/L3/biopax3-short-metabolic-pathway.owl"); Model level3 = handler.convertFromOWL(in); GSEAConverter gseaConverter = new GSEAConverter("uniprot", true); diff --git a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java index 8b118211d..d6496fd7d 100644 --- a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java +++ b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java @@ -1,5 +1,7 @@ package org.biopax.paxtools.io.jsonld; +import org.junit.jupiter.api.Test; + import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; @@ -7,8 +9,6 @@ import java.io.InputStream; import java.io.OutputStream; -import org.junit.Test; - public class JsonldBiopaxConverterTest { @Test diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index 71dc29c0c..bf5ae5441 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -265,8 +265,8 @@ public static String uri(final String xmlBase, String dbName, String idPart, if (type.equals(RelationshipTypeVocabulary.class) || ProteinReference.class.isAssignableFrom(type) || SmallMoleculeReference.class.isAssignableFrom(type) - || (type.equals(BioSource.class) && "ncbitaxon".equalsIgnoreCase(prefix) - && idPart != null && idPart.matches("^\\d+$"))) { + || (type.equals(BioSource.class) && "ncbitaxon".equalsIgnoreCase(prefix) && idPart != null && idPart.matches("^\\d+$")) + ) { // makes URL uri = Resolver.getURI(prefix, idPart); //can be null when there's id-pattern mismatch } else if (type.equals(UnificationXref.class) && !"pubmed".equalsIgnoreCase(prefix) || @@ -294,7 +294,11 @@ public static String uri(final String xmlBase, String dbName, String idPart, } String localPart = sb.toString(); String strategy = System.getProperty(PROPERTY_NORMALIZER_URI_STRATEGY, VALUE_NORMALIZER_URI_STRATEGY_MD5); - if(VALUE_NORMALIZER_URI_STRATEGY_SIMPLE.equals(strategy) || Xref.class.isAssignableFrom(type)) { + if(VALUE_NORMALIZER_URI_STRATEGY_SIMPLE.equals(strategy) + || Xref.class.isAssignableFrom(type) + || ControlledVocabulary.class.isAssignableFrom(type) + || BioSource.class.isAssignableFrom(type)) + { //for xrefs, always use the simple URI strategy (human-readable) //replace unsafe symbols with underscore localPart = localPart.replaceAll("[^-\\w]", "_"); @@ -535,12 +539,14 @@ private void normalizeCVs(Model model) { private void normalizeBioSources(Model model) { + //it's called after all the xrefs and CVs were normalized NormalizerMap map = new NormalizerMap(model); for(BioSource bs : model.getObjects(BioSource.class)) { UnificationXref uref = findPreferredUnificationXref(bs); //normally, the xref db is 'Taxonomy' (or a valid synonym) if (uref != null - && (uref.getDb().toLowerCase().contains("taxonomy") + && ( uref.getDb().equalsIgnoreCase("ncbitaxon") //should be (the preferred prefix in bioregistry.io) + || uref.getDb().toLowerCase().contains("taxonomy") //just in case.. || uref.getDb().equalsIgnoreCase("newt"))) { String idPart = uref.getId(); @@ -550,9 +556,7 @@ private void normalizeBioSources(Model model) { if(bs.getCellType()!=null && !bs.getCellType().getTerm().isEmpty()) idPart += "_" + bs.getCellType().getTerm().iterator().next(); - String uri = (idPart.equals(uref.getId()) //- no tissue or celltype were attached - && idPart.matches("^\\d+$")) //- is positive integer id - ? uri(xmlBase, uref.getDb(), idPart, BioSource.class) : "bioregistry.io/ncbitaxon:" + idPart; + String uri = uri(xmlBase, uref.getDb(), idPart, BioSource.class); //for standard db, id it makes bioregistry.io/ncbitaxon:id URI map.put(bs, uri); } else { log.debug("Won't normalize BioSource" diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java index e44b4d6a1..6cf0fadda 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java @@ -71,8 +71,7 @@ protected Resolver() { if(is != null) { try { is.close(); - } catch (IOException e) { - } + } catch (IOException ignored) {} } } } @@ -141,8 +140,9 @@ public static Namespace getNamespace(String key, boolean allowVariants) { //also try synonyms if(ns == null) { prefix = synonymap.get(key); //uppercase search - if(prefix != null) + if(prefix != null) { ns = namespaces.get(prefix.toLowerCase()); + } } if(ns == null && allowVariants) { @@ -174,7 +174,7 @@ public static String getURI(String name, String id) { * from the collection name/synonym and bio id. * @param name bio namespace/db/collection name * @param id bio identifier - * @return + * @return CURIE */ public static String getCURIE(String name, String id) { Namespace ns = getNamespace(name, true); @@ -194,17 +194,17 @@ public static String getCURIE(String name, String id) { /** * Gets the unmodifiable map of the bio identifier types registry records. - * @return + * @return prefix to Namespace object map */ public static Map getNamespaces() { return Collections.unmodifiableMap(namespaces); } /** - * Gets the unmodifiable map - mapping an identifier type name/variant/synonym - * (non-alphanumeric chars are removed) to the corresponding record/namespace "prefix". + * Gets the unmodifiable map - mapping a sanitized id-type name/variant/synonym + * (non-alphanumeric chars are removed) to the corresponding namespace prefix. * All the key/values are upper case. - * @return + * @return "sanitized" variant to prefix map */ public static Map getSpellmap() { return Collections.unmodifiableMap(spellmap); @@ -212,25 +212,37 @@ public static Map getSpellmap() { /** * Customize the mapping from a bio identifier type name/variant/synonym - * (non-alphanumeric chars should be removed) to the corresponding record/namespace "prefix". + * (non-alphanumeric chars should be removed) to the corresponding record/namespace prefix. * All the key/values should be stored in upper case. - * @return */ public static void setSpellmap(Map map) { spellmap = map; } + /** + * Gets the unmodifiable map - mapping an identifier type synonym to the corresponding namespace prefix. + * All the key/values are upper case. + * @return synonym to prefix map + */ + public static Map getSynonymap() { + return Collections.unmodifiableMap(synonymap); + } + + /** + * Customize the mapping from a bio identifier type synonym to the corresponding namespace prefix. + * All the key/values should be stored in upper case. + */ + public static void setSynonymap(Map map) { + synonymap = map; + } + /** * - * @param name - * @return + * @param name bio identifiers type/collection name + * @return true when a namespace can be found by this name or after all non-alphanumeric chars get removed */ public static boolean isKnownNameOrVariant(String name) { - return name != null && ( - namespaces.containsKey(name.toLowerCase()) - || synonymap.containsKey(name.toUpperCase()) - || spellmap.containsKey(name.toUpperCase().replaceAll("[^a-zA-Z0-9]","")) - ); + return getNamespace(name,true) != null; } } diff --git a/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java b/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java index f0f030f2b..2518e680a 100644 --- a/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java +++ b/normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java @@ -1,73 +1,84 @@ package org.biopax.paxtools.normalizer; +import org.apache.commons.lang3.StringUtils; import org.biopax.paxtools.io.SimpleIOHandler; import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.Arguments; +import org.junit.jupiter.params.provider.MethodSource; -import static org.junit.Assert.*; +import java.util.stream.Stream; + +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.params.provider.Arguments.arguments; /** * @author rodche */ public class NormalizerTest { - + static SimpleIOHandler simpleIO; - + static { simpleIO = new SimpleIOHandler(BioPAXLevel.L3); simpleIO.mergeDuplicates(true); } - @Test - public final void testUri() { - // using null or non-standard db - assertEquals(Normalizer.uri("test/", "foo", "bar", UnificationXref.class), Normalizer.uri("test/", "FOo", "bar", UnificationXref.class)); - //'pubchem' is a ambigous synonym (correct ones are: pubchem-substance, pubchem-compound, etc.) - assertEquals(Normalizer.uri("", "pubchem", "bar", UnificationXref.class), Normalizer.uri("", "PubChem", "bar", UnificationXref.class)); - assertEquals(Normalizer.uri("", null, "bar", UnificationXref.class), Normalizer.uri(null, null, "bar", UnificationXref.class)); - assertFalse(Normalizer.uri(null, "foo", "bar", UnificationXref.class).equals(Normalizer.uri(null, "foo", "BAR", UnificationXref.class))); - assertFalse(Normalizer.uri(null, "foo", "bar", UnificationXref.class).equals(Normalizer.uri(null, "foo", "bar", PublicationXref.class))); - - // using standard db names (MIRIAM) - assertEquals(Normalizer.uri("test/", "pubmed", "12345", PublicationXref.class), Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class)); - assertEquals("pubmed:12345", Normalizer.uri("test/", "PubMED", "12345", PublicationXref.class)); - assertFalse("pubmed:12345".equals(Normalizer.uri(null, "PubMED", "12345", RelationshipXref.class))); //not PublicationXref - - assertEquals("bioregistry.io/chebi:12345",Normalizer.uri("", "chebi", "CHEBI:12345", SmallMoleculeReference.class)); - assertEquals("bioregistry.io/pubchem.substance:12345",Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class)); - - System.setProperty("biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_SIMPLE); - assertEquals("SMV_mod_MOD_12345",Normalizer.uri("", "mod", "MOD:12345", SequenceModificationVocabulary.class)); - assertEquals("V_mod_MOD_12345",Normalizer.uri("", "MOD", "MOD:12345", ControlledVocabulary.class)); - System.setProperty("biopax.normalizer.uri.strategy", Normalizer.VALUE_NORMALIZER_URI_STRATEGY_MD5); - //wrong id (case-sens.) - assertFalse("bioregistry.io/chebi:12345".equals(Normalizer.uri("", "chebi", "chebi:12345", SmallMoleculeReference.class))); - - //no 'pubchem' namespace - assertFalse("bioregistry.io/pubchem:12345".equals(Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class))); - //dbName:"pubchem-substance" is mapped to the namespace prefix "pubchem.substance" - assertEquals("bioregistry.io/pubchem.substance:12345", Normalizer.uri("", "pubchem-substance", "12345", SmallMoleculeReference.class)); - - //when special symbols or spaces in the 'id' part - assertEquals("UX_foo_bar", Normalizer.uri(null, null, "foo bar", UnificationXref.class)); - - assertEquals("bioregistry.io/ncbitaxon:9606", Normalizer.uri(null, "taxonomy", "9606", BioSource.class)); - assertEquals("bioregistry.io/ncbitaxon:9606", Normalizer.uri(null, "NCBI Taxonomy", "9606", BioSource.class)); - assertEquals("bioregistry.io/ncbitaxon:9606", Normalizer.uri(null, "NEWT", "9606", BioSource.class)); - //when organism's id is not taxID (e.g., if the BioSource has tissue, cellType CVs...) - assertNotSame("bioregistry.io/ncbitaxon:9606",Normalizer.uri(null, "taxonomy", "9606_blah_blah", BioSource.class)); - - String uri = Normalizer.uri("", "UniProt", "W0C7J9", UnificationXref.class); - assertEquals("uniprot:W0C7J9", uri); + @ParameterizedTest + @MethodSource + void uri(String expected, String xmlBase, String db, String id, Class type) { + assertEquals(expected, Normalizer.uri(xmlBase, db, id, type)); + } + + // args source for the above parameterized tests + private static Stream uri() { + return Stream.of( + arguments("SMV_mod_MOD_12345", "", "mod", "MOD:12345", SequenceModificationVocabulary.class), + arguments("V_mod_MOD_12345", "", "MOD", "MOD:12345", ControlledVocabulary.class), + arguments("test/UX_foo_bar", "test/", "FOo", "bar", UnificationXref.class),//non-standard db + arguments("test/UX_foo_bar", "test/", "foo", "bar", UnificationXref.class), + //'pubchem' is ambiguous (correct: pubchem-substance, pubchem-compound) + arguments("UX_pubchem_bar", "", "pubchem", "bar", UnificationXref.class), + arguments("UX_pubchem_bar", "", "PubChem", "bar", UnificationXref.class), + arguments("UX_bar", "", null, "bar", UnificationXref.class),//null db + arguments("UX_bar", null, null, "bar", UnificationXref.class), + //different ID (case) or type makes different URI + arguments("UX_foo_BAR", null, "foo", "BAR", UnificationXref.class), + arguments("UX_foo_bar", null, "foo", "bar", UnificationXref.class), + arguments("PX_foo_bar", null, "foo", "bar", PublicationXref.class), + arguments("PX_foo_BAR", null, "foo", "BAR", PublicationXref.class), + arguments("pubmed:12345", "test/", "PubMED", "12345", PublicationXref.class), + arguments("pubmed:12345", "", "pubmed", "12345", PublicationXref.class), + arguments("pubmed:12345", "test/", "MEDLINE", "12345", PublicationXref.class), + arguments("RX_pubmed_12345", null, "PubMED", "12345", RelationshipXref.class), //not PublicationXref + arguments("bioregistry.io/chebi:12345", "", "chebi", "CHEBI:12345", SmallMoleculeReference.class), + arguments("bioregistry.io/pubchem.substance:12345", "", "pubchem-substance", "12345", SmallMoleculeReference.class), + //invalid chebi id (its "banana", if present, is case-sensitive; i.e., CHEBI:12345 or 12345 would match the pattern) + arguments("SMR_bd1c4fd7641bf774e58bda352272c720", "", "chebi", "chebi:12345", SmallMoleculeReference.class), + arguments("bioregistry.io/chebi:12345", "test/", "chebi", "12345", SmallMoleculeReference.class), + arguments("bioregistry.io/chebi:12345", "test/", "chebi", "CHEBI:12345", SmallMoleculeReference.class), + arguments("bioregistry.io/pubchem.compound:12345", "", "pubchem", "12345", SmallMoleculeReference.class), + arguments("bioregistry.io/pubchem.substance:12345", "", "pubchem-substance", "12345", SmallMoleculeReference.class), + //special symbols or spaces in the 'id' part get replaced with underscore in the URI + arguments("UX_Foo_Bar", null, null, "Foo Bar", UnificationXref.class), + arguments("UX_Foo_Bar", null, null, "Foo&Bar", UnificationXref.class), //todo: no good - makes the same URI, can mess things up... + arguments("uniprot:W0C7J9", "", "UniProt", "W0C7J9", UnificationXref.class), + arguments("bioregistry.io/ncbitaxon:9606", null, "taxonomy", "9606", BioSource.class), + arguments("bioregistry.io/ncbitaxon:9606", null, "NCBI Taxonomy", "9606", BioSource.class), + arguments("bioregistry.io/ncbitaxon:9606", null, "NEWT", "9606", BioSource.class), + //when organism's id is not taxID (e.g., if the BioSource has tissue, cellType CVs...) + arguments("BIO_taxonomy_9606_blah_blah", null, "taxonomy", "9606_blah_blah", BioSource.class) + ); } - - + + @Test - public final void testNormalize() { + void normalize() { // Note: a UniProt AC version (e.g. P68250.1 .. P68250.94) is not the same thing as isoform ID! Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); Xref ref = model.addNew(UnificationXref.class, "Xref1"); @@ -197,7 +208,7 @@ public final void testNormalize() { ux.setDb("uniprot"); //will be changed to 'uniprot isoform' ux.setId("P68250-3"); - // go normalize! + // go normalize! Normalizer normalizer = new Normalizer(); normalizer.normalize(model); @@ -244,9 +255,9 @@ public final void testNormalize() { assertEquals(1, ((Xref)bpe).getXrefOf().size()); } - + @Test - public final void testAutoName() { + void autoName() { Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); Provenance pro = model.addNew(Provenance.class, "bioregistry.io/pid.pathway/"); pro.setStandardName("foo"); @@ -255,10 +266,10 @@ public final void testAutoName() { assertTrue(pro.getName().contains("pid.pathway")); assertFalse(pro.getStandardName().equals("foo")); } - - + + @Test - public final void testNormalize2() { + void normalize2() { Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); Xref ref = model.addNew(UnificationXref.class, "Xref1"); ref.setDb("uniprot"); @@ -288,9 +299,9 @@ public final void testNormalize2() { assertNotNull(e); assertEquals(4, e.getXref().size()); } - + @Test - public final void testNormalize3() { + void normalize3() { Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); Xref ref = model.addNew(UnificationXref.class, "Xref1"); ref.setDb("uniprot"); // will be converted to 'uniprot' @@ -319,44 +330,48 @@ public final void testNormalize3() { assertNotNull(ref); assertEquals(1, ref.getXrefOf().size()); } - - + + @Test - public final void testNormalizeInoh() { - //There are two Proteins that have entityReference rdf:ID="IMR_0100366_G_alpha_s_Canonical", - //and that PR has two uniprot unification xrefs: P63092 (human) and P63095 (rat). + void normalizeInoh() { + //There are two Proteins that have entityReference (PR) rdf:ID="IMR_0100366_G_alpha_s_Canonical", + //which has two uniprot unification xrefs: P63092 (human) and P63095 (rat). //Therefore, the URI of this PR should NOT be normalized. //Also, there was a bug when replacing the PR's URI (warning: IllegalBioPAXArgumentException: Incompatible type!..) - //as the invalid PublicationXref UniProt:P63092 was getting the same normalized URI... - //To avoid all such issues (despite illegal pub. xrefs), the Normalizer won't make - //canonical URI for a PublicationXref anymore, unless xref.db is pubmed. + //as the invalid PublicationXref UniProt:P63092 was getting the same normalized URI as some PR. + //To avoid all such issues (regardless invalid pub. xrefs), the Normalizer won't make + //canonical URI for a PublicationXref anymore unless the xref.db is "pubmed" (or synonym). Model model = simpleIO.convertFromOWL(getClass().getResourceAsStream("/test-inoh.owl")); Normalizer normalizer = new Normalizer(); normalizer.setXmlBase(""); normalizer.normalize(model); - //A weird PublicationXref that uses a UniProt ID won't be normalized: - assertFalse(model.containsID("http://identifiers.org/uniprot/P63092")); - assertFalse(model.containsID("identifiers.org/uniprot/P63092")); - assertFalse(model.containsID("bioregistry.io/uniprot:P63092")); - //A PR with two UniProt IDs/unif.xrefs - human, rat - won't be normalized! - assertTrue(model.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical") instanceof ProteinReference); + + //All PublicationXref URIs either start with "pubmed:" or "PX_" prefix: + model.getObjects(PublicationXref.class).stream().forEach(px -> assertTrue(StringUtils.startsWithAny(px.getUri(),"pubmed:","PX_"))); + + BioPAXElement e = model.getByID("uniprot:P63092"); + assertTrue(e instanceof UnificationXref); + + //A PR with two different UniProt unif. xrefs - human, rat - won't be normalized! + e = model.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical"); + assertTrue(e instanceof ProteinReference); } - + private void print(XReferrable xr, Model m) { System.out.println(); - System.out.println("model=" + m.contains(xr) + ":\t" - + xr.getUri() + - " is " + xr.getModelInterface().getSimpleName() - + " and has xrefs: "); + System.out.println("model=" + m.contains(xr) + ":\t" + + xr.getUri() + + " is " + xr.getModelInterface().getSimpleName() + + " and has xrefs: "); for(Xref x : xr.getXref()) { - System.out.println("model=" + m.contains(x) + ":\t" - +" " + x + " is " - + x.getModelInterface().getSimpleName() - + " - " + x.getUri() + ", db=" + x.getDb() - + ", id=" + x.getId() + ", idVer=" + x.getIdVersion()); + System.out.println("model=" + m.contains(x) + ":\t" + +" " + x + " is " + + x.getModelInterface().getSimpleName() + + " - " + x.getUri() + ", db=" + x.getDb() + + ", id=" + x.getId() + ", idVer=" + x.getIdVersion()); for(XReferrable rx : x.getXrefOf()) { - System.out.println("model=" + m.contains(rx) + ":\t" - + " xrefOf: " + rx); + System.out.println("model=" + m.contains(rx) + ":\t" + + " xrefOf: " + rx); } } } diff --git a/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java b/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java index 4a77694ff..1c1d733f8 100644 --- a/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java +++ b/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java @@ -1,50 +1,57 @@ package org.biopax.paxtools.normalizer; -import static org.junit.Assert.*; - -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; public class ResolverTest { static final String MI = "Molecular Interactions Controlled Vocabulary"; //name corresponds to "mi" record in bioregistry.io @Test public final void getNamespace() { - assertNotNull(Resolver.getNamespace("obo.mi"));//auto-detected as "mi" - assertEquals(MI, Resolver.getNamespace("urn:miriam:mi").getName()); - assertNotNull(Resolver.getNamespace("psi-mi"));//becomes "mi" - assertNotNull(Resolver.getNamespace("MolecularInteractions Ontology", true));//misspelling variant (allowed by default) - assertNull(Resolver.getNamespace("MolecularInteractions Ontology", false));//null when spelling variants not allowed - assertNotNull(Resolver.getNamespace("http://bioregistry.io/chebi")); - assertNotNull(Resolver.getNamespace("bioregistry.io/uniprot")); - assertNotNull(Resolver.getNamespace("https://identifiers.org/psi-mi")); //matches "mi" registry prefix/namespace + Assertions.assertAll( + () -> Assertions.assertNotNull(Resolver.getNamespace("obo.mi")),//auto-detected as "mi" + () -> Assertions.assertEquals(MI, Resolver.getNamespace("urn:miriam:mi").getName()), + () -> Assertions.assertNotNull(Resolver.getNamespace("psi-mi")),//becomes "mi" + () -> Assertions.assertNotNull(Resolver.getNamespace("MolecularInteractions Ontology", true)),//misspelling variant (allowed by default) + () -> Assertions.assertNull(Resolver.getNamespace("MolecularInteractions Ontology", false)),//null when spelling variants not allowed + () -> Assertions.assertNotNull(Resolver.getNamespace("http://bioregistry.io/chebi")), + () -> Assertions.assertNotNull(Resolver.getNamespace("bioregistry.io/uniprot")), + () -> Assertions.assertNotNull(Resolver.getNamespace("https://identifiers.org/psi-mi")) //matches "mi" registry prefix/namespace + ); } @Test public final void getPattern() { - assertEquals("^\\d{4}$", Resolver.getNamespace(MI).getPattern()); + Assertions.assertEquals("^\\d{4}$", Resolver.getNamespace(MI).getPattern()); } @Test public final void checkRegExp() { - assertTrue(Resolver.checkRegExp("MI:0000", MI)); //auto-ignores "MI:" - assertTrue(Resolver.checkRegExp("0000", MI)); + Assertions.assertAll( + () -> Assertions.assertTrue(Resolver.checkRegExp("MI:0000", MI)), //auto-ignores "MI:" + () -> Assertions.assertTrue(Resolver.checkRegExp("0000", MI)) + ); } - + @Test public final void getURI() { - //standard prefix and id with "banana" prefix - assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("chebi", "CHEBI:36927")); - //old ns prefix (should auto-fix as "chebi") and id without "CHEBI:" banana... - assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("identifiers.org/chebi/", "36927")); - //similar, but using bioregistry.io/ base, with ending slash, and with banana... - assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("bioregistry.io/chebi", "CHEBI:36927")); + Assertions.assertAll( + //standard prefix and id with "banana" prefix + () -> Assertions.assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("chebi", "CHEBI:36927")), + //old ns prefix (should auto-fix as "chebi") and id without "CHEBI:" banana... + () -> Assertions.assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("identifiers.org/chebi/", "36927")), + //similar, but using bioregistry.io/ base, with ending slash, and with banana... + () -> Assertions.assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("bioregistry.io/chebi", "CHEBI:36927")) + ); } @Test public final void getCURIE() { - assertEquals("uniprot:P12345", Resolver.getCURIE("uniprot", "P12345")); - assertEquals("go:0045202", Resolver.getCURIE("go", "GO:0045202")); + Assertions.assertAll( + () -> Assertions.assertEquals("uniprot:P12345", Resolver.getCURIE("uniprot", "P12345")), + () -> Assertions.assertEquals("go:0045202", Resolver.getCURIE("go", "GO:0045202")) + ); } } diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java b/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java index 4ff1023c1..fb7c6a03c 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/DBParsers.java @@ -4,8 +4,8 @@ import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.pattern.util.HGNC; -import org.junit.Ignore; -import org.junit.Test; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; import org.w3c.dom.Document; import org.w3c.dom.NodeList; import org.xml.sax.SAXException; @@ -22,7 +22,7 @@ public class DBParsers { @Test - @Ignore + @Disabled public void extractSignalink() throws IOException { BufferedReader reader = new BufferedReader(new FileReader( @@ -121,7 +121,7 @@ private void printOrdered(final Map map, int min) } @Test - @Ignore + @Disabled public void extractSignalink2() throws IOException { BufferedReader reader = new BufferedReader(new FileReader( @@ -166,7 +166,7 @@ public void extractSignalink2() throws IOException } @Test - @Ignore + @Disabled public void printVenn() throws IOException { Set s1 = read("/home/ozgun/Projects/biopax-pattern/directed-relations.txt", true); @@ -260,7 +260,7 @@ private int reflectiveCnt(Set set) } @Test - @Ignore + @Disabled public void printNeighborsInSpike() throws IOException { String s = "DUSP1"; @@ -414,7 +414,7 @@ public Map getEG2HGNC() throws IOException } @Test - @Ignore + @Disabled public void printLines() throws IOException { BufferedReader reader = new BufferedReader(new FileReader( @@ -435,7 +435,7 @@ public void printLines() throws IOException } @Test - @Ignore + @Disabled public void printLinesContaining() throws IOException { String query = "1509498"; @@ -454,7 +454,7 @@ public void printLinesContaining() throws IOException } @Test - @Ignore + @Disabled public void searchFirstOcc() throws IOException { BufferedReader reader = new BufferedReader(new FileReader( @@ -474,7 +474,7 @@ public void searchFirstOcc() throws IOException } @Test - @Ignore + @Disabled public void readXML() throws ParserConfigurationException, IOException, SAXException { File f = new File("/home/ozgun/Desktop/signal-db/LatestSpikeDB.xml"); diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/PatternBoxTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/PatternBoxTest.java index 2eaa58e8c..933393ac5 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/PatternBoxTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/PatternBoxTest.java @@ -6,13 +6,15 @@ import org.biopax.paxtools.model.level3.Named; import org.biopax.paxtools.pattern.constraint.NonUbique; import org.biopax.paxtools.pattern.util.Blacklist; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Ignore; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; import java.io.FileInputStream; -import java.util.*; +import java.util.Collection; +import java.util.List; +import java.util.Map; /** * @author Ozgun Babur @@ -23,9 +25,8 @@ public class PatternBoxTest protected Model model_urea; protected Model model_tca; - @Before - public void setUp() throws Exception - { + @BeforeEach + public void init() { SimpleIOHandler h = new SimpleIOHandler(); model_P53 = h.convertFromOWL(PatternBoxTest.class.getResourceAsStream("AR-TP53.owl")); model_urea = h.convertFromOWL(PatternBoxTest.class.getResourceAsStream("UreaCycle.owl")); @@ -33,12 +34,12 @@ public void setUp() throws Exception } @Test - public void testInSameComplex() throws Exception + public void inSameComplex() throws Exception { List list = Searcher.search(model_P53.getByID("http://pid.nci.nih.gov/biopaxpid_33442"), PatternBox.inSameComplex()); - Assert.assertTrue(list.size() == 1); + Assertions.assertTrue(list.size() == 1); // Map> map = Searcher.search(model_P53, PatternBox.inSameComplex()); // @@ -49,23 +50,23 @@ public void testInSameComplex() throws Exception } @Test - public void testControlsStateChange() throws Exception + public void controlsStateChange() throws Exception { Map> map = Searcher.search( model_P53, PatternBox.controlsStateChange()); - Assert.assertTrue(map.size() > 0); + Assertions.assertTrue(map.size() > 0); } @Test - public void testConsecutiveCatalysis() throws Exception + public void consecutiveCatalysis() throws Exception { Pattern p = PatternBox.catalysisPrecedes(null); List list = Searcher.searchPlain(model_urea, p); int size = list.size(); - Assert.assertTrue(size > 0); + Assertions.assertTrue(size > 0); // printMatches(list, 0, 5, 10); @@ -76,21 +77,21 @@ public void testConsecutiveCatalysis() throws Exception list = Searcher.searchPlain(model_urea, p); - Assert.assertTrue(!list.isEmpty() && list.size() < size); + Assertions.assertTrue(!list.isEmpty() && list.size() < size); b = new Blacklist(PatternBoxTest.class.getResourceAsStream("blacklist.txt")); p = PatternBox.catalysisPrecedes(b); list = Searcher.searchPlain(model_tca, p); - Assert.assertTrue(list.size() > 15); + Assertions.assertTrue(list.size() > 15); // printMatches(list, 0, 5, 10); } @Test - @Ignore - public void testConsecutiveCatalysis2() throws Exception + @Disabled + public void consecutiveCatalysis2() throws Exception { SimpleIOHandler h = new SimpleIOHandler(); model_P53 = h.convertFromOWL(new FileInputStream("/home/ozgun/Desktop/NMNAT1-QPRT.owl")); diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConBoxTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConBoxTest.java index 9e81ae8cd..7b2a0533a 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConBoxTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConBoxTest.java @@ -5,10 +5,9 @@ import org.biopax.paxtools.pattern.Pattern; import org.biopax.paxtools.pattern.Searcher; import org.biopax.paxtools.pattern.util.Blacklist; -import org.junit.Assert; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; -import java.util.Collections; import java.util.List; /** @@ -17,172 +16,172 @@ public class ConBoxTest extends TestParent { @Test - public void testErToPE() throws Exception + public void erToPE() throws Exception { List list = Searcher.search(model.getByID("urn:miriam:uniprot:P04637"), //TP53 new Pattern(EntityReference.class, ConBox.erToPE(), "ER", "PE")); - Assert.assertTrue(list.size() == 5); + Assertions.assertTrue(list.size() == 5); } @Test - public void testPeToER() throws Exception + public void peToER() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_17220"), //p53 new Pattern(PhysicalEntity.class, ConBox.peToER(), "PE", "ER")); - Assert.assertTrue(list.size() == 1); + Assertions.assertTrue(list.size() == 1); } @Test - public void testDownControl() throws Exception + public void downControl() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35449"), //T-DHT/AR complex new Pattern(PhysicalEntity.class, ConBox.peToControl(), "PE", "Control")); - Assert.assertTrue(list.size() == 1); + Assertions.assertTrue(list.size() == 1); } @Test - public void testControlled() throws Exception + public void controlled() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35543"), new Pattern(Control.class, ConBox.controlled(), "Control", "Inter")); - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_35537")); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_35537")); } @Test - public void testControlToConv() throws Exception + public void controlToConv() throws Exception { // todo Test for nested controls List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35543"), new Pattern(Control.class, ConBox.controlToConv(), "Control", "Conversion")); - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_35537")); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_35537")); } @Test - public void testControlsConv() throws Exception + public void controlsConv() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35449"), new Pattern(PhysicalEntity.class, ConBox.controlsConv(), "PE", "Conv")); - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_35537")); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_35537")); } @Test - public void testGenericEquiv() throws Exception + public void genericEquiv() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_637"), // GNAO1 new Pattern(PhysicalEntity.class, ConBox.genericEquiv(), "PE", "EQ")); - Assert.assertTrue(list.size() == 2); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_623"))); + Assertions.assertTrue(list.size() == 2); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_623"))); list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_623"), // Gi Family new Pattern(PhysicalEntity.class, ConBox.genericEquiv(), "PE", "EQ")); - Assert.assertTrue(list.size() == 7); + Assertions.assertTrue(list.size() == 7); } @Test - public void testComplexMembers() throws Exception + public void complexMembers() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), // Gi family/GNB1/GNG2/GDP new Pattern(Complex.class, ConBox.complexMembers(), "Complex", "member")); - Assert.assertTrue(list.size() == 4); + Assertions.assertTrue(list.size() == 4); } @Test - public void testSimpleMembers() throws Exception + public void simpleMembers() throws Exception { // todo Test for a nested complex List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), // Gi family/GNB1/GNG2/GDP new Pattern(Complex.class, ConBox.simpleMembers(), "Complex", "SPE")); - Assert.assertTrue(list.size() == 4); + Assertions.assertTrue(list.size() == 4); } @Test - public void testWithComplexMembers() throws Exception + public void withComplexMembers() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), // Gi family/GNB1/GNG2/GDP new Pattern(PhysicalEntity.class, ConBox.withComplexMembers(), "PE", "member")); - Assert.assertTrue(list.size() == 5); + Assertions.assertTrue(list.size() == 5); } @Test - public void testWithSimpleMembers() throws Exception + public void withSimpleMembers() throws Exception { // todo Test for a nested complex List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), // Gi family/GNB1/GNG2/GDP new Pattern(PhysicalEntity.class, ConBox.withSimpleMembers(), "PE", "SPE")); - Assert.assertTrue(list.size() == 5); + Assertions.assertTrue(list.size() == 5); } @Test - public void testComplexes() throws Exception + public void complexes() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_5511"), // GNB1 new Pattern(PhysicalEntity.class, ConBox.complexes(), "PE", "Complex")); - Assert.assertTrue(list.size() == 2); + Assertions.assertTrue(list.size() == 2); } @Test - public void testWithComplexes() throws Exception + public void withComplexes() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_5511"), // GNB1 new Pattern(PhysicalEntity.class, ConBox.withComplexes(), "PE", "Complex")); - Assert.assertTrue(list.size() == 3); + Assertions.assertTrue(list.size() == 3); } @Test - public void testLeft() throws Exception + public void left() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35537"), new Pattern(Conversion.class, ConBox.left(), "Conversion", "left")); - Assert.assertTrue(list.size() == 2); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_685"))); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"))); + Assertions.assertTrue(list.size() == 2); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_685"))); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"))); } @Test - public void testRight() throws Exception + public void right() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35537"), new Pattern(Conversion.class, ConBox.right(), "Conversion", "right")); - Assert.assertTrue(list.size() == 3); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_21741"))); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_31826"))); + Assertions.assertTrue(list.size() == 3); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_21741"))); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_31826"))); } @Test - public void testParticipatesInConv() throws Exception + public void participatesInConv() throws Exception { List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_31826"), // Gi family/GTP new Pattern(PhysicalEntity.class, ConBox.participatesInConv(), "PE", "Conversion")); - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_35537"))); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_35537"))); } @Test - public void testNameEquals() throws Exception + public void nameEquals() throws Exception { Pattern p = new Pattern(Complex.class, "Complex"); p.add(ConBox.complexMembers(), "Complex", "member"); @@ -191,12 +190,12 @@ public void testNameEquals() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), // Gi family/GNB1/GNG2/GDP p); - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); } @Test - public void testNotUbique() throws Exception + public void notUbique() throws Exception { Pattern p = new Pattern(Complex.class, "Complex"); p.add(ConBox.complexMembers(), "Complex", "member"); @@ -207,7 +206,7 @@ public void testNotUbique() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), // Gi family/GNB1/GNG2/GDP p); - Assert.assertTrue(list.size() == 3); - Assert.assertFalse(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); //GDP PE ID + Assertions.assertTrue(list.size() == 3); + Assertions.assertFalse(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); //GDP PE ID } } diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConstraintTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConstraintTest.java index d1841708a..d210970a0 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConstraintTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/ConstraintTest.java @@ -6,8 +6,8 @@ import org.biopax.paxtools.model.level3.SmallMolecule; import org.biopax.paxtools.pattern.*; import org.biopax.paxtools.pattern.util.RelType; -import org.junit.Assert; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; import java.util.List; @@ -17,7 +17,7 @@ public class ConstraintTest extends TestParent { @Test - public void testAND() throws Exception + public void constraintAND() { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(new AND( @@ -27,12 +27,12 @@ public void testAND() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), p); // Gi family/GNB1/GNG2/GDP - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_678")); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_678")); } @Test - public void testType() throws Exception + public void constraintType() { Pattern p = new Pattern(Complex.class, "Complex"); p.add(ConBox.complexMembers(), "Complex", "member"); @@ -40,8 +40,8 @@ public void testType() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), p); // Gi family/GNB1/GNG2/GDP - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_678")); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(list.get(0).get(1) == model.getByID("http://pid.nci.nih.gov/biopaxpid_678")); p = new Pattern(Complex.class, "Complex"); p.add(ConBox.complexMembers(), "Complex", "member"); @@ -49,12 +49,12 @@ public void testType() throws Exception list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), p); // Gi family/GNB1/GNG2/GDP - Assert.assertTrue(list.size() == 4); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); + Assertions.assertTrue(list.size() == 4); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); } @Test - public void testEquality() throws Exception + public void constraintEquality() { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(ConBox.genericEquiv(), "PE", "eq1"); @@ -66,13 +66,13 @@ public void testEquality() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_623"), p); // Gi family - Assert.assertFalse(list.isEmpty()); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_637"))); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_638"))); + Assertions.assertFalse(list.isEmpty()); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_637"))); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_638"))); } @Test - public void testNOT() throws Exception + public void constraintNOT() { Pattern p = new Pattern(Complex.class, "Comp"); p.add(ConBox.complexMembers(), "Comp", "member"); @@ -80,12 +80,12 @@ public void testNOT() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_35409"), p); // Gi family/GNB1/GNG2/GDP - Assert.assertTrue(list.size() == 3); - Assert.assertFalse(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); + Assertions.assertTrue(list.size() == 3); + Assertions.assertFalse(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_678"))); } @Test - public void testMultiPath() throws Exception + public void constraintMultiPath() { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(new MultiPathConstraint("PhysicalEntity/controllerOf/controlled", @@ -93,13 +93,13 @@ public void testMultiPath() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_21741"), p); // GNB1/GNG2 - Assert.assertTrue(list.size() == 2); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_35537"))); + Assertions.assertTrue(list.size() == 2); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_35537"))); } @Test - public void testConversionSide() throws Exception + public void constraintConversionSide() { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(ConBox.participatesInConv(), "PE", "Conv"); @@ -107,56 +107,55 @@ public void testConversionSide() throws Exception List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_21151"), p); // p38alpha-beta - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); - Assert.assertTrue(collect(list, 2).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_17089"))); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); + Assertions.assertTrue(collect(list, 2).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_17089"))); } @Test - public void testParticipatesInConv() throws Exception + public void constraintParticipatesInConv() { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(new ParticipatesInConv(RelType.INPUT), "PE", "Conv"); List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_21151"), p); // p38alpha-beta - Assert.assertTrue(list.size() == 1); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); + Assertions.assertTrue(list.size() == 1); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); p = new Pattern(PhysicalEntity.class, "PE"); p.add(new ParticipatesInConv(RelType.OUTPUT), "PE", "Conv"); list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_21151"), p); // p38alpha-beta - Assert.assertTrue(list.isEmpty()); + Assertions.assertTrue(list.isEmpty()); } @Test - public void testSelfOrThis() throws Exception + public void constraintSelfOrThis() { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(new SelfOrThis(new ParticipatesInConv(RelType.INPUT)), "PE", "Conv"); List list = Searcher.search(model.getByID("http://pid.nci.nih.gov/biopaxpid_21151"), p); // p38alpha-beta - Assert.assertTrue(list.size() == 2); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); - Assert.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_21151"))); + Assertions.assertTrue(list.size() == 2); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_50156"))); + Assertions.assertTrue(collect(list, 1).contains(model.getByID("http://pid.nci.nih.gov/biopaxpid_21151"))); } @Test - public void testExceptions() throws Exception - { + public void exceptions() { try { Pattern p = new Pattern(PhysicalEntity.class, "PE"); p.add(new ConversionSide(ConversionSide.Type.OTHER_SIDE), "PE", "Conv", "PE2"); - Assert.assertFalse("Should have reached here", false); + Assertions.assertFalse(false, "Should have reached here"); } catch (Exception e) { - Assert.assertTrue(true); + Assertions.assertTrue(true); } } } diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java index e21905bc2..81023223c 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/constraint/TestParent.java @@ -4,8 +4,8 @@ import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.pattern.Match; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; import java.util.HashSet; import java.util.List; @@ -18,7 +18,7 @@ public class TestParent { Model model; - @Before + @BeforeEach public void setUp() throws Exception { SimpleIOHandler h = new SimpleIOHandler(); diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/MinerTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/MinerTest.java index d58befba1..5bcead4f4 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/MinerTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/MinerTest.java @@ -6,7 +6,7 @@ import org.biopax.paxtools.pattern.Pattern; import org.biopax.paxtools.pattern.constraint.ConBox; import org.biopax.paxtools.pattern.constraint.Type; -import org.junit.Ignore; +import org.junit.jupiter.api.Disabled; import java.io.*; import java.util.*; @@ -19,7 +19,7 @@ * * @author Ozgun Babur */ -@Ignore +@Disabled public class MinerTest { public static void main(String[] args) diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java index 691bdaf86..f4d57fcbf 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/miner/SIFSearcherTest.java @@ -9,15 +9,13 @@ import org.biopax.paxtools.pattern.constraint.IDConstraint; import org.biopax.paxtools.pattern.util.AdjacencyMatrix; import org.biopax.paxtools.pattern.util.Blacklist; -import org.junit.Assert; -import org.junit.Ignore; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; import java.io.*; import java.util.*; -import static org.junit.Assert.*; - /** * TODO replace the ignored "tests" (hard-coded local input paths) with normal test resources and assertions. * @@ -26,7 +24,7 @@ public class SIFSearcherTest extends PatternBoxTest { @Test - public void testGetPathways() + public void getPathways() { SIFSearcher searcher = new SIFSearcher(SIFEnum.values()); Set inters = searcher.searchSIF(model_urea); @@ -36,7 +34,7 @@ public void testGetPathways() pathways.addAll(inter.getPathways()); } - Assert.assertFalse(pathways.isEmpty()); + Assertions.assertFalse(pathways.isEmpty()); Set dataSources = new HashSet<>(); for (SIFInteraction inter : inters) @@ -44,11 +42,11 @@ public void testGetPathways() dataSources.addAll(inter.getDataSources()); } - Assert.assertFalse(dataSources.isEmpty()); + Assertions.assertFalse(dataSources.isEmpty()); } @Test - public void testGetDataSources() + public void getDataSources() { SIFSearcher searcher = new SIFSearcher(SIFEnum.values()); Set inters = searcher.searchSIF(model_urea); @@ -58,26 +56,26 @@ public void testGetDataSources() dataSources.addAll(inter.getDataSources()); } - Assert.assertFalse(dataSources.isEmpty()); + Assertions.assertFalse(dataSources.isEmpty()); } @Test - public void testAdjacencyMatrix() + public void adjacencyMatrix() { SIFSearcher searcher = new SIFSearcher(SIFEnum.CONTROLS_STATE_CHANGE_OF, SIFEnum.CHEMICAL_AFFECTS); AdjacencyMatrix matrix = searcher.searchSIFGetMatrix(model_P53); System.out.println(matrix); - Assert.assertTrue(matrix.names.length > 0); + Assertions.assertTrue(matrix.names.length > 0); } @Test - @Ignore - public void testSIFMiner() + @Disabled + public void withSIFMiner() { SIFSearcher s = new SIFSearcher(SIFEnum.CONTROLS_STATE_CHANGE_OF, SIFEnum.IN_COMPLEX_WITH); Set sif = s.searchSIF(model_P53); - Assert.assertFalse(sif.isEmpty()); + Assertions.assertFalse(sif.isEmpty()); Set pubmedIDs = new HashSet<>(); for (SIFInteraction si : sif) @@ -85,16 +83,16 @@ public void testSIFMiner() pubmedIDs.addAll(si.getPublicationIDs(true)); } - Assert.assertFalse(pubmedIDs.isEmpty()); + Assertions.assertFalse(pubmedIDs.isEmpty()); s = new SIFSearcher(SIFEnum.CATALYSIS_PRECEDES); sif = s.searchSIF(model_P53); - Assert.assertTrue(sif.isEmpty()); + Assertions.assertTrue(sif.isEmpty()); } @Test - @Ignore - public void testOldFormatWriter() throws FileNotFoundException + @Disabled + public void oldFormatWriter() throws FileNotFoundException { SIFSearcher s = new SIFSearcher(SIFEnum.CONTROLS_STATE_CHANGE_OF, SIFEnum.IN_COMPLEX_WITH); SimpleIOHandler handler = new SimpleIOHandler(); @@ -105,7 +103,7 @@ public void testOldFormatWriter() throws FileNotFoundException } @Test - @Ignore + @Disabled public void generateLargeSIFGraph() throws IOException { // String dir = "/home/ozgun/Projects/biopax-pattern/"; @@ -139,11 +137,11 @@ public void generateLargeSIFGraph() throws IOException long time = System.currentTimeMillis() - start; System.out.println("Completed in: " + getPrintable(time)); - Assert.assertTrue(2 + 2 == 4); + Assertions.assertTrue(2 + 2 == 4); } @Test - @Ignore + @Disabled public void generateSomeSIFGraph() throws IOException { long start = System.currentTimeMillis(); @@ -178,11 +176,11 @@ public Pattern constructPattern() long time = System.currentTimeMillis() - start; System.out.println("Completed in: " + getPrintable(time)); - Assert.assertTrue(2 + 2 == 4); + Assertions.assertTrue(2 + 2 == 4); } @Test - @Ignore + @Disabled public void countRelations() throws FileNotFoundException { String file = "/home/ozgun/Downloads/PC-resources/Pathway Commons.7.Comparative Toxicogenomics Database.BIOPAX.sif"; @@ -202,7 +200,7 @@ public void countRelations() throws FileNotFoundException { System.out.println(count.get(type.getTag()) + "\t" + type); } - Assert.assertTrue(2 + 2 == 4); + Assertions.assertTrue(2 + 2 == 4); } private static String getPrintable(long time) @@ -239,7 +237,7 @@ private void confirmPresenceOfUbiques(Model model, Blacklist blacklist) } @Test - public void testSIFSearcher() throws IOException + public void sifSearcher() throws IOException { // Test CommonIdFetcher vs. ConfigurableIDFetcher SIF seatch output results. final SIFType[] sifTypes = new SIFType[]{SIFEnum.IN_COMPLEX_WITH}; @@ -265,9 +263,9 @@ public void testSIFSearcher() throws IOException // Test searcher.searchSIF(model) - check no. interactions, not empty, etc... Set sifInteractions = customSifSearcher.searchSIF(model); - assertTrue(sifInteractions.isEmpty()); //no xrefs, no entity references + Assertions.assertTrue(sifInteractions.isEmpty()); //no xrefs, no entity references sifInteractions = commonSifSearcher.searchSIF(model); - assertTrue(sifInteractions.isEmpty()); //no xrefs, no entity references + Assertions.assertTrue(sifInteractions.isEmpty()); //no xrefs, no entity references //adding xrefs to PEs only does not help inferring the SIF interaction Xref prx = model.addNew(RelationshipXref.class,"prx"); @@ -280,9 +278,9 @@ public void testSIFSearcher() throws IOException //note: if xref.id were unknown/misspelled, tests would pass anyway (ER's name will be used instead) ;) pp.addXref(pprx); sifInteractions = commonSifSearcher.searchSIF(model); - assertTrue(sifInteractions.isEmpty()); //still no result (due to - no ERs?) + Assertions.assertTrue(sifInteractions.isEmpty()); //still no result (due to - no ERs?) sifInteractions = customSifSearcher.searchSIF(model); - assertTrue(sifInteractions.isEmpty()); + Assertions.assertTrue(sifInteractions.isEmpty()); //let's add entity references without any xrefs yet - ProteinReference ppr = model.addNew(ProteinReference.class,"pik3_ref"); @@ -292,26 +290,26 @@ public void testSIFSearcher() throws IOException pr.setDisplayName("RAS family"); p.setEntityReference(pr); - assertEquals(7, model.getObjects().size()); + Assertions.assertEquals(7, model.getObjects().size()); sifInteractions = customSifSearcher.searchSIF(model); - assertFalse(sifInteractions.isEmpty()); - assertEquals(1, sifInteractions.size()); + Assertions.assertFalse(sifInteractions.isEmpty()); + Assertions.assertEquals(1, sifInteractions.size()); ByteArrayOutputStream bos = new ByteArrayOutputStream(); customSifSearcher.searchSIF(model, bos); System.out.println(bos.toString());//prints (using names): "PIK3 family in-complex-with RAS family" //commonSifSearcher now also gets the same result after having recently being modified to use names when no xrefs found sifInteractions = commonSifSearcher.searchSIF(model); - assertFalse(sifInteractions.isEmpty()); //OK - assertEquals(1, sifInteractions.size()); + Assertions.assertFalse(sifInteractions.isEmpty()); //OK + Assertions.assertEquals(1, sifInteractions.size()); bos = new ByteArrayOutputStream(); commonSifSearcher.searchSIF(model, bos); System.out.println(bos.toString()); //using SimpleIDFetcher gets the result sifInteractions = simpleSifSearcher.searchSIF(model); - assertFalse(sifInteractions.isEmpty()); //OK - assertEquals(1, sifInteractions.size()); + Assertions.assertFalse(sifInteractions.isEmpty()); //OK + Assertions.assertEquals(1, sifInteractions.size()); bos = new ByteArrayOutputStream(); simpleSifSearcher.searchSIF(model, bos); System.out.println(bos.toString()); @@ -324,15 +322,15 @@ public void testSIFSearcher() throws IOException // System.out.println(bos.toString()); sifInteractions = customSifSearcher.searchSIF(model); - assertFalse(sifInteractions.isEmpty()); - assertEquals(1, sifInteractions.size()); //OK + Assertions.assertFalse(sifInteractions.isEmpty()); + Assertions.assertEquals(1, sifInteractions.size()); //OK bos = new ByteArrayOutputStream(); customSifSearcher.searchSIF(model, bos); System.out.println(bos.toString()); sifInteractions = commonSifSearcher.searchSIF(model); - assertFalse(sifInteractions.isEmpty()); - assertEquals(1, sifInteractions.size()); //OK + Assertions.assertFalse(sifInteractions.isEmpty()); + Assertions.assertEquals(1, sifInteractions.size()); //OK bos = new ByteArrayOutputStream(); commonSifSearcher.searchSIF(model, bos); System.out.println(bos.toString()); diff --git a/paxtools-archetype/README.md b/paxtools-archetype/README.md deleted file mode 100644 index a12e8d741..000000000 --- a/paxtools-archetype/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# Paxtools archetype # - -## Use ## - - mvn archetype:generate -DarchetypeRepository=https://oss.sonatype.org/content/groups/public/ -DarchetypeGroupId=org.biopax.paxtools -DarchetypeArtifactId=paxtools-archetype -DarchetypeVersion=6.0.0-SNAPSHOT -DgroupId=YOUR_GROUPID -DartifactId=YOUR_ARTIFACTID -Dversion=0.1-SNAPSHOT - -http://www.biopax.org/paxtools - diff --git a/paxtools-archetype/pom.xml b/paxtools-archetype/pom.xml deleted file mode 100644 index 100b947f0..000000000 --- a/paxtools-archetype/pom.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - 4.0.0 - - - paxtools - org.biopax.paxtools - 6.0.0-SNAPSHOT - - - paxtools-archetype - maven-archetype - Paxtools Maven Archetype - - Paxtools Maven archetype - sample Java project to quickly start using Paxtools library and BioPAX data. - - - https://biopax.github.io/Paxtools - - https://github.com/BioPAX/Paxtools - HEAD - - - - - - org.apache.maven.archetype - archetype-packaging - 2.3 - - - - - - maven-archetype-plugin - 2.3 - - - - - - diff --git a/paxtools-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml b/paxtools-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml deleted file mode 100755 index dab7fc3f1..000000000 --- a/paxtools-archetype/src/main/resources/META-INF/maven/archetype-metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - - - src/main/java - - **/*.java - - - - src/main/resources - - **/*.owl - - - - diff --git a/paxtools-archetype/src/main/resources/archetype-resources/pom.xml b/paxtools-archetype/src/main/resources/archetype-resources/pom.xml deleted file mode 100755 index 692391513..000000000 --- a/paxtools-archetype/src/main/resources/archetype-resources/pom.xml +++ /dev/null @@ -1,101 +0,0 @@ - - - 4.0.0 - - ${groupId} - ${artifactId} - jar - ${version} - - - - org.apache.maven.plugins - maven-compiler-plugin - 3.8.1 - - 11 - - - - org.apache.maven.plugins - maven-jar-plugin - 3.1.0 - - - - jar - - - - - - org.apache.maven.plugins - maven-shade-plugin - 3.2.0 - - - - com.example.Example - - - example-exec - true - - - - - package - - shade - - - - - - - - - - ossrh - OSSRH Repository - https://oss.sonatype.org/content/groups/public/ - - > - - - - org.biopax.paxtools - paxtools-core - ${version} - - - org.biopax.paxtools - pattern - ${version} - - - org.biopax.paxtools - paxtools-query - ${version} - - - log4j - log4j - 1.2.12 - runtime - true - - - commons-cli - commons-cli - 1.3 - - - junit - junit - 4.13.2 - test - - - diff --git a/paxtools-archetype/src/main/resources/archetype-resources/src/main/java/com/example/Example.java b/paxtools-archetype/src/main/resources/archetype-resources/src/main/java/com/example/Example.java deleted file mode 100755 index 2e8e16c2f..000000000 --- a/paxtools-archetype/src/main/resources/archetype-resources/src/main/java/com/example/Example.java +++ /dev/null @@ -1,84 +0,0 @@ -package com.example; - -import org.biopax.paxtools.io.SimpleIOHandler; -import org.biopax.paxtools.io.BioPAXIOHandler; -import org.biopax.paxtools.model.Model; -import org.biopax.paxtools.model.level3.*; -import org.biopax.paxtools.model.level3.Process; - -import java.io.*; -import java.util.*; - -/** - * - * Basic example that shows reading in BioPAX OWL files and simple iteration over content - * - * @author cannin - * - */ -public class Example { - public static void main(String args[]) throws IOException { - String inFileName = "dna_replication.owl"; - String outFileName = "test_result.txt"; - - BioPAXIOHandler handler = new SimpleIOHandler(); - Model rawModel = handler.convertFromOWL(Example.class.getClassLoader().getResourceAsStream(inFileName)); - - PrintStream out = null; - out = new PrintStream(new FileOutputStream(outFileName, true)); - - // Get all BiochemicalReactions - Set rawModelObjects = rawModel.getObjects(BiochemicalReaction.class); - - // Print participants in BiochemicalReactions - for (BiochemicalReaction rawModelObject : rawModelObjects) { - String tmp = "BiochemicalReaction: " + rawModelObject.getUri(); - - System.out.println(tmp); - out.println(tmp); - - // BiochemicalReactions have "right" and "left" PhysicalEntity participants - Set bpeSet = rawModelObject.getLeft(); - bpeSet.addAll(rawModelObject.getRight()); - - for(PhysicalEntity bpe : bpeSet) { - EntityReference er = null; - - // Check what type of entity - if(bpe instanceof Protein) { - Protein p = (Protein) bpe; - er = p.getEntityReference(); - } - - if(bpe instanceof SmallMolecule) { - SmallMolecule p = (SmallMolecule) bpe; - er = p.getEntityReference(); - } - - if(er instanceof EntityReference) { - // Xrefs (or cross-references) include identifier information in BioPAX - Set xrefs = er.getXref(); - - for(Xref xref : xrefs) { - tmp = "\tID: " + bpe.getUri() + - " NAME: " + bpe.getDisplayName() + - " DB: " + xref.getDb() + " DB_ID: " + xref.getId(); - - System.out.println(tmp); - out.println(tmp); - } - } else { - tmp = "\tNONE"; - - System.out.println(tmp); - out.println(tmp); - } - } - } - - out.flush(); - out.close(); - - System.out.println("DONE. Results in " + outFileName); - } -} diff --git a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/biopax3-short-metabolic-pathway.owl b/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/biopax3-short-metabolic-pathway.owl deleted file mode 100755 index a8a002ac3..000000000 --- a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/biopax3-short-metabolic-pathway.owl +++ /dev/null @@ -1,574 +0,0 @@ - - - - - - - GLK - glucokinase - - - P46880 - PMID: 15608167 - uniprot - - - - - MTKYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPGLLGSGAHLRQTLGHIL - - glucose kinase - glucokinase - GLK - - - - - 562 - taxonomy - - - Escherichia coli - - - - - GLK_ECOLI - - - - - GO:0005737 - PMID: 11483584 - Gene Ontology - - - This example is meant to provide an illustration of how various BioPAX slots should be filled; it is not intended to provide useful (or even accurate) biological information - cytoplasm - - - - - Swiss-Prot/TrEMBL - - - - - aMAZE - - - - - - - SMILES - [CH]3(n1(c2(c(nc1)c(N)ncn2)))(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)OP(O)(=O)O) - ATP - - - 1.0 - - - - - - PMID: 9847135 - C00668 - KEGG compound - - - b-D-glucose-6-phoshate - glucose-6-P - beta-D-glucose 6-phosphate - - - 260.14 - C6H13O9P - - - C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1) - beta-glucose-6-phosphate - SMILES - - - beta-D-glucose 6-phosphate - b-D-glu-6-p - - - - D-glucose-6-P - - - - Kyoto Encyclopedia of Genes and Genomes - KEGG - - - - a-D-glu-6-p - beeta-D-glucose-6-p - - - - - kegg reaction - PMID: 9847135 - R01786 - - - 5.3.1.9 - - - 1.0 - - - <FONT FACE="Symbol">b</FONT>-D-fructose-6-phosphate - - - - - C(OP(O)(O)=O)[CH]1([CH](O)[CH](O)C(O)(O1)CO) - beta-fructose-6-phosphate - SMILES - - - beta-D-fructose 6-phosphate - 260.14 - C6H13O9P - b-D-fru-6-p - - - PMID: 9847135 - C05345 - kegg compound - - - - - - - - b-D-fru-6-p - beta-D-fructose 6-phosphate - - - - - - REVERSIBLE - beta-D-glu-6-p <=> beta-D-fru-6-p - - - - - kegg reaction - R02740 - PMID: 9847135 - - - beta-D-Glucose 6-phosphate => beta-D-Fructose 6-phosphate - - b-D-glu-6-p <=> b-D-fru-6-p - - - - 0.4 - - - beta-D-Glucose 6-phosphate ketol-isomerase - - - - 1.0 - - - - - - - SMILES - c12(n(cnc(c(N)ncn1)2)[CH]3(O[CH]([CH](O)[CH](O)3)COP(=O)(O)OP(O)(=O)O)) - ADP - - - - - C00008 - PMID: 9847135 - kegg compound - - - adenosine diphosphate - C10H15N5O10P2 - ADP - 427.2 - Adenosine 5'-diphosphate - - - 2549346 - PubMed - - - PMID: 15608167 - Q9KH85 - UniProt - - - - adenosine triphosphate - 507.18 - C10H16N5O13P3 - ATP - - - C00002 - kegg compound - PMID: 9847135 - - - Adenosine 5'-triphosphate - - - Adenosine 5'-diphosphate - ADP - adenosine diphosphate - - - - - - - - - LEFT-TO-RIGHT - - - - - - - glucose-6-phosphate isomerase - - - This example is meant to provide an illustration of how various BioPAX slots should be filled; it is not intended to provide useful (or even accurate) biological information - PHI - KTFSEAIISGEWKGYTGKAITDVVNIGIGGSDLGPYMVTEALRPYKNHLNMHFVSNVDGTHIAEVLKKVNPETTLFLVASKTFTTQETMTNAHSARDWFLKAAGDEKHVAKHFAALSTNAKAVGEFGIDTANMFEFWDWVGGRYSLWSAIGLSIVLSIGFDNFVELLSGAHAMDKHFSTTPAEKNLPVLLALIGIWYNNFFGAETEAILPYDQYMHRFAAYFQQGNMESNGKYVDRNGNVVDYQTGPIIWGEPGTNGQHAFYQLIHQGTKMVPCDFIAPAITHNPLFDHHQKLLSKFFAQTEALAFGKSREVVEQEYRDQGKDPAT - - PGI - phosphohexose isomerase - phosphoglucose isomerase - glucose-6-phosphate isomerase - - GPI - - - - - PHI - - phosphoglucose isomerase - phosphohexose isomerase - PGI - GPI - - - catalysis of (beta-D-glu-6-p <=> beta-D-fruc-6-p) - LEFT-TO-RIGHT - - - PGI -> (b-d-glu-6-p <=> b-D-fru-6p) - - The source of this data did not store catalyses of reactions as separate objects, so there are no unification x-refs pointing to the source of these BioPAX instances. - - ACTIVATION - - - - - 1.0 - - - - - kegg compound - C00267 - PMID: 9847135 - - - beta-D-glucose - - - - b-D-glu - <FONT FACE="Symbol">a</FONT>-D-glucose - - - b-D-glu - - - alpha-D-glucose - C1(C(O)C(O)C(O)C(O1)CO)(O) - SMILES - - - - beta-D-glucose - C6H12O6 - 180.16 - - - - - - - - - - - - ATP - Adenosine 5'-triphosphate - - adenosine triphosphate - - - - 1.0 - - - - glucose ATP phosphotransferase - beta-D-glu + ATP => beta-D-glu-6-p + ADP - - REVERSIBLE - - - - - - 2.7.1.1 - - - true - - 2.7.1.2 - ATP:D-glucose 6-phosphotransferase - - - 1.0 - - - - b-D-glu => b-D-glu-6-p - - - glucose degradation - - glycolysis - This example is meant to provide an illustration of how various BioPAX slots should be filled; it is not intended to provide useful (or even accurate) biological information - Glycolysis Pathway - see http://www.amaze.ulb.ac.be/ - - All data within the pathway has the same availability - - - - ACTIVATION - catalysis of (alpha-D-glu <=> alpha-D-glu-6-p) - - - - The source of this data did not store catalyses of reactions as separate objects, so there are no unification x-refs pointing to the source of these BioPAX instances. - - GLK -> (a-D-glu <=> a-D-glu-6-p) - LEFT-TO-RIGHT - - - - - - Embden-Meyerhof pathway - - - - - - - - LEFT-TO-RIGHT - - - - - diff --git a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/circadian_clock.owl b/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/circadian_clock.owl deleted file mode 100755 index 22a709a1d..000000000 --- a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/circadian_clock.owl +++ /dev/null @@ -1,63790 +0,0 @@ - - - - - - - - CHEBI:15377 - ChEBI - - - - NP_001073315 - RefSeq - - - - CHEBI:43750 - ChEBI - - - - InChI=1S/ClH/h1H/p-1 - InChI - - - - NP_001191187 - RefSeq - - - - 601937 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10067 - - - - - - 605045 - omim - - - - 159819 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159819 - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 2990877 - http://www.reactome.org/biopax/46/48887#Protein12345 - Cathepsin G - - - - NM_152830 - RefSeq - - - - NM_001178 - RefSeq - - - - 179820 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2615 - - - - - - 400375 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400375 - - - - EQUAL - 63 - - - - - - - - - - ACTIVATION - - 'BMAL2:CLOCK [nucleoplasm]' positively regulates 'Expression of PAI-1' - BMAL2 (ARNTL2, CLIF) forms a heterodimer with CLOCK, binds E-boxes in the PAI-1 promoter and activates transcription of the PAI-1 gene. BMAL2 shows constitutive rather than circadian expression. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation98 - - - - Q8WV29 - UniProt - - - - NM_000098 - RefSeq - - - - 560540 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=560540 - - - - P78431 - UniProt - - - - - - MOD_RES 1592 1592 N6-acetyllysine. - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite4655 - - - - EQUAL - 84 - - - - REACT_118040 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118040.1 - - - - NM_001251825 - RefSeq - - - - 1H30 - PROTEIN DATA BANK - - - - EQUAL - 1259 - - - - ENST00000396999 - Ensembl - - - - - - - - - - Reactome DB_ID: 212391 - http://www.reactome.org/biopax/46/48887#Protein6482 - MED13 - - - - EQUAL - 614 - http://www.reactome.org/biopax/46/48887#SequenceSite20009 - - - - CHEBI:3731 - ChEBI - - - - Q5SXQ2 - UniProt - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Authored: May, B, 2010-03-11 - Reviewed: Hirota, T, 2010-06-23 - Reviewed: Delaunay, F, 2010-06-23 - http://www.reactome.org/biopax/46/48887#TemplateReaction67 - Edited: May, B, 2010-03-11 - Reviewed: Albrecht, U, 2010-06-23 - The CRYPTOCHROME-1 (CRY1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. CRY1 mRNA and protein show circadian expression. The promoter of the CRY1 gene contains an E-box which is bound by the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer (and probably also the BMAL1:NPAS2 heterodimer), which activates transcription of CRY1. - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Expression of CRYPTOCHROME-1 - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein2637 - Converted from EntitySet in Reactome - Reactome DB_ID: 389066 - Cleaved classical PDGF peptides - - - - Q9Y6Q9 - UniProt - - - - 939213 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939213 - - - - EQUAL - 32 - - - - HGNC:2299 - HGNC - - - - SS - 2.5.1.21 - Farnesyl-diphosphate farnesyltransferase - SQS - FPP:FPP farnesyltransferase - FDFT1 - - - - - - - - - - - - - - - - - FDFT_HUMAN - Squalene synthase - CATALYTIC ACTIVITY: 2 farnesyl diphosphate + NAD(P)H = squalene + 2 diphosphate + NAD(P)(+).COFACTOR: Magnesium.PATHWAY: Terpene metabolism; lanosterol biosynthesis; lanosterol from farnesyl diphosphate: step 1/3.SUBUNIT: Monomer (By similarity).SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.SIMILARITY: Belongs to the phytoene/squalene synthase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 699 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature826 - - - - ENST00000333646 - Ensembl - - - - MOD_RES N6-acetyllysine (By similarity) - - - - ENSP00000430119 - Ensembl - - - - REACT_3917 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3917.2 - - - - - - MOD_RES 71 71 Phosphothreonine; by MAPK1, MAPK3, MAPK11, MAPK12, MAPK14 and PLK3. - - - - ENSG00000140564 - Ensembl - - - - - - MOD_RES 67 67 4-carboxyglutamate. - - - - 159733 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159733 - - - - Q6YNQ1 - UniProt - - - - REACT_118005 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118005.2 - - - - REACT_5852 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5852.2 - - - - ENSP00000317665 - Ensembl - - - - NP_001010927 - RefSeq - - - - NP_056292 - RefSeq - - - - 189904 - omim - - - - - - Mediator of RNA polymerase II transcription subunit 8 - MED8_HUMAN - - - - - Reactome DB_ID: 556784 - http://www.reactome.org/biopax/46/48887#Protein6481 - MED8 - - - - ENPEP - HGNC Symbol - - - - - - - - - - - SIN3A - Histone deacetylase complex subunit Sin3a - Transcriptional corepressor Sin3a - - - - - - - - - - - - - - - - - - - - - - - - - - - - SIN3A_HUMAN - Paired amphipathic helix protein Sin3a - FUNCTION: Acts as a transcriptional repressor. Corepressor for REST. Interacts with MXI1 to repress MYC responsive genes and antagonize MYC oncogenic activities. Also interacts with MXD1-MAX heterodimers to repress transcription by tethering SIN3A to DNA (By similarity). Acts cooperatively with OGT to repress transcription in parallel with histone deacetylation.SUBUNIT: Interacts with BAZ2A, MXD3, MXD4, MBD2, NCOR1, NR4A2, REST, RLIM, SAP30, SETDB1 and SMYD2. Interacts with PHF12 in a complex composed of HDAC1, PHF12 and SAP30 (By similarity). Interacts with ARID4B, BRMS1L, DACH1, HCFC1, HDAC1, HDAC2, MXI1, SAP30L, SAP130, SFPQ, SUDS3 and TOPORS. Interacts with TET1; the interaction recruits SIN3A to gene promoters. Interacts with OGT (via TPRs 1-6); the interaction mediates transcriptional repression in parallel with histone deacetylase.SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus. Note=Recruited to the nucleolus by SAP30L.PTM: SUMO1 sumoylated by TOPORS. Probably desumoylated by SENP2.SIMILARITY: Contains 3 PAH (paired amphipathic helix) domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_24232 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24232.2 - - - - 12540854 - Sturrock, ED - Natesh, R - Schwager, SL - Acharya, KR - Pubmed - Crystal structure of the human angiotensin-converting enzyme-lisinopril complex - Nature 421:551-4 - 2003 - - - - 18786386 - Maywood, ES - O'Neill, JS - Hastings, MH - Pubmed - Cellular circadian pacemaking and the role of cytosolic rhythms - Curr Biol 18:R805-R815 - 2008 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10076 - - - - - - EQUAL - 48 - - - - Q9UG89 - UniProt - - - - - - MOD_RES 1744 1744 N6-acetyllysine. - - - - REACT_25484 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25484.4 - - - - REACT_147787 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147787.2 - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12960 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10769 - - - - ENST00000430069 - Ensembl - - - - 2DBH - PROTEIN DATA BANK - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10120 - - - - REACT_115979 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115979.1 - - - - ENST00000526580 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1794 - - - - MED21 - HGNC - - - - HGNC:13599 - HGNC - - - - NP_110389 - RefSeq - - - - 8858 - NCBI Gene - - - - - - MOD_RES 643 643 N6-acetyllysine (By similarity). - - - - REACT_12748 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12748.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10111 - - - - 184420 - omim - - - - NM_001079518 - RefSeq - - - - Q9BWK0 - UniProt - - - - Q53T93 - UniProt - - - - Q15518 - UniProt - - - - 560517 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=560517 - - - - 1509 - NCBI Gene - - - - 2065398 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065398 - - - - ENSP00000470812 - Ensembl - - - - 605344 - omim - - - - 556804 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556804 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5769 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Q9HD93 - UniProt - - - - ENST00000335681 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2401 - - - - REACT_147869 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147869.2 - - - - - - MOD_RES 116 116 N6-acetyllysine. - - - - NP_001029102 - RefSeq - - - - EQUAL - 26 - http://www.reactome.org/biopax/46/48887#SequenceSite25497 - - - - 2065406 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065406 - - - - REACT_27667 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27667.3 - - - - 939165 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939165 - - - - 1N1J - PROTEIN DATA BANK - - - - ENSP00000385988 - Ensembl - - - - REACT_115879 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115879.1 - - - - - - MOD_RES 60 60 4-carboxyglutamate. - - - - REACT_25457 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25457.2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite11624 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2731 - - - - ENST00000525566 - Ensembl - - - - EQUAL - 34 - http://www.reactome.org/biopax/46/48887#SequenceSite6200 - - - - CHEBI:44742 - ChEBI - - - - Q53XJ0 - UniProt - - - - B0I4X4 - UniProt - - - - - - MOD_RES 2151 2151 Phosphoserine. - - - - HGNC:2452 - HGNC - - - - NP_001136059 - RefSeq - - - - EQUAL - 22 - - - - 174077 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174077 - - - - NP_001254772 - RefSeq - - - - ENSG00000177200 - Ensembl - - - - 8156598 - Wang, X - Brown, MS - Sato, R - Goldstein, JL - Hua, X - Pubmed - SREBP-1, a membrane-bound transcription factor released by sterol-regulated proteolysis - Cell 77:53-62 - 1994 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of G0S2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation209 - - - - 1989791 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989791 - - - - Q71SY5 - UniProt - - - - - - MOD_RES 56 56 4-carboxyglutamate. - - - - NP_954592 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12067 - - - - - - SLC27A1 - HGNC - - - - ENST00000223190 - Ensembl - - - - - - MOD_RES 1331 1331 Phosphoserine. - - - - REACT_26870 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26870.3 - - - - CHEBI:13282 - ChEBI - - - - - NR1C3 - Nuclear receptor subfamily 1 group C member 3 - PPARG - PPAR-gamma - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PPARG_HUMAN - Peroxisome proliferator-activated receptor gamma - FUNCTION: Receptor that binds peroxisome proliferators such as hypolipidemic drugs and fatty acids. Once activated by a ligand, the receptor binds to a promoter element in the gene for acyl-CoA oxidase and activates its transcription. It therefore controls the peroxisomal beta-oxidation pathway of fatty acids. Key regulator of adipocyte differentiation and glucose homeostasis. Acts as a critical regulator of gut homeostasis by suppressing NF-kappa-B- mediated proinflammatory responses.ENZYME REGULATION: PDPK1 activates its transcriptional activity independently of its kinase activity.SUBUNIT: Forms a heterodimer with the retinoic acid receptor RXRA called adipocyte-specific transcription factor ARF6. Interacts with NCOA6 coactivator, leading to a strong increase in transcription of target genes. Interacts with coactivator PPARBP, leading to a mild increase in transcription of target genes. Interacts with FAM120B and PRDM16 (By similarity). Interacts with NOCA7 in a ligand-inducible manner. Interacts with NCOA1 and NCOA2 LXXLL motifs. Interacts with ASXL1, ASXL2, DNTTIP2, MAP2K1/MEK1, PDPK1, PRMT2 and TGFB1I1. Interacts (via DNA-binding domain) with HELZ2; the interaction stimulates the transcriptional activity of PPARG.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Redistributed from the nucleus to the cytosol through a MAP2K1/MEK1-dependent manner.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Comment=Additional isoforms seem to exist; Name=2; IsoId=P37231-1; Sequence=Displayed; Name=1; Synonyms=PPARgamma1(wt); IsoId=P37231-2; Sequence=VSP_003645; Name=3; Synonyms=PPARgamma1(tr); IsoId=P37231-3; Sequence=VSP_003645, VSP_043906, VSP_043907; Note=Exhibits dominant negative activity over isoform 1;TISSUE SPECIFICITY: Highest expression in adipose tissue. Lower in skeletal muscle, spleen, heart and liver. Also detectable in placenta, lung and ovary.PTM: O-GlcNAcylation at Thr-84 reduces transcriptional activity in adipocytes (By similarity).POLYMORPHISM: Genetic variation in PPARG may influence body mass index (BMI) [MIM:606641]. BMI reflects the amount of fat, lean mass, and body build.POLYMORPHISM: Genetic variations in PPARG influence the carotid intimal medial thickness (CIMT) [MIM:609338]. CIMT is a measure of atherosclerosis that is independently associated with traditional atherosclerotic cardiovascular disease risk factors and coronary atherosclerotic burden. 35 to 45% of the variability in multivariable-adjusted CIMT is explained by genetic factors.DISEASE: Note=Defects in PPARG can lead to type 2 insulin- resistant diabetes and hyptertension. PPARG mutations may be associated with colon cancer.DISEASE: Obesity (OBESITY) [MIM:601665]: A condition characterized by an increase of body weight beyond the limitation of skeletal and physical requirements, as the result of excessive accumulation of body fat. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.DISEASE: Lipodystrophy, familial partial, 3 (FPLD3) [MIM:604367]: A form of lipodystrophy characterized by marked loss of subcutaneous fat from the extremities. Facial adipose tissue may be increased, decreased or normal. Affected individuals show an increased preponderance of insulin resistance, diabetes mellitus and dyslipidemia. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Glioma 1 (GLM1) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. Polymorphic PPARG alleles have been found to be significantly over-represented among a cohort of American patients with sporadic glioblastoma multiforme suggesting a possible contribution to disease susceptibility.SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.SEQUENCE CAUTION: Sequence=AAN38992.2; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA23354.1; Type=Erroneous gene model prediction; Sequence=BAF83270.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAA62153.1; Type=Erroneous initiation; Note=Translation N-terminally extended;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PPARGID383ch3p25.html";WEB RESOURCE: Name=Wikipedia; Note=Peroxisome proliferator- activated receptor entry; URL="http://en.wikipedia.org/wiki/Peroxisome_proliferator-activated_receptor";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PPARG";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/pparg/";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=PPARG"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSG00000123689 - Ensembl - - - - REACT_27094 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27094.2 - - - - - - MOD_RES 560 560 Phosphoserine. - - - - NP_057144 - RefSeq - - - - REACT_117993 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117993.1 - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite4657 - - - - ENSG00000170315 - Ensembl - - - - - - ubiquitin (UBC 7) - - - - - http://www.reactome.org/biopax/46/48887#Protein2483 - Reactome DB_ID: 939862 - UBC(457-532) - - - - - - MOD_RES 162 162 N6-acetyllysine; by PCAF/KAT2B. - - - - B7WPG7 - UniProt - - - - EQUAL - 846 - http://www.reactome.org/biopax/46/48887#SequenceSite21444 - - - - NP_056287 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4777 - - - - - - ACE - HGNC Symbol - - - - EQUAL - 1336 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5624 - - - - NP_604391 - RefSeq - - - - Q8TDE5 - UniProt - - - - CHEBI:44292 - ChEBI - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4646 - - - - 19 - NCBI Gene - - - - PDGFA - HGNC Symbol - - - - - - MOD_RES 753 753 Phosphoserine. - - - - ENSG00000197905 - Ensembl - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite9872 - - - - REACT_3599 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3599.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4780 - - - - REACT_147705 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147705.2 - - - - ENST00000331163 - Ensembl - - - - P29279 - UniProt - - - - ENST00000427522 - Ensembl - - - - ENSP00000360972 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1091 - - - - 51586 - NCBI Gene - - - - CHEBI:15843 - ChEBI - - - - REACT_118635 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118635.2 - - - - - - pro-protein C light chain - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11651 - Reactome DB_ID: 159747 - 8xCbxE-3D-PROC(33-197) - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12976 - - - - - - MOD_RES 93 93 Phosphoserine (By similarity). - - - - EP300 - HGNC - - - - SKP1 - HGNC Symbol - - - - EQUAL - 417 - http://www.reactome.org/biopax/46/48887#SequenceSite23035 - - - - PPARGC1B - HGNC Symbol - - - - ENST00000354577 - Ensembl - - - - - - CREB-binding protein - CBP_HUMAN - CREBBP - - - - - Reactome DB_ID: 193545 - http://www.reactome.org/biopax/46/48887#Protein1954 - KAT3A - - - - NM_014166 - RefSeq - - - - Q2NL52 - UniProt - - - - - - - - - ARNTL:CLOCK/NPAS2 - - - - BMAL1:CLOCK/NPAS2 - Reactome DB_ID: 400360 - http://www.reactome.org/biopax/46/48887#Complex4977 - - - - REACT_111419 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111419.2 - - - - BTRC - HGNC - - - - ENST00000425457 - Ensembl - - - - MOD_RES Pyrrolidone carboxylic acid - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10176 - - - - - - B4DMC5 - UniProt - - - - O14515 - UniProt - - - - 600879 - omim - - - - ENSP00000434516 - Ensembl - - - - 381251 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381251 - - - - REACT_21133 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21133.2 - - - - EQUAL - 40 - http://www.reactome.org/biopax/46/48887#SequenceSite21724 - - - - Q9NXU9 - UniProt - - - - GZMH - HGNC - - - - MED13L - HGNC - - - - ENSP00000384074 - Ensembl - - - - 10849758 - Peters C - Schutze S - Heinrich M - Schneider-Brachert W - Winoto-Morbach S - Wickel M - Kronke M - Brunner J - Weber T - Saftig P - PubMed - Ceramide as an activator lipid of cathepsin D. - Adv Exp Med Biol 477;305-15 - 2000 - - - - EQUAL - 1347 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1838 - - - - ENST00000511206 - Ensembl - - - - - - MOD_RES 2102 2102 Phosphoserine (By similarity). - - - - REACT_27097 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27097.2 - - - - REACT_5833 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5833.2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25560 - - - - UREBDLICKHMUKA-CXSFZGCWSA-N - InChIKey - - - - 11226238 - Borchers, T - Wolfrum, C - Spener, F - Borrmann, CM - Pubmed - Fatty acids and hypolipidemic drugs regulate peroxisome proliferator-activated receptors alpha - and gamma-mediated gene expression via liver fatty acid binding protein: a signaling path to the nucleus - Proc Natl Acad Sci U S A 98:2323-8 - 2001 - - - - 116830 - omim - - - - HGNC:784 - HGNC - - - - ENST00000405666 - Ensembl - - - - Q5XX09 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10797 - - - - - - 1655716 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655716 - - - - - - ubiquitin (RPS27A) - - - - - Reactome DB_ID: 939849 - http://www.reactome.org/biopax/46/48887#Protein2472 - RPS27A(1-76) - - - - 400373 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400373 - - - - Q15562 - UniProt - - - - - Nuclear transcription factor Y subunit A - CAAT box DNA-binding protein subunit A - NFYA - NF-YA - - - - - - - - - - - - - - - - - NFYA_HUMAN - Nuclear transcription factor Y subunit alpha - FUNCTION: Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.SUBUNIT: Heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. Interacts with SP1; the interaction is inhibited by glycosylation of SP1. Interacts with ZHX1. Interacts (via N-terminus) with ZHX2 (via homeobox domain). Interacts with ZFX3.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Long; IsoId=P23511-1; Sequence=Displayed; Name=Short; IsoId=P23511-2; Sequence=VSP_000849;SIMILARITY: Belongs to the NFYA/HAP2 subunit family.SIMILARITY: Contains 1 NFYA/HAP2-type DNA-binding domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - bHLHe9 - MOP4 - NPAS2 - Member of PAS protein 4 - PASD4 - Class E basic helix-loop-helix protein 9 - PAS domain-containing protein 4 - Basic-helix-loop-helix-PAS protein MOP4 - Neuronal PAS2 - BHLHE9 - - - - - - - - - - - - - - - - NPAS2_HUMAN - Neuronal PAS domain-containing protein 2 - FUNCTION: BMAL1-NPAS2 heterodimers activate E-box element (5'- CACGTG-3') transcription of a number of proteins of the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins (By similarity).SUBUNIT: Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with another bHLH protein. Heterodimerization with CLOCK or NPAS2 is required for E-box- dependent transactivation.SUBCELLULAR LOCATION: Nucleus (By similarity).POLYMORPHISM: Variants in NPAS2 show a susceptibility to seasonal affective disorder (SAD) [MIM:608516]. SAD is a depressive condition resulting from seasonal changes, and with diurnal preference.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - MED12 - HGNC - - - - ENSP00000472264 - Ensembl - - - - Q96E94 - UniProt - - - - 3009039 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3009039 - - - - ENSP00000297347 - Ensembl - - - - ENSP00000364472 - Ensembl - - - - ENSP00000380044 - Ensembl - - - - - - MOD_RES 2083 2083 Phosphoserine. - - - - NRF1 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14062 - - - - 159790 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159790 - - - - NM_007289 - RefSeq - - - - MED11 - HGNC - - - - - DNA Containing an E-box Element - - - - E-box (DNA) - http://www.reactome.org/biopax/46/48887#PhysicalEntity622 - Reactome DB_ID: 549373 - - - - O60334 - UniProt - - - - EQUAL - 864 - - - - EQUAL - 1424 - http://www.reactome.org/biopax/46/48887#SequenceSite12337 - - - - InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+3/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-; - InChI - - - - EQUAL - 2 - - - - - - MOD_RES 1030 1030 Phosphoserine. - - - - D3DPV9 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2252 - - - - - - ENSG00000140465 - Ensembl - - - - - - MOD_RES 112 112 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval826 - - - - - - 2032767 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032767 - - - - HGNC:2551 - HGNC - - - - - - Casein kinase I isoform epsilon - CKIepsilon - - - - - http://www.reactome.org/biopax/46/48887#Protein5842 - Reactome DB_ID: 205877 - CSNK1E - - - - REACT_18117 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18117.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12002 - - - - 8841 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5645 - - - - - - ENSG00000187048 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10061 - - - - - - REACT_115943 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115943.1 - - - - ENSP00000433887 - Ensembl - - - - CHEBI:3616 - ChEBI - - - - 603866 - omim - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5781 - - - - - - MOD_RES 75 75 4-carboxyglutamate. - - - - Q5JYE0 - UniProt - - - - ENST00000276914 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9299 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature601 - - - - 1520333 - Bjornsson TD - Tao D - Yang L - Ma M - Kong AN - PubMed - Molecular cloning of the alcohol/hydroxysteroid form (hSTa) of sulfotransferase from human liver. - Biochem Biophys Res Commun 187(1);448-54 - 1992 - - - - 1989795 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989795 - - - - REACT_117957 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117957.1 - - - - - - - - - - Reactome DB_ID: 421319 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11500 - p-CLOCK/p-NPAS2 - - - - Q5T912 - UniProt - - - - - - - - - - PDGF A-chain precursor dimer - http://www.reactome.org/biopax/46/48887#Complex1210 - Reactome DB_ID: 380749 - - - - EQUAL - 301 - - - - NP_005472 - RefSeq - - - - EQUAL - 293 - - - - 603934 - omim - - - - - - ubiquitin (UBC 5) - - - - - Reactome DB_ID: 939232 - http://www.reactome.org/biopax/46/48887#Protein1053 - UBC(305-380) - - - - EQUAL - 54 - http://www.reactome.org/biopax/46/48887#SequenceSite10119 - - - - Q9NXB5 - UniProt - - - - ENST00000392543 - Ensembl - - - - 1977688 - Watt VM - Willard HF - PubMed - The human aminopeptidase N gene: isolation, chromosome localization, and DNA polymorphism analysis. - Hum Genet 85(6);651-4 - 1990 - - - - REACT_115729 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115729.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature830 - - - - Q6T5C2 - UniProt - - - - NM_001248004 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2441 - - - - - - CYPIA1 - Cytochrome P450-C - Cytochrome P450-P1 - CYP1A1 - 1.14.14.1 - Cytochrome P450 form 6 - - - - - - - - - - - - - - - - - CP1A1_HUMAN - Cytochrome P450 1A1 - FUNCTION: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.CATALYTIC ACTIVITY: RH + reduced flavoprotein + O(2) = ROH + oxidized flavoprotein + H(2)O.COFACTOR: Heme group.SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Peripheral membrane protein. Microsome membrane; Peripheral membrane protein.TISSUE SPECIFICITY: Lung, lymphocytes and placenta.INDUCTION: By 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).SIMILARITY: Belongs to the cytochrome P450 family.WEB RESOURCE: Name=Cytochrome P450 Allele Nomenclature Committee; Note=CYP1A1 alleles; URL="http://www.cypalleles.ki.se/cyp1a1.htm";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=CYP1A1";WEB RESOURCE: Name=Wikipedia; Note=CYP1A1 entry; URL="http://en.wikipedia.org/wiki/CYP1A1"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - CUL-1 - CUL1 - - - - - - - - - - - - - - - - - - - - CUL1_HUMAN - Cullin-1 - FUNCTION: Core component of multiple cullin-RING-based SCF (SKP1- CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which mediate the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as a rigid scaffold that organizes the SKP1-F-box protein and RBX1 subunits. May contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and exchange of the substrate recognition component is mediated by TIP120A/CAND1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(CCNF) directs ubiquitination of CCP110. SCF(FBXL3) and SCF(FBXL21) direct ubiquitination of CRY1 and CRY2. SCF(FBXO9) direct ubiquitination of TTI1 and TELO2.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: Component of multiple SCF (SKP1-CUL1-F-box) E3 ubiquitin- protein ligase complexes formed of CUL1, SKP1, RBX1 and a variable F-box domain-containing protein as substrate-specific subunit. Component of the SCF(FBXW11) complex containing FBXW11. Component of the SCF(SKP2) complex containing SKP2, in which it interacts directly with SKP1, SKP2 and RBX1. Component of the SCF(FBXW2) complex containing FBXw2. Component of the SCF(FBXO32) complex containing FBXO32. Component of the probable SCF(FBXO7) complex containing FBXO7. Component of the SCF(FBXO11) complex containing FBXO11. Component of the SCF(FBXO25) complex containing FBXO25. Component of the SCF(FBXO33) complex containing FBXO33. Component of the probable SCF(FBXO4) complex containing FBXO4. Component of the SCF(FBXO44) complex, composed of SKP1, CUL1 and FBXO44. Component of the SCF(BTRC) complex, composed of SKP1, CUL1 and BTRC. This complex binds phosphorylated NFKBIA. Part of a SCF complex consisting of CUL1, RBX1, SKP1 and FBXO2. Component of a SCF(SKP2)-like complex containing CUL1, SKP1, TRIM21 and SKP2. Component of the SCF(FBXO17) complex, composed of SKP1, CUL1 and FBXO17. Component of the SCF(FBXO27) complex, composed of SKP1, CUL1 and FBXO27. Component of the SCF(CCNF) complex consisting of CUL1, RBX1, SKP1 and CCNF. Component of the SCF(FBXL3) complex composed of CUL1, SKP1, RBX1 and FBXL3. Component of the SCF(FBXL21) complex composed of CUL1, SKP1, RBX1 and FBXL21. Component of the SCF(FBXO9) composed of CUL1, SKP1, RBX1 and FBXO9. Component of the SCF(FBXW7) composed of CUL1, SKP1, RBX1 and FBXW7. Interacts with CHEK2; mediates CHEK2 ubiquitination and regulates its function. Part of a complex with TIP120A/CAND1 and RBX1. The unneddylated form interacts with TIP120A/CAND1 and the interaction mediates the exchange of the F-box substrate-specific subunit. Can self-associate. Interacts with FBXW8. Interacts with RNF7. Interacts with CUL7; the interaction seems to be mediated by FBXW8. Interacts with TRIM21. Interacts with COPS2. Interacts with Epstein-Barr virus BPLF1. Interacts with human adenovirus early E1A protein; this interaction inhibits RBX1-CUL1-dependent elongation reaction of ubiquitin chains by the SCF(FBXW7) complex.TISSUE SPECIFICITY: Expressed in lung fibroblasts.PTM: Neddylated; which enhances the ubiquitination activity of SCF. Deneddylated via its interaction with the COP9 signalosome (CSN) complex. Deneddylated by Epstein-Barr virus BPLF1 leading to a S-phase-like environment that is required for efficient replication of the viral genome.SIMILARITY: Belongs to the cullin family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10153 - - - - - - 183 - NCBI Gene - - - - 1655850 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655850 - - - - EQUAL - 1597 - - - - 603134 - omim - - - - EQUAL - 54 - - - - EQUAL - 504 - - - - EQUAL - 42 - http://www.reactome.org/biopax/46/48887#SequenceSite21737 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12050 - - - - - - 19710360 - Hanniman, EA - Lazar, MA - Wu, N - Joshi, S - Yin, L - Pubmed - Negative feedback maintenance of heme homeostasis by its receptor, Rev-erbalpha - Genes Dev 23:2201-9 - 2009 - - - - REACT_118057 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118057.2 - - - - NP_004259 - RefSeq - - - - EQUAL - 2269 - - - - REACT_25429 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25429.1 - - - - ENST00000457928 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12061 - - - - - - 125263 - omim - - - - O75192 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10809 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2100 - - - - ENSP00000222553 - Ensembl - - - - ENSP00000415743 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21455 - - - - EQUAL - 554 - - - - REACT_25225 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25225.2 - - - - - - MOD_RES 114 114 Phosphoserine. - - - - 300182 - omim - - - - 49836665 - pubchem - - - - 3927292 - Faust PL - Chirgwin JM - Kornfeld S - PubMed - Cloning and sequence analysis of cDNA for human cathepsin D. - Proc Natl Acad Sci U S A 82(15);4910-4 - 1985 - - - - CHEBI:2799 - ChEBI - - - - HGNC:18047 - HGNC - - - - HGNC:7804 - HGNC - - - - ENSG00000126218 - Ensembl - - - - NM_001003802 - RefSeq - - - - P54868 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25536 - - - - - - Becaplermin - PDGFB(1-241) - PDGF-2 - Platelet-derived growth factor, B chain precursor - Platelet-derived growth factor beta polypeptide - PDGF B-chain - - - - - Reactome DB_ID: 380740 - http://www.reactome.org/biopax/46/48887#Protein2634 - c-sis - - - - EQUAL - 44 - - - - 27242 - NCBI Gene - - - - ENST00000252519 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5803 - - - - ENSP00000456245 - Ensembl - - - - - - Carboxypeptidase B2 ecNumber3.4.17.20/ecNumber - CBPB2_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein12359 - Reactome DB_ID: 3229248 - CPB2 - - - - NM_012158 - RefSeq - - - - 16474406 - Yamada, RG - Hogenesch, JB - Welsh, DK - Miraglia, LJ - Ukai, H - Ueda, HR - Baggs, JE - Sato, TK - Kobayashi, TJ - Kay, SA - Pubmed - Feedback repression is required for mammalian circadian clock function - Nat Genet 38:312-9 - 2006 - - - - 1989755 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989755 - - - - 159767 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159767 - - - - EQUAL - 85 - - - - ENSP00000331023 - Ensembl - - - - - - MOD_RES 504 504 Phosphoserine. - - - - NP_001968 - RefSeq - - - - 6667 - NCBI Gene - - - - - - MOD_RES 54 54 4-carboxyglutamate. - - - - Q96J63 - UniProt - - - - Q8IXU0 - UniProt - - - - ENST00000401424 - Ensembl - - - - - - - - - - - - - - - - Formation of PPARA:RXRA Heterodimer at Promoters of Target Genes - Edited: May, B, 2009-06-08 - Edited: May, B, 2009-05-30 16:45:51 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4673 - Authored: May, B, 2009-05-30 16:45:51 - Peroxisome proliferator-activated receptor alpha (PPAR-alpha) is a type II nuclear receptor (its subcellular location is independent of ligand binding) related to PPAR-beta/delta and PPAR-gamma. PPAR-alpha is expressed highly in the liver where if functions to control lipid metabolism, especially fatty acid oxidation. <br>PPAR-alpha forms heterodimers with Retinoid X receptor alpha (RXR-alpha). The heterodimers bind peroxisome proliferator receptor elements (PPREs) in and around genes regulated by PPAR-alpha. - - - - - ENST00000317276 - Ensembl - - - - 442496 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442496 - - - - - - - - - - INHIBITION - - 'lisinopril [extracellular region]' negatively regulates 'ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control306 - - - - 11994399 - Brown, MS - Horton, JD - Goldstein, JL - Pubmed - SREBPs: activators of the complete program of cholesterol and fatty acid synthesis in the liver - J Clin Invest 109:1125-31 - 2002 - - - - CCRN4L - CCR4 - NOC - CCR4 protein homolog - - - - - - - - - - - - - - - - NOCT_HUMAN - Nocturnin - FUNCTION: Component of the circadian clock or downstream effector of clock function. Exhibits a high amplitude circadian rhythm with maximal levels in early evening. In constant darkness or constant light, the amplitude of the rhythm decreases (By similarity).SIMILARITY: Belongs to the CCR4/nocturin family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12366 - - - - CRY2 - HGNC Symbol - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1846 - - - - - - - - Circadian pacemaker protein Rigui - hPER1 - RIGUI - PER1 - PER - Circadian clock protein PERIOD 1 - KIAA0482 - - - - - - - - - - - - - - - - PER1_HUMAN - Period circadian protein homolog 1 - FUNCTION: Component of the circadian clock mechanism which is essential for generating circadian rhythms. Negative element in the circadian transcriptional loop. Influences clock function by interacting with other circadian regulatory proteins and transporting them to the nucleus. Negatively regulates CLOCK|NPAS2-BMAL1|BMAL2-induced transactivation. Can bind heme (By similarity).SUBUNIT: Homodimer (By similarity). Component of the circadian core oscillator, which includes the CRY proteins, CLOCK or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E, TIMELESS, and the PER proteins. Interacts directly with TIMELESS, PER2, PER3 and, through a C-terminal domain, with CRY1 and CRY2. Interaction with CSNK1D or CSNK1E promotes nuclear location of PER proteins. Interacts with GPRASP1 (By similarity). Binding to CSNK1G2 triggers proteasomal degradation.SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm (By similarity). Note=Mainly nuclear. Nucleocytoplasmic shuttling is effected by interaction with other circadian core oscillator proteins and/or by phosphorylation. Retention of PER1 in the cytoplasm occurs through PER1-PER2 heterodimer formation or by interaction with CSNK1E and/or phosphorylation which appears to mask the PER1 nuclear localization signal. Also translocated to the nucleus by CRY1 or CRY2 (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Comment=Additional isoforms seem to exist; Name=Rigui 4.7; IsoId=O15534-1; Sequence=Displayed; Name=Rigui 3.0; IsoId=O15534-2; Sequence=Not described; Name=Rigui 6.6; Synonyms=Truncated; IsoId=O15534-3; Sequence=Not described;TISSUE SPECIFICITY: Widely expressed. Found in heart, brain, placenta, lung, liver, skeletal muscle, pancreas, kidney, spleen, thymus, prostate, testis, ovary and small intestine. Highest level in skeletal muscle. Low level in kidney.INDUCTION: Serum-induced levels in fibroblasts show circadian oscillations. Maximum levels after 1 hour stimulation, minimum levels after 12 hours. Another peak is then observed after 20 hours. Protein levels show maximum levels at 6 hours, decrease to reach minimum levels at 20 hours, and increase again to reach a second peak after 26 hours. Levels then decrease slightly and then increase to maximum levels at 32 hours. Levels of phosphorylated form increase between 3 hours and 12 hours.PTM: Phosphorylated on serine residues by CSNK1E. Also can be phosphorylated by the delta isoform. Phosphorylation by CSNK1 retains PER1 in the cytoplasm and leads to its ubiquitination and subsequent degradation.PTM: Ubiquitinated (By similarity).SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.SEQUENCE CAUTION: Sequence=BAC06326.2; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 2180 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10812 - - - - - - 20561910 - Cui, A - Kong, X - Zhu, L - Gupta, N - Fang, F - Cui, Y - Chen, Q - Shao, D - Liu, X - Liu, Y - Chang, Y - Qiao, A - Pubmed - PGC-1 beta-regulated mitochondrial biogenesis and function in myotubes is mediated by NRF-1 and ERR alpha - Mitochondrion 10:516-27 - 2010 - - - - - 8.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12956 - - - - ENSP00000421934 - Ensembl - - - - PTHR23042:SF3 - PANTHER Family - - - - - NP_443109 - RefSeq - - - - NP_001003802 - RefSeq - - - - EQUAL - 231 - - - - EQUAL - 400 - http://www.reactome.org/biopax/46/48887#SequenceSite21690 - - - - NP_001234933 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2096 - - - - EQUAL - 622 - http://www.reactome.org/biopax/46/48887#SequenceSite21661 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5095 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9715 - - - - 603348 - omim - - - - - - prothrombin (factor II) - 10xCbxE-F2(44-622) - - - - - - - - - - - - - - Reactome DB_ID: 159845 - http://www.reactome.org/biopax/46/48887#Protein11661 - 10xCbxE-F2 - - - - Q8TCU0 - UniProt - - - - 8648 - NCBI Gene - - - - 561169 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561169 - - - - EQUAL - 211 - http://www.reactome.org/biopax/46/48887#SequenceSite4957 - - - - CPT2 - HGNC - - - - - - - - - - Authored: May, B, 2011-11-08 - The PEX11A gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction160 - Expression of PEX11A - - - - ENSG00000115486 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5806 - - - - - - PIMT - - - - - http://www.reactome.org/biopax/46/48887#Protein6511 - Reactome DB_ID: 400176 - TGS1 - - - - HGNC:1723 - HGNC - - - - NM_001256662 - RefSeq - - - - 381367 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381367 - - - - EQUAL - 59 - - - - REACT_117959 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117959.1 - - - - ENST00000342783 - Ensembl - - - - NM_000859 - RefSeq - - - - EQUAL - 872 - - - - TEAD1 - HGNC - - - - GO:0005576 - Gene Ontology - - - - 612915 - omim - - - - ENSP00000384851 - Ensembl - - - - 1EFH - PROTEIN DATA BANK - - - - NM_001030272 - RefSeq - - - - ENST00000467467 - Ensembl - - - - ENST00000413513 - Ensembl - - - - ENSG00000136146 - Ensembl - - - - HGNC:12458 - HGNC - - - - NP_060062 - RefSeq - - - - - - p-S-BMAL1 - BMAL1_HUMAN, phosphorylated - Aryl hydrocarbon receptor nuclear translocator-like protein 1, phosphorylated - p-S-ARNTL - - - - - - Reactome DB_ID: 421312 - http://www.reactome.org/biopax/46/48887#Protein11499 - p-ARNTL - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5790 - - - - Q9UPV5 - UniProt - - - - 12738229 - Vaughan, DE - Eren, M - Johnson, CH - Painter, CA - Schoenhard, JA - Smith, LH - Pubmed - Regulation of the PAI-1 promoter by circadian clock components: differential activation by BMAL1 and BMAL2 - J Mol Cell Cardiol 35:473-81 - 2003 - - - - P49674 - UniProt - - - - IPCSVZSSVZVIGE-UHFFFAOYSA-N - InChIKey - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12014 - - - - ENSG00000063322 - Ensembl - - - - 3325591 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3325591 - - - - ENSG00000023330 - Ensembl - - - - 879741 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879741 - - - - EQUAL - 183 - http://www.reactome.org/biopax/46/48887#SequenceSite21654 - - - - D3DNQ9 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10140 - - - - - - MOD_RES 89 89 Phosphoserine; by AMPK. - - - - EQUAL - 251 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5608 - - - - REACT_950 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_950.2 - - - - - bHLH-PAS protein JAP3 - PASD3 - PAS domain-containing protein 3 - ARNTL - Member of PAS protein 3 - MOP3 - Class E basic helix-loop-helix protein 5 - BMAL1 - bHLHe5 - Brain and muscle ARNT-like 1 - Basic-helix-loop-helix-PAS protein MOP3 - BHLHE5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BMAL1_HUMAN - Aryl hydrocarbon receptor nuclear translocator-like protein 1 - FUNCTION: ARNTL-CLOCK heterodimers activate E-box element (5'- CACGTG-3') transcription of a number of proteins of the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins (By similarity).SUBUNIT: Interacts with CRY2 (By similarity). Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, ARNTL or ARNTL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with another bHLH protein. Heterodimerization with CLOCK is required for E-box-dependent transactivation, for CLOCK nuclear translocation and degradation, and, for phosphorylation of both CLOCK and ARNTL. Interaction with PER and CRY proteins requires translocation to the nucleus. Interaction of the CLOCK-ARNTL heterodimer with PER or CRY inhibits transcription activation. Interacts with HSP90; with AHR in vitro, but not in vivo. Part of a nuclear complex which also includes GNB2L1/RACK1 and PRKCA; GNB2L1 and PRKCA are recruited to the complex in a circadian manner.SUBCELLULAR LOCATION: Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=9; Comment=Additional isoforms seem to exist; Name=BMAL1B; Synonyms=JAP3; IsoId=O00327-2; Sequence=Displayed; Name=BMAL1A; IsoId=O00327-1; Sequence=VSP_002094; Name=BMAL1C; IsoId=O00327-3; Sequence=VSP_002096, VSP_002097; Name=BMAL1D; IsoId=O00327-4; Sequence=VSP_002098; Name=BMAL1E; IsoId=O00327-5; Sequence=VSP_002099, VSP_002100; Name=BMAL1F; IsoId=O00327-6; Sequence=VSP_002101, VSP_002102; Name=MOP3; IsoId=O00327-7; Sequence=VSP_002095; Name=8; IsoId=O00327-8; Sequence=VSP_035457; Name=9; IsoId=O00327-9; Sequence=VSP_002094, VSP_035457;TISSUE SPECIFICITY: Highly expressed in the adult brain, skeletal muscle and heart.PTM: Acetylated on Lys-538 upon dimerization with CLOCK. Acetylation facilitates CRY1-mediated repression (By similarity).PTM: Phosphorylated upon dimerization with CLOCK (By similarity).PTM: Sumoylated on Lys-259 upon dimerization with CLOCK (By similarity).MISCELLANEOUS: CLOCK-ARNTL double mutations within the PAS domains result in syngernistic desensitization to high levels of CRY on repression of CLOCK-ARNTL transcriptional activity of PER1 and, disrupt circadian rhythmicity.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_005027 - RefSeq - - - - A6NLA4 - UniProt - - - - REACT_1644 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1644.3 - - - - 609751 - omim - - - - ENST00000403510 - Ensembl - - - - MED27 - HGNC Symbol - - - - 11994355 - Schick F - Haring HU - Kellerer M - Jacob S - Loblein K - Stumvoll M - Thamer C - Tschritter O - Machann J - Haap M - PubMed - Metabolic characterization of a woman homozygous for the Ser113Leu missense mutation in carnitine palmitoyl transferase II. - J Clin Endocrinol Metab 87(5);2139-43 - 2002 - - - - ENSP00000223095 - Ensembl - - - - EQUAL - 71 - - - - - - - - Pro-factor X is transported from the endoplasmic reticulum to the Golgi apparatus - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3894 - In this reaction, 1 molecule of 'pro-factor X' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - - - - - EQUAL - 305 - http://www.reactome.org/biopax/46/48887#SequenceSite4661 - - - - Q14339 - UniProt - - - - 400255 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400255 - - - - EQUAL - 33 - http://www.reactome.org/biopax/46/48887#SequenceSite21707 - - - - 879833 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879833 - - - - - - MOD_RES 887 887 Phosphothreonine. - - - - PTHR23042:SF10 - PANTHER Family - - - - - MOD_RES 4-carboxyglutamate - - - - NM_005647 - RefSeq - - - - ENSP00000422390 - Ensembl - - - - 606013 - omim - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite15685 - - - - EQUAL - 350 - - - - PTHR11269:SF9 - PANTHER Family - - - - - 11533495 - pubchem-substance - - - - ENSP00000290863 - Ensembl - - - - ENSP00000361258 - Ensembl - - - - 517831 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=517831 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10813 - - - - - - Q14815 - UniProt - - - - 602691 - omim - - - - NP_004371 - RefSeq - - - - Q9NTT9 - UniProt - - - - 11745043 - Jacquemin E - PubMed - Role of multidrug resistance 3 deficiency in pediatric and adult liver disease: one gene for three diseases. - Semin Liver Dis 21(4);551-62 - 2001 - - - - ENSP00000407746 - Ensembl - - - - REACT_148206 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148206.1 - - - - EQUAL - 1023 - http://www.reactome.org/biopax/46/48887#SequenceSite25541 - - - - Q8IUY9 - UniProt - - - - - - MOD_RES 2142 2142 Asymmetric dimethylarginine; by CARM1; alternate. - - - - O15410 - UniProt - - - - ENSP00000378529 - Ensembl - - - - PTHR13992:SF10 - PANTHER Family - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#TemplateReaction76 - The CPT1A gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - Edited: May, B, 2011-10-23 - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-10-23 - Expression of CPT1A - - - - Q96TD3 - UniProt - - - - ENSP00000378402 - Ensembl - - - - E9PGV6 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10002 - - - - REACT_148584 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148584.2 - - - - ENSP00000439084 - Ensembl - - - - - - MOD_RES 19 19 Phosphoserine. - - - - REACT_4000 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4000.2 - - - - ENSG00000101849 - Ensembl - - - - REACT_1860 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1860.3 - - - - Q9UHV7 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8334 - - - - NM_001876 - RefSeq - - - - ANPEP - HGNC Symbol - - - - ENSG00000118523 - Ensembl - - - - - - ubiquitin (UBC 3) - - - - - Reactome DB_ID: 939258 - http://www.reactome.org/biopax/46/48887#Protein1051 - UBC(153-228) - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2110 - - - - - - TEAD3 - HGNC Symbol - - - - REACT_148107 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148107.1 - - - - 708327 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=708327 - - - - ENST00000400206 - Ensembl - - - - ENST00000293777 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1042 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14057 - - - - NP_068576 - RefSeq - - - - REACT_24537 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24537.2 - - - - ENSP00000352135 - Ensembl - - - - 2065432 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065432 - - - - NP_003874 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval825 - - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1852 - - - - B7Z3Y9 - UniProt - - - - - - MOD_RES 289 289 Phosphoserine. - - - - ATP6AP2 - HGNC Symbol - - - - EQUAL - 586 - http://www.reactome.org/biopax/46/48887#SequenceSite21478 - - - - Q9UG43 - UniProt - - - - - - MOD_RES 267 267 N6-acetyllysine. - - - - - - Platelet-derived growth factor, B chain with retention motif - - - - - http://www.reactome.org/biopax/46/48887#Protein2130 - Reactome DB_ID: 381904 - PDGFB(82-241) - - - - EQUAL - 283 - http://www.reactome.org/biopax/46/48887#SequenceSite5736 - - - - 400174 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400174 - - - - ENSG00000079459 - Ensembl - - - - EQUAL - 403 - - - - P78454 - UniProt - - - - BHLHE41 - HGNC Symbol - - - - EQUAL - 300 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21435 - - - - REACT_148648 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148648.1 - - - - EQUAL - 80 - http://www.reactome.org/biopax/46/48887#SequenceSite10128 - - - - NP_003930 - RefSeq - - - - 99313641 - pubchem - - - - - - MOD_RES 66 66 4-carboxyglutamate. - - - - - - MOD_RES 80 80 4-carboxyglutamate. - - - - EQUAL - 437 - - - - Q6VBP9 - UniProt - - - - Q9BUE0 - UniProt - - - - 1989792 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989792 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12068 - - - - - - - bHLHe8 - Class E basic helix-loop-helix protein 8 - 2.3.1.48 - hCLOCK - KIAA0334 - BHLHE8 - CLOCK - - - - - - - - - - - - - - - - - - - - - - - CLOCK_HUMAN - Circadian locomoter output cycles protein kaput - FUNCTION: ARNTL/2-CLOCK heterodimers activate E-box element (5'- CACGTG-3') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression (By similarity). Acetylates primarily histones H3 and H4 (By similarity). Acetylates also a non-histone substrate: ARNTL (By similarity). Plays a role in DNA damage response (DDR) signaling during the S phase.CATALYTIC ACTIVITY: Acetyl-CoA + [histone] = CoA + acetyl- [histone].SUBUNIT: Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, ARNTL or ARNTL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with another bHLH protein. Heterodimerization with ARNTL is required for E-box-dependent transactivation, for CLOCK nuclear translocation and degradation, and, for phosphorylation of both CLOCK and ARNTL. Interaction with PER and CRY proteins requires translocation to the nucleus. Interaction of the CLOCK-ARNTL heterodimer with PER or CRY inhibits transcription activation. Binds weakly ARNTL and ARNTL2 to form heterodimers which bind poorly to the E-box motif (By similarity).SUBCELLULAR LOCATION: Nucleus. Chromosome. Cytoplasm (By similarity). Nucleus (By similarity). Note=Shuffling between the cytoplasm and the nucleus is under circadian regulation and is ARNTL-dependent. Phosphorylated form located in the nucleus (By similarity). Localizes to sites of DNA damage in a H2AX- independent manner.TISSUE SPECIFICITY: Expressed in all tissues examined including spleen, thymus, prostate, testis, ovary, small intestine, colon, leukocytes, heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Highest levels in testis and skeletal muscle. Low levels in thymus, lung and liver. Expressed in all brain regions with highest levels in cerebellum. Highly expressed in the suprachiasmatic nucleus (SCN).PTM: Phosphorylation is dependent on CLOCK-ARNTL heterodimer formation (By similarity).MISCELLANEOUS: CLOCK-ARNTL double mutations within the PAS domains result in syngernistic desensitization to high levels of CRY on repression of CLOCK-ARNTL transcriptional activity of PER1 and disrupt circadian rhythmicity.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.SEQUENCE CAUTION: Sequence=BAA20792.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12074 - - - - - - Q9HBX1 - UniProt - - - - ENST00000355815 - Ensembl - - - - Q9UPC9 - UniProt - - - - 1989789 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989789 - - - - - - CLOCK_HUMAN, phosphorylated - Circadian locomoter output cycles protein kaput, phosphorylated - p-S-CLOCK - - - - - - http://www.reactome.org/biopax/46/48887#Protein11501 - Reactome DB_ID: 421310 - p-CLOCK - - - - EQUAL - 241 - http://www.reactome.org/biopax/46/48887#SequenceSite4969 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5777 - - - - ENST00000282441 - Ensembl - - - - - - MOD_RES 86 86 4-carboxyglutamate. - - - - EQUAL - 267 - - - - HGNC:2707 - HGNC - - - - ESRRA - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5633 - - - - - - EQUAL - 255 - http://www.reactome.org/biopax/46/48887#SequenceSite15686 - - - - ACE2 - HGNC - - - - Q86TN8 - UniProt - - - - - - MOD_RES 750 750 Phosphoserine. - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4779 - - - - - - - - - - KIAA1025 - THRAP2 - Mediator complex subunit 13-like - Thyroid hormone receptor-associated protein 2 - TRAP240L - PROSIT240 - Thyroid hormone receptor-associated protein complex 240 kDa component-like - MED13L - - - - - - - - - - - - - - - - - - MD13L_HUMAN - Mediator of RNA polymerase II transcription subunit 13-like - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. This subunit may specifically regulate transcription of targets of the Wnt signaling pathway and SHH signaling pathway.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).TISSUE SPECIFICITY: Highly expressed in brain (cerebellum), heart (aorta), skeletal muscle, kidney, placenta and peripheral blood leukocytes. Highly expressed in fetal brain.DISEASE: Transposition of the great arteries dextro-looped 1 (DTGA1) [MIM:608808]: A congenital heart defect consisting of complete inversion of the great vessels, so that the aorta incorrectly arises from the right ventricle and the pulmonary artery incorrectly arises from the left ventricle. This creates completely separate pulmonary and systemic circulatory systems, an arrangement that is incompatible with life. The presence or absence of associated cardiac anomalies defines the clinical presentation and surgical management of patients with transposition of the great arteries. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Note=A chromosomal aberration involving MED13L is found in a patient with transposition of the great arteries, dextro- looped and mental retardation. Translocation t(12;17)(q24.1;q21).SIMILARITY: Belongs to the Mediator complex subunit 13 family.SEQUENCE CAUTION: Sequence=BAB14697.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_117927 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117927.1 - - - - ENSP00000342343 - Ensembl - - - - A8K866 - UniProt - - - - - - ferriprotoheme IX - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule969 - Reactome DB_ID: 1237011 - ferriheme b - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1169 - - - - - - - - - Expression of Farnesyldiphosphate Farnesyltransferase (FDFT1, Squalene Synthase) - Authored: May, B, 2011-09-28 - Reviewed: Liang, Guosheng, 2012-08-25 - The FDFT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-09-28 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4678 - - - - - HGNC:11806 - HGNC - - - - REACT_20402 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20402.3 - - - - ENST00000216338 - Ensembl - - - - A4LAZ5 - UniProt - - - - ENSP00000300060 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10065 - - - - - - - - MED15_HUMAN - Mediator of RNA polymerase II transcription subunit 15 - - - - - Reactome DB_ID: 556827 - http://www.reactome.org/biopax/46/48887#Protein6491 - MED15 - - - - ENSP00000287820 - Ensembl - - - - - - Fatty acid-binding protein, liver - FABPL_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein13756 - Reactome DB_ID: 1989743 - FABP1 - - - - Q14192 - UniProt - - - - EQUAL - 714 - - - - - - - - - - - - TEAD:YAP1 - http://www.reactome.org/biopax/46/48887#Complex4781 - Reactome DB_ID: 2032772 - - - - 159866 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159866 - - - - NM_001256091 - RefSeq - - - - 10408760 - Park EA - Cook GA - PubMed - Expression and regulation of carnitine palmitoyltransferase-Ialpha and -Ibeta genes. - Am J Med Sci 318(1);43-8 - 1999 - - - - ENSP00000265350 - Ensembl - - - - MI:2163 - Molecular Interactions Ontology - - - - REACT_7081 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7081.4 - - - - 2HZD - PROTEIN DATA BANK - - - - - - MOD_RES 152 152 Phosphoserine. - - - - Q13354 - UniProt - - - - - - MOD_RES 500 500 N6-acetyllysine. - - - - 18981473 - Lefterova, MI - Cristancho, A - Schupp, M - Steger, DJ - Zhang, Y - Stoeckert CJ, Jr - Lazar, MA - Liu, XS - Zhuo, D - Schug, J - Feng, D - Pubmed - PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale - Genes Dev 22:2941-52 - 2008 - - - - ENSP00000288599 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10121 - - - - 1961767 - DiDonato S - Taroni F - Liras Martin A - Colombo I - Tarelli GT - Rocchi M - Finocchiaro G - PubMed - cDNA cloning, sequence analysis, and chromosomal localization of human carnitine palmitoyltransferase. - Proc Natl Acad Sci U S A 88(23);10981 - 1991 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10122 - - - - GO:0005811 - Gene Ontology - - - - - - MOD_RES 424 424 Sulfotyrosine (Potential). - - - - MYMOFIZGZYHOMD-UHFFFAOYSA-N - InChIKey - - - - EQUAL - 56 - - - - EQUAL - 2016 - - - - 1408 - NCBI Gene - - - - 603426 - omim - - - - HGNC:3551 - HGNC - - - - 8145523 - pubchem-substance - - - - NP_055267 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1101 - - - - Q13000 - UniProt - - - - EQUAL - 558 - - - - EQUAL - 79 - http://www.reactome.org/biopax/46/48887#SequenceSite9871 - - - - ENSP00000340816 - Ensembl - - - - MOD_RES Omega-N-methylated arginine - - - - - - Angiotensin-(3-8) - ANGT_HUMAN - ANG3-8 - Angiotensin IV - AGT(36-41) - - - - - Reactome DB_ID: 2022355 - http://www.reactome.org/biopax/46/48887#Protein12354 - AGT - - - - - - - - - - Nuclear receptor coactivator 6-interacting protein - 2.1.1.- - PIMT - NCOA6IP - PRIP-interacting protein with methyltransferase motif - HCA137 - Hepatocellular carcinoma-associated antigen 137 - CLL-associated antigen KW-2 - TGS1 - PIPMT - Cap-specific guanine-N2 methyltransferase - - - - - - - - - - - - - - - - - - TGS1_HUMAN - Trimethylguanosine synthase - FUNCTION: Catalyzes the 2 serial methylation steps for the conversion of the 7-monomethylguanosine (m(7)G) caps of snRNAs and snoRNAs to a 2,2,7-trimethylguanosine (m(2,2,7)G) cap structure. The enzyme is specific for guanine, and N7 methylation must precede N2 methylation. Hypermethylation of the m7G cap of U snRNAs leads to their concentration in nuclear foci, their colocalization with coilin and the formation of canonical Cajal bodies (CBs). Plays a role in transcriptional regulation.CATALYTIC ACTIVITY: S-adenosyl-L-methionine + m(7)G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(2,7)G(5')pppR-RNA.CATALYTIC ACTIVITY: S-adenosyl-L-methionine + m(2,7)G(5')pppR-RNA = S-adenosyl-L-homocysteine + m(2,2,7)G(5')pppR-RNA.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=30 uM for m(7)GDP; KM=5 uM for S-adenosyl-L-methionine; pH dependence: Optimum pH is 8.5-9.5;SUBUNIT: May form homooligomers. Interacts with CREBBP/CBP, EED/WAIT1, EP300/P300, NCOA6/PRIP, PPARBP/PBP and SMN.SUBCELLULAR LOCATION: Cytoplasm. Nucleus, Cajal body. Note=A 90 kDa isoform is found in the nucleus while a 55 kDa isoform is found in the cytoplasm and colocalizes with the tubulin network.TISSUE SPECIFICITY: Ubiquitously expressed. High expression in heart, skeletal muscle, kidney, liver and placenta.SIMILARITY: Belongs to the methyltransferase superfamily. Trimethylguanosine synthase family.SEQUENCE CAUTION: Sequence=AAH11999.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15516.1; Type=Erroneous initiation; Note=Translation N-terminally extended; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_20368 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20368.2 - - - - 1989762 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989762 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10186 - - - - - - 159727 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159727 - - - - EQUAL - 505 - http://www.reactome.org/biopax/46/48887#SequenceSite18499 - - - - EQUAL - 55 - - - - NFYB - HGNC Symbol - - - - HGNC:6997 - HGNC - - - - 184206 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=184206 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14070 - - - - EQUAL - 593 - http://www.reactome.org/biopax/46/48887#SequenceSite21486 - - - - NP_001327 - RefSeq - - - - 1989752 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989752 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4730 - - - - - - - NM_006534 - RefSeq - - - - Q53SQ3 - UniProt - - - - - MED19 - Mediator complex subunit 19 - Lung cancer metastasis-related protein 1 - LCMR1 - - - - - - - - - - - - - - MED19_HUMAN - Mediator of RNA polymerase II transcription subunit 19 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=A0JLT2-1; Sequence=Displayed; Name=2; IsoId=A0JLT2-2; Sequence=VSP_028121, VSP_028122; Note=No experimental confirmation available;SIMILARITY: Belongs to the Mediator complex subunit 19 family.SEQUENCE CAUTION: Sequence=AAN16075.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - AVP - HGNC - - - - Q5SZU2 - UniProt - - - - - - MOD_RES 603 603 Phosphothreonine. - - - - NP_002599 - RefSeq - - - - ENSP00000229418 - Ensembl - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of TNFRSF21' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation219 - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction158 - Edited: May, B, 2011-11-08 - The HMGCS2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - Expression of HMGCS2 - - - - - - MOD_RES 116 116 Phosphothreonine. - - - - ENSP00000387672 - Ensembl - - - - 4209 - NCBI Gene - - - - 9012850 - Li, X - Ring, HZ - McKnight, SL - Russell, DW - Barnard, M - Tian, H - Francke, U - Shelton, J - Richardson, J - Zhou, YD - Pubmed - Molecular characterization of two mammalian bHLH-PAS domain proteins selectively expressed in the central nervous system - Proc Natl Acad Sci U S A 94:713-8 - 1997 - - - - Q9UCU6 - UniProt - - - - CTSD - HGNC Symbol - - - - MOD_RES N-acetylmethionine - - - - NM_001193350 - RefSeq - - - - PTHR22844:SF13 - PANTHER Family - - - - - EQUAL - 84 - http://www.reactome.org/biopax/46/48887#SequenceSite10129 - - - - 133522 - NCBI Gene - - - - - - MOD_RES 149 149 Phosphoserine. - - - - HGNC:7670 - HGNC - - - - ENST00000353205 - Ensembl - - - - ENSG00000126368 - Ensembl - - - - 1989759 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989759 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5652 - - - - - - Q09472 - UniProt - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite21697 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature187 - - - - EQUAL - 1529 - - - - 8060328 - Ohba, Y - Kawabe, Y - Matsumoto, A - Nabata, H - Endo, A - Wada, Y - Suzuki, T - Yazaki, Y - Itakura, H - Honda, M - Pubmed - Sterol mediated regulation of SREBP-1a,1b,1c and SREBP-2 in cultured human cells - Biochem Biophys Res Commun 202:1460-7 - 1994 - - - - - - MOD_RES 862 862 Phosphoserine. - - - - EQUAL - 2261 - http://www.reactome.org/biopax/46/48887#SequenceSite25353 - - - - MEF2C - HGNC - - - - - - MOD_RES 61 61 4-carboxyglutamate. - - - - EQUAL - 176 - - - - - - MOD_RES 2063 2063 Phosphoserine. - - - - ENST00000341376 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12810 - - - - Q96BK2 - UniProt - - - - NP_001001653 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature819 - - - - Q6IB05 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10764 - - - - SERPINE1 - HGNC Symbol - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of PPARA' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation101 - - - - - - MOD_RES 245 245 N6-acetyllysine. - - - - HELZ2 - HGNC - - - - EQUAL - 200 - http://www.reactome.org/biopax/46/48887#SequenceSite12391 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10038 - - - - ENSP00000312617 - Ensembl - - - - Q9NYE7 - UniProt - - - - NM_005765 - RefSeq - - - - Q9Y660 - UniProt - - - - EQUAL - 72 - - - - ENSP00000353847 - Ensembl - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep3057 - - - - CYP7A1 - HGNC Symbol - - - - HGNC:19971 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10072 - - - - - - - - alpha-linolenic acid - - - - Reactome DB_ID: 400174 - http://www.reactome.org/biopax/46/48887#SmallMolecule737 - ALA - - - - HGNC:2082 - HGNC - - - - HGNC:3355 - HGNC - - - - 159822 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159822 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5657 - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12828 - - - - ENSG00000113580 - Ensembl - - - - 605732 - omim - - - - Regeneration-associated protein 3 - Apo-AV - APOA5 - Apolipoprotein A5 - RAP3 - ApoA-V - - - - - - - - - - - - - - - - - - - APOA5_HUMAN - Apolipoprotein A-V - FUNCTION: Minor apolipoprotein mainly associated with HDL and to a lesser extent with VLDL. May also be associated with chylomicrons. Important determinant of plasma triglyceride (TG) levels by both being a potent stimulator of apo-CII lipoprotein lipase (LPL) TG hydrolysis and a inhibitor of the hepatic VLDL-TG production rate (without affecting the VLDL-apoB production rate) (By similarity). Activates poorly lecithin:cholesterol acyltransferase (LCAT) and does not enhance efflux of cholesterol from macrophages.SUBUNIT: Interacts with GPIHBP1.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Liver and plasma.INDUCTION: Up-regulated by PPARA agonists, which are used clinically to lower serum TG (such as fibrates).PTM: Phosphorylation sites are present in the extracellular medium.POLYMORPHISM: Three common alleles are known: allele APOA5*1, APOA5*2 and APOA5*3. The APOA5*2 haplotype, which consists of 3 non-coding SNPs, is present in approximately 16% of Caucasians and is associated with increased plasma triglyceride concentrations. APOA5*3 haplotype is defined by the rare Ser-19-Trp substitution. Together, the APOA5*2 and APOA5*3 haplotypes are found in 25 to 50% of African Americans, Hispanics, and Caucasians.DISEASE: Hypertriglyceridemia, familial (FHTR) [MIM:145750]: A common inherited disorder in which the concentration of very low density lipoprotein (VLDL) is elevated in the plasma. This leads to increased risk of heart disease, obesity, and pancreatitis. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Hyperlipoproteinemia 5 (HLPP5) [MIM:144650]: Characterized by increased amounts of chylomicrons and very low density lipoprotein (VLDL) and decreased low density lipoprotein (LDL) and high density lipoprotein (HDL) in the plasma after a fast. Numerous conditions cause this phenotype, including insulin- dependent diabetes mellitus, contraceptive steroids, alcohol abuse, and glycogen storage disease type 1A (GSD1A). Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: Induced in early phase of liver regeneration.SIMILARITY: Belongs to the apolipoprotein A1/A4/E family.CAUTION: It is uncertain whether Met-1 or Met-4 is the initiator.SEQUENCE CAUTION: Sequence=AAF25661.1; Type=Erroneous initiation; Sequence=AAF25662.1; Type=Erroneous initiation; Sequence=AAQ89109.1; Type=Erroneous termination; Positions=275; Note=Translated as Gln; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_13014 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13014.2 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The APOA1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction144 - Reviewed: Kersten, S, 2009-06-08 - Expression of APOA1 - - - - 8336730 - Brancolini, C - Avanzi, G - Manfioletti, G - Schneider, C - Pubmed - The protein encoded by a growth arrest-specific gene (gas6) is a new member of the vitamin K-dependent proteins related to protein S, a negative coregulator in the blood coagulation cascade - Mol Cell Biol 13:4976-85 - 1993 - - - - REACT_117955 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117955.1 - - - - EQUAL - 776 - http://www.reactome.org/biopax/46/48887#SequenceSite5365 - - - - ENST00000256379 - Ensembl - - - - 400199 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400199 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5783 - - - - UBA52 - HGNC - - - - EQUAL - 66 - - - - - DNA Containing an ROR Element - - - - RORE (DNA) - http://www.reactome.org/biopax/46/48887#PhysicalEntity621 - Reactome DB_ID: 1368102 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21489 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10133 - - - - 607956 - omim - - - - EQUAL - 180 - - - - ENSP00000416498 - Ensembl - - - - - - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule1078 - Reactome DB_ID: 2065401 - enalaprilat - - - - - - MOD_RES 157 157 Phosphothreonine. - - - - REACT_8056 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_8056.1 - - - - Neuronal cell death-inducible putative kinase - NIPK - C20orf97 - TRB-3 - p65-interacting inhibitor of NF-kappa-B - SKIP3 - TRIB3 - SINK - TRB3 - - - - - - - - - - - - - - - - - - TRIB3_HUMAN - Tribbles homolog 3 - FUNCTION: Disrupts insulin signaling by binding directly to Akt kinases and blocking their activation. May bind directly to and mask the 'Thr-308' phosphorylation site in AKT1. Binds to ATF4 and inhibits its transcriptional activation activity. Interacts with the NF-kappa-B transactivator p65 RELA and inhibits its phosphorylation and thus its transcriptional activation activity. Interacts with MAPK kinases and regulates activation of MAP kinases. May play a role in programmed neuronal cell death but does not appear to affect non-neuronal cells. Does not display kinase activity. Inhibits the transcriptional activity of DDIT3/CHOP and is involved in DDIT3/CHOP-dependent cell death during ER stress. Can inhibit APOBEC3A editing of nuclear DNA.SUBUNIT: Interacts with AKT1, AKT2, ATF4, MAP2K1 and MAP2K7. Interacts with DDIT3/CHOP and inhibits its interaction with EP300/P300. Interacts (via N-terminus) with APOBEC3A. Interacts with APOBEC3C.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Highest expression in liver, pancreas, peripheral blood leukocytes and bone marrow. Also highly expressed in a number of primary lung, colon and breast tumors. Expressed in spleen, thymus, and prostate and is undetectable in other examined tissues, including testis, ovary, small intestine, colon, leukocyte, heart, brain, placenta, lung, skeletal muscle, and kidney.INDUCTION: By hypoxia, TNF, and by nutrient starvation. Expression is PI 3-kinase and/or NF-kappa-B-dependent. Induced by ER stress via ATF4-DDIT3/CHOP pathway and can downregulate its own induction by repression of ATF4-DDIT3/CHOP functions.DOMAIN: The protein kinase domain is predicted to be catalytically inactive.SIMILARITY: Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. Tribbles subfamily.SIMILARITY: Contains 1 protein kinase domain.CAUTION: The role of this protein in Akt activation has been demonstrated by Du et al (PubMed:12791994) for the mouse ortholog but Iynedjian (PubMed:15469416) has not been able to reproduce the result in rat hepatocytes. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2337 - - - - Q92883 - UniProt - - - - EQUAL - 154 - - - - Q96NW8 - UniProt - - - - REACT_147760 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147760.2 - - - - NM_199141 - RefSeq - - - - 607008 - omim - - - - ENSP00000385097 - Ensembl - - - - 3158 - NCBI Gene - - - - ANPEP - HGNC - - - - 1480021 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1480021 - - - - ENST00000469224 - Ensembl - - - - 1R42 - PROTEIN DATA BANK - - - - CPB1 - HGNC Symbol - - - - B4DX67 - UniProt - - - - EQUAL - 691 - http://www.reactome.org/biopax/46/48887#SequenceSite21692 - - - - - - MOD_RES 651 651 Phosphothreonine; by PKC/PRKCZ. - - - - A9IZ92 - UniProt - - - - 1606710 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1606710 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10193 - - - - - - EQUAL - 66 - - - - - - MOD_RES 76 76 4-carboxyglutamate. - - - - ENSG00000196498 - Ensembl - - - - Q8NI33 - UniProt - - - - HGNC:601 - HGNC - - - - 11906282 - Kuntz ID - Huo S - Kollman PA - Wang J - Cieplak P - PubMed - Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. - J Med Chem 45(7);1412-9 - 2002 - - - - - - MOD_RES 1554 1554 N6-acetyllysine; by autocatalysis. - - - - 1605563 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1605563 - - - - - - F-box-like/WD repeat-containing protein - TBL1R_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein3202 - Reactome DB_ID: 351643 - TBL1XR1 - - - - - - UBC(1-76) - ubiquitin (UBC 1) - - - - - Reactome DB_ID: 939871 - http://www.reactome.org/biopax/46/48887#Protein2477 - UBC - - - - P22891 - UniProt - - - - 8921389 - Bootsma, D - Kobayashi, K - Takao, M - Yasui, A - Eker, AP - van der Spek, PJ - Pubmed - Cloning, tissue expression, and mapping of a human photolyase homolog with similarity to plant blue-light receptors - Genomics 37:177-82 - 1996 - - - - 1989797 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989797 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21453 - - - - C7ECU1 - UniProt - - - - NP_858045 - RefSeq - - - - EQUAL - 161 - - - - ATF2 - HGNC - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ACOX1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation193 - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-06-18 - http://www.reactome.org/biopax/46/48887#TemplateReaction61 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - The DEC2 (BHLHE41, BHLHB3) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds E-box elements in the DEC2 promoter and activates transcription of DEC2. - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Authored: May, B, 2010-06-18 - Expression of DEC2 (BHLHE41, BHLHB3) - - - - - HD3 - RPD3-2 - HDAC3 - 3.5.1.98 - SMAP45 - - - - - - - - - - - - - - - - - HDAC3_HUMAN - Histone deacetylase 3 - FUNCTION: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4), and some other non-histone substrates. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Probably participates in the regulation of transcription through its binding to the zinc-finger transcription factor YY1; increases YY1 repression activity. Required to repress transcription of the POU1F1 transcription factor. Acts as a molecular chaperone for shuttling phosphorylated NR2C1 to PML bodies for sumoylation (By similarity).CATALYTIC ACTIVITY: Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.SUBUNIT: Interacts with HDAC7 and HDAC9. Forms a heterologous complex at least with YY1. Interacts with DAXX, HDAC10 and DACH1. Found in a complex with NCOR1 and NCOR2. Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1R, CORO2A and GPS2. Interacts with BCOR, MJD2A/JHDM3A, NRIP1, PRDM6 and SRY. Interacts with BTBD14B. Interacts with GLIS2. Interacts (via the DNA-binding domain) with NR2C1; the interaction recruits phosphorylated NR2C1 to PML bodies for sumoylation (By similarity). Component of the Notch corepressor complex. Interacts with CBFA2T3 and NKAP. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with and deacetylates MAPK14. Interacts with ZMYND15 (By similarity).SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=RPD3-2B; IsoId=O15379-1; Sequence=Displayed; Name=2; Synonyms=RPD3-2A; IsoId=O15379-2; Sequence=VSP_002079;TISSUE SPECIFICITY: Widely expressed.PTM: Sumoylated in vitro.SIMILARITY: Belongs to the histone deacetylase family. HD type 1 subfamily.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/HDAC3ID40804ch5q31.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5664 - - - - - - ENST00000546179 - Ensembl - - - - Q7KYV3 - UniProt - - - - - - MOD_RES 1032 1032 Phosphothreonine; by MAPK1 or MAPK3. - - - - EQUAL - 46 - http://www.reactome.org/biopax/46/48887#SequenceSite21716 - - - - 1KKQ - PROTEIN DATA BANK - - - - EQUAL - 30 - http://www.reactome.org/biopax/46/48887#SequenceSite23010 - - - - CHEBI:44701 - ChEBI - - - - REACT_148333 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148333.1 - - - - EQUAL - 1457 - - - - - - MOD_RES 156 156 Phosphothreonine. - - - - ENSP00000379322 - Ensembl - - - - NM_001136198 - RefSeq - - - - ABCA1 - HGNC Symbol - - - - O95477 - UniProt - - - - Q86UY2 - UniProt - - - - NM_000029 - RefSeq - - - - 561161 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561161 - - - - NM_001139467 - RefSeq - - - - 2906314 - Schneider C - Kooiman PM - van der Bliek AM - Borst P - PubMed - Sequence of mdr3 cDNA encoding a human P-glycoprotein. - Gene 71(2);401-11 - 1988 - - - - EQUAL - 79 - - - - NP_001180279 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10124 - - - - EQUAL - 684 - http://www.reactome.org/biopax/46/48887#SequenceSite1791 - - - - EQUAL - 408 - - - - EQUAL - 586 - http://www.reactome.org/biopax/46/48887#SequenceSite21484 - - - - 1EGC - PROTEIN DATA BANK - - - - ENSP00000385523 - Ensembl - - - - - - MOD_RES 758 758 N6-acetyllysine (By similarity). - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature820 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12813 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1033 - - - - 1KLT - PROTEIN DATA BANK - - - - - 6.3.2.19 - - - - - Ubiquitination of PER Proteins - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3864 - Edited: May, B, 2010-02-20 - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Polyubiquitination of PER proteins is directed by the Beta-TrCP1 component of SCF E3 ubiquitin ligase. The polyubiquitinated PER proteins are recognized and degraded by the 26S proteasome. Degradation of PER proteins occurs during the night and is necessary to allow new transcription of BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) targets in the morning during the circadian cycle. - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12934 - - - - EQUAL - 750 - - - - - ANPEP Hydrolyzes Angiotensin-(2-8) to Yield Angiotensin-(3-8) - - - - - - - - ANPEP Hydrolyzes Angiotensin III to Yield Angiotensin IV - Authored: May, B, 2011-11-19 - Aminopeptidase N (APN, ANPEP, aminopeptidase M, alanyl aminopeptidase) hydrolyzes angiotensin-(2-8) (angiotensin III) to yield angiotensin-(3-8) (angiotensin IV) (see the positive control reactions in Diaz-Perales et al. 2005). Aminopeptidase O (AOPEP) also hydrolyzes angiotensin-(2-8) to angiotensin-(3-8) in vitro (Diaz-Perales et al. 2005) but AOPEP is located in the nucleolus in vivo (Axton et al. 2008) and angiotensin-(2-8) has not been observed in the nucleus. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4050 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - - - - - 442481 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442481 - - - - - 6.3.2.19 - - - - - - - Ubiquitination of Emi1 by SCF-beta-TrCP - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2158 - Reviewed: Peters, JM, 2006-03-27 22:55:09 - Edited: Matthews, L, 2006-01-30 00:00:00 - Following its association with SCF-βTrCP, phospho-Emi1 is poly-ubiquitinated. - Authored: Lorca, T, Castro, A, 2006-01-26 00:00:00 - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1814 - - - - - - EQUAL - 18 - http://www.reactome.org/biopax/46/48887#SequenceSite23020 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10018 - - - - ENSP00000386526 - Ensembl - - - - Q8NF16 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5791 - - - - EQUAL - 73 - http://www.reactome.org/biopax/46/48887#SequenceSite21686 - - - - NM_134262 - RefSeq - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite23008 - - - - ENSP00000405574 - Ensembl - - - - 11533142 - pubchem - - - - ABCB4 - HGNC - - - - REACT_25684 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25684.2 - - - - - 12.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12929 - - - - 186785 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=186785 - - - - ENSP00000410369 - Ensembl - - - - REACT_20839 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20839.3 - - - - Q14340 - UniProt - - - - ENSP00000290866 - Ensembl - - - - ENST00000360851 - Ensembl - - - - Q9Y3N1 - UniProt - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite10123 - - - - CHEBI:13285 - ChEBI - - - - B5MEC2 - UniProt - - - - ENST00000358129 - Ensembl - - - - - - MOD_RES 59 59 4-carboxyglutamate. - - - - REACT_1864 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1864.2 - - - - Q5JR00 - UniProt - - - - 12011767 - Chyczewski L - Olszewska E - Chodynicki S - PubMed - Immunohistochemical investigations of cathepsin D activity in the structures of cholesteatoma. - Med Sci Monit 8(5);BR184-6 - 2002 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1106 - - - - EQUAL - 28 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5796 - - - - ENSP00000431574 - Ensembl - - - - EQUAL - 38 - http://www.reactome.org/biopax/46/48887#SequenceSite21746 - - - - EQUAL - 247 - - - - ENST00000372455 - Ensembl - - - - 18288277 - Kersten, S - Pubmed - Peroxisome proliferator activated receptors and lipoprotein metabolism - PPAR Res 2008:132960 - 2008 - - - - 20110263 - Kersten, S - de Groot, PJ - de Vries, SC - Muller, M - Degenhardt, T - Carlberg, C - Vaisanen, S - Heinaniemi, M - van der Meer, DL - Pubmed - Profiling of promoter occupancy by PPAR{alpha} in human hepatoma cells via ChIP-chip analysis - Nucleic Acids Res - 2010 - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite21722 - - - - EQUAL - 1592 - - - - P38435 - UniProt - - - - OYHQOLUKZRVURQ-HZJYTTRNSA-N - InChIKey - - - - REACT_6992 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6992.2 - - - - - - phospho-CREB - p-S133-CREB1 - cAMP response element binding protein - - - - - - Reactome DB_ID: 111910 - http://www.reactome.org/biopax/46/48887#Protein216 - CREB - - - - - TIG1 - TNRC7 - TIG-1 - Mediator complex subunit 15 - PC2 glutamine/Q-rich-associated protein - Activator-recruited cofactor 105 kDa component - TPA-inducible gene 1 protein - Trinucleotide repeat-containing gene 7 protein - CTG repeat protein 7a - MED15 - Positive cofactor 2 glutamine/Q-rich-associated protein - PCQAP - ARC105 - CTG7A - - - - - - - - - - - - - - - - - - - - - - - - - - - MED15_HUMAN - Mediator of RNA polymerase II transcription subunit 15 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Required for cholesterol-dependent gene regulation. Positively regulates the Nodal signaling pathway.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with SMAD2, SMAD3, SREBF1 and SREBF2. Interacts with WWTR1. Interacts with TRIM11.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q96RN5-1; Sequence=Displayed; Name=2; IsoId=Q96RN5-2; Sequence=VSP_003922; Name=3; IsoId=Q96RN5-3; Sequence=VSP_013024, VSP_003922; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in all tissues examined, including heart, brain, lung, spleen, thymus, pancreas, blood leukocyte and placenta. However, the level of expression varied, with highest expression in the placenta and peripheral blood and lowest in the pancreas and kidney.INDUCTION: By 12-O-tetradecanoylphorbol-13-acetate (TPA).PTM: Ubiquitinated by TRIM11, leading to proteasomal degradation.POLYMORPHISM: The poly-Gln region from amino acids 235-262 of PCQAP is polymorphic. There are from 15 to 18 repeats in the Italian population.SIMILARITY: Belongs to the Mediator complex subunit 15 family.SEQUENCE CAUTION: Sequence=AAC12944.1; Type=Frameshift; Positions=13, 600, 749; Sequence=BAB85034.1; Type=Miscellaneous discrepancy; Note=Several sequencing errors; Sequence=BAC03446.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 699 699 Phosphoserine (By similarity). - - - - ENST00000510942 - Ensembl - - - - REACT_1743 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1743.2 - - - - Q6PK58 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10115 - - - - NP_060489 - RefSeq - - - - CPA3 - HGNC - - - - 2158 - NCBI Gene - - - - Q9Y297 - UniProt - - - - 380749 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380749 - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of FATP1 (SLC27A1)' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation207 - - - - EQUAL - 439 - - - - Q99743 - UniProt - - - - Q9P122 - UniProt - - - - O95403 - UniProt - - - - REACT_119390 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119390.1 - - - - NM_000820 - RefSeq - - - - CHEBI:15756 - ChEBI - - - - REACT_118642 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118642.2 - - - - - - SREBP1 - SRBP1_HUMAN - SREBF1(1-1147) - Sterol regulatory element-binding protein 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein11547 - Reactome DB_ID: 1368141 - SREBF1 - - - - - - Aryl hydrocarbon receptor nuclear translocator-like protein 2 - BMAL2 - BMAL2_HUMAN - ARNTL2 - - - - - Reactome DB_ID: 879826 - http://www.reactome.org/biopax/46/48887#Protein11508 - CLIF - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12949 - - - - 26697309 - pubchem-substance - - - - - PPARGC1 - PPARGC-1-beta - PPAR-gamma coactivator 1-beta - PGC1B - PERC - PGC1 - PGC-1-beta - PPARGC1B - PGC-1-related estrogen receptor alpha coactivator - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PRGC2_HUMAN - Peroxisome proliferator-activated receptor gamma coactivator 1-beta - FUNCTION: Plays a role of stimulator of transcription factors and nuclear receptors activities. Activates transcritional activity of estrogen receptor alpha, nuclear respiratory factor 1 (NRF1) and glucocorticoid receptor in the presence of glucocorticoids. May play a role in constitutive non-adrenergic-mediated mitochondrial biogenesis as suggested by increased basal oxygen consumption and mitochondrial number when overexpressed. May be involved in fat oxidation and non-oxidative glucose metabolism and in the regulation of energy expenditure.SUBUNIT: Interacts with hepatocyte nuclear factor 4-alpha/HNF4A, Sterol regulatory binding transcription factor 1/SREBF1, PPAR- alpha/PPARA, thyroid hormone receptor beta/THRB and host cell factor/HCFC1. Interacts with estrogen-related receptor gamma/ESRRG and alpha/ESRRA. Interacts with PRDM16 (By similarity). Interacts with estrogen receptor alpha/ESR1.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Name=1; Synonyms=PGC1beta-1a; IsoId=Q86YN6-1; Sequence=Displayed; Name=2; Synonyms=PGC1beta-2a; IsoId=Q86YN6-2; Sequence=VSP_019299; Name=3; Synonyms=PGC1beta-1b; IsoId=Q86YN6-3; Sequence=VSP_019301; Name=4; Synonyms=PGC1beta-2b; IsoId=Q86YN6-4; Sequence=VSP_019299, VSP_019301; Name=5; Synonyms=PERC-s; IsoId=Q86YN6-5; Sequence=VSP_019300; Note=Lacks LXXLL motif 1 and has a reduced ability to enhance the hormone-dependent activity of estrogen receptor alpha; Name=6; IsoId=Q86YN6-6; Sequence=VSP_043374, VSP_019300; Note=No experimental confirmation available;TISSUE SPECIFICITY: Ubiquitous with higher expression in heart, brain and skeletal muscle.INDUCTION: Repressed by saturated fatty acids such as palmitate and stearate in skeletal muscle cells. Induced by insulin and reduced by aging in skeletal muscle biopsies. Down-regulated in type 2 diabetes mellitus subjects as well as in pre-diabetics.DOMAIN: Contains 2 Leu-Xaa-Xaa-Leu-Leu (LXXLL) motif, which are usually required for the association with nuclear receptors (By similarity).POLYMORPHISM: Variation of PPARGC1B may contribute to the pathogenesis of obesity, with a widespread Ala-203 allele being a risk factor for the development of this common disorders.SIMILARITY: Contains 1 RRM (RNA recognition motif) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000371502 - Ensembl - - - - NR3C1 - HGNC - - - - 2022403 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022403 - - - - EQUAL - 773 - - - - - - MOD_RES 347 347 N6-acetyllysine (By similarity). - - - - EQUAL - 389 - - - - D3DQF4 - UniProt - - - - 7296 - NCBI Gene - - - - ENST00000517625 - Ensembl - - - - EQUAL - 519 - http://www.reactome.org/biopax/46/48887#SequenceSite25551 - - - - NM_001270522 - RefSeq - - - - ENSEMBL:ENSG00000113161 HMGCR - - HMGCR - http://www.reactome.org/biopax/46/48887#DnaReference29 - - - - - 612914 - omim - - - - - - ubiquitin (UBC 3) - - - - - Reactome DB_ID: 939853 - http://www.reactome.org/biopax/46/48887#Protein2479 - UBC(153-228) - - - - - - MED16_HUMAN - Mediator of RNA polymerase II transcription subunit 16 - - - - - Reactome DB_ID: 556802 - http://www.reactome.org/biopax/46/48887#Protein6480 - MED16 - - - - - - MOD_RES 59 59 4-carboxyglutamate. - - - - EQUAL - 2438 - - - - 8145136 - pubchem-substance - - - - - - MOD_RES 2065 2065 Phosphoserine. - - - - NM_005920 - RefSeq - - - - EQUAL - 106 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature821 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of GLIPR1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation210 - - - - Q9HBY3 - UniProt - - - - ENSG00000166825 - Ensembl - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12941 - - - - - - MOD_RES 884 884 Phosphoserine; by MAPK; in vitro. - - - - Q15409 - UniProt - - - - - - ubiquitin (UBC 5) - - - - - http://www.reactome.org/biopax/46/48887#Protein2481 - Reactome DB_ID: 939863 - UBC(305-380) - - - - NM_019616 - RefSeq - - - - 11533495 - pubchem - - - - REN - HGNC Symbol - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1269 - - - - NP_001166170 - RefSeq - - - - 90390 - NCBI Gene - - - - Q9UDL6 - UniProt - - - - 10748155 - Vinarov DA - Chun KY - Miziorko HM - Zajicek J - PubMed - 3-Hydroxy-3-methylglutaryl-CoA synthase. A role for glutamate 95 in general acid/base catalysis of C-C bond formation. - J Biol Chem 275(24);17946-53 - 2000 - - - - ENSP00000361535 - Ensembl - - - - Q15648 - UniProt - - - - APOA2 - HGNC Symbol - - - - REACT_115927 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115927.1 - - - - 610197 - omim - - - - 12147324 - Cellini E - Bartoli A - Ortenzi L - Nacmias B - Bagnoli S - Petruzzi C - Serio A - Ciantelli M - Sorbi S - Tedde A - Guarnieri BM - PubMed - Cathepsin D polymorphism in Italian sporadic and familial Alzheimer's disease. - Neurosci Lett 328(3);273-6 - 2002 - - - - NP_703151 - RefSeq - - - - ENST00000325110 - Ensembl - - - - EQUAL - 884 - - - - EQUAL - 664 - - - - - - - - - ACTIVATION - - 'ROR-alpha:Coactivator [nucleoplasm]' positively regulates 'Expression of NR1D1 (REV-ERBA)' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation107 - RORA binds the NR1D1 (REV-ERBA) promoter and activates transcription. - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - Q6UWK9 - UniProt - - - - REACT_5650 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5650.2 - - - - 159735 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159735 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4764 - - - - - - EQUAL - 101 - - - - 2022412 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022412 - - - - - - MOD_RES 1223 1223 Phosphoserine. - - - - ENSG00000005339 - Ensembl - - - - 186822 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=186822 - - - - ENST00000522855 - Ensembl - - - - ENSP00000378416 - Ensembl - - - - EQUAL - 4 - - - - - - ubiquitin (UBC 9) - - - - - http://www.reactome.org/biopax/46/48887#Protein2485 - Reactome DB_ID: 939868 - UBC(609-684) - - - - FBX5 - Early mitotic inhibitor 1 - FBXO5 - EMI1 - - - - - - - - - - - - - - - - - - - - FBX5_HUMAN - F-box only protein 5 - FUNCTION: Regulates progression through early mitosis by inhibiting the anaphase promoting complex/cyclosome (APC). Binds to the APC activators CDC20 and FZR1/CDH1 to prevent APC activation. Can also bind directly to the APC to inhibit substrate-binding.SUBUNIT: Part of a SCF (SKP1-cullin-F-box) protein ligase complex (By similarity). Interacts with BTRC, FZR1/CDH1 and the N-terminal substrate-binding domain of CDC20. Also interacts with EVI5 which blocks its phosphorylation by PLK1 and prevents its subsequent binding to BTRC and degradation.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Cytoplasm, cytoskeleton, spindle. Note=In interphase, localizes in a punctate manner in the nucleus and cytoplasm with some perinuclear concentration. In mitotic cells, localizes throughout the cell, particularly at the spindle.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9UKT4-1; Sequence=Displayed; Name=2; IsoId=Q9UKT4-2; Sequence=VSP_041362;DEVELOPMENTAL STAGE: Accumulates in late G1 phase, levels rise during S phase and drop in early mitosis.DOMAIN: The C-terminal region is required for inhibition of APC activity.PTM: Phosphorylation by CDK2 and subsequently by PLK1 triggers degradation during early mitosis through ubiquitin-mediated proteolysis by the SCF ubiquitin ligase complex containing the F- box protein BTRC. This degradation is necessary for the activation of APC in late mitosis and subsequent mitotic progression.PTM: Ubiquitinated by the by the SCF(BTRC) complex following phosphorylation by PLK1.SIMILARITY: Contains 1 F-box domain.SIMILARITY: Contains 1 IBR-type zinc finger. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - pro-protein C light chain, uncarboxylated - - - - - - http://www.reactome.org/biopax/46/48887#Protein11636 - Reactome DB_ID: 159768 - 3D-PROC(33-197) - - - - F-box/LRR-repeat protein 3A - F-box and leucine-rich repeat protein 3A - FBL3A - FBXL3A - FBXL3 - - - - - - - - - - - - - - FBXL3_HUMAN - F-box/LRR-repeat protein 3 - FUNCTION: Substrate-recognition component of the SCF(FBXL3) E3 ubiquitin ligase complex involved in circadian rhythm function. Plays a key role in the maintenance of both the speed and the robustness of the circadian clock oscillation. The SCF(FBXL3) complex mainly acts in the nucleus and mediates ubiquitination and subsequent degradation of CRY1 and CRY2. Activity of the SCF(FBXL3) complex is counteracted by the SCF(FBXL21) complex. FBXL3 probably recognizes and binds phosphorylated CRY1 and CRY2.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: Part of the SCF (SKP1-CUL1-F-box) E3 ubiquitin-protein ligase complex SCF(FBXL3) composed of CUL1, SKP1, RBX1 and FBXL3. Interacts with CRY1 and CRY2.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Predominantly nuclear.TISSUE SPECIFICITY: Widely expressed.SIMILARITY: Contains 1 F-box domain.SIMILARITY: Contains 7 LRR (leucine-rich) repeats. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21433 - - - - 9333243 - Ozawa, R - Hirose, M - Fukuhara, C - Sakaki, Y - Okamura, H - Tei, H - Shigeyoshi, Y - Pubmed - Circadian oscillation of a mammalian homologue of the Drosophila period gene - Nature 389:512-6 - 1997 - - - - - - MOD_RES 58 58 4-carboxyglutamate. - - - - 174249 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174249 - - - - P34991 - UniProt - - - - - - PER2_HUMAN - Period circadian protein homolog 2 - - - - - - Reactome DB_ID: 3325591 - http://www.reactome.org/biopax/46/48887#Protein11529 - p-S-PER2 - - - - REACT_20026 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20026.4 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature8623 - - - - REACT_148301 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148301.1 - - - - REACT_20362 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20362.1 - - - - CTSG - HGNC Symbol - - - - - - MOD_RES 190 190 Phosphoserine; by PKA (By similarity). - - - - - - Oxygen - - - - Reactome DB_ID: 113534 - http://www.reactome.org/biopax/46/48887#SmallMolecule743 - O2 - - - - - - (9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid - 9(S')-HODE - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule733 - Reactome DB_ID: 381251 - 9S-HODE - - - - Q8N190 - UniProt - - - - 2022414 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022414 - - - - ENST00000359206 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10147 - - - - - - MOD_RES 419 419 Sulfotyrosine (Potential). - - - - P35398 - UniProt - - - - GLIPR1 - HGNC Symbol - - - - CHEBI:13283 - ChEBI - - - - 79718 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5610 - - - - ENST00000227665 - Ensembl - - - - ENSG00000106366 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1766 - - - - REACT_120315 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120315.1 - - - - Q9UD53 - UniProt - - - - B2RP56 - UniProt - - - - UBC - HGNC - - - - 189438 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=189438 - - - - REACT_24153 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24153.2 - - - - - - - - - - - - - - - - PPARA:RXRA Repressor Complex - Reactome DB_ID: 400196 - http://www.reactome.org/biopax/46/48887#Complex5478 - - - - ENST00000337672 - Ensembl - - - - Q6GU45 - UniProt - - - - Q9UCS8 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8359 - - - - HGNC:11716 - HGNC - - - - Q6P9H7 - UniProt - - - - 939188 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939188 - - - - BUFJIHPUGZHTHL-NKFFZRIASA-N - InChIKey - - - - TEAD4 - HGNC - - - - 8402897 - Wang, X - Brown, MS - Admon, A - Briggs, MR - Goldstein, JL - Hua, X - Wu, J - Yokoyama, C - Pubmed - SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene - Cell 75:187-97 - 1993 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21487 - - - - EQUAL - 127 - - - - - - MOD_RES 1215 1215 Phosphothreonine. - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis669 - - - - 159868 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159868 - - - - - - MOD_RES 980 980 Phosphoserine. - - - - Q96J12 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10049 - - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21443 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite11628 - - - - - - MOD_RES 640 640 N6-acetyllysine. - - - - 15270719 - Pouyssegur, J - Chauvet, C - Berra, E - Danan, JL - Bois-Joyeux, B - Pubmed - The gene encoding human retinoic acid-receptor-related orphan receptor alpha is a target for hypoxia-inducible factor 1 - Biochem J 384:79-85 - 2004 - - - - - - MOD_RES 939 939 Phosphoserine. - - - - (2S,3R)-3-hydroxyaspartic acid - - - - - - - - - - - - - - - - - - - - ubiquitin - - - - http://www.reactome.org/biopax/46/48887#Protein1043 - Converted from EntitySet in Reactome - Reactome DB_ID: 113595 - Ub - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5654 - - - - - - - - PER2_HUMAN - Period circadian protein homolog 2 - - - - - http://www.reactome.org/biopax/46/48887#Protein11514 - Reactome DB_ID: 400399 - PER2 - - - - 349685 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=349685 - - - - - - - - - - Edited: May, B, 2011-06-22 - http://www.reactome.org/biopax/46/48887#TemplateReaction74 - The RORA gene is transcribed to yield mRNA and the mRNA is transcribed to yield protein. - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - Expression of RORA (ROR-alpha) - - - - ENSG00000018408 - Ensembl - - - - - - - - - - - Active PDGF dimers (AA, AB, BB) - Reactome DB_ID: 380760 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Complex891 - - - - - - MOD_RES 66 66 4-carboxyglutamate. - - - - 381935 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381935 - - - - CHEBI:13352 - ChEBI - - - - 400183 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400183 - - - - ENSP00000378268 - Ensembl - - - - EQUAL - 540 - - - - L-gamma-carboxyglutamic acid - - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ABCA1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation190 - - - - O-phospho-L-serine - - - - - O-phospho-L-threonine - - - - - ENSP00000361738 - Ensembl - - - - ENSP00000389610 - Ensembl - - - - REACT_2383 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2383.2 - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12944 - - - - NM_181491 - RefSeq - - - - 9427249 - Zylka, MJ - Reppert, SM - Kolakowski LF, Jr - Weaver, DR - Shearman, LP - Pubmed - Two period homologs: circadian expression and photic regulation in the suprachiasmatic nuclei - Neuron 19:1261-9 - 1997 - - - - PROZ - HGNC Symbol - - - - NM_001122 - RefSeq - - - - Q4F964 - UniProt - - - - 12177166 - Ohashi, K - Hasty, AH - Tamura, Y - Kimura, S - Ishibashi, S - Matsuzaka, T - Iizuka, Y - Yamada, N - Yoshikawa, T - Yahagi, N - Shimano, H - Sato, R - Okazaki, H - Harada, K - Osuga, J - Gotoda, T - Amemiya-Kudo, M - Pubmed - Transcriptional activities of nuclear SREBP-1a, -1c, and -2 to different target promoters of lipogenic and cholesterogenic genes - J Lipid Res 43:1220-35 - 2002 - - - - - - MOD_RES 601 601 Omega-N-methylated arginine (By similarity). - - - - NP_671766 - RefSeq - - - - ENST00000395901 - Ensembl - - - - Q6LBS3 - UniProt - - - - O15421 - UniProt - - - - Q9UQV5 - UniProt - - - - Q9HD95 - UniProt - - - - EQUAL - 39 - http://www.reactome.org/biopax/46/48887#SequenceSite21743 - - - - ENST00000240055 - Ensembl - - - - 389058 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389058 - - - - A4D1D5 - UniProt - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite21719 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1047 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10755 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8356 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2747 - - - - F7 - HGNC Symbol - - - - Q15067 - UniProt - - - - ENST00000261523 - Ensembl - - - - REACT_25677 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25677.2 - - - - - - MOD_RES 47 47 4-carboxyglutamate. - - - - EQUAL - 1111 - - - - HGNC:30281 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2097 - - - - - - MOD_RES 445 445 N6-(pyridoxal phosphate)lysine (Probable). - - - - EQUAL - 349 - http://www.reactome.org/biopax/46/48887#SequenceSite20847 - - - - 14718380 - pubchem - - - - REACT_24312 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24312.2 - - - - MED20 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8322 - - - - ESRRA - HGNC Symbol - - - - EQUAL - 89 - - - - REACT_26285 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26285.2 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1083 - - - - NP_001900 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8320 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5635 - - - - - - PTHR22952:SF15 - PANTHER Family - - - - - Q5JUY8 - UniProt - - - - - - Carboxypeptidase B ecNumber3.4.17.2/ecNumber - CBPB1_HUMAN - - - - - Reactome DB_ID: 3229247 - http://www.reactome.org/biopax/46/48887#Protein12358 - CPB1 - - - - - - FBXL3_HUMAN - F-box/LRR-repeat protein 3 - - - - - Reactome DB_ID: 400380 - http://www.reactome.org/biopax/46/48887#Protein11536 - FBXL3 - - - - - - SIN3B_HUMAN - SIN3B isoform 1 - Paired amphipathic helix protein Sin3b - - - - - Reactome DB_ID: 349685 - http://www.reactome.org/biopax/46/48887#Protein13755 - SIN3B-1 - - - - P35399 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5636 - - - - 1.1.4.1 - VKOR - VKORC1 - Vitamin K1 2,3-epoxide reductase subunit 1 - - - - - - - - - - - - - - - - - - - - - VKOR1_HUMAN - Vitamin K epoxide reductase complex subunit 1 - FUNCTION: Involved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin K 2,3-epoxide to active vitamin K.CATALYTIC ACTIVITY: 2-methyl-3-phytyl-1,4-naphthoquinone + oxidized dithiothreitol = 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl- 1,4-naphthoquinone + 1,4-dithiothreitol.SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=MST576; IsoId=Q9BQB6-1; Sequence=Displayed; Name=2; Synonyms=MST134; IsoId=Q9BQB6-2; Sequence=VSP_013363; Name=3; IsoId=Q9BQB6-3; Sequence=VSP_043407; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed at highest levels in fetal and adult liver, followed by fetal heart, kidney, and lung, adult heart, and pancreas.DISEASE: Combined deficiency of vitamin K-dependent clotting factors 2 (VKCFD2) [MIM:607473]: VKCFD leads to a bleeding tendency that is usually reversed by oral administration of vitamin K. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Coumarin resistance (CMRES) [MIM:122700]: A condition characterized by partial or complete resistance to warfarin or other 4-hydroxycoumarin derivatives. These drugs are used as anti- coagulants for the prevention of thromboembolic diseases in subjects with deep vein thrombosis, atrial fibrillation, or mechanical heart valve replacement. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: The location of two cysteine active-site residues within a proposed transmembrane is consistent both with the known hydrophobic environment of the thiol redox site of the enzyme and with the lipophilicity of vitamin K and warfarin.SIMILARITY: Belongs to the VKOR family.SEQUENCE CAUTION: Sequence=AAQ88821.1; Type=Erroneous initiation;WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/vkorc1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 421315 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421315 - - - - EQUAL - 136 - - - - APOA2 - HGNC - - - - Q9UPX5 - UniProt - - - - TXNRD1 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21429 - - - - REACT_25790 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25790.2 - - - - - - - - Pro-prothrombin is transported from the endoplasmic reticulum to the Golgi apparatus - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3895 - In this reaction, 1 molecule of 'pro-prothrombin (factor II)' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5647 - - - - - - ENSP00000363929 - Ensembl - - - - 1989761 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989761 - - - - GO:0005741 - Gene Ontology - - - - - - MOD_RES 89 89 Phosphoserine; by LATS2. - - - - 3932474 - Martin, LF - Wallin, R - Pubmed - Vitamin K-dependent carboxylation and vitamin K metabolism in liver. Effects of warfarin. - J Clin Invest 76:1879-84 - 1985 - - - - REACT_148506 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148506.1 - - - - 400272 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400272 - - - - NP_001070729 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12951 - - - - Q8N3P2 - UniProt - - - - 212418 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212418 - - - - ENST00000545634 - Ensembl - - - - - - MOD_RES 766 766 Phosphoserine (By similarity). - - - - 159845 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159845 - - - - NCOR1 - HGNC Symbol - - - - EQUAL - 136 - - - - - - MOD_RES 636 636 N6-acetyllysine. - - - - EQUAL - 61 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4905 - - - - CD36 - HGNC Symbol - - - - - - - - - - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein12335 - Reactome DB_ID: 2990850 - Renin - - - - REACT_120341 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120341.1 - - - - NP_000812 - RefSeq - - - - - - MOD_RES 254 254 N6-acetyllysine (By similarity). - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8346 - - - - WWTR1 - HGNC - - - - NP_001013417 - RefSeq - - - - ENSP00000352929 - Ensembl - - - - ENST00000368053 - Ensembl - - - - 600046 - omim - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12935 - - - - ENST00000408038 - Ensembl - - - - 446172 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=446172 - - - - ENSP00000233838 - Ensembl - - - - NP_000490 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4956 - - - - ENSP00000324494 - Ensembl - - - - REACT_26573 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26573.3 - - - - ENSG00000109819 - Ensembl - - - - ENST00000287820 - Ensembl - - - - FDFT1 - HGNC - - - - NM_001242539 - RefSeq - - - - D3DQ98 - UniProt - - - - REACT_2437 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2437.2 - - - - - - NEP_HUMAN - Neprilysin - - - - - Reactome DB_ID: 2022342 - http://www.reactome.org/biopax/46/48887#Protein12351 - MME - - - - - - - - - - - - - - - - - pro-GAS6, uncarboxylated + 11 CO2 + 11 O2 + 11 vitamin K hydroquinone -> pro-GAS6 + 11 H2O + 11 vitamin K epoxide - Edited: D'Eustachio, P, 0000-00-00 00:00:00 - The details of the gamma-carboxylation of GAS6 have not been determined directly, but are inferred from those worked out for protein S (Manfioletti et al. 1993). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3891 - Authored: D'Eustachio, P, 2005-05-07 21:30:29 - - - - - - - REACT_27942 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27942.3 - - - - REACT_420 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_420.3 - - - - - - - - - - - - - - - - - ACTIVATION - - 'SREBP1A/1C/2:NF-Y:HMGCS1 gene [nucleoplasm]' positively regulates 'Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1)' - http://www.reactome.org/biopax/46/48887#Control387 - SREBF1A/1C/2 (SREBP1A/1C/2) and NF-Y bind the promoter of the Hydroxymethylglutaryl coenzyme A synthase (HMGCS1) gene and enhance transcription (Shimano et al. 1996, Shimano et al. 1997, Horton et al. 1998, Inoue et al. 1998, Pai et al. 1998, Sakakura et al. 2001, Amemiya-Kudo et al. 2002, Reed et al. 2008, reviewed in Horton et al. 2002). - - - - 8144514 - pubchem - - - - Q53RY2 - UniProt - - - - EQUAL - 82 - http://www.reactome.org/biopax/46/48887#SequenceSite3903 - - - - EQUAL - 499 - http://www.reactome.org/biopax/46/48887#SequenceSite10451 - - - - ENSP00000343205 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14067 - - - - ENST00000406310 - Ensembl - - - - - - MOD_RES 1468 1468 Phosphoserine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12814 - - - - EQUAL - 406 - http://www.reactome.org/biopax/46/48887#SequenceSite12411 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12016 - - - - B9TX55 - UniProt - - - - NP_061828 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12378 - - - - 16857194 - Chong, NW - Codd, V - Samani, NJ - Chan, D - Pubmed - Circadian clock genes cause activation of the human PAI-1 gene promoter with 4G/5G allelic preference - FEBS Lett 580:4469-72 - 2006 - - - - D3DN28 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5639 - - - - - - NP_001171968 - RefSeq - - - - CHEBI:23011 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2231 - - - - EQUAL - 372 - - - - Q5JWT4 - UniProt - - - - 159759 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159759 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10150 - - - - NM_001253881 - RefSeq - - - - ENSP00000301645 - Ensembl - - - - REACT_148083 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148083.2 - - - - EQUAL - 2 - - - - EQUAL - 437 - - - - EQUAL - 550 - - - - 2022405 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022405 - - - - REACT_26103 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26103.3 - - - - REACT_118659 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118659.2 - - - - ENSG00000112237 - Ensembl - - - - MED29 - HGNC - - - - 10024026 - Loew GH - Chang YT - PubMed - Homology modeling and substrate binding study of human CYP4A11 enzyme. - Proteins 34(3);403-15 - 1999 - - - - EQUAL - 854 - - - - MED30 - HGNC Symbol - - - - EQUAL - 1482 - - - - EQUAL - 119 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10075 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10189 - - - - - - - Secreted Angiotensin-converting Enzyme Hydrolyzes Angiotensin I to Yield Angiotensin II - - - - - - - - - - - - - - Secreted ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8) - Authored: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4041 - Edited: May, B, 2011-11-19 - Secreted angiotensin-converting enzyme (ACE) cleaves 2 amino acid residues from the C-terminus of angiotensin-(1-10) (angiotensin I) to yield angiotensin-(1-8) (angiotensin II) (Wei et al. 1991). This reaction is inhibited by drugs used to treat hypertension (angiotensin converting enzyme inhibitors, ACEI) including captopril (Gronhagen-Riska and Fyhrquist 1980, Stewart et al. 1981, Ehlers et al. 1986, Hayakari et al. 1989, Wei et al. 1991, Baudin and Beneteau-Burnat 1999), enalaprilat (metablized from the prodrug enalapril, Wei et al. 1991, Baudin and Beneteau-Burnat 1999), lisinopril ( Ehlers et al. 1991, Natesh et al. 2003), and ramiprilat (metabolized from the prodrug ramipril, Baudin and Beneteau-Burnat 1999). ACE is secreted ("shed") from membranes of endothelial cells by cleavage in the C-terminal region that removes the membrane anchor. - Reviewed: Joseph, J, 2012-08-06 - - - - - EQUAL - 24 - - - - CHEBI:41356 - ChEBI - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The TXNRD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction167 - Expression of TXNRD1 - - - - Q9ULH8 - UniProt - - - - - - MOD_RES 61 61 4-carboxyglutamate. - - - - ENSP00000359206 - Ensembl - - - - ENSG00000146072 - Ensembl - - - - EQUAL - 636 - http://www.reactome.org/biopax/46/48887#SequenceSite21442 - - - - EQUAL - 419 - - - - NM_003213 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8335 - - - - EQUAL - 273 - - - - 9062341 - Brown, MS - Horton, JD - Shimano, H - Hammer, RE - Goldstein, JL - Shimomura, I - Pubmed - Isoform 1c of sterol regulatory element binding protein is less active than isoform 1a in livers of transgenic mice and in cultured cells - J Clin Invest 99:846-54 - 1997 - - - - H0Y308 - UniProt - - - - HGNC:16840 - HGNC - - - - REACT_117940 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117940.3 - - - - 9062340 - Brown, MS - Horton, JD - Shimano, H - Goldstein, JL - Shimomura, I - Pubmed - Differential expression of exons 1a and 1c in mRNAs for sterol regulatory element binding protein-1 in human and mouse organs and cultured cells - J Clin Invest 99:838-45 - 1997 - - - - - - MOD_RES 215 215 Phosphoserine. - - - - NM_014391 - RefSeq - - - - 400267 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400267 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12843 - - - - P15088 - UniProt - - - - EQUAL - 1 - - - - - Processed sterol regulatory element-binding protein 2 - SREBP2 - bHLHd2 - Class D basic helix-loop-helix protein 2 - SREBP-2 - Sterol regulatory element-binding transcription factor 2 - BHLHD2 - SREBF2 - - - - - - - - - - - - - - - - SRBP2_HUMAN - Sterol regulatory element-binding protein 2 - FUNCTION: Transcriptional activator required for lipid homeostasis. Regulates transcription of the LDL receptor gene as well as the cholesterol and to a lesser degree the fatty acid synthesis pathway (By similarity). Binds the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3') found in the flanking region of the LDRL and HMG-CoA synthase genes.SUBUNIT: Forms a tight complex with SCAP in the ER membrane. Efficient DNA binding of the soluble transcription factor fragment requires dimerization with another bHLH protein. Interacts with LMNA. Component of SCAP/SREBP complex composed of SREBF2, SCAP and RNF139; the complex hampers the interaction between SCAP and SEC24B, thereby reducing SREBF2 proteolytic processing. Interacts (via C-terminus domain) with RNF139.SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein. Cytoplasmic vesicle, COPII-coated vesicle membrane; Multi-pass membrane protein. Note=Moves from the endoplasmic reticulum to the Golgi in the absence of sterols.SUBCELLULAR LOCATION: Processed sterol regulatory element-binding protein 2: Nucleus.TISSUE SPECIFICITY: Ubiquitously expressed in adult and fetal tissues.PTM: At low cholesterol the SCAP/SREBP complex is recruited into COPII vesicles for export from the ER. In the Golgi complex SREBPs are cleaved sequentially by site-1 and site-2 protease. The first cleavage by site-1 protease occurs within the luminal loop, the second cleavage by site-2 protease occurs within the first transmembrane domain and releases the transcription factor from the Golgi membrane. Apoptosis triggers cleavage by the cysteine proteases caspase-3 and caspase-7.PTM: Phosphorylated by AMPK, leading to suppress protein processing and nuclear translocation, and repress target gene expression (By similarity).SIMILARITY: Belongs to the SREBP family.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SEQUENCE CAUTION: Sequence=AAH51799.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - FBXL3 - HGNC Symbol - - - - EQUAL - 36 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5599 - - - - CLOCK - HGNC - - - - NP_001181973 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4712 - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1)' - http://www.reactome.org/biopax/46/48887#Control388 - - - - 52623 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=52623 - - - - P05121 - UniProt - - - - 400282 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400282 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14059 - - - - EQUAL - 33 - http://www.reactome.org/biopax/46/48887#SequenceSite21664 - - - - MED17 - HGNC Symbol - - - - EQUAL - 397 - - - - ENST00000367531 - Ensembl - - - - 159772 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159772 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21644 - - - - P04798 - UniProt - - - - Q6PCB7 - UniProt - - - - 14980219 - Glass, CK - Rose, DW - Aggarwal, A - Perissi, V - Rosenfeld, MG - Pubmed - A corepressor/coactivator exchange complex required for transcriptional activation by nuclear receptors and other regulated transcription factors - Cell 116:511-26 - 2004 - - - - EQUAL - 1454 - http://www.reactome.org/biopax/46/48887#SequenceSite12379 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4705 - - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12964 - - - - REACT_19517 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19517.3 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25558 - - - - - - MOD_RES 554 554 Phosphoserine; by GSK3-beta (By similarity). - - - - NM_021961 - RefSeq - - - - EQUAL - 110 - - - - - - MOD_RES 553 553 Phosphoserine. - - - - - - MOD_RES 537 537 Phosphoserine. - - - - - - Perilipin-2 - Adipophilin - PLIN2 - ADFP_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein13779 - Reactome DB_ID: 400160 - ADFP - - - - REACT_115593 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115593.1 - - - - Q6UX90 - UniProt - - - - 1PO4 - PROTEIN DATA BANK - - - - - - NOCT_HUMAN - Nocturnin - - - - - Reactome DB_ID: 508391 - http://www.reactome.org/biopax/46/48887#Protein11507 - CCRN4L - - - - 15821743 - Akashi, M - Takumi, T - Pubmed - The orphan nuclear receptor RORalpha regulates circadian transcription of the mammalian core-clock Bmal1 - Nat Struct Mol Biol 12:441-8 - 2005 - - - - EQUAL - 635 - - - - 1N83 - PROTEIN DATA BANK - - - - ENST00000601519 - Ensembl - - - - F8VUC2 - UniProt - - - - 400198 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400198 - - - - HGNC:8799 - HGNC - - - - - - MOD_RES 39 39 Phosphoserine; by CK2. - - - - 605653 - omim - - - - - - growth-arrest-specific protein 6 propeptide - GAS6 propeptide - - - - - http://www.reactome.org/biopax/46/48887#Protein11670 - Reactome DB_ID: 163840 - GAS6(31-38) - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10167 - - - - - - NP_057347 - RefSeq - - - - - - MOD_RES 1347 1347 Phosphoserine. - - - - Q8TCV7 - UniProt - - - - 3091 - NCBI Gene - - - - 174230 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174230 - - - - - - MED19_HUMAN - Mediator of RNA polymerase II transcription subunit 19 - - - - - Reactome DB_ID: 556819 - http://www.reactome.org/biopax/46/48887#Protein6486 - MED19 - - - - - - - - Peroxisome Proliferator Receptor Element (PPRE) - http://www.reactome.org/biopax/46/48887#PhysicalEntity296 - Reactome DB_ID: 422139 - - - - HGNC:9456 - HGNC - - - - NM_001003891 - RefSeq - - - - CHEBI:43228 - ChEBI - - - - ENST00000404735 - Ensembl - - - - REACT_7570 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7570.2 - - - - - - MOD_RES 151 151 Phosphoserine. - - - - 9079689 - Bradfield, CA - Hogenesch, JB - Brown, RC - Pray-Grant, M - Gu, YZ - Chan, WK - Jackiw, VH - Perdew, GH - Pubmed - Characterization of a subset of the basic-helix-loop-helix-PAS superfamily that interacts with components of the dioxin signaling pathway - J Biol Chem 272:8581-93 - 1997 - - - - Q9Y3W6 - UniProt - - - - - - ubiquitin (UBC 8) - - - - - Reactome DB_ID: 939239 - http://www.reactome.org/biopax/46/48887#Protein1056 - UBC(533-608) - - - - - - Nuclear receptor ROR-alpha - RORA_HUMAN - - - - - Reactome DB_ID: 400325 - http://www.reactome.org/biopax/46/48887#Protein11495 - RORA - - - - - - Cytochrome P450 4A11 - P450-HL-omega - CYP4AII - Fatty acid omega-hydroxylase - CYPIVA11 - Lauric acid omega-hydroxylase - P-450 HK omega - - - - - http://www.reactome.org/biopax/46/48887#Protein13766 - Reactome DB_ID: 52649 - CYP4A11 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2603 - - - - REACT_3979 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3979.1 - - - - EQUAL - 289 - - - - HGNC:30092 - HGNC - - - - HGNC:2370 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5649 - - - - - - NP_000481 - RefSeq - - - - TNFRSF21 - HGNC Symbol - - - - NP_001120915 - RefSeq - - - - REACT_5866 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5866.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5675 - - - - - - EQUAL - 424 - - - - ENSP00000411411 - Ensembl - - - - - - - - - INHIBITION - - 'NR1D1 (REV-ERBA):heme:Corepressor [nucleoplasm]' negatively regulates 'Expression of NPAS2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation89 - - - - 400382 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400382 - - - - 113534 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113534 - - - - NP_000124 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10159 - - - - - - NM_001142588 - RefSeq - - - - REACT_115945 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115945.2 - - - - 123 - NCBI Gene - - - - NP_001167559 - RefSeq - - - - REACT_148325 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148325.1 - - - - Q7M4L4 - UniProt - - - - - - - - - - - - - - - - NR1D1 (REV-ERBA):heme:Corepressor - http://www.reactome.org/biopax/46/48887#Complex4975 - Reactome DB_ID: 1368079 - - - - EQUAL - 2177 - http://www.reactome.org/biopax/46/48887#SequenceSite12377 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5650 - - - - - - 290 - NCBI Gene - - - - 2069717 - Heckendorf B - Hasilik A - Grosch HW - Redecker B - Mersmann G - PubMed - Molecular organization of the human cathepsin D gene. - DNA Cell Biol 10(6);423-31 - - - - 51343 - NCBI Gene - - - - REACT_116863 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116863.3 - - - - EQUAL - 413 - - - - ARNTL - HGNC Symbol - - - - ENST00000599595 - Ensembl - - - - ENST00000324883 - Ensembl - - - - NP_001884 - RefSeq - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction146 - Reviewed: Kersten, S, 2009-06-08 - The APOA5 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of APOA5 - - - - EQUAL - 70 - - - - 1989778 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989778 - - - - NP_001434 - RefSeq - - - - 5465 - NCBI Gene - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12356 - - - - HGNC:25701 - HGNC - - - - 603732 - omim - - - - - hSRB11 - SRB11 homolog - CCNC - - - - - - - - - - - - - - - - - - - - CCNC_HUMAN - Cyclin-C - FUNCTION: Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Binds to and activates cyclin-dependent kinase CDK8 that phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The cylin/CDK pair formed by CCNC/CDK8 also associates with the large subunit of RNA polymerase II.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P24863-1; Sequence=Displayed; Name=2; IsoId=P24863-2; Sequence=VSP_043075; Note=No experimental confirmation available;TISSUE SPECIFICITY: Highest levels in pancreas. High levels in heart, liver, skeletal muscle and kidney. Low levels in brain.SIMILARITY: Belongs to the cyclin family. Cyclin C subfamily.SIMILARITY: Contains 1 cyclin N-terminal domain.SEQUENCE CAUTION: Sequence=AAC50825.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10021 - - - - - - MOD_RES 211 211 Phosphoserine. - - - - - - MOD_RES 681 681 Phosphothreonine; by PKC/PRKCZ. - - - - 192169 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=192169 - - - - EQUAL - 1463 - - - - ENSP00000342351 - Ensembl - - - - EQUAL - 133 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature822 - - - - NM_000780 - RefSeq - - - - CHEBI:13291 - ChEBI - - - - CHEBI:10298 - ChEBI - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1085 - - - - EQUAL - 264 - - - - - 3.4.21 - - - - - pro-GAS6 -> GAS6 + GAS6 propeptide - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3907 - Edited: D'Eustachio, P, 0000-00-00 00:00:00 - The details of the gamma-carboxylation of GAS6 have not been determined directly, but are inferred from those worked out for protein S (Manfioletti et al. 1993). - Authored: D'Eustachio, P, 2005-05-07 21:30:29 - - - - - - - - PDGFA isoform 1 - Platelet-derived growth factor, A chain precursor - - - - - Reactome DB_ID: 380743 - http://www.reactome.org/biopax/46/48887#Protein2633 - PDGFA-1(1-211) - - - - EQUAL - 208 - http://www.reactome.org/biopax/46/48887#SequenceSite12353 - - - - 3F1S - PROTEIN DATA BANK - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10136 - - - - - - MOD_RES 433 433 Phosphoserine (By similarity). - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1862 - - - - 9969 - NCBI Gene - - - - - - - - - - - - - RIP160 - SRC1 - bHLHe74 - Protein Hin-2 - NCoA-1 - Renal carcinoma antigen NY-REN-52 - NCOA1 - SRC-1 - Class E basic helix-loop-helix protein 74 - BHLHE74 - 2.3.1.48 - Steroid receptor coactivator 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NCOA1_HUMAN - Nuclear receptor coactivator 1 - FUNCTION: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.CATALYTIC ACTIVITY: Acetyl-CoA + [histone] = CoA + acetyl- [histone].SUBUNIT: Interacts with the methyltransferase CARM1 (By similarity). Interacts with NCOA6 and NCOA2. Interacts with the FDL motif of STAT5A and STAT5B. Interacts with the LXXLL motif of STAT6. Interacts with STAT3 following IL-6 stimulation. Interacts with the basal transcription factor GTF2B. Interacts with the histone acetyltransferases EP300 and CREBBP. Interacts with PCAF, COPS5, NR3C1 and TTLL5/STAMP. Interacts with PSMB9. Interacts with UBE2L3; they functionally interact to regulate progesterone receptor transcriptional activity. Interacts with PRMT2 and DDX5. Interacts with ASXL1.SUBCELLULAR LOCATION: Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=SRC-1A, SRC1a; IsoId=Q15788-1; Sequence=Displayed; Name=2; Synonyms=SRC-1E, SRC1e; IsoId=Q15788-2; Sequence=VSP_011739; Note=Major form. Contains a domain at its C-terminus (1241-1399) that is able to mediate transactivation; Name=3; Synonyms=SRC-1 (-Q); IsoId=Q15788-3; Sequence=VSP_011738;TISSUE SPECIFICITY: Widely expressed.DOMAIN: The C-terminal (1107-1441) part mediates the histone acetyltransferase (HAT) activity.DOMAIN: Contains 7 Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs. LXXLL motifs 3, 4 and 5 are essential for the association with nuclear receptors. LXXLL motif 7, which is not present in isoform 2, increases the affinity for steroid receptors in vitro.PTM: Sumoylated; sumoylation increases its interaction with PGR and prolongs its retention in the nucleus. It does not prevent its ubiquitination and does not exert a clear effect on the stability of the protein.PTM: Ubiquitinated; leading to proteasome-mediated degradation. Ubiquitination and sumoylation take place at different sites.DISEASE: Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.SIMILARITY: Belongs to the SRC/p160 nuclear receptor coactivator family.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAS (PER-ARNT-SIM) domain.SEQUENCE CAUTION: Sequence=AAA64187.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAC50305.1; Type=Erroneous initiation; Note=Translation N-terminally extended;WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/ncoa1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 14999402 - Kersten, S - Mandard, S - Muller, M - Pubmed - Peroxisome proliferator-activated receptor alpha target genes - Cell Mol Life Sci 61:393-416 - 2004 - - - - - - MOD_RES 419 419 Phosphoserine; by MAPK7. - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4720 - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Reviewed: Hirota, T, 2010-06-23 - The DEC1 (BHLHE40, BHLHB2) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The DEC1 gene contains E-box elements in its promoter which bind the BMAL:CLOCK (ARNTL:CLOCK) heterodimer and confer circadian rhythm on its expression. - Edited: May, B, 2010-06-18 - http://www.reactome.org/biopax/46/48887#TemplateReaction60 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Authored: May, B, 2010-06-18 - Expression of DEC1 (BHLHE40, BHLHB2) - - - - 10413 - NCBI Gene - - - - NP_000771 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10165 - - - - - - - - - - - ACTIVATION - - 'ROR-alpha:Coactivator [nucleoplasm]' positively regulates 'Expression of CPT1A' - As inferred from mouse, ROR-alpha binds the promoter of the CPT1A gene and, together with coactivators EP300 and PGC-1alpha, enhances transcription. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation119 - - - - EQUAL - 60 - - - - 192340 - omim - - - - 421319 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421319 - - - - Q86V36 - UniProt - - - - NP_115662 - RefSeq - - - - Q6NWN9 - UniProt - - - - - - Angiotensin-1 - Angiotensin-(1-10) - Angiotensin I - AGT(34-43) - ANG1-10 - ANGT_HUMAN - - - - - Reactome DB_ID: 2022346 - http://www.reactome.org/biopax/46/48887#Protein12334 - AGT - - - - MOD_RES Methionine sulfoxide - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2251 - - - - - - REACT_117973 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117973.1 - - - - 1605584 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1605584 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1812 - - - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1264 - - - - REACT_115777 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115777.1 - - - - O14516 - UniProt - - - - Q5QTQ7 - UniProt - - - - - - MOD_RES 2269 2269 Phosphoserine. - - - - NM_002518 - RefSeq - - - - EQUAL - 89 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1054 - - - - - - NCOA2_HUMAN - - - - - Reactome DB_ID: 376398 - http://www.reactome.org/biopax/46/48887#Protein6500 - NCOA2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8342 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5628 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1838 - - - - - - MOD_RES 231 231 Phosphoserine. - - - - - - - - - ACTIVATION - - 'Renin:Prorenin Receptor [plasma membrane]' positively regulates 'Renin:Prorenin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10)' - http://www.reactome.org/biopax/46/48887#Control302 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12025 - - - - 603618 - omim - - - - HMGCS1 - HGNC Symbol - - - - ENSEMBL:ENSG00000023330 ALAS1 - - ALAS1 - http://www.reactome.org/biopax/46/48887#DnaReference30 - - - - - ENST00000394975 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5784 - - - - A4D7V1 - UniProt - - - - NM_006930 - RefSeq - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12972 - - - - EQUAL - 803 - - - - - - Casein kinase I isoform epsilon - CKIepsilon - - - - - http://www.reactome.org/biopax/46/48887#Protein11531 - Reactome DB_ID: 421306 - CSNK1E - - - - EQUAL - 299 - http://www.reactome.org/biopax/46/48887#SequenceSite21497 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25548 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5656 - - - - - - NP_003205 - RefSeq - - - - 2990852 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2990852 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12066 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Circadian Clock - Reviewed: Kay, SA, 2010-06-23 - Reviewed: Hirota, T, 2010-06-23 - http://www.reactome.org/biopax/46/48887#Pathway875 - Edited: May, B, 2009-05-17 22:04:50 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - At the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening. During the night CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning. <br>Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA (NR1D1), both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha (RORA) activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1. <br>BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show different tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phosphorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nucleus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY complexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening. <br>PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type component of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type component of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitinated and proteolyzed by the 26S proteasome.<br>The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients. - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - - - - - - ACTIVATION - - 'MEF2C/D:PPARGC1A [nucleoplasm]' positively regulates 'Expression of PPARGC1A (PGC-1alpha)' - As inferred from mouse, MEF2C or MEF2D with PGC-1alpha activate expression of PGC-1alpha (Handschin et al. 2003). - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation113 - - - - ENST00000539158 - Ensembl - - - - HGNC:5008 - HGNC - - - - NP_000434 - RefSeq - - - - - - MOD_RES 61 61 4-carboxyglutamate. - - - - ENSP00000326804 - Ensembl - - - - 1368116 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368116 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10039 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10070 - - - - - - 159754 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159754 - - - - NM_001995 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8351 - - - - A8MY84 - UniProt - - - - ENST00000372653 - Ensembl - - - - HGNC:13469 - HGNC - - - - ENST00000371697 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5605 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10794 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12065 - - - - - - CHEBI:7860 - ChEBI - - - - B5BU73 - UniProt - - - - EQUAL - 266 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10810 - - - - - - P36509 - UniProt - - - - - - MOD_RES 1216 1216 N6-acetyllysine. - - - - Q15178 - UniProt - - - - REACT_13032 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13032.2 - - - - ENST00000461783 - Ensembl - - - - 380743 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380743 - - - - 1989777 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989777 - - - - Q9NTZ9 - UniProt - - - - 176930 - omim - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CYP4A11' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation203 - - - - Cofactor required for Sp1 transcriptional activation subunit 3 - ARC130 - CRSP3 - MED23 - Mediator complex subunit 23 - hSur-2 - Activator-recruited cofactor 130 kDa component - Protein sur-2 homolog - CRSP complex subunit 3 - DRIP130 - Transcriptional coactivator CRSP130 - Vitamin D3 receptor-interacting protein complex 130 kDa component - KIAA1216 - SUR2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MED23_HUMAN - Mediator of RNA polymerase II transcription subunit 23 - FUNCTION: Required for transcriptional activation subsequent to the assembly of the preinitiation complex (By similarity). Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Required for transcriptional activation by adenovirus E1A protein. Required for ELK1-dependent transcriptional activation in response to activated Ras signaling.SUBUNIT: Interacts with ELK1 (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with CEBPB, CTNNB1, and GLI3. Interacts with the adenovirus E1A protein.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Comment=Experimental confirmation may be lacking for some isoforms; Name=1; IsoId=Q9ULK4-1; Sequence=Displayed; Name=2; IsoId=Q9ULK4-2; Sequence=VSP_004034, VSP_004036, VSP_004037; Name=3; IsoId=Q9ULK4-3; Sequence=VSP_004034, VSP_004035; Name=4; IsoId=Q9ULK4-4; Sequence=VSP_004035; Name=5; IsoId=Q9ULK4-5; Sequence=VSP_028380; Name=6; IsoId=Q9ULK4-6; Sequence=VSP_047860, VSP_047861;DISEASE: Mental retardation, autosomal recessive 18 (MRT18) [MIM:614249]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the Mediator complex subunit 23 family.SEQUENCE CAUTION: Sequence=AAD12724.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAD31729.1; Type=Frameshift; Positions=945, 950; Sequence=BAA86530.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 1586 1586 N6-acetyllysine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12943 - - - - Adipose differentiation-related protein - ADFP - Adipophilin - PLIN2 - ADRP - - - - - - - - - - - - - PLIN2_HUMAN - Perilipin-2 - FUNCTION: May be involved in development and maintenance of adipose tissue (By similarity).SUBCELLULAR LOCATION: Membrane; Peripheral membrane protein.TISSUE SPECIFICITY: Milk lipid globules.PTM: Acylated; primarily with C14, C16 and C18 fatty acids.SIMILARITY: Belongs to the perilipin family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q53HU1 - UniProt - - - - ENSP00000260129 - Ensembl - - - - ENSP00000374357 - Ensembl - - - - - - MOD_RES 55 55 4-carboxyglutamate. - - - - 400237 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400237 - - - - - - pro-protein S, uncarboxylated - - - - - http://www.reactome.org/biopax/46/48887#Protein11639 - Reactome DB_ID: 159758 - PROS1(25-676) - - - - ENSP00000377977 - Ensembl - - - - 191329 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=191329 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5364 - - - - NP_000030 - RefSeq - - - - Q8NEV5 - UniProt - - - - 211 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10128 - - - - - - MOD_RES 110 110 Phosphotyrosine (By similarity). - - - - ENSG00000112972 - Ensembl - - - - EQUAL - 2057 - - - - EQUAL - 2525 - http://www.reactome.org/biopax/46/48887#SequenceSite5774 - - - - PTHR11945:SF25 - PANTHER Family - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21465 - - - - EQUAL - 832 - - - - 602408 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10127 - - - - TBL1X - HGNC Symbol - - - - NP_001240810 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12342 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10185 - - - - - - - - - Casein kinase I delta or Casein kinase I epsilon - - - - Reactome DB_ID: 421289 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11519 - CSNK1E/CSNK1D - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature122 - - - - HGNC:17556 - HGNC - - - - - - MOD_RES 1057 1057 Phosphothreonine. - - - - ENST00000544915 - Ensembl - - - - 25942 - NCBI Gene - - - - REACT_116407 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116407.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval834 - - - - - - 2022355 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022355 - - - - REACT_25627 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25627.2 - - - - ENST00000355619 - Ensembl - - - - ENSG00000132326 - Ensembl - - - - P14798 - UniProt - - - - Q15101 - UniProt - - - - REACT_27510 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27510.3 - - - - ENSP00000377020 - Ensembl - - - - P02652 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4966 - - - - Q8TAI6 - UniProt - - - - Q53GU4 - UniProt - - - - NM_000506 - RefSeq - - - - ENST00000262735 - Ensembl - - - - 1X4K - PROTEIN DATA BANK - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1049 - - - - EQUAL - 1734 - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-06-18 - The DBP gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind E-boxes in the DBP promoter and activate transcription of DBP. - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Authored: May, B, 2010-06-18 - http://www.reactome.org/biopax/46/48887#TemplateReaction59 - Expression of DBP - - - - 1989821 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989821 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14048 - - - - REACT_115949 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115949.1 - - - - NP_009218 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10051 - - - - - - - - MOD_RES 21 21 Phosphoserine (By similarity). - - - - REACT_148518 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148518.1 - - - - TGS1 - HGNC Symbol - - - - ENST00000360366 - Ensembl - - - - Q9NY21 - UniProt - - - - - - MOD_RES 372 372 Phosphoserine. - - - - EQUAL - 200 - http://www.reactome.org/biopax/46/48887#SequenceSite21666 - - - - ENSP00000370348 - Ensembl - - - - 2065430 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065430 - - - - - - - PRMT4 - 2.1.1.- - 2.1.1.125 - Protein arginine N-methyltransferase 4 - Coactivator-associated arginine methyltransferase 1 - CARM1 - - - - - - - - - - - - - - - CARM1_HUMAN - Histone-arginine methyltransferase CARM1 - FUNCTION: Methylates (mono- and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in several proteins involved in DNA packaging, transcription regulation, pre-mRNA splicing, and mRNA stability. Recruited to promoters upon gene activation together with histone acetyltransferases from EP300/P300 and p160 families, methylates histone H3 at 'Arg-17' (H3R17me), forming mainly asymmetric dimethylarginine (H3R17me2a), leading to activate transcription via chromatin remodeling. During nuclear hormone receptor activation and TCF7L2/TCF4 activation, acts synergically with EP300/P300 and either one of the p160 histone acetyltransferases NCOA1/SRC1, NCOA2/GRIP1 and NCOA3/ACTR or CTNNB1/beta-catenin to activate transcription. During myogenic transcriptional activation, acts together with NCOA3/ACTR as a coactivator for MEF2C. During monocyte inflammatory stimulation, acts together with EP300/P300 as a coactivator for NF-kappa-B. Acts as coactivator for PPARG, promotes adipocyte differentiation and the accumulation of brown fat tissue. Plays a role in the regulation of pre-mRNA alternative splicing by methylation of splicing factors. Also seems to be involved in p53/TP53 transcriptional activation. Methylates EP300/P300, both at 'Arg- 2142', which may loosen its interaction with NCOA2/GRIP1, and at 'Arg-580' and 'Arg-604' in the KIX domain, which impairs its interaction with CREB and inhibits CREB-dependent transcriptional activation. Also methylates arginine residues in RNA-binding proteins PABPC1, ELAVL1 and ELAV4, which may affect their mRNA- stabilizing properties and the half-life of their target mRNAs.CATALYTIC ACTIVITY: S-adenosyl-L-methionine + arginine-[histone] = S-adenosyl-L-homocysteine + N(omega)-methyl-arginine-[histone].ENZYME REGULATION: Methylation of H3R17 (H3R17me) by CARM1 is stimulated by preacetylation of H3 'Lys-18' (H3K18ac) H3 'Lys-23' (H3K23ac) by EP300 and blocked by citrullination of H3 'Arg-17' (H3R17ci) by PADI4 (By similarity).SUBUNIT: Homodimer (Probable). Interacts with the C-terminus of NCOA2/GRIP1, NCO3/ACTR and NCOA1/SRC1. Part of a complex consisting of CARM1, EP300/P300 and NCOA2/GRIP1. Interacts with FLII, TP53, myogenic factor MEF2, EP300/P300, TRIM24, CREBBP and CTNNB1. Identified in a complex containing CARM1, TRIM24 and NCOA2/GRIP1. Interacts with NCOA3/SRC3. Interacts with SNRPC (By similarity). Interacts with NR1H4. Interacts with RELA. Interacts with HTLV-1 Tax-1.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Mainly nuclear during the G1, S and G2 phases of the cell cycle. Cytoplasmic during mitosis, after breakup of the nuclear membrane.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=3; IsoId=Q86X55-3; Sequence=Displayed; Name=1; IsoId=Q86X55-1; Sequence=VSP_039876; Name=2; IsoId=Q86X55-2; Sequence=VSP_012506, VSP_012507; Note=No experimental confirmation available;TISSUE SPECIFICITY: Overexpressed in prostate adenocarcinomas and high-grade prostatic intraepithelial neoplasia.PTM: Auto-methylated on Arg-550. Methylation enhances transcription coactivator activity. Methylation is required for its role in the regulation of pre-mRNA alternative splicing (By similarity).PTM: Phosphorylation at Ser-216 interferes with S-adenosyl-L- methionine binding and strongly reduces methyltransferase activity (By similarity). Phosphorylation at Ser-216 is strongly increased during mitosis, and decreases rapidly to a very low, basal level after entry into the G1 phase of the cell cycle. Phosphorylation at Ser-216 may promote location in the cytosol.SIMILARITY: Belongs to the protein arginine N-methyltransferase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000229758 - Ensembl - - - - ENSG00000118137 - Ensembl - - - - - - - - OPA-containing protein - KIAA0192 - Trinucleotide repeat-containing gene 11 protein - TRAP230 - HOPA - MED12 - CAG repeat protein 45 - ARC240 - Mediator complex subunit 12 - Activator-recruited cofactor 240 kDa component - CAGH45 - Thyroid hormone receptor-associated protein complex 230 kDa component - Trap230 - TNRC11 - - - - - - - - - - - - - - - - - - - - MED12_HUMAN - Mediator of RNA polymerase II transcription subunit 12 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. This subunit may specifically regulate transcription of targets of the Wnt signaling pathway and SHH signaling pathway.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Also interacts with CTNNB1 and GLI3.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q93074-1; Sequence=Displayed; Name=2; IsoId=Q93074-2; Sequence=VSP_035520; Name=3; IsoId=Q93074-3; Sequence=VSP_035521; Note=No experimental confirmation available;TISSUE SPECIFICITY: Ubiquitous.DISEASE: Opitz-Kaveggia syndrome (OKS) [MIM:305450]: X-linked disorder characterized by mental retardation, relative macrocephaly, hypotonia and constipation. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Lujan-Fryns syndrome (LUJFRYS) [MIM:309520]: Clinically, Lujan-Fryns syndrome can be distinguished from Opitz-Kaveggia syndrome by tall stature, hypernasal voice, hyperextensible digits and high nasal root. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Ohdo syndrome, X-linked (OHDOX) [MIM:300895]: A syndrome characterized by mental retardation, feeding problems, and distinctive facial appearance with coarse facial features, severe blepharophimosis, ptosis, a bulbous nose, micrognathia and a small mouth. Dental hypoplasia and deafness can be considered as common manifestations of the syndrome. Male patients show cryptorchidism and scrotal hypoplasia. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the Mediator complex subunit 12 family.SEQUENCE CAUTION: Sequence=AAD22033.1; Type=Erroneous initiation;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/MED12"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 11786931 - Maier W - Heun R - Schmitz S - Papassotiropoulos A - Bagli M - Lohmann PL - Kolsch H - Majores M - Rao ML - PubMed - Cathepsin D: screening for new polymorphisms using single-strand conformation polymorphism analysis. - Int J Mol Med 9(2);185-7 - 2002 - - - - - - MOD_RES 63 63 4-carboxyglutamate. - - - - P09958 - UniProt - - - - EQUAL - 350 - http://www.reactome.org/biopax/46/48887#SequenceSite23003 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5641 - - - - NM_003847 - RefSeq - - - - ENSP00000261178 - Ensembl - - - - 11241162 - Ognjanovic, S - Samal, B - Yamamoto, SY - Garibay-Tupas, J - Bryant-Greenwood, GD - Bao, S - Pubmed - Genomic organization of the gene coding for human pre-B-cell colony enhancing factor and expression in human fetal membranes - J Mol Endocrinol 26:107-17 - 2001 - - - - Q9BQ77 - UniProt - - - - - - - - ACTIVATION - - 'TEAD:YAP1 [nucleoplasm]' positively regulates 'Expression of CTGF' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation81 - - - - Q5T9K2 - UniProt - - - - Q8WYA3 - UniProt - - - - NP_000495 - RefSeq - - - - 549355 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549355 - - - - CPT2 - HGNC Symbol - - - - 6500 - NCBI Gene - - - - ENSP00000361736 - Ensembl - - - - REACT_148166 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148166.2 - - - - REACT_19435 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19435.1 - - - - NM_021027 - RefSeq - - - - EQUAL - 121 - - - - EQUAL - 560 - - - - REACT_23065 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23065.3 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10765 - - - - - - - - - FYR - FZR1 - FZR - CDC20-like protein 1 - KIAA1242 - Fzr - CDH1 - hCDH1 - Cdh1/Hct1 homolog - - - - - - - - - - - - - - - - - - - - - - - - - - - - FZR_HUMAN - Fizzy-related protein homolog - FUNCTION: Key regulator of ligase activity of the anaphase promoting complex/cyclosome (APC/C), which confers substrate specificity upon the complex. Associates with the APC/C in late mitosis, in replacement of CDC20, and activates the APC/C during anaphase and telophase. The APC/C remains active in degrading substrates to ensure that positive regulators of the cell cycle do not accumulate prematurely. At the G1/S transition FZR1 is phosphorylated, leading to its dissociation from the APC/C. Following DNA damage, it is required for the G2 DNA damage checkpoint: its dephosphorylation and reassociation with the APC/C leads to the ubiquitination of PLK1, preventing entry into mitosis.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: The unphosphorylated form interacts with APC/C during mitosis. Interacts with NINL. Interacts (in complex with the anaphase promoting complex APC) with MAD2L2; inhibits FZR1- mediated APC/C activation. Interacts with USP37. Interacts (via WD repeats) with MAK.SUBCELLULAR LOCATION: Isoform 2: Nucleus.SUBCELLULAR LOCATION: Isoform 3: Cytoplasm.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q9UM11-1; Sequence=Displayed; Name=2; Synonyms=CDH1alpha, Fzr1; IsoId=Q9UM11-2; Sequence=VSP_008504; Note=Major; Name=3; Synonyms=CDH1beta, Fzr2; IsoId=Q9UM11-3; Sequence=VSP_008503, VSP_008504; Note=Minor;TISSUE SPECIFICITY: Isoform 2 is expressed at high levels in heart, liver, spleen and some cancer cell lines whereas isoform 3 is expressed only at low levels in these tissues.PTM: Phosphorylated during mitosis, probably by maturation promoting factor (MPF), leading to its dissociation of the APC/C. Following DNA damage, it is dephosphorylated by CDC14B in G2 phase, leading to its reassociation with the APC/C, and allowing an efficient G2 DNA damage checkpoint. Phosphorylated by MAK.SIMILARITY: Belongs to the WD repeat CDC20/Fizzy family.SIMILARITY: Contains 7 WD repeats.SEQUENCE CAUTION: Sequence=AAD26623.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part; Sequence=AAD26624.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part; Sequence=BAA86556.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite1304 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1168 - - - - MME - HGNC - - - - EQUAL - 449 - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12940 - - - - 79365 - NCBI Gene - - - - EQUAL - 328 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5642 - - - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12974 - - - - 1989790 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989790 - - - - 2065355 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065355 - - - - - - MOD_RES 2 2 N-acetylserine. - - - - NP_001243019 - RefSeq - - - - NP_062562 - RefSeq - - - - - - MOD_RES 453 453 Phosphothreonine; by MAPK1 AND MAPK3. - - - - NM_000443 - RefSeq - - - - 446159 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=446159 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of PLIN2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation215 - - - - APOA5 - HGNC - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4957 - - - - - Q495X4 - UniProt - - - - - - MOD_RES 49 49 4-carboxyglutamate. - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4953 - - - - - - - - - - - - - - - MOD_RES 499 499 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1658 - - - - EQUAL - 588 - - - - ENST00000513440 - Ensembl - - - - Q9H3Q5 - UniProt - - - - - - - - - INHIBITION - - 'ramiprilat [extracellular region]' negatively regulates 'ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control308 - - - - ENSP00000363868 - Ensembl - - - - 610237 - omim - - - - 111910 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=111910 - - - - - - MOD_RES 310 310 N6-succinyllysine (By similarity). - - - - EQUAL - 151 - - - - EQUAL - 184 - - - - EQUAL - 501 - http://www.reactome.org/biopax/46/48887#SequenceSite25555 - - - - EQUAL - 72 - http://www.reactome.org/biopax/46/48887#SequenceSite9911 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8326 - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12961 - - - - 11533142 - pubchem-substance - - - - NP_005457 - RefSeq - - - - NP_001521 - RefSeq - - - - - - - - - - ENPEP Dimer - Reactome DB_ID: 2022357 - http://www.reactome.org/biopax/46/48887#Complex5111 - - - - - - p-S-PER1 - Phosphorylated Period circadian protein homolog 1 - PER1_HUMAN - - - - - - Reactome DB_ID: 400310 - http://www.reactome.org/biopax/46/48887#Protein11525 - p-PER1 - - - - EQUAL - 604 - - - - NM_000176 - RefSeq - - - - - C9H15NO3S - (2S)-1-[(2S)-2-methyl-3-sulfanylpropanoyl]pyrrolidine-2-carboxylic acid - D-3-mercapto-2-methylpropanoyl-L-proline - 1-[(2S)-2-methyl-3-sulfanylpropanoyl]-L-proline - Captopryl - L-Captopril - D-2-methyl-3-mercaptopropanoyl-L-proline - CP - - - - - 217.28635 - captopril - captopril - A proline derivative in which <stereo>L</stereo>-proline is substituted on nitrogen with a (2<stereo>S</stereo>)-2-methyl-3-sulfanylpropanoyl group. It is used as an anti-hypertensive ACE inhibitor drug. - - - - ENST00000367195 - Ensembl - - - - 549373 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549373 - - - - EQUAL - 1014 - - - - REACT_25601 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25601.2 - - - - 159808 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159808 - - - - 421320 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421320 - - - - NP_001129669 - RefSeq - - - - NM_001204262 - RefSeq - - - - Q8NC83 - UniProt - - - - 1AM9 - PROTEIN DATA BANK - - - - Q9NRP8 - UniProt - - - - - - MOD_RES 73 73 4-carboxyglutamate. - - - - 2022346 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022346 - - - - REACT_120333 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120333.1 - - - - REACT_20168 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20168.1 - - - - 400304 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400304 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10020 - - - - REACT_120342 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120342.1 - - - - REACT_20348 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20348.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12022 - - - - NP_000304 - RefSeq - - - - 8145133 - pubchem - - - - ENSP00000445317 - Ensembl - - - - REACT_117969 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117969.1 - - - - - - - - - - - - - - - - - - - - - - - - 65 kDa Yes-associated protein - YAP1 - YAP65 - - - - - - - - - - - - - - - - - - - - - - - - - - YAP1_HUMAN - Yorkie homolog - FUNCTION: Transcriptional regulator which can act both as a coactivator and a corepressor and is the critical downstream regulatory target in the Hippo signaling pathway that plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Plays a key role to control cell proliferation in response to cell contact. Phosphorylation of YAP1 by LATS1/2 inhibits its translocation into the nucleus to regulate cellular genes important for cell proliferation, cell death, and cell migration. The presence of TEAD transcription factors are required for it to stimulate gene expression, cell growth, anchorage-independent growth, and epithelial mesenchymal transition (EMT) induction. Isoform 2 and isoform 3 can activate the C-terminal fragment (CTF) of ERBB4 (isoform 3).SUBUNIT: Binds to the SH3 domain of the YES kinase. Binds to WBP1 and WBP2. Binds, in vitro, through the WW1 domain, to neural isoforms of ENAH that contain the PPSY motif (By similarity). The phosphorylated form interacts with YWHAB. Interacts (via WW domains) with LATS1 (via PPxY motif 2). Interacts with LATS2. Isoform 2 and isoform 3 interact (via WW domain 1) with isoform 3 of ERBB4 (via PPxY motif 2). Interacts with TEAD1, TEAD2, TEAD3 and TEAD4. Interacts with TP73. Interacts with RUNX1. Interacts with HCK. Interacts (via WW domains) with PTPN14 (via PPxY motif 2); this interaction leads to the cytoplasmic sequestration of YAP1 and inhibits its transcriptional coactivator activity.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Both phosphorylation and cell density can regulate its subcellular localization. Phosphorylation sequesters it in the cytoplasm by inhibiting its translocation into the nucleus. At low density, predominantly nuclear and is translocated to the cytoplasm at high density. PTPN14 induces translocation from the nucleus to the cytoplasm.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Comment=Additional isoforms lacking the transactivation domain exist; Name=1; Synonyms=YAP2L; IsoId=P46937-1; Sequence=Displayed; Name=2; Synonyms=YAP2; IsoId=P46937-2; Sequence=VSP_039054; Name=3; Synonyms=YAP1; IsoId=P46937-3; Sequence=VSP_039053, VSP_039055; Name=4; IsoId=P46937-4; Sequence=VSP_045190; Note=No experimental confirmation available;TISSUE SPECIFICITY: Increased expression seen in some liver and prostate cancers. Isoforms lacking the transactivation domain found in striatal neurons of patients with Huntington disease (at protein level).PTM: Phosphorylated by LATS1 and LATS2; leading to cytoplasmic translocation and inactivation. Phosphorylated by ABL1; leading to YAP1 stabilization, enhanced interaction with TP73 and recruitment onto proapoptotic genes; in response to DNA damage. Phosphorylation at Ser-400 and Ser-403 by CK1 is triggered by previous phosphorylation at Ser-397 by LATS proteins and leads to YAP1 ubiquitination by SCF(beta-TRCP) E3 ubiquitin ligase and subsequent degradation. Phosphorylated at Thr-119, Ser-138, Thr- 154, Ser-367 and Thr-412 by MAPK8/JNK1 and MAPK9/JNK2, which is required for the regukation of apoptosis by YAP1.PTM: Ubiquitinated by SCF(beta-TRCP) E3 ubiquitin ligase.SIMILARITY: Belongs to the YORKIE family.SIMILARITY: Contains 2 WW domains.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/YAP1ID42855ch11q22.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q3B7B7 - UniProt - - - - ENSP00000300056 - Ensembl - - - - 11855939 - Deschauer M - Schroder R - Wieser T - Zierz S - PubMed - A novel nonsense mutation (515del4) in muscle carnitine palmitoyltransferase II deficiency. - Mol Genet Metab 75(2);181-5 - 2002 - - - - ENST00000432207 - Ensembl - - - - NM_001193347 - RefSeq - - - - REN - HGNC - - - - S-palmitoyl-L-cysteine - - - - - ENST00000272190 - Ensembl - - - - 607776 - omim - - - - ENST00000309157 - Ensembl - - - - 9171241 - Wahli, W - Parker, MG - L'Horset, F - Krey, G - Perroud, M - Kalkhoven, E - Braissant, O - Pubmed - Fatty acids, eicosanoids, and hypolipidemic agents identified as ligands of peroxisome proliferator-activated receptors by coactivator-dependent receptor ligand assay - Mol Endocrinol 11:779-91 - 1997 - - - - ENST00000395856 - Ensembl - - - - 2022341 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022341 - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - The CRYPTOCHROME-2 (CRY2) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, the CRY2 protein shows circadian rhythm in the suprachiasmatic nucleus (SCN) and in peripheral tissues. The mRNA shows circadian rhythm in muscle but not in the SCN. Expression is dependent on CLOCK. - Authored: May, B, 2010-03-11 - Reviewed: Hirota, T, 2010-06-23 - Reviewed: Delaunay, F, 2010-06-23 - Edited: May, B, 2010-03-11 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - http://www.reactome.org/biopax/46/48887#TemplateReaction68 - Expression of CRYPTOCHROME-2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10025 - - - - ENSP00000254658 - Ensembl - - - - REACT_27639 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27639.2 - - - - - - ubiquitin (UBC 4) - - - - - http://www.reactome.org/biopax/46/48887#Protein2480 - Reactome DB_ID: 939857 - UBC(229-304) - - - - EQUAL - 200 - http://www.reactome.org/biopax/46/48887#SequenceSite21705 - - - - EQUAL - 275 - - - - 212398 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212398 - - - - 1368187 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368187 - - - - 10720750 - Teubner W - Pabel U - Jones AL - Andrae U - Engelke CE - Coughtrie MW - Falany CN - Meinl W - Glatt H - PubMed - Sulfotransferases: genetics and role in toxicology. - Toxicol Lett 112-113;341-8 - 2000 - - - - NM_147223 - RefSeq - - - - 212401 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212401 - - - - 26271 - NCBI Gene - - - - ENSP00000376146 - Ensembl - - - - - TEAD-3 - TEAD5 - DTEF-1 - TEF5 - TEAD3 - TEA domain family member 3 - - - - - - - - - - - - - - - TEAD3_HUMAN - Transcriptional enhancer factor TEF-5 - FUNCTION: Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein MST1/MST2, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Acts by mediating gene expression of YAP1 and WWTR1/TAZ, thereby regulating cell proliferation, migration and epithelial mesenchymal transition (EMT) induction. Binds to multiple functional elements of the human chorionic somatomammotropin-B gene enhancer.SUBUNIT: Interacts with YAP1 and WWTR1/TAZ.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Preferentially expressed in the placenta.SIMILARITY: Contains 1 TEA DNA-binding domain.SEQUENCE CAUTION: Sequence=AAH27877.1; Type=Miscellaneous discrepancy; Note=Unusual initiator. The initiator methionine is coded by a non-canonical ATA isoleucine codon; Sequence=AAH91488.2; Type=Miscellaneous discrepancy; Note=Unusual initiator. The initiator methionine is coded by a non-canonical ATA isoleucine codon; Sequence=CAA64213.2; Type=Miscellaneous discrepancy; Note=Unusual initiator. The initiator methionine is coded by a non-canonical ATA isoleucine codon; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 1359 - NCBI Gene - - - - ENSG00000104973 - Ensembl - - - - REACT_116079 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116079.1 - - - - SULT2A1 - HGNC Symbol - - - - Q96QU3 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1069 - - - - REACT_24369 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24369.2 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1045 - - - - EQUAL - 664 - - - - ENSP00000405087 - Ensembl - - - - ENSG00000124641 - Ensembl - - - - Q5JVF2 - UniProt - - - - NP_006157 - RefSeq - - - - EQUAL - 72 - http://www.reactome.org/biopax/46/48887#SequenceSite9993 - - - - 185641 - omim - - - - NM_001143946 - RefSeq - - - - EQUAL - 687 - - - - EQUAL - 380 - http://www.reactome.org/biopax/46/48887#SequenceSite4662 - - - - ENSG00000164758 - Ensembl - - - - 1368108 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368108 - - - - - - NF-YB - - - - - Reactome DB_ID: 381067 - http://www.reactome.org/biopax/46/48887#Protein12433 - NFYB - - - - ENSP00000470507 - Ensembl - - - - MED4 - HGNC - - - - NM_001166107 - RefSeq - - - - ENST00000435530 - Ensembl - - - - - - MOD_RES 1597 1597 N6-acetyllysine. - - - - ENST00000375323 - Ensembl - - - - EQUAL - 111 - http://www.reactome.org/biopax/46/48887#SequenceSite23036 - - - - EQUAL - 62 - http://www.reactome.org/biopax/46/48887#SequenceSite9997 - - - - - - MOD_RES 550 550 Dimethylated arginine (By similarity). - - - - GO:0004842 - GENE ONTOLOGY - - - - - EQUAL - 138 - - - - A1L469 - UniProt - - - - Q9UQ18 - UniProt - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of Farnesyldiphosphate Farnesyltransferase (FDFT1, Squalene Synthase)' - http://www.reactome.org/biopax/46/48887#Control385 - - - - ENSP00000417079 - Ensembl - - - - ENSP00000340874 - Ensembl - - - - 15236580 - Sturrock, ED - Natesh, R - Schwager, SL - Acharya, KR - Evans, HR - Pubmed - Structural details on the binding of antihypertensive drugs captopril and enalaprilat to human testicular angiotensin I-converting enzyme - Biochemistry 43:8718-24 - 2004 - - - - ENST00000234071 - Ensembl - - - - REACT_26137 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26137.4 - - - - HGNC:2377 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10157 - - - - - - EQUAL - 51 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8332 - - - - ENSP00000473039 - Ensembl - - - - EQUAL - 46 - - - - 159768 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159768 - - - - NM_001256093 - RefSeq - - - - HGNC:13557 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5800 - - - - - - MOD_RES 105 105 Phosphoserine. - - - - 1215 - NCBI Gene - - - - PTHR19304:SF9 - PANTHER Family - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5366 - - - - Q96T10 - UniProt - - - - NP_001230013 - RefSeq - - - - 1480006 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1480006 - - - - HGNC:16228 - HGNC - - - - NM_012177 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8347 - - - - CPB1 - HGNC - - - - REACT_27725 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27725.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10048 - - - - - - - - KC1D_HUMAN - Casein kinase I isoform delta - - - - - http://www.reactome.org/biopax/46/48887#Protein11532 - Reactome DB_ID: 421305 - CSNK1D - - - - 4289389 - Goldblatt, H - Haas, E - Pubmed - Kinetic constants of the human renin and human angiotensinogen reaction - Circ Res 20:45-55 - 1967 - - - - 2022378 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022378 - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13188 - - - - ENSP00000362948 - Ensembl - - - - REACT_148209 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148209.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2088 - - - - MED25 - HGNC Symbol - - - - - - 12xCbxE-3D-F9 - 12xCbxE-3D-F9(47-461) - - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11656 - Reactome DB_ID: 159822 - factor IX - - - - 173510 - omim - - - - HMGCS2 - HGNC Symbol - - - - ENSG00000180210 - Ensembl - - - - ENSP00000376326 - Ensembl - - - - 2384150 - Noshiro, M - Okuda, K - Pubmed - Molecular cloning and sequence analysis of cDNA encoding human cholesterol 7 alpha-hydroxylase - FEBS Lett 268:137-40 - 1990 - - - - P41215 - UniProt - - - - 879828 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879828 - - - - EQUAL - 447 - http://www.reactome.org/biopax/46/48887#SequenceSite20837 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10009 - - - - - - 9xCbxE-F7(21-466) - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11646 - Reactome DB_ID: 159767 - pro-factor VII - - - - ENSG00000148677 - Ensembl - - - - ENSG00000198911 - Ensembl - - - - ENSP00000236850 - Ensembl - - - - EQUAL - 4 - - - - CHEBI:17351 - ChEBI - - - - TIAM2 - HGNC - - - - - - Ub-p-S-CRY1 - CRY1_HUMAN - Ubiquitinated Phosphorylated Cryptochrome-1 - - - - - - - Reactome DB_ID: 517931 - http://www.reactome.org/biopax/46/48887#Protein11538 - ub-p-CRY1 - - - - - - Cleaved fragment of PDGF B-chain (191-241) - - - - - Reactome DB_ID: 396945 - http://www.reactome.org/biopax/46/48887#Protein2640 - PDGFB(191-241) - - - - EQUAL - 444 - - - - EQUAL - 178 - - - - 1989754 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989754 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10796 - - - - - - EQUAL - 461 - http://www.reactome.org/biopax/46/48887#SequenceSite21647 - - - - 11232563 - He, Y - Ptácek, LJ - Virshup, DM - Fu, YH - Eide, EJ - Jones, CR - Hinz, WA - Toh, KL - Pubmed - An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome - Science 291:1040-3 - 2001 - - - - ENST00000597451 - Ensembl - - - - NP_612482 - RefSeq - - - - ENSP00000308528 - Ensembl - - - - EQUAL - 412 - http://www.reactome.org/biopax/46/48887#SequenceSite21434 - - - - REACT_147799 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147799.2 - - - - - - - - - Reactome DB_ID: 2065395 - http://www.reactome.org/biopax/46/48887#SmallMolecule1076 - captopril - - - - Q92869 - UniProt - - - - O00315 - UniProt - - - - 8647822 - Sanchez, HB - Osborne, TF - Rosenfeld, JM - Vallett, SM - Pubmed - A direct role for sterol regulatory element binding protein in activation of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene - J Biol Chem 271:12247-53 - 1996 - - - - EQUAL - 426 - http://www.reactome.org/biopax/46/48887#SequenceSite20835 - - - - EQUAL - 2 - - - - ENSP00000387160 - Ensembl - - - - REACT_27330 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27330.1 - - - - EQUAL - 468 - http://www.reactome.org/biopax/46/48887#SequenceSite12423 - - - - - - MOD_RES 89 89 4-carboxyglutamate. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1100 - - - - 517830 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=517830 - - - - EQUAL - 846 - http://www.reactome.org/biopax/46/48887#SequenceSite21422 - - - - CHEBI:10744 - ChEBI - - - - HGNC:9234 - HGNC - - - - EQUAL - 913 - - - - 159744 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159744 - - - - Q96D86 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2113 - - - - - - EQUAL - 61 - - - - - - MOD_RES 110 110 Phosphothreonine (By similarity). - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12008 - - - - ENSP00000377534 - Ensembl - - - - EQUAL - 550 - - - - ENSP00000346588 - Ensembl - - - - EQUAL - 59 - - - - ENST00000308733 - Ensembl - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5770 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25570 - - - - 1989745 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989745 - - - - REACT_12685 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12685.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10153 - - - - ENSG00000130589 - Ensembl - - - - - - omim - - - - EQUAL - 40 - http://www.reactome.org/biopax/46/48887#SequenceSite23023 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1038 - - - - Q6LDN9 - UniProt - - - - - - MOD_RES 285 285 Phosphoserine. - - - - REACT_27920 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27920.3 - - - - EQUAL - 85 - http://www.reactome.org/biopax/46/48887#SequenceSite9869 - - - - Q86YN5 - UniProt - - - - - - MOD_RES 46 46 4-carboxyglutamate. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2782 - - - - - - 7835883 - Inaba, T - Khatib, ZA - Valentine, M - Look, AT - Pubmed - Chromosomal localization and cDNA cloning of the human DBP and TEF genes - Genomics 23:344-51 - 1994 - - - - EQUAL - 1029 - - - - EQUAL - 196 - http://www.reactome.org/biopax/46/48887#SequenceSite4955 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5625 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2117 - - - - - - 159771 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159771 - - - - REACT_26547 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26547.2 - - - - 163820 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163820 - - - - 2443571 - Goldstein, SM - Wintroub, BU - Proud, D - Schwartz, LB - Irani, AM - Kaempfer, CE - Pubmed - Detection and partial characterization of a human mast cell carboxypeptidase - J Immunol 139:2724-9 - 1987 - - - - ENSG00000123095 - Ensembl - - - - 163813 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163813 - - - - 3671094 - Elliott WH - May BK - Borthwick IA - Bawden MJ - Healy HM - Morris CP - PubMed - Sequence of human 5-aminolevulinate synthase cDNA. - Nucleic Acids Res 15(20);8563 - 1987 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5614 - - - - NM_024665 - RefSeq - - - - 10924499 - Christie, G - Turner, AJ - Karran, E - Hooper, NM - Tipnis, SR - Hyde, R - Pubmed - A human homolog of angiotensin-converting enzyme. Cloning and functional expression as a captopril-insensitive carboxypeptidase - J Biol Chem 275:33238-43 - 2000 - - - - CPT1A - HGNC - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12948 - - - - EQUAL - 321 - - - - NP_056973 - RefSeq - - - - - - - - - - Authored: May, B, 2011-11-08 - The UGT1A9 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction168 - Expression of UGT1A9 - - - - 608628 - omim - - - - G0S2 - HGNC - - - - REACT_111441 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111441.1 - - - - EQUAL - 60 - - - - CRY1 - HGNC - - - - - - vitamin K epoxide - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule971 - Reactome DB_ID: 159835 - VKO - - - - - - - - ACTIVATION - - Glucocorticoids enhance rhythmic transcription of PER2 - As inferred from mouse, glucocorticoids bind the glucocorticoid receptor at the promoter of the PER2 gene and enhance rhythmic transcription. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation105 - - - - NP_006303 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2200 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25534 - - - - InChI=1S/C31H48O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,18-20,22-24,32-33H,9-17,21H2,1-6H3/b25-20+/t23-,24-/m1/s1 - InChI - - - - 400247 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400247 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5640 - - - - Q9UH79 - UniProt - - - - EQUAL - 69 - - - - HGNC:2532 - HGNC - - - - 7736787 - Otterness DM - Weinshilboum RM - Mohrenweiser HW - Brandriff BF - PubMed - Dehydroepiandrosterone sulfotransferase gene (STD): localization to human chromosome band 19q13.3. - Cytogenet Cell Genet 70(1-2);45-7 - 1995 - - - - ENSP00000392247 - Ensembl - - - - - - MOD_RES 241 241 N6-acetyllysine. - - - - NP_000167 - RefSeq - - - - REACT_118045 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118045.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12042 - - - - - - ENSP00000426665 - Ensembl - - - - 2155 - NCBI Gene - - - - 381254 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381254 - - - - REACT_148661 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148661.1 - - - - EQUAL - 74 - http://www.reactome.org/biopax/46/48887#SequenceSite9873 - - - - EQUAL - 412 - - - - 602633 - omim - - - - - - MOD_RES 476 476 Phosphothreonine. - - - - 1989813 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989813 - - - - - - - - - - PDGF B-chain precursor dimer - Reactome DB_ID: 380748 - http://www.reactome.org/biopax/46/48887#Complex1211 - - - - NP_066940 - RefSeq - - - - EQUAL - 384 - - - - EQUAL - 241 - http://www.reactome.org/biopax/46/48887#SequenceSite3904 - - - - EQUAL - 753 - - - - D3DXC4 - UniProt - - - - REACT_148553 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148553.2 - - - - Q96ST3 - UniProt - - - - EQUAL - 73 - - - - Q6VB42 - UniProt - - - - Q13616 - UniProt - - - - 8618898 - Ho, WT - Miao, CH - Greenberg, D - Chung, DW - Davie, EW - Pubmed - Liver-specific expression of the human factor VII gene - Proc Natl Acad Sci U S A 92:12347-51 - 1995 - - - - ELOVL3 - HGNC - - - - EQUAL - 476 - - - - ENST00000449337 - Ensembl - - - - - - pro-GAS6, uncarboxylated - pro-growth-arrest-specific protein 6, uncarboxylated - - - - - Reactome DB_ID: 163812 - http://www.reactome.org/biopax/46/48887#Protein11643 - GAS6(31-691) - - - - 560473 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=560473 - - - - MED4 - HGNC Symbol - - - - EQUAL - 885 - - - - EQUAL - 780 - - - - NCOA6 - HGNC - - - - EP300 - HGNC Symbol - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12010 - - - - NM_001142587 - RefSeq - - - - O75787 - UniProt - - - - 7912658 - Gros P - Ruetz S - PubMed - Phosphatidylcholine translocase: a physiological role for the mdr2 gene. - Cell 77(7);1071-81 - 1994 - - - - Q13644 - UniProt - - - - 11840502 - Sanchez-Guerra M - Gonzalez-Garcia J - Infante J - del Molino JP - Berciano J - Mateo I - Llorca J - Combarros O - PubMed - Lack of association between cathepsin D genetic polymorphism and Alzheimer disease in a Spanish sample. - Am J Med Genet 114(1);31-3 - 2002 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10034 - - - - 12927775 - Fuhrer, W - Herold, P - Rasetti, V - Maibaum, J - Cumin, F - Göschke, R - Stanton, A - Baum, HP - Cohen, NC - Schnell, CR - Rüger, H - Jensen, C - Mah, R - Rahuel, J - Grütter, MG - Yamaguchi, Y - Bedigian, MP - Schilling, W - Wood, JM - Rigollier, P - O'Brien, E - Stutz, S - Pubmed - Structure-based design of aliskiren, a novel orally effective renin inhibitor - Biochem Biophys Res Commun 308:698-705 - 2003 - - - - EQUAL - 956 - - - - - - Histone acetyltransferase p300 - KAT3B - EP300 - EP300_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein506 - Reactome DB_ID: 381325 - p300 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25574 - - - - NM_001256134 - RefSeq - - - - - - MOD_RES 739 739 Phosphothreonine; by MAPK1, MAPK3 AND MAPK8. - - - - - - - - - Binding of FBXL3 to Phosphorylated CRY proteins - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2009-05-17 22:04:50 - FBXL3 is an F-box type component of a particular SKP/CUL/F-Box E3 ubiquitin ligase. FBXL3 interacts specifically with CRY1 and CRY2 in the cytosol to direct the polyubiquitination of CRY1 and CRY2. It is unknown if FBXL3 requires phosphorylation or other modification of CRY proteins in order to bind and ubiquitinate them. Phosphorylation of CRY by Adenosine monophosphate-dependent kinase increases degradation of CRY, apparently by increasing association of CRY with FBXL3 Polyubiquitination of CRY proteins directs them to the 26S proteasome for degradation. - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3862 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - ENSP00000348610 - Ensembl - - - - P12821 - UniProt - - - - ENST00000346342 - Ensembl - - - - 49491 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=49491 - - - - 442499 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442499 - - - - HGNC:18305 - HGNC - - - - - - APOA1(25-266) - apolipoprotein A-I - - - - - Reactome DB_ID: 174720 - http://www.reactome.org/biopax/46/48887#Protein578 - apoA-I - - - - - - MOD_RES 449 449 Phosphoserine. - - - - 879850 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879850 - - - - 2022396 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022396 - - - - Q96RN5 - UniProt - - - - - - - - - INHIBITION - - 'NR1D1 (REV-ERBA):heme:Corepressor [nucleoplasm]' negatively regulates 'Expression of NR1D1 (REV-ERBA)' - NR1D1 (REV-ERBA) binds its own promoter and represses its own expression. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation108 - - - - ENSP00000262367 - Ensembl - - - - 1543 - NCBI Gene - - - - Q86YN3 - UniProt - - - - 3325590 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3325590 - - - - NM_002616 - RefSeq - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 400230 - http://www.reactome.org/biopax/46/48887#Protein11527 - p-S-PER1,2 - - - - ENSG00000135218 - Ensembl - - - - Q5JVF6 - UniProt - - - - 2022345 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022345 - - - - Q9C094 - UniProt - - - - EQUAL - 114 - - - - Q0VGB6 - UniProt - - - - NP_060108 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2229 - - - - NM_001836 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7596 - - - - A4D7U4 - UniProt - - - - NM_021117 - RefSeq - - - - 549572 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549572 - - - - 159730 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159730 - - - - AGT - HGNC - - - - 1368069 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368069 - - - - EQUAL - 266 - http://www.reactome.org/biopax/46/48887#SequenceSite21496 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4724 - - - - - EQUAL - 63 - - - - NAMPT - HGNC Symbol - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5798 - - - - EQUAL - 69 - http://www.reactome.org/biopax/46/48887#SequenceSite18497 - - - - NM_018019 - RefSeq - - - - REACT_17391 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17391.2 - - - - - - UBB(1-76) - ubiquitin (UBB 1) - - - - - http://www.reactome.org/biopax/46/48887#Protein1046 - Reactome DB_ID: 939214 - UBB - - - - REACT_25528 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25528.2 - - - - EQUAL - 1136 - - - - EQUAL - 512 - http://www.reactome.org/biopax/46/48887#SequenceSite25549 - - - - EQUAL - 676 - http://www.reactome.org/biopax/46/48887#SequenceSite21673 - - - - EQUAL - 9 - - - - REACT_147959 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147959.1 - - - - 11441146 - Wu, LC - McKnight, SL - Reick, M - Rutter, J - Pubmed - Regulation of clock and NPAS2 DNA binding by the redox state of NAD cofactors - Science 293:510-4 - 2001 - - - - 11441147 - Dudley, C - McKnight, SL - Garcia, JA - Reick, M - Pubmed - NPAS2: an analog of clock operative in the mammalian forebrain - Science 293:506-9 - 2001 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2442 - - - - - - ENSP00000437955 - Ensembl - - - - EQUAL - 93 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10129 - - - - EQUAL - 1481 - - - - EQUAL - 59 - - - - REACT_116133 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116133.1 - - - - B2RDI9 - UniProt - - - - REACT_27753 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27753.3 - - - - ACOX1 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8327 - - - - 600441 - omim - - - - 1989775 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989775 - - - - - - MOD_RES 83 83 N6-acetyllysine (By similarity). - - - - REACT_27383 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27383.3 - - - - MED6 - HGNC - - - - NP_001124468 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12815 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12390 - - - - MED13L - HGNC Symbol - - - - GO:0005886 - Gene Ontology - - - - GO:0008234 - GENE ONTOLOGY - - - - - ENSP00000345702 - Ensembl - - - - Q6VBP4 - UniProt - - - - O60834 - UniProt - - - - EQUAL - 2063 - http://www.reactome.org/biopax/46/48887#SequenceSite12415 - - - - ENSP00000380311 - Ensembl - - - - REACT_147733 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147733.2 - - - - 561148 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561148 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ANKRD1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation197 - - - - Q9UK86 - UniProt - - - - B2R4Z6 - UniProt - - - - 8145820 - pubchem-substance - - - - NM_017592 - RefSeq - - - - - - - - Pro-protein S is transported from the endoplasmic reticulum to the Golgi apparatus - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3897 - In this reaction, 1 molecule of 'pro-protein S' is translocated from endoplasmic reticulum membrane to Golgi membrane.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - - - - - - TaxREB302 - Tax-responsive enhancer element-binding protein 302 - DBP - Albumin D box-binding protein - Albumin D-element-binding protein - - - - - - - - - - - - - DBP_HUMAN - D site-binding protein - FUNCTION: This transcriptional activator recognizes and binds to the sequence 5'-RTTAYGTAAY-3' found in the promoter of genes such as albumin, CYP2A4 and CYP2A5. It is not essential for circadian rhythm generation, but modulates important clock output genes. May be a direct target for regulation by the circadian pacemaker component clock. May affect circadian period and sleep regulation.SUBUNIT: Binds DNA as a homodimer or a heterodimer. Can form a heterodimer with TEF.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Ubiquitously expressed. Expressed in the suprachiasmatic nuclei (SCN) and in most peripheral tissues, with a strong circadian rhythmicity.SIMILARITY: Belongs to the bZIP family. PAR subfamily.SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 728 728 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1857 - - - - - - - - - - - - - - BMAL1:CLOCK/NPAS2:CRY - Reactome DB_ID: 549449 - http://www.reactome.org/biopax/46/48887#Complex4981 - - - - - - MOD_RES 641 641 Phosphoserine; by PKC/PRKCZ; alternate. - - - - ENSG00000100450 - Ensembl - - - - - - MOD_RES 1529 1529 N6-acetyllysine. - - - - 159827 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159827 - - - - - - MOD_RES 1555 1555 N6-acetyllysine. - - - - A6NIQ6 - UniProt - - - - Q8WYA4 - UniProt - - - - HGNC:2300 - HGNC - - - - B0I4X3 - UniProt - - - - - - - - Pro-protein C is transported from the endoplasmic reticulum to the Golgi apparatus - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3896 - In this reaction, 1 molecule of 'pro-protein C' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - - - - - EQUAL - 493 - - - - REACT_21644 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21644.2 - - - - - - MOD_RES 63 63 4-carboxyglutamate. - - - - Q6FI38 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry5026 - - - - EQUAL - 241 - http://www.reactome.org/biopax/46/48887#SequenceSite4959 - - - - TBL1X - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2092 - - - - NP_598395 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10071 - - - - - - 25819 - NCBI Gene - - - - EQUAL - 326 - - - - NM_030762 - RefSeq - - - - 5627 - NCBI Gene - - - - 212391 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212391 - - - - NP_001243063 - RefSeq - - - - EQUAL - 609 - http://www.reactome.org/biopax/46/48887#SequenceSite4669 - - - - - GGCX - GC - Gamma-glutamyl carboxylase - Peptidyl-glutamate 4-carboxylase - 4.1.1.90 - Vitamin K gamma glutamyl carboxylase - - - - - - - - - - - - - - - - - - - - - - - - - VKGC_HUMAN - Vitamin K-dependent gamma-carboxylase - FUNCTION: Mediates the vitamin K-dependent carboxylation of glutamate residues to calcium-binding gamma-carboxyglutamate (Gla) residues with the concomitant conversion of the reduced hydroquinone form of vitamin K to vitamin K epoxide.CATALYTIC ACTIVITY: [Peptidyl]-4-carboxyglutamate + 2,3- epoxyphylloquinone + H(2)O = [peptidyl]-glutamate + CO(2) + O(2) + phylloquinone.BIOPHYSICOCHEMICAL PROPERTIES: pH dependence: Optimum pH is 7;SUBUNIT: Monomer. May interact with CALU (By similarity).SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P38435-1; Sequence=Displayed; Name=2; IsoId=P38435-2; Sequence=VSP_046179; Note=No experimental confirmation available;DISEASE: Combined deficiency of vitamin K-dependent clotting factors 1 (VKCFD1) [MIM:277450]: VKCFD leads to a bleeding tendency that is usually reversed by oral administration of vitamin K. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Pseudoxanthoma elasticum-like disorder with multiple coagulation factor deficiency (PXEL-MCFD) [MIM:610842]: Characterized by hyperlaxity of the skin involving the entire body. Important phenotypic differences with classical PXE include much more severe skin laxity with spreading toward the trunk and limbs with thick, leathery skin folds rather than confinement to flexural areas, and no decrease in visual acuity. Moreover, detailed electron microscopic analyzes revealed that alterations of elastic fibers as well as their mineralization are slightly different from those in classic PXE. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: The vitamin K-dependent protein substrates of carboxylase have usually a propeptide that binds to a high- affinity site on the carboxylase. CO(2), O(2) and reduced vitamin K are cosubstrates.SIMILARITY: Belongs to the vitamin K-dependent gamma-carboxylase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 549467 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549467 - - - - NM_002943 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5741 - - - - ENSP00000442438 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite20836 - - - - EQUAL - 1391 - - - - - - - - - - ACTIVATION - - 'p-PPARGC1A [nucleoplasm]' positively regulates 'Expression of PPARGC1A (PGC-1alpha)' - PGC-1alpha (PPARGC1A) enhances expression of its own gene in mouse (Jager et al.2007) and in rat hepatocytes (Lin et al. 2003) - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation114 - - - - REACT_119524 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119524.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9755 - - - - - - ENSP00000384403 - Ensembl - - - - 1368079 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368079 - - - - Q7KZ19 - UniProt - - - - EQUAL - 676 - http://www.reactome.org/biopax/46/48887#SequenceSite21738 - - - - 2022362 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022362 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4968 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8314 - - - - O75148 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10035 - - - - ENSP00000388107 - Ensembl - - - - EQUAL - 207 - http://www.reactome.org/biopax/46/48887#SequenceSite23171 - - - - - C18H19N3O3S - BRL-49653 - 5-(4-{2-[methyl(pyridin-2-yl)amino]ethoxy}benzyl)-1,3-thiazolidine-2,4-dione - 5-((4-(2-(methyl-2-pyridinylamino)ethoxy)phenyl)methyl)-2,4-thiazolidinedione - - - - - 357.427 - rosiglitazone - rosiglitazone - - - - EQUAL - 428 - http://www.reactome.org/biopax/46/48887#SequenceSite4694 - - - - EQUAL - 504 - - - - ENST00000472167 - Ensembl - - - - REACT_2524 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2524.2 - - - - ENSP00000265723 - Ensembl - - - - REACT_24758 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24758.2 - - - - - - Glucocorticoid receptor - GCR_HUMAN - - - - - Reactome DB_ID: 879837 - http://www.reactome.org/biopax/46/48887#Protein11515 - NR3C1 - - - - O75557 - UniProt - - - - EQUAL - 658 - http://www.reactome.org/biopax/46/48887#SequenceSite25477 - - - - EQUAL - 119 - - - - 551 - NCBI Gene - - - - ENSP00000229758 - Ensembl - - - - 8804575 - Huang SM - Chang GG - Chou WY - PubMed - Nonidentity of the cDNA sequence of human breast cancer cell malic enzyme to that from the normal human cell. - J Protein Chem 15(3);273-9 - 1996 - - - - EQUAL - 21 - - - - 8575776 - Simard J - Morissette J - Durocher F - Dufort I - Luu-The V - PubMed - Genetic linkage mapping of the dehydroepiandrosterone sulfotransferase (STD) gene on the chromosome 19q13.3 region. - Genomics 29(3);781-3 - 1995 - - - - - - - - SREBP1A,1C,2 cleaved by S2P - - - - http://www.reactome.org/biopax/46/48887#Protein13770 - Converted from EntitySet in Reactome - Reactome DB_ID: 1655720 - SREBF1A,1C,2 cleaved by S2P - - - - 1AV1 - PROTEIN DATA BANK - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12831 - - - - 601737 - omim - - - - 611265 - omim - - - - - 3.4.23 - Renin Bound to Renin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin I - - - - - - - - - Renin:Prorenin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10) - Renin bound to the (pro)renin receptor (ATP6AP2) hydrolyzes angiotensinogen to yield angiotensin-(1-10) (angiotensin I) (Nguyen et al. 2002). Binding to the (pro)renin receptor increases the catalytic efficiency of renin 4-fold (Nguyen et al. 2002). Aliskiren, a drug used clinically to treat hypertension, inhibits cleavage of angiotensinogen by renin (Gossas et al. 2011, Wood et al. 2003, reviewed in Gerc et al. 2009). - Authored: May, B, 2011-11-19 - Edited: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4038 - Reviewed: Joseph, J, 2012-08-06 - - - - - - - MOD_RES 88 88 N6-acetyllysine. - - - - - - - - - - - - p55CDC - CDC20 - - - - - - - - - - - - - - - - - - - CDC20_HUMAN - Cell division cycle protein 20 homolog - FUNCTION: Required for full ubiquitin ligase activity of the anaphase promoting complex/cyclosome (APC/C) and may confer substrate specificity upon the complex. Is regulated by MAD2L1: in metaphase the MAD2L1-CDC20-APC/C ternary complex is inactive and in anaphase the CDC20-APC/C binary complex is active in degrading substrates. The CDC20-APC/C complex positively regulates the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons. CDC20-APC/C-induced degradation of NEUROD2 induces presynaptic differentiation.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: Found in a complex with CDC20, CDC27, SPATC1 and TUBG1. Interacts with SPATC1. Interacts with NEUROD2 (By similarity). Interacts with MAD2L1 and BUB1B. The phosphorylated form interacts with APC/C. Interacts with NINL. May interact with MAD2L2. Interacts with CDK5RAP2. Interacts with isoform 1 of NEK2.SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cytoplasm, cytoskeleton, spindle pole.DEVELOPMENTAL STAGE: Synthesis is initiated at G1/S, protein level peaks in M phase and protein is abruptly degraded at M/G1 transition.PTM: Phosphorylated during mitosis, probably by maturation promoting factor (MPF). Phosphorylated by BUB1 at Ser-41; Ser-72; Ser-92; Ser-153; Thr-157 and Ser-161. Phosphorylated by NEK2.PTM: Dephosphorylated by CTDP1.PTM: Ubiquitinated and degraded by the proteasome during spindle assembly checkpoint. Deubiquitinated by USP44, leading to stabilize the MAD2L1-CDC20-APC/C ternary complex, thereby preventing premature activation of the APC/C. Ubiquitinated at Lys-490 during prometaphase. Ubiquitination at Lys-485 and Lys-490 has no effect on its ability to bind the APC/C complex.SIMILARITY: Belongs to the WD repeat CDC20/Fizzy family.SIMILARITY: Contains 7 WD repeats.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CDC20ID40003ch1p34.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc20/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 2436 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2757 - - - - - - EQUAL - 482 - http://www.reactome.org/biopax/46/48887#SequenceSite21436 - - - - GO:0002003 - GENE ONTOLOGY - - - - - PER1 - HGNC - - - - NPAS2 - HGNC - - - - APOA1 - HGNC Symbol - - - - EQUAL - 416 - http://www.reactome.org/biopax/46/48887#SequenceSite11121 - - - - EQUAL - 247 - http://www.reactome.org/biopax/46/48887#SequenceSite25573 - - - - ENST00000360490 - Ensembl - - - - ENSP00000392983 - Ensembl - - - - Q53G18 - UniProt - - - - - - factor VII propeptide - - - - - http://www.reactome.org/biopax/46/48887#Protein11657 - Reactome DB_ID: 159847 - F7(21-60) - - - - Q9NPJ6 - UniProt - - - - ENSP00000303192 - Ensembl - - - - REACT_24411 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24411.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5632 - - - - Q6LCY0 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry3486 - - - - 23309 - NCBI Gene - - - - NP_001034581 - RefSeq - - - - EQUAL - 383 - - - - P15086 - UniProt - - - - - - MOD_RES 101 101 Phosphoserine; by ATM. - - - - 17306620 - Yu, S - Reddy, JK - Pubmed - Transcription coactivators for peroxisome proliferator-activated receptors - Biochim Biophys Acta 1771:936-51 - 2007 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5773 - - - - EQUAL - 131 - - - - ENSP00000384517 - Ensembl - - - - - - GPIIIB - PAS IV - 4xPalmC-CD36 - CD36 antigen - PAS-4 protein - Platelet glycoprotein IV - - - - - - - - - - Reactome DB_ID: 51645 - http://www.reactome.org/biopax/46/48887#Protein817 - GPIV - - - - REACT_148338 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148338.1 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction155 - Reviewed: Kersten, S, 2009-06-08 - The G0S2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of G0S2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10879 - - - - - - REACT_117967 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117967.1 - - - - REACT_117932 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117932.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21477 - - - - - - Arachidonate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule738 - Reactome DB_ID: 400137 - AA - - - - - - MOD_RES 67 67 4-carboxyglutamate. - - - - EQUAL - 640 - - - - 948 - NCBI Gene - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1036 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4717 - - - - - - MOD_RES 612 612 Phosphoserine; alternate. - - - - 1385 - NCBI Gene - - - - EQUAL - 539 - - - - NP_002945 - RefSeq - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12926 - - - - 400273 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400273 - - - - 2990875 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2990875 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2099 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10043 - - - - - - Mediator complex subunit 20 - TRFP - hTRFP - MED20 - TRF-proximal protein homolog - - - - - - - - - - - - - - - MED20_HUMAN - Mediator of RNA polymerase II transcription subunit 20 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Interacts with PPARG (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 20 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000400117 - Ensembl - - - - NM_001174088 - RefSeq - - - - EQUAL - 1147 - - - - 7893153 - Haro D - Hegardt FG - Ortiz JA - Buesa C - Mascaro C - PubMed - Molecular cloning and tissue expression of human mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase. - Arch Biochem Biophys 317(2);385-90 - 1995 - - - - - - MOD_RES 112 112 Phosphoserine; by MAPK (By similarity). - - - - ENSP00000272317 - Ensembl - - - - 2022368 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022368 - - - - Q9NYR5 - UniProt - - - - ENSP00000252595 - Ensembl - - - - EQUAL - 1473 - - - - NP_003882 - RefSeq - - - - EQUAL - 527 - - - - - 13.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12968 - - - - Q15179 - UniProt - - - - ENSP00000309753 - Ensembl - - - - EQUAL - 34 - http://www.reactome.org/biopax/46/48887#SequenceSite22996 - - - - 1368081 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368081 - - - - FZR1 - HGNC Symbol - - - - O60244 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12012 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5619 - - - - 189906 - omim - - - - 159770 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159770 - - - - NP_068370 - RefSeq - - - - CHEBI:44952 - ChEBI - - - - Q96S56 - UniProt - - - - EQUAL - 87 - http://www.reactome.org/biopax/46/48887#SequenceSite4966 - - - - 300196 - omim - - - - 1636 - NCBI Gene - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4964 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5633 - - - - REACT_164455 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164455.1 - - - - Q16001 - UniProt - - - - REACT_17226 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17226.2 - - - - HIF1A - HGNC Symbol - - - - 1A6Y - PROTEIN DATA BANK - - - - ENST00000424173 - Ensembl - - - - 8363569 - Brown S - Acharya SK - Bell DR - Ateitalla I - Elias E - Rider CG - Davies MH - Na L - Jenkins NA - Plant NJ - PubMed - Species-specific induction of cytochrome P-450 4A RNAs: PCR cloning of partial guinea-pig, human and mouse CYP4A cDNAs. - Biochem J 294 ( Pt 1);173-80 - 1993 - - - - 1989793 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989793 - - - - ENSP00000280614 - Ensembl - - - - HGNC:8852 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1096 - - - - ENST00000393230 - Ensembl - - - - ENSG00000167910 - Ensembl - - - - bHLHe41 - Class B basic helix-loop-helix protein 3 - bHLHb3 - DEC2 - Enhancer-of-split and hairy-related protein 1 - hDEC2 - SHARP-1 - Differentially expressed in chondrocytes protein 2 - BHLHE41 - SHARP1 - BHLHB3 - - - - - - - - - - - - - BHE41_HUMAN - Class E basic helix-loop-helix protein 41 - FUNCTION: May be a transcriptional repressor that represses both basal and activated transcription.SUBUNIT: Homodimerize.SUBCELLULAR LOCATION: Nucleus (By similarity).TISSUE SPECIFICITY: Highly expressed in skeletal muscle and brain, moderately expressed in pancreas and heart, weakly expressed in placenta, lung, liver and kidney.POLYMORPHISM: Genetic variations in BHLHE41 are associated with the short sleep phenotype [MIM:612975]. Individuals with this trait require less sleep in any 24-hour period than is typical for their age group.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 Orange domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000327315 - Ensembl - - - - - - MOD_RES 554 554 Phosphoserine. - - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction149 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The CYP4A11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of CYP4A11 - - - - NM_000602 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1077 - - - - NP_003661 - RefSeq - - - - REACT_27658 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27658.3 - - - - 8145132 - pubchem - - - - REACT_116159 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116159.1 - - - - REACT_117935 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117935.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12981 - - - - ENSP00000301608 - Ensembl - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13189 - - - - AGT - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25352 - - - - 26697064 - pubchem-substance - - - - 87324641 - pubchem-substance - - - - ENSP00000323326 - Ensembl - - - - REACT_116112 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116112.2 - - - - EQUAL - 160 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10244 - - - - ENSG00000105516 - Ensembl - - - - EQUAL - 211 - - - - B4E1A7 - UniProt - - - - - - MOD_RES 1024 1024 N6-acetyllysine; alternate. - - - - A4D1D3 - UniProt - - - - REACT_164052 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164052.1 - - - - - - MDR3_HUMAN - Multidrug resistance protein 3 - - - - - Reactome DB_ID: 400167 - http://www.reactome.org/biopax/46/48887#Protein13758 - ABCB4 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8348 - - - - - - - - - - - ACE Hydrolyzes Angiotensin-(1-9) to Yield Angiotensin-(1-7) - Authored: May, B, 2011-11-19 - Edited: May, B, 2011-11-19 - Angiotensin-converting enzyme (ACE) hydrolyzes angiotensin-(1-9) to yield angiotensin-(1-7) (Rice et al. 2004). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4046 - Reviewed: Joseph, J, 2012-08-06 - - - - - 442469 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442469 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4711 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2870 - - - - ENST00000324817 - Ensembl - - - - 10025 - NCBI Gene - - - - O00316 - UniProt - - - - NM_024831 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5667 - - - - - - 2558510 - Hayakari, M - Amano, K - Izumi, H - Murakami, S - Pubmed - Purification of angiotensin-converting enzyme from human intestine - Adv Exp Med Biol 247:365-70 - 1989 - - - - 2677 - NCBI Gene - - - - REACT_117999 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117999.1 - - - - 1639841 - Heldin, CH - Westermark, B - Thyberg, J - Ostman, A - Pubmed - PDGF-AA and PDGF-BB biosynthesis: proprotein processing in the Golgi complex and lysosomal degradation of PDGF-BB retained intracellularly - J Cell Biol 118:509-19 - 1992 - - - - ENST00000396000 - Ensembl - - - - DRIP80 - Vitamin D3 receptor-interacting protein complex 80 kDa component - Thyroid hormone receptor-associated protein complex 80 kDa component - CRSP6 - Mediator complex subunit 17 - ARC77 - Transcriptional coactivator CRSP77 - TRAP80 - CRSP complex subunit 6 - MED17 - Trap80 - Cofactor required for Sp1 transcriptional activation subunit 6 - Activator-recruited cofactor 77 kDa component - DRIP77 - - - - - - - - - - - - - - - - - - - MED17_HUMAN - Mediator of RNA polymerase II transcription subunit 17 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Interacts with GATA1 and PPARG (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with STAT2.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9NVC6-1; Sequence=Displayed; Name=2; IsoId=Q9NVC6-2; Sequence=VSP_028115, VSP_028116;TISSUE SPECIFICITY: Ubiquitous.DISEASE: Microcephaly, postnatal progressive, with seizures and brain atrophy (MCPHSBA) [MIM:613668]: A disorder characterized by postnatal progressive microcephaly and severe developmental retardation associated with cerebral and cerebellar atrophy. Infants manifest swallowing difficulties leading to failure to thrive, jitteriness, poor visual fixation, truncal arching, seizures. There is no acquisition of developmental milestones and patients suffer from marked spasticity and profound retardation. Progressive microcephaly becomes evident few months after birth. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the Mediator complex subunit 17 family.SEQUENCE CAUTION: Sequence=AAD30856.1; Type=Frameshift; Positions=333, 335, 341, 346; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSG00000007866 - Ensembl - - - - - - ubiquitin (UBC 2) - - - - - http://www.reactome.org/biopax/46/48887#Protein2478 - Reactome DB_ID: 939869 - UBC(77-152) - - - - 159841 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159841 - - - - REACT_27127 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27127.2 - - - - ENSP00000227665 - Ensembl - - - - NP_056529 - RefSeq - - - - EQUAL - 75 - http://www.reactome.org/biopax/46/48887#SequenceSite9992 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8357 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4967 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12824 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1098 - - - - MOD_RES N-acetylserine - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein2125 - Converted from EntitySet in Reactome - Reactome DB_ID: 381940 - Active platelet-derived growth factor A chain isoforms - - - - ENSG00000005812 - Ensembl - - - - REACT_19786 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19786.1 - - - - - - MOD_RES 110 110 Methionine sulfoxide. - - - - ENST00000318981 - Ensembl - - - - - - 11xCbxE-PROS1(25-676) - - - - - - - - - - - - - - - Reactome DB_ID: 159850 - http://www.reactome.org/biopax/46/48887#Protein11652 - pro-protein S - - - - NM_003670 - RefSeq - - - - 549364 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549364 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10150 - - - - - - REACT_120364 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120364.1 - - - - P04151 - UniProt - - - - REACT_27076 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27076.3 - - - - - - MOD_RES 979 979 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10768 - - - - A2RUN0 - UniProt - - - - ENSP00000000442 - Ensembl - - - - 7698013 - Bishop DF - Cotter PD - Smith DI - Drabkin HA - Varkony T - PubMed - Assignment of the human housekeeping delta-aminolevulinate synthase gene (ALAS1) to chromosome band 3p21.1 by PCR analysis of somatic cell hybrids. - Cytogenet Cell Genet 69(3-4);207-8 - 1995 - - - - 200994 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=200994 - - - - ENSP00000426745 - Ensembl - - - - ENSP00000347834 - Ensembl - - - - PROS1 - HGNC Symbol - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of NOCTURNIN' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation97 - The phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds an E-box element in the promoter of the NOCTURNIN gene and activates transcription of NOCTURNIN. NPAS2 is predicted to act redundantly with CLOCK. - - - - F8WD53 - UniProt - - - - Q9UBK2 - UniProt - - - - EQUAL - 400 - http://www.reactome.org/biopax/46/48887#SequenceSite21675 - - - - - - - - - - ANPEP Dimer - http://www.reactome.org/biopax/46/48887#Complex5112 - Reactome DB_ID: 2022361 - - - - - - MOD_RES 53 53 4-carboxyglutamate. - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite25322 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12821 - - - - - - NRF1_HUMAN - Nuclear respiratory factor 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein13762 - Reactome DB_ID: 1592205 - NRF1 - - - - 8145109 - pubchem-substance - - - - NP_148937 - RefSeq - - - - EQUAL - 646 - http://www.reactome.org/biopax/46/48887#SequenceSite23575 - - - - - - MOD_RES 226 226 Phosphoserine. - - - - 14718380 - pubchem-substance - - - - EQUAL - 95 - - - - Q9UD54 - UniProt - - - - - - TBL1X_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein3201 - Reactome DB_ID: 351644 - TBL1X - - - - MOD_RES (3S)-3-hydroxyasparagine - - - - Q06413 - UniProt - - - - 1358792 - Lusis AJ - Russell DW - Cohen JC - Mehrabian M - Hobbs HH - Sparkes RS - Cali JJ - Jelinek DF - PubMed - Cloning of the human cholesterol 7 alpha-hydroxylase gene (CYP7) and localization to chromosome 8q11-q12. - Genomics 14(1);153-61 - 1992 - - - - NP_001180278 - RefSeq - - - - HGNC:45 - HGNC - - - - WWTR1 - HGNC Symbol - - - - NM_021705 - RefSeq - - - - ENSP00000269814 - Ensembl - - - - ENSP00000420389 - Ensembl - - - - EQUAL - 146 - - - - EQUAL - 247 - http://www.reactome.org/biopax/46/48887#SequenceSite5187 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The AGT gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction142 - Expression of AGT - - - - Q9HD94 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21467 - - - - ENSP00000434459 - Ensembl - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite4650 - - - - REACT_115770 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115770.1 - - - - NP_001258558 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10062 - - - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite21437 - - - - Nuclear transcription factor Y subunit C - Transactivator HSM-1/2 - NFYC - NF-YC - CAAT box DNA-binding protein subunit C - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NFYC_HUMAN - Nuclear transcription factor Y subunit gamma - FUNCTION: Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.SUBUNIT: Heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=7; Name=3; Synonyms=DS2.8; IsoId=Q13952-1; Sequence=Displayed; Name=1; Synonyms=Gamma; IsoId=Q13952-2; Sequence=VSP_000851, VSP_000852; Name=2; IsoId=Q13952-3; Sequence=VSP_000851; Name=4; IsoId=Q13952-4; Sequence=VSP_043348, VSP_000851, VSP_000852; Note=No experimental confirmation available; Name=5; IsoId=Q13952-5; Sequence=VSP_000852; Note=No experimental confirmation available; Name=6; IsoId=Q13952-6; Sequence=VSP_043349, VSP_000851, VSP_000852; Note=No experimental confirmation available; Name=7; IsoId=Q13952-7; Sequence=VSP_000851, VSP_046350, VSP_000852; Note=No experimental confirmation available;SIMILARITY: Belongs to the NFYC/HAP5 subunit family.SEQUENCE CAUTION: Sequence=BAD92212.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_7039 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7039.1 - - - - ALAS1 - HGNC Symbol - - - - Q6VBP2 - UniProt - - - - Q5JVF5 - UniProt - - - - - - MOD_RES 703 703 N6-acetyllysine. - - - - EQUAL - 683 - - - - 10891 - NCBI Gene - - - - EQUAL - 271 - - - - ENST00000236671 - Ensembl - - - - 1655826 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655826 - - - - REACT_25694 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25694.3 - - - - Q86U66 - UniProt - - - - EQUAL - 461 - http://www.reactome.org/biopax/46/48887#SequenceSite21649 - - - - 57761 - NCBI Gene - - - - 159848 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159848 - - - - 939191 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939191 - - - - REACT_4023 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4023.3 - - - - Q9UEV0 - UniProt - - - - REACT_116996 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116996.4 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4693 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2774 - - - - - - O00314 - UniProt - - - - Q6BEB4 - uniprot - - - - EQUAL - 164 - - - - ENST00000595683 - Ensembl - - - - ENSP00000363518 - Ensembl - - - - NP_001137417 - RefSeq - - - - 2022373 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022373 - - - - NP_036250 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5616 - - - - 1FQV - PROTEIN DATA BANK - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8323 - - - - ENST00000372651 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5774 - - - - EQUAL - 1119 - - - - MED8 - HGNC Symbol - - - - Q8IWY5 - UniProt - - - - Q96QX2 - UniProt - - - - Q9BPZ8 - UniProt - - - - REACT_19502 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19502.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4759 - - - - - - - - - - - - P08473 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4723 - - - - - - 190040 - omim - - - - ENST00000372462 - Ensembl - - - - ENSP00000356501 - Ensembl - - - - EQUAL - 58 - - - - - - - - - - - - INHIBITION - - 'enalaprilat [extracellular region]' negatively regulates 'ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control307 - - - - ENSP00000446108 - Ensembl - - - - Q9UHM2 - UniProt - - - - NM_000789 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25546 - - - - EQUAL - 400 - http://www.reactome.org/biopax/46/48887#SequenceSite21740 - - - - - - MOD_RES 119 119 N6-acetyllysine. - - - - CDK8 - HGNC Symbol - - - - EQUAL - 57 - - - - 1368165 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368165 - - - - 1368102 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368102 - - - - - - Cathepsin D ecNumber3.4.23.5/ecNumber component recommendedName: Cathepsin D light chain /component component recommendedName: Cathepsin D heavy chain /component - CATD_HUMAN - CTSD(65-412) - - - - - http://www.reactome.org/biopax/46/48887#Protein12341 - Reactome DB_ID: 2990852 - CTSD - - - - ENST00000409177 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21425 - - - - 400210 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400210 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10762 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10760 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2108 - - - - - - NP_056075 - RefSeq - - - - NP_000020 - RefSeq - - - - 556821 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556821 - - - - ENSP00000331831 - Ensembl - - - - NM_133263 - RefSeq - - - - ENSP00000357223 - Ensembl - - - - 1989767 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989767 - - - - ENSP00000420393 - Ensembl - - - - EQUAL - 60 - http://www.reactome.org/biopax/46/48887#SequenceSite21720 - - - - NP_001091742 - RefSeq - - - - Q3MIL8 - UniProt - - - - ENST00000325222 - Ensembl - - - - NM_005502 - RefSeq - - - - NP_001191191 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10036 - - - - EQUAL - 676 - http://www.reactome.org/biopax/46/48887#SequenceSite21710 - - - - 174608 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174608 - - - - - - - - - - - - - - Activated PPARA:RXRA Heterodimer - Reactome DB_ID: 422412 - http://www.reactome.org/biopax/46/48887#Complex3140 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12072 - - - - - - 8622974 - Laudet, V - Bègue, A - Adelmant, G - Stéhelin, D - Pubmed - A functional Rev-erb alpha responsive element located in the human Rev-erb alpha promoter mediates a repressing activity - Proc Natl Acad Sci U S A 93:3553-8 - 1996 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8360 - - - - EQUAL - 65 - http://www.reactome.org/biopax/46/48887#SequenceSite9885 - - - - ENSP00000404427 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1035 - - - - - - - - - ACTIVATION - - 'ALAS1 gene:NRF1:PPARGC1B [nucleoplasm]' positively regulates 'Expression of ALAS1' - http://www.reactome.org/biopax/46/48887#Control383 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2588 - - - - EQUAL - 239 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21483 - - - - - - - SREBF1A/2 Dimer - - - - SREBP1A/2 Dimer - Reactome DB_ID: 2065551 - http://www.reactome.org/biopax/46/48887#Complex5481 - - - - Q59GY8 - UniProt - - - - 9440 - NCBI Gene - - - - EQUAL - 1403 - - - - MED15 - HGNC Symbol - - - - EQUAL - 29 - http://www.reactome.org/biopax/46/48887#SequenceSite21648 - - - - 191343 - omim - - - - - - MOD_RES 127 127 Phosphoserine; by LATS1 and LATS2. - - - - - - MOD_RES 46 46 Phosphoserine; by CK2. - - - - ENSP00000364697 - Ensembl - - - - - - - - - NRF1 - Alpha palindromic-binding protein - NRF-1 - Alpha-pal - - - - - - - - - - - - - - - - - - - - - NRF1_HUMAN - Nuclear respiratory factor 1 - FUNCTION: Transcription factor that activates the expression of the EIF2S1 (EIF2-alpha) gene. Links the transcriptional modulation of key metabolic genes to cellular growth and development. Implicated in the control of nuclear genes required for respiration, heme biosynthesis, and mitochondrial DNA transcription and replication.SUBUNIT: Homodimer. Binds DNA as a dimer. Interacts with PPRC1.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Long; IsoId=Q16656-1; Sequence=Displayed; Name=Short; IsoId=Q16656-2; Sequence=VSP_003598;TISSUE SPECIFICITY: Ubiquitously expressed with strongest expression in skeletal muscle.PTM: Phosphorylation enhances DNA binding.SIMILARITY: Belongs to the NRF1/Ewg family.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/NRF1ID44233ch7q32.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 505 - http://www.reactome.org/biopax/46/48887#SequenceSite12325 - - - - EQUAL - 873 - - - - PTHR11909:SF59 - PANTHER Family - - - - - REACT_3039 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3039.2 - - - - - - - - - NR3C1:Dexamethasone - Glucocorticoid receptor:Dexamethasone Complex - - - - GR:Dexamethasone - Reactome DB_ID: 879850 - http://www.reactome.org/biopax/46/48887#Complex4980 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14069 - - - - MOD:00047 - Protein Modification Ontology - - - - EQUAL - 113 - - - - ENST00000292733 - Ensembl - - - - EQUAL - 2102 - - - - - - Class E basic helix-loop-helix protein 40 - BHE40_HUMAN - - - - - Reactome DB_ID: 879741 - http://www.reactome.org/biopax/46/48887#Protein11504 - BHLHE40 - - - - EQUAL - 826 - http://www.reactome.org/biopax/46/48887#SequenceSite6185 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4725 - - - - - - - - - - - - - - - - Transcriptional intermediary factor 2 - NCOA2 - bHLHe75 - TIF2 - Class E basic helix-loop-helix protein 75 - hTIF2 - BHLHE75 - NCoA-2 - - - - - - - - - - - - - - NCOA2_HUMAN - Nuclear receptor coactivator 2 - FUNCTION: Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF- 2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.SUBUNIT: Present in a complex containing CARM1 and EP300/P300, and interacts with CARM1 and NR3C2 (By similarity). Present in a complex containing NCOA3, IKKA, IKKB, IKBKG and CREBBP. Interacts (via C-terminus) with CREBBP. Interacts with HIF1A, NCOA1, APEX and NR3C1. Interacts with CASP8AP2 and TTLL5/STAMP. Interacts with ESR1, RARA and RXRA. Interacts with PSMB9 and DDX5.SUBCELLULAR LOCATION: Nucleus.DOMAIN: Contains four Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs. The LXXLL motifs are essential for the association with nuclear receptors and are, at least in part, functionally redundant.DOMAIN: The LLXXLXXXL motif is involved in transcriptional coactivation and CREBBP/CBP binding.DOMAIN: Contains 2 C-terminal transcription activation domains (AD1 and AD2) that can function independently.DISEASE: Note=Chromosomal aberrations involving NCOA2 may be a cause of acute myeloid leukemias. Inversion inv(8)(p11;q13) generates the KAT6A-NCOA2 oncogene, which consists of the N- terminal part of KAT6A and the C-terminal part of NCOA2/TIF2. KAT6A-NCOA2 binds to CREBBP and disrupts its function in transcription activation.SIMILARITY: Belongs to the SRC/p160 nuclear receptor coactivator family.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAS (PER-ARNT-SIM) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_25432 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25432.3 - - - - EQUAL - 608 - http://www.reactome.org/biopax/46/48887#SequenceSite1789 - - - - 335 - NCBI Gene - - - - - - - - - - Binding of Beta-TrCP1 to phosphorylated PER proteins - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - Beta-TrCP1 is an F-box type component of a particular SKP/CUL/F-Box (SCF) E3 ubiquitin ligase. Beta-TrCP1 interacts specifically with phosphorylated PER proteins and directs their polyubiquitination. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3861 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - EQUAL - 555 - - - - Q15596 - UniProt - - - - - - - - - - - - Renin:Prorenin Receptor - Reactome DB_ID: 2022360 - http://www.reactome.org/biopax/46/48887#Complex5109 - - - - - - CLOCK_HUMAN - Circadian locomoter output cycles protein kaput - - - - - Reactome DB_ID: 400392 - http://www.reactome.org/biopax/46/48887#Protein11496 - CLOCK - - - - 9845520 - Wu, SM - Stafford, DW - Lanir, N - Brenner, B - Sanchez-Vega, B - Solera, J - Pubmed - A missense mutation in gamma-glutamyl carboxylase gene causes combined deficiency of all vitamin K-dependent blood coagulation factors - Blood 92:4554-9 - 1998 - - - - CHEBI:15378 - ChEBI - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of TXNRD1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation221 - - - - - - phospho-Emi1(Ser 182) - - - - - - Reactome DB_ID: 177324 - http://www.reactome.org/biopax/46/48887#Protein6076 - p-S182-FBXO5 - - - - - - MOD_RES 1112 1112 Phosphoserine. - - - - Q9HAX0 - UniProt - - - - 1374 - NCBI Gene - - - - EQUAL - 601 - - - - - - MOD_RES 553 553 Phosphothreonine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8345 - - - - 2168 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature825 - - - - Q5VX33 - UniProt - - - - REACT_152034 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_152034.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12982 - - - - EQUAL - 113 - - - - NP_005756 - RefSeq - - - - NM_001256661 - RefSeq - - - - ENSG00000084676 - Ensembl - - - - - - - - - - - - - - bHLHe78 - PASD8 - ARNT-interacting protein - HIF1-alpha - PAS domain-containing protein 8 - HIF1A - MOP1 - Member of PAS protein 1 - HIF-1-alpha - Basic-helix-loop-helix-PAS protein MOP1 - Class E basic helix-loop-helix protein 78 - BHLHE78 - - - - - - - - - - - - - - - - - - - - - - - - - - HIF1A_HUMAN - Hypoxia-inducible factor 1-alpha - FUNCTION: Functions as a master transcriptional regulator of the adaptive response to hypoxia. Under hypoxic conditions, activates the transcription of over 40 genes, including erythropoietin, glucose transporters, glycolytic enzymes, vascular endothelial growth factor, HILPDA, and other genes whose protein products increase oxygen delivery or facilitate metabolic adaptation to hypoxia. Plays an essential role in embryonic vascularization, tumor angiogenesis and pathophysiology of ischemic disease. Binds to core DNA sequence 5'-[AG]CGTG-3' within the hypoxia response element (HRE) of target gene promoters. Activation requires recruitment of transcriptional coactivators such as CREBPB and EP300. Activity is enhanced by interaction with both, NCOA1 or NCOA2. Interaction with redox regulatory protein APEX seems to activate CTAD and potentiates activation by NCOA1 and CREBBP. Involved in the axonal distribution and transport of mitochondria in neurons during hypoxia.SUBUNIT: Interacts with the HIF1A beta/ARNT subunit; heterodimerization is required for DNA binding. Interacts with COPS5; the interaction increases the transcriptional activity of HIF1A through increased stability (By similarity). Interacts with EP300 (via TAZ-type 1 domains); the interaction is stimulated in response to hypoxia and inhibited by CITED2. Interacts with CREBBP (via TAZ-type 1 domains). Interacts with NCOA1, NCOA2, APEX and HSP90. Interacts (hydroxylated within the ODD domain) with VHLL (via beta domain); the interaction, leads to polyubiquitination and subsequent HIF1A proteasomal degradation. During hypoxia, sumoylated HIF1A also binds VHL; the interaction promotes the ubiquitination of HIF1A. Interacts with SENP1; the interaction desumoylates HIF1A resulting in stabilization and activation of transcription. Interacts (Via the ODD domain) with ARD1A; the interaction appears not to acetylate HIF1A nor have any affect on protein stability, during hypoxia. Interacts with RWDD3; the interaction enhances HIF1A sumoylation. Interacts with TSGA10 (By similarity). Interacts with RORA (via the DNA binding domain); the interaction enhances HIF1A transcription under hypoxia through increasing protein stability. Interaction with PSMA7 inhibits the transactivation activity of HIF1A under both normoxic and hypoxia- mimicking conditions. Interacts with USP20. Interacts with GNB2L1/RACK1; promotes HIF1A ubiquitination and proteasome- mediated degradation. Interacts (via N-terminus) with USP19.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Cytoplasmic in normoxia, nuclear translocation in response to hypoxia. Colocalizes with SUMO1 in the nucleus, under hypoxia.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q16665-1; Sequence=Displayed; Name=2; IsoId=Q16665-2; Sequence=VSP_047335, VSP_007738; Note=No experimental confirmation available; Name=3; Synonyms=I.3; IsoId=Q16665-3; Sequence=VSP_044942; Note=Up-regulated in peripheral T lymphocytes after T-cell receptor stimulation. Highest expression in peripheral blood leukocytes and thymus;TISSUE SPECIFICITY: Expressed in most tissues with highest levels in kidney and heart. Overexpressed in the majority of common human cancers and their metastases, due to the presence of intratumoral hypoxia and as a result of mutations in genes encoding oncoproteins and tumor suppressors.INDUCTION: Under reduced oxygen tension. Induced also by various receptor-mediated factors such as growth factors, cytokines, and circulatory factors such as PDGF, EGF, FGF2, IGF2, TGFB1, HGF, TNF, IL1B/interleukin-1 beta, angiotensin-2 and thrombin. However, this induction is less intense than that stimulated by hypoxia. Repressed by HIPK2 and LIMD1.DOMAIN: Contains two independent C-terminal transactivation domains, NTAD and CTAD, which function synergistically. Their transcriptional activity is repressed by an intervening inhibitory domain (ID).PTM: In normoxia, is hydroxylated on Pro-402 and Pro-564 in the oxygen-dependent degradation domain (ODD) by EGLN1/PHD1 and EGLN2/PHD2. EGLN3/PHD3 has also been shown to hydroxylate Pro-564. The hydroxylated prolines promote interaction with VHL, initiating rapid ubiquitination and subsequent proteasomal degradation. Deubiquitinated by USP20. Under hypoxia, proline hydroxylation is impaired and ubiquitination is attenuated, resulting in stabilization.PTM: In normoxia, is hydroxylated on Asn-803 by HIF1AN, thus abrogating interaction with CREBBP and EP300 and preventing transcriptional activation. This hydroxylation is inhibited by the Cu/Zn-chelator, Clioquinol.PTM: S-nitrosylation of Cys-800 may be responsible for increased recruitment of p300 coactivator necessary for transcriptional activity of HIF-1 complex.PTM: Requires phosphorylation for DNA-binding. Phosphorylation at Ser-247 by CSNK1D/CK1 represses kinase activity and impairs ARNT binding. Phosphorylation by GSK3-beta and PLK3 promote degradation by the proteasome.PTM: Sumoylated; with SUMO1 under hypoxia. Sumoylation is enhanced through interaction with RWDD3. Desumoylation by SENP1 leads to increased HIF1A stability and transriptional activity (By similarity).PTM: Ubiquitinated; in normoxia, following hydroxylation and interaction with VHL. Lys-532 appears to be the principal site of ubiquitination. Clioquinol, the Cu/Zn-chelator, inhibits ubiquitination through preventing hydroxylation at Asn-803.PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of asparagine is (S) stereospecific within HIF CTAD domains.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.WEB RESOURCE: Name=Wikipedia; Note=Hypoxia inducible factor entry; URL="http://en.wikipedia.org/wiki/Hypoxia_inducible_factor"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - SULT2A1 - HGNC - - - - 10790862 - Keesler, GA - Yao, Z - Virshup, D - Camacho, F - Mondadori, C - Guo, Y - Pubmed - Phosphorylation and destabilization of human period I clock protein by human casein kinase I epsilon - Neuroreport 11:951-5 - 2000 - - - - REACT_117188 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117188.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5641 - - - - - - REACT_20113 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20113.2 - - - - HGNC:12437 - HGNC - - - - NP_005638 - RefSeq - - - - EQUAL - 619 - - - - EQUAL - 47 - - - - ENSP00000377021 - Ensembl - - - - ENSP00000346242 - Ensembl - - - - ENSP00000386892 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2440 - - - - - - - - MOD_RES 576 576 Phosphoserine; by PLK3. - - - - 396945 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=396945 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8355 - - - - ENSG00000134317 - Ensembl - - - - EQUAL - 55 - http://www.reactome.org/biopax/46/48887#SequenceSite10120 - - - - ENST00000564845 - Ensembl - - - - NP_001441 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1849 - - - - REACT_3836 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3836.2 - - - - REACT_5533 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5533.3 - - - - 12118000 - Barbier, O - Blanquart, C - Fruchart, JC - Glineur, C - Staels, B - Pubmed - Peroxisome proliferator-activated receptor alpha (PPARalpha ) turnover by the ubiquitin-proteasome system controls the ligand-induced expression level of its target genes - J Biol Chem 277:37254-9 - 2002 - - - - - - MOD_RES 2076 2076 Phosphoserine. - - - - HGNC:4168 - HGNC - - - - 600663 - omim - - - - XLYOFNOQVPJJNP-UHFFFAOYSA-N - InChIKey - - - - - - ubiquitin (UBC 8) - - - - - http://www.reactome.org/biopax/46/48887#Protein2484 - Reactome DB_ID: 939866 - UBC(533-608) - - - - 2065425 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065425 - - - - PTHR11461:SF49 - PANTHER Family - - - - - EQUAL - 2 - - - - NM_152221 - RefSeq - - - - Q86YY0 - UniProt - - - - REACT_4290 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4290.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5629 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5640 - - - - - - HGNC:28760 - HGNC - - - - - - MOD_RES 104 104 N6-acetyllysine. - - - - REACT_115807 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115807.1 - - - - GZMH - HGNC Symbol - - - - ENSP00000369131 - Ensembl - - - - REACT_913 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_913.3 - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12946 - - - - REACT_115962 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115962.1 - - - - Q15304 - UniProt - - - - Q15114 - UniProt - - - - 12202481 - Chen JY - Cooper AD - Goodart S - Levy-Wilson B - PubMed - Mice expressing the human CYP7A1 gene in the mouse CYP7A1 knock-out background lack induction of CYP7A1 expression by cholesterol feeding and have increased hypercholesterolemia when fed a high fat diet. - J Biol Chem 277(45);42588-95 - 2002 - - - - Q6P143 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12368 - - - - EQUAL - 456 - http://www.reactome.org/biopax/46/48887#SequenceSite4664 - - - - 1989806 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989806 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2115 - - - - - - Q07869 - UniProt - - - - GAS6 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12842 - - - - EQUAL - 304 - http://www.reactome.org/biopax/46/48887#SequenceSite1781 - - - - - - - - - - - - - - - - - hPER2 - PER2 - Circadian clock protein PERIOD 2 - KIAA0347 - - - - - - - - - - - - - - - - - - - - PER2_HUMAN - Period circadian protein homolog 2 - FUNCTION: Component of the circadian clock mechanism which is essential for generating circadian rhythms. Negative element in the circadian transcriptional loop. Influences clock function by interacting with other circadian regulatory proteins and transporting them to the nucleus. Negatively regulates CLOCK|NPAS2-BMAL1|BMAL2-induced transactivation (By similarity).SUBUNIT: Homodimer. Component of the circadian core oscillator, which includes the CRY proteins, CLOCK or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E, TIMELESS, and the PER proteins. Interacts directly with PER1 and PER3, and through a C-terminal domain, with CRY1 and CRY2. Interaction with CSNK1D or CSNK1E promotes nuclear location of PER proteins. Interacts, via its second PAS domain, with TIMELESS in vitro. Interacts with NFIL3 (By similarity). Interacts with PML (By similarity).SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm (By similarity). Cytoplasm, perinuclear region (By similarity). Note=Mainly nuclear. Nucleocytoplasmic shuttling is effected by interaction with other circadian core oscillator proteins and/or by phosphorylation. Retention of PER1 in the cytoplasm occurs through PER1-PER2 heterodimer formation or by interaction with CSNK1E and/or phosphorylation which appears to mask the PER nuclear localization signal. Also translocated to the nucleus by CRY1 or CRY2 (By similarity). PML regulates its nuclear localization (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O15055-1; Sequence=Displayed; Name=2; Synonyms=PER2S; IsoId=O15055-2; Sequence=VSP_021653, VSP_021654; Note=No experimental confirmation available;TISSUE SPECIFICITY: Widely expressed. Found in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. High levels in skeletal muscle and pancreas. Low level in lung.INDUCTION: Serum-induced levels in fibroblasts show circadian oscillations. Maximum levels after 1 hour stimulation, minimum levels after 12 hours. Another peak is then observed after 24 hours.PTM: Phosphorylated by CSNK1E and CSNK1D. Phosphorylation results in PER2 protein degradation.DISEASE: Advanced sleep phase syndrome, familial, 1 (FASPS1) [MIM:604348]: A disorder characterized by very early sleep onset and offset. Individuals are 'morning larks' with a 4 hours advance of the sleep, temperature and melatonin rhythms. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.SEQUENCE CAUTION: Sequence=BAA20804.2; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_001193349 - RefSeq - - - - 103195 - omim - - - - NM_017638 - RefSeq - - - - NM_000821 - RefSeq - - - - NM_001336 - RefSeq - - - - Q9Y2G6 - UniProt - - - - - - Mediator of RNA polymerase II transcription subunit 23 - MED23_HUMAN - - - - - Reactome DB_ID: 556823 - http://www.reactome.org/biopax/46/48887#Protein6470 - MED23 - - - - REACT_120337 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120337.1 - - - - Q5JWT3 - UniProt - - - - - - - - - - INHIBITION - - 'lisinopril [extracellular region]' negatively regulates 'Secreted ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control313 - - - - - - GLIP1_HUMAN - Glioma pathogenesis-related protein 1 - - - - - Reactome DB_ID: 561145 - http://www.reactome.org/biopax/46/48887#Protein13774 - GLIPR1 - - - - 1998759 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1998759 - - - - 159729 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159729 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10117 - - - - ENST00000406961 - Ensembl - - - - 136950 - omim - - - - B2R524 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5602 - - - - TBL1XR1 - HGNC - - - - Surfeit locus protein 5 - SURF5 - MED22 - Mediator complex subunit 22 - Surf-5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MED22_HUMAN - Mediator of RNA polymerase II transcription subunit 22 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Surf5B; IsoId=Q15528-1; Sequence=Displayed; Name=Surf5A; IsoId=Q15528-2; Sequence=VSP_006309;SIMILARITY: Belongs to the Mediator complex subunit 22 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_27983 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27983.2 - - - - - - MOD_RES 275 275 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12047 - - - - - - NP_599023 - RefSeq - - - - O00327 - UniProt - - - - CHEBI:29889 - ChEBI - - - - CPT1A - HGNC Symbol - - - - - - ubiquitin (UBC 6) - - - - - Reactome DB_ID: 939191 - http://www.reactome.org/biopax/46/48887#Protein1054 - UBC(381-456) - - - - ENST00000514015 - Ensembl - - - - ENSG00000100311 - Ensembl - - - - CSNK1E - HGNC - - - - ENSP00000321800 - Ensembl - - - - - - MOD_RES 60 60 4-carboxyglutamate. - - - - ENST00000372004 - Ensembl - - - - EQUAL - 153 - - - - - - Prorenin receptor - Renin receptor - RENR_HUMAN - - - - - Reactome DB_ID: 2022356 - http://www.reactome.org/biopax/46/48887#Protein12338 - ATP6AP2 - - - - EQUAL - 157 - - - - Q5VZL3 - UniProt - - - - ENST00000261178 - Ensembl - - - - CHEBI:5585 - ChEBI - - - - REACT_19370 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19370.2 - - - - NP_005112 - RefSeq - - - - EQUAL - 1042 - - - - 2022399 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022399 - - - - ENSG00000151014 - Ensembl - - - - Q9Y652 - UniProt - - - - ENST00000367029 - Ensembl - - - - 9353271 - Staels, B - Schoonjans, K - Auwerx, J - Martin, G - Lefebvre, AM - Pubmed - Coordinate regulation of the expression of the fatty acid transport protein and acyl-CoA synthetase genes by PPARalpha and PPARgamma activators - J Biol Chem 272:28210-7 - 1997 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1051 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8313 - - - - Q9Y667 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10023 - - - - - - MOD_RES 154 154 Phosphothreonine; by MAPK8 and MAPK9. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1848 - - - - ENSG00000153002 - Ensembl - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ABCB4' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation191 - - - - 939230 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939230 - - - - ENPEP - HGNC - - - - ENST00000395837 - Ensembl - - - - CYP4A11 - HGNC - - - - - - MOD_RES 1112 1112 Phosphoserine. - - - - NP_001180277 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2225 - - - - ENSP00000424606 - Ensembl - - - - CHEBI:3380 - ChEBI - - - - GGIDWJQWCUJYRY-RGGAHWMASA-L - InChIKey - - - - - - MOD_RES 444 444 Phosphoserine. - - - - REACT_24883 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24883.2 - - - - 5464096 - PubChem Compound - - - - NP_009219 - RefSeq - - - - EQUAL - 698 - http://www.reactome.org/biopax/46/48887#SequenceSite25539 - - - - 2065429 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065429 - - - - - - - - - - - Formation of ROR-alpha Coactivator Complex - As inferred from mouse, RORA binds DNA and recruits the coactivators PGC-1alpha (PPARGC1A) and p300 (EP300, a histone acetylase). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3865 - Edited: May, B, 2011-06-22 - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1076 - - - - 227600 - omim - - - - NP_001827 - RefSeq - - - - - - apoA-V - apolipoprotein A-V - - - - - Reactome DB_ID: 174608 - http://www.reactome.org/biopax/46/48887#Protein13645 - APOA5 - - - - 2426135 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2426135 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1272 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12396 - - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction163 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The SULT2A1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of SULT2A1 - - - - InChI=1S/CO2/c2-1-3 - InChI - - - - TEAD-4 - TEF3 - RTEF1 - TEAD4 - TCF13L1 - Transcription factor RTEF-1 - Transcription factor 13-like 1 - TEA domain family member 4 - - - - - - - - - - - - - - - - - - - - - TEAD4_HUMAN - Transcriptional enhancer factor TEF-3 - FUNCTION: Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein MST1/MST2, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Acts by mediating gene expression of YAP1 and WWTR1/TAZ, thereby regulating cell proliferation, migration and epithelial mesenchymal transition (EMT) induction. Binds specifically and non-cooperatively to the Sph and GT-IIC 'enhansons' (5'-GTGGAATGT-3') and activates transcription. Binds to the M-CAT motif.SUBUNIT: Interacts with YAP1 and WWTR1/TAZ.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q15561-1; Sequence=Displayed; Name=2; IsoId=Q15561-2; Sequence=VSP_043099; Note=No experimental confirmation available; Name=3; IsoId=Q15561-3; Sequence=VSP_045657; Note=No experimental confirmation available;TISSUE SPECIFICITY: Preferentially expressed in skeletal muscle. Lower levels in pancreas, placenta, and heart.SIMILARITY: Contains 1 TEA DNA-binding domain.SEQUENCE CAUTION: Sequence=CAA64212.2; Type=Miscellaneous discrepancy; Note=Unusual initiator. The initiator methionine is coded by a non-canonical ATA isoleucine codon; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - TEAD-2 - TEF4 - TEAD2 - TEA domain family member 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TEAD2_HUMAN - Transcriptional enhancer factor TEF-4 - FUNCTION: Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein MST1/MST2, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Acts by mediating gene expression of YAP1 and WWTR1/TAZ, thereby regulating cell proliferation, migration and epithelial mesenchymal transition (EMT) induction. Binds to the SPH and GT-IIC 'enhansons' (5'- GTGGAATGT-3'). May be involved in the gene regulation of neural development. Binds to the M-CAT motif.SUBUNIT: Interacts with YAP1 and WWTR1/TAZ.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q15562-1; Sequence=Displayed; Name=2; IsoId=Q15562-2; Sequence=VSP_045127; Name=3; IsoId=Q15562-3; Sequence=VSP_045126, VSP_045127;SIMILARITY: Contains 1 TEA DNA-binding domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - B2R7E4 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5597 - - - - EQUAL - 485 - http://www.reactome.org/biopax/46/48887#SequenceSite22995 - - - - NM_001204259 - RefSeq - - - - 159728 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159728 - - - - HGNC:9451 - HGNC - - - - B4DUS6 - UniProt - - - - 14718224 - pubchem - - - - 4360430 - Vallotton, MB - Favre, L - Pubmed - Kinetics of the reaction of human renin with natural substrates and tetradecapeptide substrate - Biochim Biophys Acta 327:471-80 - 1973 - - - - ENST00000374796 - Ensembl - - - - NM_001079846 - RefSeq - - - - EQUAL - 55 - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of SULT2A1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation217 - - - - - - MOD_RES 940 940 Phosphoserine. - - - - EQUAL - 83 - - - - - - - - - - Reactome DB_ID: 212414 - http://www.reactome.org/biopax/46/48887#Protein6493 - MED25 - - - - NM_182742 - RefSeq - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21735 - - - - ENSP00000473048 - Ensembl - - - - ENSG00000160563 - Ensembl - - - - GO:0004674 - GENE ONTOLOGY - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12364 - - - - HGNC:11108 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4964 - - - - - AVP-NPII - AVP - Copeptin - ARVP - VP - Arg-vasopressin - Neurophysin 2 - Arginine-vasopressin - Neurophysin-II - - - - - - - - - - - - - - - NEU2_HUMAN - Vasopressin-neurophysin 2-copeptin - FUNCTION: Neurophysin 2 specifically binds vasopressin.FUNCTION: Vasopressin has a direct antidiuretic action on the kidney, it also causes vasoconstriction of the peripheral vessels.SUBCELLULAR LOCATION: Secreted.DISEASE: Diabetes insipidus, neurohypophyseal (NDI) [MIM:125700]: A disease characterized by persistent thirst, polydipsia and polyuria. Affected individuals are apparently normal at birth, but characteristically develop symptoms of vasopressin deficiency during childhood. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the vasopressin/oxytocin family.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/AVP";WEB RESOURCE: Name=Wikipedia; Note=Vasopressin entry; URL="http://en.wikipedia.org/wiki/Vasopressin"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_004379 - RefSeq - - - - 1DQ8 - PROTEIN DATA BANK - - - - NM_001001683 - RefSeq - - - - HGNC:6983 - HGNC - - - - CDC20 - HGNC Symbol - - - - HGNC:24042 - HGNC - - - - 7913466 - Haro D - Hegardt FG - Rodriguez JC - Gil-Gomez G - PubMed - Peroxisome proliferator-activated receptor mediates induction of the mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase gene by fatty acids. - J Biol Chem 269(29);18767-72 - 1994 - - - - - - MOD_RES 555 555 Phosphothreonine; by GSK3-beta. - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CPT1A' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation118 - - - - 400360 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400360 - - - - ENST00000460393 - Ensembl - - - - 2065414 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065414 - - - - HGNC:4854 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1062 - - - - 1454 - NCBI Gene - - - - EQUAL - 68 - - - - 602700 - omim - - - - ENSP00000309259 - Ensembl - - - - PPARGC1A - HGNC - - - - - - - - - Stabilization of Unphosphorylated BMAL1:CLOCK/NPAS2 Heterodimer by CRY Proteins - Reviewed: Kay, SA, 2010-06-23 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3856 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-03-19 - Reviewed: Delaunay, F, 2010-06-23 - Authored: May, B, 2010-03-19 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - CRY1 and CRY2 bind the unphosphorylated BMAL1:CLOCK (ARNTL:CLOCK) heterodimer (and by homology the BMAL1:NPAS2 (ARNTL:NPAS2) heterodimer) and prolong its half-life. The unphosphorylated BMAL1:CLOCK heterodimer only weakly activates transcription and is therefore believed to competitively reduce transcription by phosphorylated BMAL1:CLOCK heterodimer. The complex of unphosphorylated BMAL1:CLOCK with CRY may contain additional components and may traffic into the nucleus. - - - - - EQUAL - 611 - - - - NP_002560 - RefSeq - - - - ENST00000394965 - Ensembl - - - - 159795 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159795 - - - - InChI=1S/C18H19N3O3S/c1-21(16-4-2-3-9-19-16)10-11-24-14-7-5-13(6-8-14)12-15-17(22)20-18(23)25-15/h2-9,15H,10-12H2,1H3,(H,20,22,23) - InChI - - - - - - - - - - - - - - - - - - - - pro-prothrombin, uncarboxylated + 10 CO2 + 10 O2 + 10 vitamin K hydroquinone -> pro-prothrombin + 10 H2O + 10 vitamin K epoxide - At the beginning of this reaction, 10 molecules of 'Oxygen', 10 molecules of 'vitamin K hydroquinone', 10 molecules of 'CO2', and 1 molecule of 'pro-prothrombin (factor II), uncarboxylated' are present. At the end of this reaction, 1 molecule of 'pro-prothrombin (factor II)', 10 molecules of 'H2O', and 10 molecules of 'vitamin K epoxide' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3887 - - - - - - - NP_001025444 - RefSeq - - - - EQUAL - 923 - - - - ENSP00000454651 - Ensembl - - - - ENSP00000220584 - Ensembl - - - - NM_004035 - RefSeq - - - - Q9UIT8 - UniProt - - - - 1851160 - Wei, L - Corvol, P - Clauser, E - Alhenc-Gelas, F - Pubmed - The two homologous domains of human angiotensin I-converting enzyme are both catalytically active - J Biol Chem 266:9002-8 - 1991 - - - - NP_001094286 - RefSeq - - - - - - MOD_RES 2438 2438 Phosphoserine. - - - - HGNC:17288 - HGNC - - - - ENSG00000080618 - Ensembl - - - - - 3.4.21 - Cathepsin G Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8) - - - - - - - - - Cathepsin G Hydrolyzes Angiotensin I to Yield Angiotensin II - Authored: May, B, 2011-11-19 - Cathepsin G hydrolyzes angiotensin-(1-10) (angiotensin I) to yield angiotensin-(1-8) (angiotensin II) (Reilly et al. 1982, Owen and Campbell 1998, Raymond et al. 2010). Cathepsin bound to the plasma membrane of neutrophils has a higher activity than does soluble cathepsin G (Owen and Campbell 1998). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4043 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - - - - - - - MOD_RES 1299 1299 Phosphoserine. - - - - 1A2C - PROTEIN DATA BANK - - - - NM_033423 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1797 - - - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - The PERIOD-1 (PER1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The promoter of the PER1 gene contains E-boxes which are bound by the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer (and probably also the BMAL1:NPAS2 (ARNTL:NPAS2) heterodimer). The BMAL1:CLOCK heterodimer activates transcription of PER1. - Authored: May, B, 2010-03-11 - Reviewed: Hirota, T, 2010-06-23 - Reviewed: Delaunay, F, 2010-06-23 - Edited: May, B, 2010-03-11 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - http://www.reactome.org/biopax/46/48887#TemplateReaction69 - Expression of PERIOD-1 - - - - NP_001177369 - RefSeq - - - - REACT_119451 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119451.2 - - - - 1989760 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989760 - - - - EQUAL - 32 - http://www.reactome.org/biopax/46/48887#SequenceSite21723 - - - - - - MOD_RES 569 569 Phosphoserine. - - - - REACT_4157 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4157.2 - - - - REACT_18157 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18157.1 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6471 - Reactome DB_ID: 212331 - MED24 - - - - NP_208384 - RefSeq - - - - - 3.4.21 - - - - pro-factor VII -> factor VII + factor VII propeptide - At the beginning of this reaction, 1 molecule of 'pro-factor VII' is present. At the end of this reaction, 1 molecule of 'factor VII', and 1 molecule of 'factor VII propeptide' are present.<br><br> This reaction takes place in the 'Golgi membrane' and is mediated by the 'furin activity' of 'furin'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3901 - - - - - - 1988962 - DiDonato S - Taroni F - Colombo I - Martin AL - Tarelli GT - Rocchi M - Finocchiaro G - PubMed - cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase. - Proc Natl Acad Sci U S A 88(2);661-5 - 1991 - - - - - - MOD_RES 247 247 Phosphoserine; by CK1. - - - - NP_002509 - RefSeq - - - - NM_139314 - RefSeq - - - - HGNC:2328 - HGNC - - - - REACT_17456 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17456.1 - - - - EQUAL - 197 - http://www.reactome.org/biopax/46/48887#SequenceSite21734 - - - - ENST00000372457 - Ensembl - - - - - 3.4.21 - - - - - - Processing of classical PDGFs - After dimerization of the PDGF-A and PDGF-B chains in the ER of producing cells, the dimers are proteolytically cleaved in the trans-Golgi network during protein maturation and secretion. The dibasic-specific proprotein convertase, furin, or related convertases are involved in the conversion of proPDGF forms to active PDGF forms. - Edited: Garapati, P V, Jassal, B, 2008-11-24 10:14:27 - Reviewed: Heldin, CH, 2008-11-23 19:29:34 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction798 - Authored: Garapati, P V, Jassal, B, 2008-11-24 10:14:27 - - - - - - - - - - - - Reactome DB_ID: 400343 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11498 - CLOCK/NPAS2 - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2011-06-29 - Reviewed: Delaunay, F, 2010-06-23 - Edited: May, B, 2011-06-29 - Reviewed: Albrecht, U, 2010-06-23 - The NAMPT (NamPRT) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer enhances transcription of NAMPT. - http://www.reactome.org/biopax/46/48887#TemplateReaction66 - Expression of NAMPT (NamPRT, PBEF, Visfatin) - - - - - - MOD_RES 564 564 4-hydroxyproline. - - - - ENSG00000113161 - Ensembl - - - - 9616112 - Wilsbacher, LD - Davis, FC - Staknis, D - Weitz, CJ - Takahashi, JS - King, DP - Gekakis, N - Nguyen, HB - Pubmed - Role of the CLOCK protein in the mammalian circadian mechanism - Science 280:1564-9 - 1998 - - - - 601933 - omim - - - - ENSP00000234071 - Ensembl - - - - NP_958849 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1844 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2361 - - - - - - - - MED27_HUMAN - Mediator of RNA polymerase II transcription subunit 27 - - - - - http://www.reactome.org/biopax/46/48887#Protein6478 - Reactome DB_ID: 556761 - MED27 - - - - REACT_27846 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27846.2 - - - - NP_001180276 - RefSeq - - - - PTHR24265:SF40 - PANTHER Family - - - - - B0LPG8 - UniProt - - - - - - - - - - - - - 3.6.4.12 - KISH2 - Chromatin-remodeling factor CHROM1 - PRIC320 - ATP-dependent helicase CHD9 - CHD-9 - PPAR-alpha-interacting complex protein 320 kDa - CHD9 - Chromatin-related mesenchymal modulator - Kismet homolog 2 - CReMM - KIAA0308 - Peroxisomal proliferator-activated receptor A-interacting complex 320 kDa protein - - - - - - - - - - - - - - - - - - - - - - - - - CHD9_HUMAN - Chromodomain-helicase-DNA-binding protein 9 - FUNCTION: Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA. Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis (By similarity).CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Interacts with PPARA. Probably interacts with ESR1 and NR1I3.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q3L8U1-1; Sequence=Displayed; Name=2; IsoId=Q3L8U1-2; Sequence=VSP_018086; Name=3; IsoId=Q3L8U1-3; Sequence=VSP_018085, VSP_018086;TISSUE SPECIFICITY: Widely expressed at low levels. In bone marrow, expression is restricted to osteoprogenitor cells adjacent to mature osteoblasts.PTM: Phosphorylated on serine and tyrosine residues.SIMILARITY: Belongs to the SNF2/RAD54 helicase family.SIMILARITY: Contains 2 chromo domains.SIMILARITY: Contains 1 helicase ATP-binding domain.SIMILARITY: Contains 1 helicase C-terminal domain.SEQUENCE CAUTION: Sequence=AAF24170.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=BAB14112.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_020183 - RefSeq - - - - 163825 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163825 - - - - 10529898 - Wahli, W - Desvergne, B - Pubmed - Peroxisome proliferator-activated receptors: nuclear control of metabolism - Endocr Rev 20:649-88 - 1999 - - - - 16790432 - Ishii, Y - Hattori, A - Mizutani, S - Goto, Y - Tsujimoto, M - Pubmed - Enzymatic properties of human aminopeptidase A. Regulation of its enzymatic activity by calcium and angiotensin IV - J Biol Chem 281:23503-13 - 2006 - - - - 351657 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=351657 - - - - Q9NQV4 - UniProt - - - - - 13.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12965 - - - - REACT_117432 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117432.4 - - - - EQUAL - 338 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14054 - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite21652 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14049 - - - - MOD_RES N6-acetyllysine - - - - ENSG00000112029 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10052 - - - - - - ENST00000538308 - Ensembl - - - - 2065393 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065393 - - - - EQUAL - 67 - - - - 8145109 - pubchem - - - - Q8IV02 - UniProt - - - - NP_000007 - RefSeq - - - - - - MOD_RES 2073 2073 Phosphothreonine. - - - - ENSP00000441153 - Ensembl - - - - MED29 - HGNC Symbol - - - - REACT_26408 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26408.2 - - - - Q16656 - UniProt - - - - - - Transcription factor Sp1 - SP1_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein3066 - Reactome DB_ID: 1592223 - SP1 - - - - - - ACSL1 variant1 - - - - - http://www.reactome.org/biopax/46/48887#Protein13760 - Reactome DB_ID: 400123 - ACSL1 - - - - NP_002934 - RefSeq - - - - Q5GH23 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite6152 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4654 - - - - - - MOD_RES 1734 1734 Phosphoserine. - - - - NM_004599 - RefSeq - - - - 892 - NCBI Gene - - - - Q6MZR9 - UniProt - - - - ENST00000309964 - Ensembl - - - - 939869 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939869 - - - - EQUAL - 211 - http://www.reactome.org/biopax/46/48887#SequenceSite4967 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10837 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2109 - - - - - - Q53SX3 - UniProt - - - - ENST00000287936 - Ensembl - - - - Q6VB40 - UniProt - - - - SIN3A - HGNC - - - - NM_030973 - RefSeq - - - - REACT_7036 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7036.2 - - - - Q14143 - UniProt - - - - Q9NS70 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite5362 - - - - ENSG00000082014 - Ensembl - - - - REACT_23225 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23225.4 - - - - 400340 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400340 - - - - NP_001191193 - RefSeq - - - - Q7Z2R4 - UniProt - - - - EQUAL - 22 - http://www.reactome.org/biopax/46/48887#SequenceSite5186 - - - - ENSG00000101981 - Ensembl - - - - P11310 - UniProt - - - - HGNC:17001 - HGNC - - - - 2022410 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022410 - - - - 2022365 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022365 - - - - HGNC:2330 - HGNC - - - - EQUAL - 696 - - - - ENST00000538539 - Ensembl - - - - REACT_115815 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115815.1 - - - - HGNC:3528 - HGNC - - - - - - F-box/WD repeat-containing protein 1A - Beta-TrCP - - - - - http://www.reactome.org/biopax/46/48887#Protein2848 - Reactome DB_ID: 174237 - BTRC - - - - - - MOD_RES 662 662 Phosphoserine. - - - - EQUAL - 152 - - - - - - MOD_RES 134 134 Phosphoserine. - - - - - - Glutamyl aminopeptidase - AMPE_HUMAN - - - - - Reactome DB_ID: 2022341 - http://www.reactome.org/biopax/46/48887#Protein12353 - ENPEP - - - - ENSG00000155868 - Ensembl - - - - Q9NTU0 - UniProt - - - - NM_001204261 - RefSeq - - - - - - MOD_RES 704 704 Phosphoserine. - - - - 212440 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212440 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10011 - - - - HGNC:11289 - HGNC - - - - - - MOD_RES 281 281 Phosphotyrosine. - - - - EQUAL - 798 - http://www.reactome.org/biopax/46/48887#SequenceSite12335 - - - - ENSP00000357047 - Ensembl - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis312 - - - - 125290 - omim - - - - 1UKL - PROTEIN DATA BANK - - - - 4208 - NCBI Gene - - - - Q9UN07 - UniProt - - - - REACT_20244 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20244.3 - - - - ENST00000397786 - Ensembl - - - - Q9UBJ3 - UniProt - - - - Q4ZG49 - UniProt - - - - REACT_117956 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117956.1 - - - - ENST00000393232 - Ensembl - - - - ENSP00000429686 - Ensembl - - - - 1D7G - PROTEIN DATA BANK - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval828 - - - - - - B5BUM8 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5797 - - - - EQUAL - 234 - - - - - - Cyclic AMP-dependent transcription factor ATF-2 (phosphorylated) - - - - - - - Reactome DB_ID: 450243 - http://www.reactome.org/biopax/46/48887#Protein9962 - p-T69,T71-ATF2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8352 - - - - Q8NCG0 - UniProt - - - - ENSP00000379180 - Ensembl - - - - Q9UIY4 - UniProt - - - - ENSP00000308541 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21439 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1041 - - - - REACT_116914 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116914.2 - - - - EQUAL - 255 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5642 - - - - - - MOD_RES 403 403 Phosphoserine; by CK1. - - - - - - p-S-PER2 - Phosphorylated Period circadian protein homolog 2 - PER2_HUMAN - - - - - - Reactome DB_ID: 400331 - http://www.reactome.org/biopax/46/48887#Protein11526 - p-PER2 - - - - - - MOD_RES 775 775 Phosphoserine; by CK2. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9999 - - - - EQUAL - 49 - - - - 12083803 - Huttler S - Sandhoff K - Laurent-Matha V - Lucas A - Rochefort H - Garcia M - PubMed - Procathepsin D interacts with prosaposin in cancer cells but its internalization is not mediated by LDL receptor-related protein. - Exp Cell Res 277(2);210-9 - 2002 - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4708 - - - - - Q16797 - UniProt - - - - NP_001113 - RefSeq - - - - - - - - - - Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1) - Authored: May, B, 2011-09-28 - The HMGCS1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Liang, Guosheng, 2012-08-25 - Edited: May, B, 2011-09-28 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4679 - Reviewed: Kersten, S, 2009-06-08 - - - - - - - MOD_RES 1119 1119 Phosphoserine. - - - - EQUAL - 2 - - - - 561143 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561143 - - - - 1368161 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368161 - - - - 8358442 - DiDonato S - Taroni F - Dworzak F - Willems PJ - Cavadini P - Verderio E - PubMed - Identification of a common mutation in the carnitine palmitoyltransferase II gene in familial recurrent myoglobinuria patients. - Nat Genet 4(3);314-20 - 1993 - - - - - - PER1_HUMAN - Ubiquitinated Phosphorylated Period circadian protein homolog 1 - Ub-p-S-PER1 - - - - - - - Reactome DB_ID: 517831 - http://www.reactome.org/biopax/46/48887#Protein11541 - ub-p-PER1 - - - - 9442 - NCBI Gene - - - - Q9Y2X0 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10053 - - - - - - - - MOD_RES 619 619 N6-acetyllysine; by CREBBP. - - - - Q86V96 - UniProt - - - - 19324877 - Zhao, B - Zhao, S - Zhang, H - Lei, Q - Zha, ZY - Yao, J - Guan, KL - Liu, CY - Xiong, Y - Pubmed - TEAD transcription factors mediate the function of TAZ in cell growth and epithelial-mesenchymal transition - J Biol Chem 284:13355-62 - 2009 - - - - 19324876 - Chong, YF - Loo, LS - Lim, CJ - Huang, C - Chan, SW - Hong, W - Pubmed - TEADs mediate nuclear retention of TAZ to promote oncogenic transformation - J Biol Chem 284:14347-58 - 2009 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4727 - - - - Q13420 - UniProt - - - - REACT_148350 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148350.2 - - - - REACT_24708 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24708.2 - - - - NP_001003891 - RefSeq - - - - EQUAL - 7 - http://www.reactome.org/biopax/46/48887#SequenceSite1305 - - - - REACT_9726 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9726.2 - - - - ENSP00000380195 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10766 - - - - ENST00000311907 - Ensembl - - - - - - MOD_RES 56 56 4-carboxyglutamate. - - - - ENSG00000143947 - Ensembl - - - - ENSP00000435123 - Ensembl - - - - - 8.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12953 - - - - EQUAL - 55 - http://www.reactome.org/biopax/46/48887#SequenceSite21679 - - - - EQUAL - 116 - - - - 1989824 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989824 - - - - REACT_618 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_618.2 - - - - 1989803 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989803 - - - - NM_138711 - RefSeq - - - - Q6IC31 - UniProt - - - - HGNC:3703 - HGNC - - - - 2022376 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022376 - - - - EQUAL - 553 - - - - - - eicosapentaenoic acid - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule739 - Reactome DB_ID: 400199 - EPA - - - - 1655720 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655720 - - - - ENSP00000251871 - Ensembl - - - - ENSG00000101200 - Ensembl - - - - ENSP00000419234 - Ensembl - - - - 18434626 - Akimoto, T - Yan, Z - Li, P - Pubmed - Functional interaction of regulatory factors with the Pgc-1alpha promoter in response to exercise by in vivo imaging - Am J Physiol Cell Physiol 295:C288-92 - 2008 - - - - 159846 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159846 - - - - ENST00000255764 - Ensembl - - - - - - MOD_RES 362 362 Phosphothreonine. - - - - EQUAL - 31 - http://www.reactome.org/biopax/46/48887#SequenceSite21693 - - - - 1LYA - PROTEIN DATA BANK - - - - PASP - PCPB - CPB - 3.4.17.2 - CPB1 - Pancreas-specific protein - - - - - - - - - - - - - - - - CBPB1_HUMAN - Carboxypeptidase B - CATALYTIC ACTIVITY: Preferential release of a C-terminal lysine or arginine amino acid.COFACTOR: Binds 1 zinc ion per subunit.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Pancreas.SIMILARITY: Belongs to the peptidase M14 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 380739 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380739 - - - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - http://www.reactome.org/biopax/46/48887#TemplateReaction64 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-03-19 - Reviewed: Delaunay, F, 2010-06-23 - Authored: May, B, 2010-03-19 - Reviewed: Albrecht, U, 2010-06-23 - The PAI-1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The PAI-1 gene shows circadian expression due to direct transcriptional activation by the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer and the BMAL2:CLOCK (CLIF:CLOCK, ARNTL2:CLOCK) heterodimer. - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Expression of PAI-1 - - - - - - - - - - PDGF B homodimer - http://www.reactome.org/biopax/46/48887#Complex893 - Reactome DB_ID: 184206 - - - - HGNC:11957 - HGNC - - - - ENSP00000217233 - Ensembl - - - - ENSG00000023330 - Ensembl - - - - MC-CPA - Carboxypeptidase A3 - CPA3 - 3.4.17.1 - - - - - - - - - - - - CBPA3_HUMAN - Mast cell carboxypeptidase A - CATALYTIC ACTIVITY: Release of a C-terminal amino acid, but little or no action with -Asp, -Glu, -Arg, -Lys or -Pro.COFACTOR: Binds 1 zinc ion per subunit (By similarity).SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle. Note=Secretory granules.SIMILARITY: Belongs to the peptidase M14 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12227 - - - - ENSP00000456911 - Ensembl - - - - Q9UM10 - UniProt - - - - 159757 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159757 - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite8669 - - - - EQUAL - 119 - - - - 400161 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400161 - - - - - - - - - - Authored: May, B, 2011-11-08 - The ANKRD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction143 - Expression of ANKRD1 - - - - RLAWWYSOJDYHDC-BZSNNMDCSA-N - InChIKey - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite3511 - - - - EQUAL - 779 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10183 - - - - - - Q59F52 - UniProt - - - - REACT_3995 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3995.3 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1075 - - - - CHEBI:42043 - ChEBI - - - - EQUAL - 625 - - - - Q9NR51 - UniProt - - - - REACT_25419 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25419.2 - - - - NP_006525 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12009 - - - - 11330046 - Zhu, Y - Qi, C - Reddy, JK - Pubmed - Peroxisome proliferator-activated receptors, coactivators, and downstream targets - Cell Biochem Biophys 32:187-204 - 2000 - - - - 6721 - NCBI Gene - - - - 1848554 - Soubrier, F - Wei, L - Corvol, P - Michaud, A - Clauser, E - Alhenc-Gelas, F - Pubmed - Expression and characterization of recombinant human angiotensin I-converting enzyme. Evidence for a C-terminal transmembrane anchor and for a proteolytic processing of the secreted recombinant and plasma enzymes - J Biol Chem 266:5540-6 - 1991 - - - - HGNC:10995 - HGNC - - - - - - MOD_RES 49 49 Methionine sulfoxide. - - - - ENSG00000163751 - Ensembl - - - - - - Granzyme H ecNumber3.4.21.-/ecNumber - GRAH_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein12346 - Reactome DB_ID: 2990875 - GZMH - - - - ENSP00000439495 - Ensembl - - - - ENSP00000325612 - Ensembl - - - - NP_001257558 - RefSeq - - - - - - MOD_RES 121 121 Phosphoserine; by PKA. - - - - EQUAL - 620 - - - - Q7Z7N3 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10839 - - - - ENSP00000377855 - Ensembl - - - - 2022417 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022417 - - - - ENSG00000066136 - Ensembl - - - - 4862 - NCBI Gene - - - - REACT_13890 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13890.1 - - - - Q8TEF3 - UniProt - - - - Q9Y5P7 - UniProt - - - - ENST00000343730 - Ensembl - - - - - - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 - SMRD3_HUMAN - - - - - Reactome DB_ID: 400141 - http://www.reactome.org/biopax/46/48887#Protein6510 - SMARCD3 - - - - 159751 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159751 - - - - Q9H9V7 - UniProt - - - - NP_001072986 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5630 - - - - - - CDK19 - HGNC - - - - EQUAL - 655 - http://www.reactome.org/biopax/46/48887#SequenceSite25581 - - - - REACT_26012 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26012.2 - - - - 15067378 - Fukamizu, A - Shimamoto, Y - Hirota, K - Pubmed - Effect of peroxisome proliferator-activated receptor alpha on human angiotensinogen promoter - Int J Mol Med 13:729-33 - 2004 - - - - NM_001204258 - RefSeq - - - - 351643 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=351643 - - - - REACT_22461 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22461.3 - - - - Q96SV3 - UniProt - - - - 442488 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442488 - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite9679 - - - - 2032773 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032773 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12003 - - - - NM_001013399 - RefSeq - - - - NM_134261 - RefSeq - - - - REACT_148020 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148020.2 - - - - EQUAL - 74 - http://www.reactome.org/biopax/46/48887#SequenceSite10126 - - - - B2RU05 - UniProt - - - - ENSP00000357907 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4700 - - - - - - - - - - - - - - - - - - - - 1RJK - PROTEIN DATA BANK - - - - - - water - - - - Reactome DB_ID: 109276 - http://www.reactome.org/biopax/46/48887#SmallMolecule64 - H2O - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-06-18 - http://www.reactome.org/biopax/46/48887#TemplateReaction58 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - The AVP gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind an E-box enhancer in the promoter of the AVP gene and activate transcription of AVP. - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Authored: May, B, 2010-06-18 - Expression of AVP - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1092 - - - - 1P22 - PROTEIN DATA BANK - - - - NM_015979 - RefSeq - - - - EQUAL - 65 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4721 - - - - - EQUAL - 54 - http://www.reactome.org/biopax/46/48887#SequenceSite9889 - - - - - - MOD_RES 714 714 Phosphoserine (By similarity). - - - - REACT_19669 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19669.1 - - - - MOD_RES N6-(pyridoxal phosphate)lysine (Probable) - - - - ENSP00000413389 - Ensembl - - - - REACT_148101 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148101.2 - - - - NP_005493 - RefSeq - - - - Q6IA79 - UniProt - - - - - - MOD_RES 589 589 Nitrated tyrosine (By similarity). - - - - ENSP00000429472 - Ensembl - - - - HGNC:396 - HGNC - - - - - - protein C heavy chain - - - - - Reactome DB_ID: 159827 - http://www.reactome.org/biopax/46/48887#Protein11650 - PROC(200-461) - - - - - - MOD_RES 826 826 Phosphoserine. - - - - Q6NWN7 - UniProt - - - - - - Becaplermin - c-sis - PDGF-2 - Platelet-derived growth factor beta polypeptide - PDGF B-chain - Platelet-derived growth factor, B chain - - - - - http://www.reactome.org/biopax/46/48887#Protein2129 - Reactome DB_ID: 184201 - PDGFB - - - - EQUAL - 2037 - - - - - - MOD_RES 264 264 N6-acetyllysine. - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4729 - - - - - - - - ENSG00000130772 - Ensembl - - - - - - pro-factor VII - - - - - http://www.reactome.org/biopax/46/48887#Protein11506 - Reactome DB_ID: 159848 - F7(21-466) - - - - 12213890 - Sahlin S - Rudling M - Olivecrona H - Stahle L - Bjorkhem I - Reihner E - Einarsson C - Angelin B - PubMed - Regulation of hepatic low-density lipoprotein receptor, 3-hydroxy-3-methylglutaryl coenzyme A reductase, and cholesterol 7alpha-hydroxylase mRNAs in human liver. - J Clin Endocrinol Metab 87(9);4307-13 - 2002 - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12837 - - - - Q99541 - UniProt - - - - ENSP00000380210 - Ensembl - - - - HGNC:8568 - HGNC - - - - - - MOD_RES 86 86 4-carboxyglutamate. - - - - TRIB3 - HGNC Symbol - - - - 18802415 - Ko, CH - Takahashi, JS - Hong, HK - McDearmon, EL - Pubmed - The genetics of mammalian circadian order and disorder: implications for physiology and disease - Nat Rev Genet 9:764-75 - 2008 - - - - - - - - - - INHIBITION - - 'aliskiren [extracellular region]' negatively regulates 'Prorenin:Prorenin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10)' - http://www.reactome.org/biopax/46/48887#Control303 - - - - - - SIN3A_HUMAN - Paired amphipathic helix protein Sin3a - - - - - http://www.reactome.org/biopax/46/48887#Protein5371 - Reactome DB_ID: 351657 - SIN3A - - - - G0/G1 switch regulatory protein 2 - G0S2 - Putative lymphocyte G0/G1 switch gene - - - - - - - - - - - - G0S2_HUMAN - G0/G1 switch protein 2 - FUNCTION: Promotes apoptosis by binding to BCL2, hence preventing the formation of protective BCL2-BAX heterodimers.SUBUNIT: Directly interacts with BCL2; this interaction prevents the formation of the anti-apoptotic BAX-BCL2 complex.SUBCELLULAR LOCATION: Mitochondrion.TISSUE SPECIFICITY: Widely expressed with highest levels in peripheral blood, skeletal muscle and heart, followed by kidney and liver.INDUCTION: Induced by TNF through the activation of the NFKB pathway. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 879832 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879832 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite11626 - - - - REACT_118734 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118734.2 - - - - REACT_27555 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27555.2 - - - - - - MOD_RES 300 300 Phosphothreonine; by MAPK14. - - - - EQUAL - 32 - http://www.reactome.org/biopax/46/48887#SequenceSite21656 - - - - REACT_1423 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1423.3 - - - - 1989764 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989764 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1090 - - - - EQUAL - 70 - - - - REACT_25637 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25637.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5338 - - - - EQUAL - 771 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4400 - - - - ENSP00000333125 - Ensembl - - - - - - MOD_RES 2016 2016 Phosphoserine. - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ACADM' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation192 - - - - Q8WVC8 - UniProt - - - - EQUAL - 2897 - http://www.reactome.org/biopax/46/48887#SequenceSite12421 - - - - D3DNJ9 - UniProt - - - - HGNC:7673 - HGNC - - - - - - MOD_RES 451 451 N6-acetyllysine (By similarity). - - - - - - MOD_RES 2436 2436 Phosphoserine. - - - - ENSP00000231487 - Ensembl - - - - InChI=1S/C20H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22/h3-4,6-7,9-10,12-13,15-16H,2,5,8,11,14,17-19H2,1H3,(H,21,22)/b4-3-,7-6-,10-9-,13-12-,16-15- - InChI - - - - ENSG00000167397 - Ensembl - - - - 7798189 - Kusunose E - Kishimoto T - Kikuta Y - Kinoshita H - Tanaka S - Yamamoto S - Kawashima H - Kusunose M - PubMed - Purification and cDNA cloning of human liver CYP4A fatty acid omega-hydroxylase. - J Biochem (Tokyo) 116(1);74-80 - 1994 - - - - Q3MIX4 - UniProt - - - - REACT_25499 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25499.2 - - - - REACT_119570 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119570.1 - - - - - - MOD_RES 59 59 Phosphoserine; by CK2 (By similarity). - - - - - - ubiquitin (UBC 9) - - - - - Reactome DB_ID: 939165 - http://www.reactome.org/biopax/46/48887#Protein1057 - UBC(609-684) - - - - 1368172 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368172 - - - - EQUAL - 877 - http://www.reactome.org/biopax/46/48887#SequenceSite12359 - - - - 2991279 - Carney, D - Sausville, E - Battey, J - Pubmed - The human vasopressin gene is linked to the oxytocin gene and is selectively expressed in a cultured lung cancer cell line - J Biol Chem 260:10236-41 - 1985 - - - - EQUAL - 660 - http://www.reactome.org/biopax/46/48887#SequenceSite25537 - - - - EQUAL - 795 - - - - NP_004765 - RefSeq - - - - NP_001169 - RefSeq - - - - 1989801 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989801 - - - - CHEBI:42857 - ChEBI - - - - ENSP00000326767 - Ensembl - - - - EQUAL - 62 - http://www.reactome.org/biopax/46/48887#SequenceSite10046 - - - - EQUAL - 62 - - - - CD36 - HGNC - - - - REACT_27077 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27077.2 - - - - EQUAL - 226 - - - - CHEBI:4786 - ChEBI - - - - - ARC32 - MED8 - Mediator complex subunit 8 - Activator-recruited cofactor 32 kDa component - - - - - - - - - - - - - - - - - - - - - - - - MED8_HUMAN - Mediator of RNA polymerase II transcription subunit 8 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May play a role as a target recruitment subunit in E3 ubiquitin-protein ligase complexes and thus in ubiquitination and subsequent proteasomal degradation of target proteins.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. May be part of a multisubunit E3 ubiquitin-protein ligase complex with the elongin BC complex (TCEB1 and TCEB2), CUL2 and RBX1.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q96G25-1; Sequence=Displayed; Name=2; IsoId=Q96G25-2; Sequence=VSP_007524; Name=3; IsoId=Q96G25-3; Sequence=VSP_035507; Note=No experimental confirmation available;DOMAIN: The elongin BC complex binding domain is also known as BC- box with the consensus [APST]-L-x(3)-C-x(3)-[AILV].SIMILARITY: Belongs to the Mediator complex subunit 8 family.SEQUENCE CAUTION: Sequence=BG722466; Type=Frameshift; Positions=258; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 381 - http://www.reactome.org/biopax/46/48887#SequenceSite4663 - - - - ENSP00000445002 - Ensembl - - - - ENSP00000281928 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5552 - - - - EQUAL - 56 - http://www.reactome.org/biopax/46/48887#SequenceSite10049 - - - - ENST00000452400 - Ensembl - - - - ENST00000493237 - Ensembl - - - - Q5SXQ6 - UniProt - - - - EQUAL - 6 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of AGT' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation196 - - - - REACT_27492 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27492.1 - - - - NM_006166 - RefSeq - - - - EQUAL - 311 - http://www.reactome.org/biopax/46/48887#SequenceSite12355 - - - - MED16 - HGNC Symbol - - - - HGNC:11715 - HGNC - - - - Q9UN09 - UniProt - - - - ENSP00000385971 - Ensembl - - - - - - - - - ARNTL:CLOCK/NPAS2:CRY:PER - - - - BMAL1:CLOCK/NPAS2:CRY:PER - http://www.reactome.org/biopax/46/48887#Complex4985 - Reactome DB_ID: 400273 - - - - HGNC:29 - HGNC - - - - EQUAL - 191 - http://www.reactome.org/biopax/46/48887#SequenceSite4968 - - - - EQUAL - 483 - http://www.reactome.org/biopax/46/48887#SequenceSite12417 - - - - ENSG00000161920 - Ensembl - - - - ENST00000264867 - Ensembl - - - - 22193701 - Danielson, UH - Henderson, I - Vrang, L - Sedig, S - Sahlberg, C - Lindström, E - Gossas, T - Pubmed - Aliskiren displays long-lasting interactions with human renin - Naunyn Schmiedebergs Arch Pharmacol - 2011 - - - - MED24 - HGNC - - - - NM_001139466 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1087 - - - - ENSG00000196549 - Ensembl - - - - Q9UPX2 - UniProt - - - - Q9NWA0 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9365 - - - - - - EQUAL - 104 - - - - EQUAL - 1258 - - - - EQUAL - 543 - - - - - - MOD_RES 55 55 Phosphoserine. - - - - EQUAL - 131 - http://www.reactome.org/biopax/46/48887#SequenceSite12395 - - - - REACT_1565 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1565.3 - - - - - - - - - - - Authored: May, B, 2011-11-08 - The TNFRSF21 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction165 - Expression of TNFRSF21 - - - - HGNC:16039 - HGNC - - - - EQUAL - 31 - http://www.reactome.org/biopax/46/48887#SequenceSite21745 - - - - NP_004590 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2112 - - - - - - 421305 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421305 - - - - 8274222 - Gonzalez FJ - Ogawa H - Kimura S - Imaoka S - PubMed - Complete cDNA sequence and cDNA-directed expression of CYP4A11, a fatty acid omega-hydroxylase expressed in human kidney. - DNA Cell Biol 12(10);893-9 - 1993 - - - - - - - - - ACTIVATION - - 'Steroid hormone receptor ERR1 [nucleoplasm]' positively regulates 'Expression of ALAS1' - ERR1 (ERRalpha) probably interacts with coactivator PG-1beta to activate ALAS1 (Shao et al. Shao et al. 2010). - http://www.reactome.org/biopax/46/48887#Control384 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5767 - - - - - MED23 - HGNC - - - - REACT_15261 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15261.2 - - - - EQUAL - 337 - - - - ENST00000372184 - Ensembl - - - - 7893760 - Schinkel AH - van Deemter L - Mol CA - Wagenaar E - Smit JJ - Borst P - PubMed - Characterization of the promoter region of the human MDR3 P-glycoprotein gene. - Biochim Biophys Acta 1261(1);44-56 - 1995 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12811 - - - - 11774469 - Holmes KV - Wentworth DE - PubMed - Addition of a single glycosylation site to hAPN blocks human coronavirus-229E receptor activity. - Adv Exp Med Biol 494;199-204 - 2001 - - - - ENSP00000407911 - Ensembl - - - - - - (9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule732 - Reactome DB_ID: 381254 - 13(S')-HODE - - - - ENSP00000292733 - Ensembl - - - - - - - - - - - - - - - - - - - - - - - - - PPARBP - PPAR-binding protein - TRAP220 - Peroxisome proliferator-activated receptor-binding protein - TRIP-2 - DRIP230 - PPARGBP - Thyroid receptor-interacting protein 2 - Vitamin D receptor-interacting protein complex component DRIP205 - Thyroid hormone receptor-associated protein complex 220 kDa component - Trap220 - DRIP205 - CRSP200 - TRIP2 - CRSP1 - TR-interacting protein 2 - PBP - Mediator complex subunit 1 - Activator-recruited cofactor 205 kDa component - p53 regulatory protein RB18A - RB18A - MED1 - ARC205 - - - - - - - - - - - - - - - - - - - - - MED1_HUMAN - Mediator of RNA polymerase II transcription subunit 1 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Interacts with GATA1 and YWHAH (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This subunit specifically interacts with a number of nuclear receptors in a ligand-dependent fashion including AR, ESR1, ESR2, PPARA, PPARG, RXRA, RXRG, THRA, THRB and VDR. Interacts with CTNNB1, GABPA, GLI3, PPARGC1A and TP53. Binds DNA.SUBCELLULAR LOCATION: Nucleus. Note=A subset of the protein may enter the nucleolus subsequent to phosphorylation by MAPK1 or MAPK3.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q15648-1; Sequence=Displayed; Name=2; IsoId=Q15648-3; Sequence=VSP_027906, VSP_027907;TISSUE SPECIFICITY: Ubiquitously expressed.PTM: Phosphorylated by MAPK1 or MAPK3 during G2/M phase which may enhance protein stability and promote entry into the nucleolus.SIMILARITY: Belongs to the Mediator complex subunit 1 family.SEQUENCE CAUTION: Sequence=AAC39854.1; Type=Frameshift; Positions=543, 545; Sequence=AAH06517.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=CAA73867.1; Type=Frameshift; Positions=4; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - HGNC:14248 - HGNC - - - - 9305755 - Mitchell GA - Boukaftane Y - PubMed - Cloning and characterization of the human mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase gene. - Gene 195(2);121-6 - 1997 - - - - - - Connective tissue growth factor - CTGF_HUMAN - - - - - Reactome DB_ID: 561148 - http://www.reactome.org/biopax/46/48887#Protein11198 - CTGF - - - - F-box and WD repeats protein beta-TrCP - BTRC - FBW1A - pIkappaBalpha-E3 receptor subunit - E3RSIkappaB - Epididymis tissue protein Li 2a - BTRCP - FBXW1A - - - - - - - - - - - - - - - - - - - - - - FBW1A_HUMAN - F-box/WD repeat-containing protein 1A - FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes and binds to phosphorylated target proteins. SCF(BTRC) mediates the ubiquitination of CTNNB1 and participates in Wnt signaling. SCF(BTRC) mediates the ubiquitination of NFKBIA, NFKBIB and NFKBIE; the degradation frees the associated NFKB1 to translocate into the nucleus and to activate transcription. Ubiquitination of NFKBIA occurs at 'Lys- 21' and 'Lys-22'. SCF(BTRC) mediates the ubiquitination of phosphorylated NFKB1/nuclear factor NF-kappa-B p105 subunit, ATF4, SMAD3, SMAD4, CDC25A, DLG1, FBXO5 and probably NFKB2. SCF(BTRC) mediates the ubiquitination of phosphorylated SNAI1. May be involved in ubiquitination and subsequent proteasomal degradation through a DBB1-CUL4 E3 ubiquitin-protein ligase. Required for activation of NFKB-mediated transcription by IL1B, MAP3K14, MAP3K1, IKBKB and TNF. Required for proteolytic processing of GLI3.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: Homodimer. Self-associates. Component of the SCF(BTRC) complex formed of CUL1, SKP1, RBX1 and a BTRC dimer. Direct interaction with SKP1 occurs via the F-box domain. Interacts with phosphorylated ubiquitination substrates SMAD3 and SMAD4. Interacts with phosphorylated ubiquitination substrates CTNNB1, NFKBIA, NFKBIB, NFKBIE, NFKB1/nuclear factor NF-kappa-B p105 subunit, ATF4, CDC25A, DLG1, FBXO5 and SNAI1; the interaction requires the phosphorylation of the 2 serine residues in the substrate destruction motif D-S-G-X(2,3,4)-S. Binds UBQLN1. Interacts with CDC34 and UBE2R2. Interacts with FBXW11. Interacts with CUL4A and DDB1. Part of a SCF(BTRC)-like complex lacking CUL1, which is associated with phosphorylated NKBIA and RELA; RELA interacts directly with NFKBIA. Interacts with HIV-1 Vpu. Interacts with the phosphorylated form of GLI3. Interacts with CLU.SUBCELLULAR LOCATION: Cytoplasm. Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9Y297-1; Sequence=Displayed; Name=2; IsoId=Q9Y297-2; Sequence=VSP_006764;TISSUE SPECIFICITY: Expressed in epididymis (at protein level).DOMAIN: The N-terminal D domain mediates homodimerization.SIMILARITY: Contains 1 F-box domain.SIMILARITY: Contains 7 WD repeats.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org//Genes/BTRCID451ch10q24.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q9UKT7 - UniProt - - - - GAS6 - HGNC Symbol - - - - - - - - ABC-1 - ABC1 - CERP - ATP-binding cassette 1 - ATP-binding cassette transporter 1 - Cholesterol efflux regulatory protein - ABCA1 - - - - - - - - - - - - - - - - - - - - ABCA1_HUMAN - ATP-binding cassette sub-family A member 1 - FUNCTION: cAMP-dependent and sulfonylurea-sensitive anion transporter. Key gatekeeper influencing intracellular cholesterol transport.SUBUNIT: Interacts with MEGF10.SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.TISSUE SPECIFICITY: Widely expressed, but most abundant in macrophages.INDUCTION: By bacterial lipopolysaccharides (LPS). LPS regulates expression through a liver X receptor (LXR) -independent mechanism. Repressed by ZNF202.DOMAIN: Multifunctional polypeptide with two homologous halves, each containing a hydrophobic membrane-anchoring domain and an ATP binding cassette (ABC) domain.PTM: Phosphorylation on Ser-2054 regulates phospholipid efflux.PTM: Palmitoylation by DHHC8 is essential for membrane localization.POLYMORPHISM: Genetic variations in ABCA1 define the high density lipoprotein cholesterol level quantitative trait locus 13 (HDLCQ13) [MIM:600046].DISEASE: High density lipoprotein deficiency 1 (HDLD1) [MIM:205400]: Recessive disorder characterized by absence of high density lipoprotein (HDL) cholesterol from plasma, accumulation of cholesteryl esters, premature coronary artery disease (CAD), hepatosplenomegaly, recurrent peripheral neuropathy and progressive muscle wasting and weakness. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: High density lipoprotein deficiency 2 (HDLD2) [MIM:604091]: Inherited as autosomal dominant trait. It is characterized by moderately low HDL cholesterol, predilection toward premature coronary artery disease (CAD) and a reduction in cellular cholesterol efflux. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the ABC transporter superfamily. ABCA family.SIMILARITY: Contains 2 ABC transporter domains.SEQUENCE CAUTION: Sequence=AAD49849.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAA10005.1; Type=Erroneous initiation; Note=Translation N-terminally extended;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ABCA1";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=ABCA1";WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=O95477"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#TemplateReaction75 - Edited: May, B, 2011-06-22 - The SREBF1 (SREBP1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - Expression of SREBF1 (SREBP1) - - - - 2426128 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2426128 - - - - - - AMPN_HUMAN - Aminopeptidase N - - - - - Reactome DB_ID: 2022340 - http://www.reactome.org/biopax/46/48887#Protein12355 - ANPEP - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8318 - - - - F5GYQ8 - UniProt - - - - NM_015477 - RefSeq - - - - - - MOD_RES 1218 1218 N6-acetyllysine. - - - - Q3KQV0 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1046 - - - - ENSP00000222002 - Ensembl - - - - - - MOD_RES 184 184 N6-acetyllysine (By similarity). - - - - 8386511 - Green, S - Latruffe, N - Bardot, O - Aldridge, TC - Pubmed - PPAR-RXR heterodimer activates a peroxisome proliferator response element upstream of the bifunctional enzyme gene - Biochem Biophys Res Commun 192:37-45 - 1993 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12975 - - - - A2RRQ6 - UniProt - - - - EQUAL - 2073 - - - - Q6T7F5 - UniProt - - - - EQUAL - 488 - http://www.reactome.org/biopax/46/48887#SequenceSite21700 - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite21689 - - - - - - MOD_RES 70 70 4-carboxyglutamate. - - - - 84246 - NCBI Gene - - - - - - CPT1 (liver) - carnitine palmitoyltransferase 1A (liver) - - - - - http://www.reactome.org/biopax/46/48887#Protein11548 - Reactome DB_ID: 400161 - CPT1A - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10135 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5655 - - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4732 - - - - ENSG00000269571 - Ensembl - - - - - 13.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12969 - - - - ENSP00000408045 - Ensembl - - - - Q9UPG7 - UniProt - - - - 9445487 - Nowak NJ - Gerhard DS - Weber BH - Stohr H - Cooper PR - Shows TB - Rivera A - Marquardt A - PubMed - A gene map of the Best's vitelliform macular dystrophy region in chromosome 11q12-q13.1. - Genome Res 8(1);48-56 - 1998 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1769 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6489 - Reactome DB_ID: 212343 - MED12 - - - - 2347585 - Henderson AS - Astrin KH - Bishop DF - PubMed - Human delta-aminolevulinate synthase: assignment of the housekeeping gene to 3p21 and the erythroid-specific gene to the X chromosome. - Genomics 7(2);207-14 - 1990 - - - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 400207 - http://www.reactome.org/biopax/46/48887#Protein13754 - Corepressors of PPARalpha - - - - NP_001135994 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5648 - - - - - - REACT_24415 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24415.2 - - - - NP_004266 - RefSeq - - - - ENSP00000381522 - Ensembl - - - - 7679927 - Griffin KJ - Johnson EF - Muerhoff AS - Richardson TH - Hsu MH - Clark JE - Palmer CN - PubMed - Characterization of a cDNA encoding a human kidney, cytochrome P-450 4A fatty acid omega-hydroxylase and the cognate enzyme expressed in Escherichia coli. - Biochim Biophys Acta 1172(1-2);161-6 - 1993 - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite21653 - - - - PDGFB - HGNC - - - - NP_005181 - RefSeq - - - - - - MOD_RES 178 178 Phosphothreonine; by AMPK (By similarity). - - - - EQUAL - 47 - http://www.reactome.org/biopax/46/48887#SequenceSite21717 - - - - 2022388 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022388 - - - - SLC27A1 - HGNC Symbol - - - - 4311 - NCBI Gene - - - - 400344 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400344 - - - - PTHR24254:SF0 - PANTHER Family - - - - - 381929 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381929 - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - The PPARA gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind the scond intron of the PPARA gene and activate transcription of PPARA. - http://www.reactome.org/biopax/46/48887#TemplateReaction65 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-06-18 - Reviewed: Kersten, S, 2009-06-08 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Authored: May, B, 2010-06-18 - Expression of PPARA - - - - ENSG00000133794 - Ensembl - - - - ENSP00000265162 - Ensembl - - - - ENSP00000346969 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5313 - - - - - - - - MOD_RES 408 408 Phosphoserine (By similarity). - - - - REACT_117960 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117960.1 - - - - - - MOD_RES 540 540 Phosphoserine (By similarity). - - - - Activator-recruited cofactor 70 kDa component - ARC70 - CRSP7 - CRSP complex subunit 7 - MED26 - Transcriptional coactivator CRSP70 - Mediator complex subunit 26 - Cofactor required for Sp1 transcriptional activation subunit 7 - - - - - - - - - - - - - - MED26_HUMAN - Mediator of RNA polymerase II transcription subunit 26 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O95402-1; Sequence=Displayed; Name=2; IsoId=O95402-2; Sequence=VSP_028151, VSP_028152; Note=No experimental confirmation available;SIMILARITY: Belongs to the Mediator complex subunit 26 family.SIMILARITY: Contains 1 TFIIS N-terminal domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000424646 - Ensembl - - - - MOD_RES S-nitrosocysteine (Probable) - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5794 - - - - 1368127 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368127 - - - - REACT_5090 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5090.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10110 - - - - 2EQR - PROTEIN DATA BANK - - - - PLIN2 - HGNC Symbol - - - - - - MOD_RES 48 48 4-carboxyglutamate. - - - - REACT_13943 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13943.2 - - - - 11018023 - Lee, ME - Perrella, MA - de la Monte, SM - Chin, MT - Hsieh, CM - Layne, MD - Yet, SF - Maemura, K - Pubmed - CLIF, a novel cycle-like factor, regulates the circadian oscillation of plasminogen activator inhibitor-1 gene expression - J Biol Chem 275:36847-51 - 2000 - - - - ENST00000599551 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14064 - - - - NP_000811 - RefSeq - - - - CMA1 - HGNC Symbol - - - - EQUAL - 98 - - - - NP_005002 - RefSeq - - - - ACE - HGNC - - - - ENSP00000344818 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12980 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12829 - - - - HNICUWMFWZBIFP-IRQZEAMPSA-N - InChIKey - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12833 - - - - MED1 - HGNC - - - - REACT_17491 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17491.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2073 - - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1053 - - - - D3DPJ1 - UniProt - - - - 607372 - omim - - - - HGNC:8845 - HGNC - - - - NP_001243020 - RefSeq - - - - CHEBI:10745 - ChEBI - - - - ENSG00000101255 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1854 - - - - 159752 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159752 - - - - - - NADP-dependent malic enzyme - MAOX_HUMAN - - - - - Reactome DB_ID: 400119 - http://www.reactome.org/biopax/46/48887#Protein13777 - ME1 - - - - 1234135 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1234135 - - - - 174720 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174720 - - - - ENSP00000351172 - Ensembl - - - - CYP4A2 - 1.14.15.3 - 20-HETE synthase - Fatty acid omega-hydroxylase - Cytochrome P-450HK-omega - CYP4A11 - Cytochrome P450HL-omega - CYP4AII - 20-hydroxyeicosatetraenoic acid synthase - CYPIVA11 - Lauric acid omega-hydroxylase - - - - - - - - - - - - - - - - - - - - - - - - - - - CP4AB_HUMAN - Cytochrome P450 4A11 - FUNCTION: Catalyzes the omega- and (omega-1)-hydroxylation of various fatty acids such as laurate, myristate and palmitate. Has little activity toward prostaglandins A1 and E1. Oxidizes arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE).CATALYTIC ACTIVITY: Octane + reduced rubredoxin + O(2) = 1-octanol + oxidized rubredoxin + H(2)O.COFACTOR: Heme group (By similarity).SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Peripheral membrane protein. Microsome membrane; Peripheral membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q02928-1; Sequence=Displayed; Name=2; IsoId=Q02928-2; Sequence=VSP_034595;TISSUE SPECIFICITY: Kidney and liver.POLYMORPHISM: CYP4A11v seems to be a rare allelic variant of CYP4A11, it seems to be unstable and not to metabolize lauric acid.SIMILARITY: Belongs to the cytochrome P450 family.WEB RESOURCE: Name=Cytochrome P450 Allele Nomenclature Committee; Note=CYP4A11 alleles; URL="http://www.cypalleles.ki.se/cyp4a11.htm";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/cyp4a11/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000544913 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10757 - - - - ENST00000220584 - Ensembl - - - - 7711730 - Finocchiaro, G - Wang, H - Lamantea, E - Taroni, F - Gellera, C - DiDonato, S - Montermini, L - Cavadini, P - Verderio, E - Pubmed - Carnitine palmitoyltransferase II deficiency: structure of the gene and characterization of two novel disease-causing mutations - Hum Mol Genet 4:19-29 - 1995 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1249 - - - - HGNC:2376 - HGNC - - - - Q14D51 - UniProt - - - - 12764228 - Lin, J - Spiegelman, BM - Tarr, PT - Handschin, C - Rhee, J - Pubmed - An autoregulatory loop controls peroxisome proliferator-activated receptor gamma coactivator 1alpha expression in muscle - Proc Natl Acad Sci U S A 100:7111-6 - 2003 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12346 - - - - 421289 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421289 - - - - REACT_118055 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118055.1 - - - - ENSG00000187079 - Ensembl - - - - - - TRB3_HUMAN - Tribbles homolog 3 - - - - - http://www.reactome.org/biopax/46/48887#Protein2180 - Reactome DB_ID: 199447 - TRIB3 - - - - NP_112235 - RefSeq - - - - EQUAL - 268 - http://www.reactome.org/biopax/46/48887#SequenceSite12361 - - - - 15207811 - Li, H - Fredriksson, L - Eriksson, U - Pubmed - The PDGF family: four gene products form five dimeric isoforms - Cytokine Growth Factor Rev 15:197-204 - 2004 - - - - - - - - - - - Cofactor required for Sp1 transcriptional activation subunit 2 - TRAP170 - hRGR1 - Vitamin D3 receptor-interacting protein complex 150 kDa component - RGR1 homolog - CRSP2 - Mediator complex subunit 14 - MED14 - Activator-recruited cofactor 150 kDa component - Transcriptional coactivator CRSP150 - CRSP complex subunit 2 - EXLM1 - RGR1 - CXorf4 - Trap170 - Thyroid hormone receptor-associated protein complex 170 kDa component - ARC150 - DRIP150 - - - - - - - - - - - - - - MED14_HUMAN - Mediator of RNA polymerase II transcription subunit 14 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Interacts with GATA1 (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with AR, ESR1, SREBF1 and STAT2.SUBCELLULAR LOCATION: Nucleus (Probable).TISSUE SPECIFICITY: Ubiquitous.SIMILARITY: Belongs to the Mediator complex subunit 14 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10761 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8333 - - - - 12140763 - Platet N - Liaudet-Coopman E - Derocq D - Glondu M - Rochefort H - Garcia M - PubMed - Down-regulation of cathepsin-D expression by antisense gene transfer inhibits tumor growth and experimental lung metastasis of human breast cancer cells. - Oncogene 21(33);5127-34 - 2002 - - - - NM_015149 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10003 - - - - LZFZMUMEGBBDTC-QEJZJMRPSA-N - InChIKey - - - - D3DVC0 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1040 - - - - ENST00000598780 - Ensembl - - - - EQUAL - 618 - http://www.reactome.org/biopax/46/48887#SequenceSite25567 - - - - EQUAL - 556 - http://www.reactome.org/biopax/46/48887#SequenceSite21420 - - - - EAP - Differentiation antigen gp160 - 3.4.11.7 - CD249 - Aminopeptidase A - AP-A - ENPEP - - - - - - - - - - - - - AMPE_HUMAN - Glutamyl aminopeptidase - FUNCTION: Appears to have a role in the catabolic pathway of the renin-angiotensin system. Probably plays a role in regulating growth and differentiation of early B-lineage cells.CATALYTIC ACTIVITY: Release of N-terminal glutamate (and to a lesser extent aspartate) from a peptide.COFACTOR: Binds 1 zinc ion per subunit (By similarity).SUBUNIT: Homodimer; disulfide-linked.SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein.TISSUE SPECIFICITY: Expressed by epithelial cells of the proximal tubule cells and the glomerulus of the nephron. Also found in a variety of other tissues.SIMILARITY: Belongs to the peptidase M1 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_001177413 - RefSeq - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4713 - - - - - ENST00000427410 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2758 - - - - - - - - MOD_RES 2 2 N-acetylserine. - - - - - - RecName: Full=Vasopressin-neurophysin 2-copeptin; AltName: Full=AVP-NPII; Contains: RecName: Full=Arg-vasopressin; Contains: RecName: Full=Neurophysin 2; AltName: Full=Neurophysin-II; Contains: RecName: Full=Copeptin; Flags: Precursor;<br>GN Name=AVP; Synonyms=ARVP, VP;<br>OS Homo sapiens - NEU2_HUMAN - Arg vasopressin - AVP(20-28) - - - - - http://www.reactome.org/biopax/46/48887#Protein3366 - Reactome DB_ID: 388474 - AVP - - - - - - - - Pro-factor VII is transported from the endoplasmic reticulum to the Golgi apparatus - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3893 - In this reaction, 1 molecule of 'pro-factor VII' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - - - - - NM_001003801 - RefSeq - - - - ENSG00000261579 - Ensembl - - - - 3229246 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3229246 - - - - 159746 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159746 - - - - 156993 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=156993 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21475 - - - - O15416 - UniProt - - - - - - MOD_RES 1970 1970 N6-acetyllysine. - - - - HGNC:23393 - HGNC - - - - NP_005028 - RefSeq - - - - Q9UC55 - UniProt - - - - 6095 - NCBI Gene - - - - - - prothrombin (factor II) propeptide - - - - - Reactome DB_ID: 159759 - http://www.reactome.org/biopax/46/48887#Protein11662 - F2(25-43) - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10877 - - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5326 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8328 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1860 - - - - - - MOD_RES 46 46 N6-acetyllysine. - - - - NM_004176 - RefSeq - - - - ENST00000491289 - Ensembl - - - - Q3C2G2 - UniProt - - - - Q6IMN1 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10158 - - - - - - EQUAL - 580 - - - - O15401 - UniProt - - - - ubiquitinylated lysine - - - - - 1989800 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989800 - - - - PTHR24040:SF0 - PANTHER Family - - - - - 2564851 - Peiper SC - Ashmun RA - Shapiro LH - Look AT - PubMed - Human myeloid plasma membrane glycoprotein CD13 (gp150) is identical to aminopeptidase N. - J Clin Invest 83(4);1299-307 - 1989 - - - - EQUAL - 63 - http://www.reactome.org/biopax/46/48887#SequenceSite9996 - - - - ENSG00000141551 - Ensembl - - - - O15025 - UniProt - - - - REACT_17845 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17845.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5637 - - - - - - EQUAL - 640 - - - - P49336 - UniProt - - - - ENST00000275246 - Ensembl - - - - ENST00000402802 - Ensembl - - - - ENSP00000376558 - Ensembl - - - - 107680 - omim - - - - B4DK61 - UniProt - - - - EQUAL - 500 - - - - MEF2C - HGNC Symbol - - - - ENST00000538643 - Ensembl - - - - ENST00000290663 - Ensembl - - - - 8145194 - pubchem - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - EQUAL - 1487 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4962 - - - - Q49AN0 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25540 - - - - - - MOD_RES 1258 1258 Phosphoserine. - - - - 2032774 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032774 - - - - - - MOD_RES 138 138 N6-acetyllysine; by PCAF/KAT2B. - - - - EQUAL - 421 - http://www.reactome.org/biopax/46/48887#SequenceSite25498 - - - - Q6I9Y9 - UniProt - - - - O75448 - UniProt - - - - EQUAL - 244 - http://www.reactome.org/biopax/46/48887#SequenceSite12371 - - - - 85441 - NCBI Gene - - - - 16503871 - Gouni-Berthold, I - Krone, W - Pubmed - Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis - Curr Drug Targets Cardiovasc Haematol Disord 5:513-23 - 2005 - - - - - - Cathepsin D ecNumber3.4.23.5/ecNumber component recommendedName: Cathepsin D light chain /component component recommendedName: Cathepsin D heavy chain /component - CATD_HUMAN - CTSD(65-412) - - - - - http://www.reactome.org/biopax/46/48887#Protein12337 - Reactome DB_ID: 2990853 - CTSD - - - - - - MOD_RES 279 279 N6-acetyllysine. - - - - 600863 - omim - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21500 - - - - P14793 - UniProt - - - - REACT_22509 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22509.3 - - - - MED11 - HGNC Symbol - - - - REACT_27826 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27826.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12011 - - - - - C18H32O2 - acido linoleico - Telfairic acid - linolic acid - acide cis-linoleique - C18:2, n-6,9 all-cis - (9Z,12Z)-octadeca-9,12-dienoic acid - LA - C18:2 9c, 12c omega6 todos cis-9,12-octadienoico - cis,cis-linoleic acid - 9Z,12Z-octadecadienoic acid - cis-Delta(9,12)-octadecadienoic acid - all-cis-9,12-octadecadienoic acid - acide linoleique - cis,cis-9,12-octadecadienoic acid - - - - - - - - 280.4455 - linoleic acid - linoleic acid - An octadecadienoic acid containing two <stereo>Z</stereo> (<stereo>cis</stereo>) double bonds at positions 9 and 12. - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4955 - - - - - - - - - - - - - - MOD_RES 1185 1185 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10060 - - - - - - A6NJQ5 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5604 - - - - 113519 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113519 - - - - 400328 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400328 - - - - MED31 - HGNC - - - - NP_001135741 - RefSeq - - - - ENSG00000081189 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry3487 - - - - ENST00000402126 - Ensembl - - - - - - Chromodomain-helicase-DNA-binding protein 9 - CHD9_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6512 - Reactome DB_ID: 400163 - CHD9 - - - - 1655873 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655873 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval827 - - - - - - P22680 - UniProt - - - - NP_963851 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1082 - - - - 1368087 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368087 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1843 - - - - CYP4A11 - HGNC Symbol - - - - - 3.4.21 - - - - pro-factor X -> factor X + factor X propeptide - At the beginning of this reaction, 1 molecule of 'pro-factor X' is present. At the end of this reaction, 1 molecule of 'factor X light chain propeptide', and 1 molecule of 'factor X' are present.<br><br> This reaction takes place in the 'Golgi membrane' and is mediated by the 'furin activity' of 'furin'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3902 - - - - - - 1989808 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989808 - - - - 3229248 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3229248 - - - - EQUAL - 129 - - - - Q53YX9 - UniProt - - - - 7598806 - Dufort I - Labrie F - Reimnitz G - Luu-The V - Paquet N - PubMed - Structural characterization and expression of the human dehydroepiandrosterone sulfotransferase gene. - DNA Cell Biol 14(6);511-8 - 1995 - - - - ENSP00000364731 - Ensembl - - - - 19233136 - Yoshioka, T - Sakai, M - Hosooka, T - Inagaki, K - Watanabe, E - Noguchi, T - Kasuga, M - Ogawa, W - Iguchi, H - Matsuki, Y - Hiramatsu, R - Pubmed - Identification and characterization of an alternative promoter of the human PGC-1alpha gene - Biochem Biophys Res Commun 381:537-43 - 2009 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8343 - - - - NP_000893 - RefSeq - - - - - - Induction of Platelet glycoprotein IV (PAS IV, CD36, GPIV) Expression During Adipogenesis - - - - - The Platelet glycoprotein IV gene (CD36, PAS IV, GPIV) is transcribed to yield mRNA and the mRNA is translated to yield proteind. - Reviewed: D'Eustachio, P, 2009-05-26 22:09:50 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction46 - Edited: May, B, 2010-03-23 - Reviewed: Sethi, JK, 2011-02-09 - Authored: May, B, 2010-03-23 - Expression of CD36 (platelet glycoprotein IV, FAT) - - - - ENSP00000281455 - Ensembl - - - - ENSP00000353638 - Ensembl - - - - - - MOD_RES 67 67 4-carboxyglutamate. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12032 - - - - - - EQUAL - 226 - - - - HGNC:7669 - HGNC - - - - EQUAL - 1970 - - - - B4DXI3 - UniProt - - - - ENST00000324907 - Ensembl - - - - ENST00000261646 - Ensembl - - - - NP_064568 - RefSeq - - - - - - - - - - - - - - - - - - KIAA1047 - N-CoR - NCOR1 - N-CoR1 - - - - - - - - - - - - - - - - - - - - - - - - - - - NCOR1_HUMAN - Nuclear receptor corepressor 1 - FUNCTION: Mediates transcriptional repression by certain nuclear receptors. Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors.SUBUNIT: Interacts with C1D, SIAH2, HDAC7, SAP30, SIN3A and SIN3B (By similarity). Forms a large corepressor complex that contains. SIN3A/B and histone deacetylases HDAC1 and HDAC2. This complex associates with the thyroid (TR) and the retinoid acid receptors (RAR) in the absence of ligand. Interacts directly with RARA; the interaction is faciliated with RARA trimethylation. Interacts with DACH1. Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1XR1, CORO2A and GPS2. Interacts with TRIM28 and KDM3A. Interacts with ZBTB33; the interaction serves to recruit the N-CoR complex to promoter regions containing methylated CpG dinucleotides. Interacts with HDAC9 (via its catalytic domain). Interacts with CBFA2T3 and HEXIM1. Interacts (via the RRFD1 domain) with BAZ1A (via its N-terminal); the interaction corepresses a number of NCOR1-regulated genes. May interact with DEAF1.SUBCELLULAR LOCATION: Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=O75376-1; Sequence=Displayed; Name=2; IsoId=O75376-2; Sequence=VSP_010207, VSP_010208; Name=3; Synonyms=b; IsoId=O75376-3; Sequence=VSP_046468, VSP_010207, VSP_046469, VSP_046470; Note=No experimental confirmation available;DOMAIN: The N-terminal region contains three independent domains that are capable of mediating transcriptional repression (RD1, RD2 and RD3).DOMAIN: The C-terminal region contains two separate nuclear receptor-interacting domains (ID1 and ID2), each of which contains a conserved sequence referred to as the CORNR box. This motif is necessary and sufficient for binding to unligated nuclear hormone receptors, while sequences flanking the CORNR box determine the precise nuclear hormone receptor specificity (By similarity).PTM: Ubiquitinated; mediated by SIAH2 and leading to its subsequent proteasomal degradation (By similarity).SIMILARITY: Belongs to the N-CoR nuclear receptor corepressors family.SIMILARITY: Contains 2 SANT domains.SEQUENCE CAUTION: Sequence=BAA82999.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Pre-B-cell colony-enhancing factor 1 - NAMPT - Nampt - Visfatin - Pre-B cell-enhancing factor - PBEF - NAmPRTase - 2.4.2.12 - PBEF1 - - - - - - - - - - - - - - - - - - NAMPT_HUMAN - Nicotinamide phosphoribosyltransferase - FUNCTION: Catalyzes the condensation of nicotinamide with 5- phosphoribosyl-1-pyrophosphate to yield nicotinamide mononucleotide, an intermediate in the biosynthesis of NAD. It is the rate limiting component in the mammalian NAD biosynthesis pathway (By similarity).CATALYTIC ACTIVITY: Nicotinamide D-ribonucleotide + diphosphate = nicotinamide + 5-phospho-alpha-D-ribose 1-diphosphate.ENZYME REGULATION: Inhibited by FK866. FK866 competes for the same binding site as nicotinamide, but due to its very low dissociation rate, it is essentially an irreversible inhibitor.PATHWAY: Cofactor biosynthesis; NAD(+) biosynthesis; nicotinamide D-ribonucleotide from 5-phospho-alpha-D-ribose 1-diphosphate and nicotinamide: step 1/1.SUBUNIT: Homodimer.SUBCELLULAR LOCATION: Cytoplasm (By similarity).TISSUE SPECIFICITY: Expressed in large amounts in bone marrow, liver tissue, and muscle. Also present in heart, placenta, lung, and kidney tissues.SIMILARITY: Belongs to the NAPRTase family.CAUTION: Was originally (PubMed:8289818) thought to be a cytokine which acts on early B-lineage precursor cells, by enhancing the effect of IL-7 and SCF on pre-B-cell colony formation.SEQUENCE CAUTION: Sequence=AAQ96862.1; Type=Erroneous gene model prediction; Sequence=EAL24400.1; Type=Erroneous gene model prediction;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/NAMPTID43890ch7q22.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 49836649 - pubchem-substance - - - - Q9BQB6 - UniProt - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12958 - - - - HGNC:2375 - HGNC - - - - EQUAL - 343 - - - - - - MOD_RES 530 530 Phosphoserine (By similarity). - - - - - - MOD_RES 343 343 Phosphoserine. - - - - - - pro-growth-arrest-specific protein 6 - 11xCbxE-GAS6(31-691) - - - - - - - - - - - - - - - - Reactome DB_ID: 163805 - http://www.reactome.org/biopax/46/48887#Protein11654 - pro-GAS6 - - - - - - MED22_HUMAN - Mediator of RNA polymerase II transcription subunit 22 - - - - - Reactome DB_ID: 556779 - http://www.reactome.org/biopax/46/48887#Protein6496 - MED22 - - - - - - MOD_RES 41 41 Phosphoserine. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite398 - - - - ENST00000409833 - Ensembl - - - - EQUAL - 282 - - - - 7892212 - McGarry, JD - Foster, DW - Esser, V - Zhang, B - Britton, CH - Schultz, RA - Pubmed - Human liver mitochondrial carnitine palmitoyltransferase I: characterization of its cDNA and chromosomal localization and partial analysis of the gene - Proc Natl Acad Sci U S A 92:1984-8 - 1995 - - - - - 3.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7595 - - - - 177332 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=177332 - - - - NM_015260 - RefSeq - - - - - 3.4.21 - - - - pro-prothrombin -> prothrombin + prothrombin propeptide - At the beginning of this reaction, 1 molecule of 'pro-prothrombin (factor II)' is present. At the end of this reaction, 1 molecule of 'prothrombin (factor II) propeptide', and 1 molecule of 'prothrombin (factor II)' are present.<br><br> This reaction takes place in the 'Golgi membrane' and is mediated by the 'furin activity' of 'furin'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3903 - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6498 - Reactome DB_ID: 212429 - MED31 - - - - EQUAL - 347 - - - - 602550 - omim - - - - - - - - - INHIBITION - - 'NR1D1 (REV-ERBA):heme:Corepressor [nucleoplasm]' negatively regulates 'Expression of ELOVL3' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation110 - As inferred from mouse, REV-ERBA (NR1D1) binds the promoter of the ELOVL3 gene and represses transcription, possibly by recruiting corepressors. - - - - - - MOD_RES 311 311 Phosphoserine; by LATS2. - - - - B4DTY1 - UniProt - - - - EQUAL - 54 - http://www.reactome.org/biopax/46/48887#SequenceSite9916 - - - - EQUAL - 1560 - - - - 601993 - omim - - - - NCOA3 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5737 - - - - - - - - - - - - Beta-TrCP1:PER - http://www.reactome.org/biopax/46/48887#Complex4986 - Reactome DB_ID: 400368 - - - - 18853057 - Bersanetti, PA - Hial, V - Lopes, IC - Carmona, AK - Gomes, RA - Teodoro, LG - Pubmed - Angiotensin-converting enzyme in pericardial fluid: comparative study with serum activity - Arq Bras Cardiol 91:156-61, 172-8 - 2008 - - - - 604256 - omim - - - - 2022393 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022393 - - - - HGNC:22963 - HGNC - - - - 400310 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400310 - - - - Q59GM0 - UniProt - - - - - 12.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12928 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8358 - - - - Q6Q785 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10042 - - - - - - EQUAL - 1223 - - - - EQUAL - 57 - http://www.reactome.org/biopax/46/48887#SequenceSite25544 - - - - NM_001871 - RefSeq - - - - REACT_5343 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5343.1 - - - - 600848 - omim - - - - ENSG00000177565 - Ensembl - - - - EQUAL - 110 - - - - REACT_119389 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119389.1 - - - - NCOA6 - HGNC Symbol - - - - Q96A79 - UniProt - - - - 174159 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174159 - - - - P20393 - UniProt - - - - - - ACE(30-1306) - ACE_HUMAN - Angiotensin-converting enzyme - - - - - http://www.reactome.org/biopax/46/48887#Protein12343 - Reactome DB_ID: 508496 - ACE - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2121 - - - - - - Q9UFZ6 - UniProt - - - - REACT_147935 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147935.2 - - - - ENST00000557220 - Ensembl - - - - REACT_15002 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15002.1 - - - - EQUAL - 141 - - - - PTHR11932:SF19 - PANTHER Family - - - - - REACT_26345 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26345.2 - - - - 163834 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163834 - - - - - - Renin - RENI_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein12340 - Reactome DB_ID: 2022352 - REN - - - - 1989756 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989756 - - - - 939868 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939868 - - - - 1W1C - PROTEIN DATA BANK - - - - EQUAL - 68 - http://www.reactome.org/biopax/46/48887#SequenceSite10124 - - - - REACT_148677 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148677.1 - - - - - - MOD_RES 95 95 4-carboxyglutamate. - - - - ENSP00000367697 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature124 - - - - PTHR11705:SF17 - PANTHER Family - - - - - 9616204 - Brown, MS - Shimano, H - Horton, JD - Hammer, RE - Goldstein, JL - Shimomura, I - Pubmed - Activation of cholesterol synthesis in preference to fatty acid synthesis in liver and adipose tissue of transgenic mice overproducing sterol regulatory element-binding protein-2 - J Clin Invest 101:2331-9 - 1998 - - - - B4DH32 - UniProt - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction159 - The ME1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - Expression of ME1 - - - - REACT_27168 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27168.2 - - - - - - - - - - - - PPARA: Fatty Acid Complex (Activated PPARA) - Reactome DB_ID: 422413 - http://www.reactome.org/biopax/46/48887#Complex3141 - - - - NM_000490 - RefSeq - - - - ENSP00000447486 - Ensembl - - - - 600864 - omim - - - - EQUAL - 73 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1059 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25538 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature823 - - - - 9443 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4773 - - - - - EQUAL - 22 - - - - EQUAL - 1546 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of TRIB3' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation220 - - - - REACT_119693 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119693.2 - - - - Q53H04 - UniProt - - - - ENSG00000121671 - Ensembl - - - - - - MOD_RES 2214 2214 Phosphoserine. - - - - ENSP00000338283 - Ensembl - - - - REACT_26326 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26326.2 - - - - NR1F1 - Nuclear receptor subfamily 1 group F member 1 - Retinoid-related orphan receptor-alpha - Nuclear receptor RZR-alpha - RORA - RZRA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RORA_HUMAN - Nuclear receptor ROR-alpha - FUNCTION: Orphan nuclear receptor. Binds DNA as a monomer to hormone response elements (HRE) containing a single core motif half-site preceded by a short A-T-rich sequence. This isomer binds to the consensus sequence 5'-[AT][TA]A[AT][CGT]TAGGTCA-3'. Regulates a number of genes involved in lipid metabolism such as apolipoproteins AI, APOA5, CIII, CYP71 and PPARgamma, in cerebellum and photoreceptor development including PCP2, OPN1SW, OPN1SM AND ARR3, in circadian rhythm with BMAL1, and skeletal muscle development with MYOD1. Possible receptor for cholesterol or one of its derivatives.ENZYME REGULATION: Activated by CaMK4.SUBUNIT: Monomer. Interacts (via the DNA-binding domain) with HIF1; the interaction enhances HIF1A transcription under hypoxia through increasing protein stability.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Name=Alpha-2; IsoId=P35398-1; Sequence=Displayed; Name=Alpha-1; IsoId=P35398-2; Sequence=VSP_003655; Name=Alpha-3; IsoId=P35398-3; Sequence=VSP_003656; Name=Alpha-4; IsoId=P35398-4; Sequence=VSP_003657; Note=Ref.2 (AAA02963) sequence is in conflict in position: 8:A->E;TISSUE SPECIFICITY: Widely expressed in a number of tissues.INDUCTION: By hypoxia and melatonin.PTM: Phosphorylation by PKC in neurons inhibits transcriptional activity. Phosphorylated on Thr-216 by ERK2 in vitro.PTM: Sumoylated by SENP1 and SENP2. Sumoylation, promoted by PIAS2, PIAS3, PIASy but not PIAS1, enhances the transcriptional activity. Desumoylated by SENP1.PTM: Ubiquitinated. Ubiquitination is required for efficient transcriptional activity and is prevented by Hairless.SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR)' - http://www.reactome.org/biopax/46/48887#Control381 - - - - ENST00000353411 - Ensembl - - - - - - MOD_RES 780 780 N6-acetyllysine. - - - - REACT_5451 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5451.2 - - - - ENST00000323817 - Ensembl - - - - EQUAL - 461 - http://www.reactome.org/biopax/46/48887#SequenceSite21706 - - - - EQUAL - 758 - http://www.reactome.org/biopax/46/48887#SequenceSite21651 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13186 - - - - - - MOD_RES 1207 1207 Phosphoserine. - - - - NM_001145357 - RefSeq - - - - Q6NS89 - UniProt - - - - REACT_12848 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12848.3 - - - - EQUAL - 1255 - http://www.reactome.org/biopax/46/48887#SequenceSite21454 - - - - ENSP00000355627 - Ensembl - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of PPARA' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation100 - As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind E-boxes in the second intron of the PPARA gene and activate transcription of PPARA. - - - - - - MOD_RES 533 533 Phosphoserine (By similarity). - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13223 - - - - NM_014452 - RefSeq - - - - EQUAL - 504 - http://www.reactome.org/biopax/46/48887#SequenceSite5339 - - - - REACT_27106 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27106.2 - - - - 421310 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421310 - - - - REACT_13363 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13363.3 - - - - ENSP00000435602 - Ensembl - - - - ENST00000372654 - Ensembl - - - - B3KMR9 - UniProt - - - - - - RENI_HUMAN - REN(24-406) - Prorenin - - - - - http://www.reactome.org/biopax/46/48887#Protein12342 - Reactome DB_ID: 2065391 - REN - - - - EQUAL - 1147 - http://www.reactome.org/biopax/46/48887#SequenceSite21501 - - - - 607392 - omim - - - - 54797 - NCBI Gene - - - - GO:0005788 - Gene Ontology - - - - 879770 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879770 - - - - NM_002608 - RefSeq - - - - REACT_120147 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120147.1 - - - - REACT_27515 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27515.3 - - - - EQUAL - 54 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10772 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Mediator Complex (consensus) - http://www.reactome.org/biopax/46/48887#Complex3134 - Reactome DB_ID: 556786 - - - - - - MOD_RES 2234 2234 Phosphoserine. - - - - ENSP00000008527 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10793 - - - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12836 - - - - EQUAL - 407 - - - - ENSP00000441403 - Ensembl - - - - EQUAL - 109 - - - - 159786 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159786 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4954 - - - - - - - - - - - - - HGNC:9237 - HGNC - - - - 1EZF - PROTEIN DATA BANK - - - - ENST00000313639 - Ensembl - - - - - - 13xCbxE-PROZ(24-400) - - - - - - - - - - - - - - - - - - Reactome DB_ID: 163838 - http://www.reactome.org/biopax/46/48887#Protein11642 - pro-protein Z - - - - ENST00000407236 - Ensembl - - - - Q9BYF1 - UniProt - - - - Q9UN08 - UniProt - - - - EQUAL - 451 - - - - REACT_3151 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3151.2 - - - - ENSP00000376924 - Ensembl - - - - 400138 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400138 - - - - 159731 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159731 - - - - - - MOD_RES 73 73 4-carboxyglutamate. - - - - - - factor X heavy chain - - - - - Reactome DB_ID: 159776 - http://www.reactome.org/biopax/46/48887#Protein11631 - F10(183-488) - - - - REACT_27560 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27560.2 - - - - 19934321 - Tian, L - Hyslop, T - Wang, M - Casimiro, MC - Ojeifo, JO - Pestell, RG - Wang, C - Liang, B - Zhou, J - Pubmed - Activating peroxisome proliferator-activated receptor gamma mutant promotes tumor growth in vivo by enhancing angiogenesis - Cancer Res 69:9236-44 - 2009 - - - - EQUAL - 945 - - - - ENSG00000113161 - Ensembl - - - - - - MOD_RES 370 370 Phosphoserine (By similarity). - - - - MED16 - DRIP92 - Mediator complex subunit 16 - Trap95 - Thyroid hormone receptor-associated protein 5 - Thyroid hormone receptor-associated protein complex 95 kDa component - THRAP5 - Vitamin D3 receptor-interacting protein complex 92 kDa component - - - - - - - - - - - - - - - - - - - - - - - - MED16_HUMAN - Mediator of RNA polymerase II transcription subunit 16 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=5; Name=1; IsoId=Q9Y2X0-1; Sequence=Displayed; Name=2; IsoId=Q9Y2X0-2; Sequence=VSP_051724; Name=3; IsoId=Q9Y2X0-3; Sequence=VSP_051722, VSP_051724; Note=No experimental confirmation available; Name=4; IsoId=Q9Y2X0-4; Sequence=VSP_051721, VSP_051723; Note=No experimental confirmation available; Name=5; IsoId=Q9Y2X0-5; Sequence=VSP_028749, VSP_028750; Note=No experimental confirmation available;SIMILARITY: Belongs to the Mediator complex subunit 16 family.SIMILARITY: Contains 5 WD repeats.CAUTION: It is uncertain whether Met-1 or Met-13 is the initiator.SEQUENCE CAUTION: Sequence=AAD31087.1; Type=Frameshift; Positions=609; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 986 - - - - Q5VUF3 - UniProt - - - - 549428 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549428 - - - - EQUAL - 428 - http://www.reactome.org/biopax/46/48887#SequenceSite21482 - - - - - - - p-PGC-1alpha - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 1592227 - http://www.reactome.org/biopax/46/48887#Protein11544 - p-PPARGC1A - - - - REACT_3453 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3453.1 - - - - 9862 - NCBI Gene - - - - REACT_148672 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148672.1 - - - - EQUAL - 383 - - - - HGNC:2372 - HGNC - - - - REACT_148025 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148025.1 - - - - - - MOD_RES 878 878 N6-acetyllysine. - - - - 50486 - NCBI Gene - - - - 12807885 - Lin, J - Puigserver, P - Yang, R - Newgard, CB - Spiegelman, BM - Tarr, PT - Rhee, J - Pubmed - PGC-1beta in the regulation of hepatic glucose and energy metabolism - J Biol Chem 278:30843-8 - 2003 - - - - Q5VTA5 - UniProt - - - - REACT_115875 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115875.1 - - - - ENSP00000268171 - Ensembl - - - - - - MOD_RES 803 803 (3S)-3-hydroxyasparagine. - - - - - - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule970 - Reactome DB_ID: 156540 - H+ - - - - REACT_7348 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7348.1 - - - - - - MOD_RES 1195 1195 Phosphoserine. - - - - 5054 - NCBI Gene - - - - - - MOD_RES 1674 1674 N6-acetyllysine. - - - - Q5FBE1 - UniProt - - - - Q5T6L1 - UniProt - - - - 603101 - omim - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6495 - Reactome DB_ID: 212430 - MED7 - - - - - - MOD_RES 86 86 Phosphoserine. - - - - - - 12xCbxE-3D-F9(29-461) - - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11628 - Reactome DB_ID: 159866 - pro-factor IX - - - - Q9Y3C7 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4767 - - - - - - - - MOD_RES 1648 1648 Phosphothreonine (By similarity). - - - - 199938 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=199938 - - - - - - G0S2_HUMAN - G0/G1 switch regulatory protein 2 - - - - - http://www.reactome.org/biopax/46/48887#Protein13773 - Reactome DB_ID: 1989741 - G0S2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2253 - - - - - - - - MOD_RES 413 413 N6-acetyllysine (By similarity). - - - - 879827 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879827 - - - - Q9Y2W0 - UniProt - - - - EQUAL - 43 - http://www.reactome.org/biopax/46/48887#SequenceSite22997 - - - - 7685352 - Conrad, DG - Jiang, G - Shechter, I - McKenzie, TL - Pubmed - Transcriptional regulation by lovastatin and 25-hydroxycholesterol in HepG2 cells and molecular cloning and expression of the cDNA for the human hepatic squalene synthase - J Biol Chem 268:12818-24 - 1993 - - - - - KM-102-derived reductase-like factor - Gene associated with retinoic and interferon-induced mortality 12 protein - Thioredoxin reductase TR1 - TXNRD1 - Gene associated with retinoic and IFN-induced mortality 12 protein - KDRF - TR - GRIM12 - GRIM-12 - 1.8.1.9 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TRXR1_HUMAN - Thioredoxin reductase 1, cytoplasmic - FUNCTION: Isoform 1 may possess glutaredoxin activity as well as thioredoxin reductase activity and induces actin and tubulin polymerization, leading to formation of cell membrane protrusions. Isoform 4 enhances the transcriptional activity of estrogen receptors alpha and beta while isoform 5 enhances the transcriptional activity of the beta receptor only. Isoform 5 also mediates cell death induced by a combination of interferon-beta and retinoic acid.CATALYTIC ACTIVITY: Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH.COFACTOR: Binds 1 FAD per subunit.SUBUNIT: Homodimer. Isoform 4 interacts with ESR1 and ESR2. Interacts with HERC5.SUBCELLULAR LOCATION: Cytoplasm (By similarity).SUBCELLULAR LOCATION: Isoform 4: Cytoplasm. Nucleus.SUBCELLULAR LOCATION: Isoform 5: Cytoplasm.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Name=1; Synonyms=V, TXNRD1_v3; IsoId=Q16881-1; Sequence=Displayed; Note=Minor isoform; Name=2; Synonyms=II, TXNRD1_v4; IsoId=Q16881-2; Sequence=VSP_031560, VSP_031565; Name=3; Synonyms=III, TXNRD1_v5; IsoId=Q16881-3; Sequence=VSP_031562, VSP_031563; Name=4; Synonyms=IV, TXNRD1_v2, TrxR1b; IsoId=Q16881-4; Sequence=VSP_031561, VSP_031564; Name=5; Synonyms=I, TXNRD1_v1, TrxR1a; IsoId=Q16881-5; Sequence=VSP_031558; Note=Major isoform. The N-terminus of the sequence is processed into a mature form that lacks residues Met-151 and Asn-152 at the N-terminus; Name=6; Synonyms=VI; IsoId=Q16881-6; Sequence=VSP_031559;TISSUE SPECIFICITY: Isoform 1 is expressed predominantly in Leydig cells (at protein level). Also expressed in ovary, spleen, heart, liver, kidney and pancreas and in a number of cancer cell lines. Isoform 4 is widely expressed with highest levels in kidney, testis, uterus, ovary, prostate, placenta and fetal liver.INDUCTION: Isoform 5 is induced by a combination of interferon- beta and retinoic acid (at protein level). Isoform 1 is induced by estradiol or testosterone in HeLa cells.DOMAIN: The N-terminal glutaredoxin domain found in isoform 1 does not contain the C-P-Y-C redox-active motif normally found in glutaredoxins and has been found to be inactive in classical glutaredoxin assays.PTM: The N-terminus of isoform 5 is blocked.PTM: ISGylated (Probable).MISCELLANEOUS: The thioredoxin reductase active site is a redox- active disulfide bond. The selenocysteine residue is also essential for catalytic activity.SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.SIMILARITY: Contains 1 glutaredoxin domain.SEQUENCE CAUTION: Sequence=AAB35418.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=AAC69621.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=AAF15900.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=AAV38446.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=AAZ67916.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=BAA13674.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=CAA04503.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=CAA62629.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec; Sequence=CAG38744.1; Type=Erroneous termination; Positions=648; Note=Translated as Sec;WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/txnrd1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - A2I2N8 - UniProt - - - - NM_001142590 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10170 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10172 - - - - - - - - MOD_RES 51 51 4-carboxyglutamate. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BMAL1:CLOCK/NPAS2 Activates Circadian Expression - Reviewed: Kay, SA, 2010-06-23 - As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in Munoz and Baler 2003). - Edited: May, B, 2011-06-22 - Reviewed: Hirota, T, 2010-06-23 - http://www.reactome.org/biopax/46/48887#Pathway876 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Authored: May, B, 2011-06-22 - - - - - 2022374 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022374 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10763 - - - - EQUAL - 103 - http://www.reactome.org/biopax/46/48887#SequenceSite25563 - - - - EQUAL - 245 - - - - ENST00000565731 - Ensembl - - - - C0LZJ3 - UniProt - - - - NM_052877 - RefSeq - - - - 2028294 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2028294 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21431 - - - - CHEBI:36144 - ChEBI - - - - Q9NZL5 - UniProt - - - - 2708524 - Goldstein, SM - Wintroub, BU - Kealey, JT - Kaempfer, CE - Pubmed - Human mast cell carboxypeptidase. Purification and characterization - J Clin Invest 83:1630-6 - 1989 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite21502 - - - - - - MOD_RES 109 109 Phosphoserine; by LATS1 and LATS2. - - - - 400380 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400380 - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite4651 - - - - 14729975 - Osumi, T - Gonzalez, FJ - Tsukamoto, T - Shimizu, M - Takeshita, A - Pubmed - Tissue-selective, bidirectional regulation of PEX11 alpha and perilipin genes through a common peroxisome proliferator response element - Mol Cell Biol 24:1313-23 - 2004 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5799 - - - - 549564 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549564 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12026 - - - - NP_001257451 - RefSeq - - - - ENST00000375559 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10068 - - - - - - 5154 - NCBI Gene - - - - ENSG00000055130 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5787 - - - - MED31 - HGNC Symbol - - - - AVP - HGNC Symbol - - - - EQUAL - 2 - - - - - - ANKR1_HUMAN - Ankyrin repeat domain-containing protein 1 - - - - - Reactome DB_ID: 561143 - http://www.reactome.org/biopax/46/48887#Protein13764 - ANKRD1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12362 - - - - NM_001039667 - RefSeq - - - - NP_057063 - RefSeq - - - - REACT_17313 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17313.1 - - - - 9282 - NCBI Gene - - - - - - - - - - - - - SREBF1A/1C/2:NF-Y:SP1:FDFT1 gene - - - - SREBP1A/1C/2:NF-Y:SP1:FDFT1 gene - Reactome DB_ID: 2426135 - http://www.reactome.org/biopax/46/48887#Complex5483 - - - - - - MOD_RES 61 61 Phosphoserine; by LATS1 and LATS2. - - - - 939184 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939184 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10152 - - - - ENSP00000264867 - Ensembl - - - - - - MOD_RES 1006 1006 Phosphoserine. - - - - - - UBA52(1-76) - ubiquitin (UBA52) - - - - - http://www.reactome.org/biopax/46/48887#Protein1045 - Reactome DB_ID: 939203 - UBA52 - - - - 4802 - NCBI Gene - - - - REACT_27103 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27103.3 - - - - ENSP00000383889 - Ensembl - - - - REACT_27403 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27403.2 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1104 - - - - REACT_1307 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1307.3 - - - - ENSG00000241119 - Ensembl - - - - Q16866 - UniProt - - - - HGNC:24824 - HGNC - - - - 7004 - NCBI Gene - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25582 - - - - Cardiac ankyrin repeat protein - CARP - HA1A2 - ANKRD1 - Cytokine-inducible gene C-193 protein - Cytokine-inducible nuclear protein - C193 - - - - - - - - - - - - - ANKR1_HUMAN - Ankyrin repeat domain-containing protein 1 - FUNCTION: May play an important role in endothelial cell activation. May act as a nuclear transcription factor that negatively regulates the expression of cardiac genes. Induction seems to be correlated with apoptotic cell death in hepatoma cells.SUBUNIT: Interacts with YBX1 (By similarity). Interacts with TTN/titin.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Mainly expressed in activated vascular endothelial cells. To a lower extent, also expressed in hepatoma cells.INDUCTION: By TNF, IL1A/interleukin-1 alpha and parthenolide.DISEASE: Total anomalous pulmonary venous return (TAPVR) [MIM:106700]: Rare congenital heart disease (CHD) in which the pulmonary veins fail to connect to the left atrium during cardiac development, draining instead into either the right atrium or one of its venous tributaries. This disease accounts for 1.5% of all CHDs and has a prevalence of approximately 1 out of 15'000 live births. Note=The disease may be caused by mutations affecting the gene represented in this entry.SIMILARITY: Contains 5 ANK repeats. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 56 - http://www.reactome.org/biopax/46/48887#SequenceSite9888 - - - - ENST00000371486 - Ensembl - - - - EQUAL - 788 - http://www.reactome.org/biopax/46/48887#SequenceSite12381 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10155 - - - - - - NP_148983 - RefSeq - - - - P48060 - UniProt - - - - Q9Y5B3 - UniProt - - - - REACT_5064 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5064.2 - - - - Q86X55 - UniProt - - - - 163844 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163844 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4774 - - - - - ENST00000344469 - Ensembl - - - - - - MOD_RES 271 271 Phosphoserine; by HIPK2. - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21703 - - - - 8106172 - Oude Elferink RP - Schinkel AH - van Deemter L - Ottenhoff R - van Roon MA - Groen AK - Wagenaar E - Mol CA - Smit JJ - van der Lugt NM - PubMed - Homozygous disruption of the murine mdr2 P-glycoprotein gene leads to a complete absence of phospholipid from bile and to liver disease. - Cell 75(3);451-62 - 1993 - - - - ENST00000296861 - Ensembl - - - - NM_005190 - RefSeq - - - - ENSG00000118260 - Ensembl - - - - MED30 - HGNC - - - - Golgi membrane - - - - - 7678732 - Comer, KA - Falany, CN - Falany, JL - Pubmed - Cloning and expression of human liver dehydroepiandrosterone sulphotransferase - Biochem J 289:233-40 - 1993 - - - - Q9BUH1 - UniProt - - - - - Vitamin D3 receptor-interacting protein complex 36 kDa component - MED4 - Mediator complex subunit 4 - Activator-recruited cofactor 36 kDa component - ARC36 - VDRIP - DRIP36 - TRAP/SMCC/PC2 subunit p36 subunit - - - - - - - - - - - - - - - - - - - - - - - - MED4_HUMAN - Mediator of RNA polymerase II transcription subunit 4 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9NPJ6-1; Sequence=Displayed; Name=2; IsoId=Q9NPJ6-2; Sequence=VSP_047072;SIMILARITY: Belongs to the Mediator complex subunit 4 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval831 - - - - - - CHEBI:23901 - ChEBI - - - - 18587630 - Peng, X - Zhang, Y - Li, R - Cao, JM - Qiang, B - Zhou, L - Hao, W - Yuan, J - Yue, J - Ding, JM - Pubmed - CLOCK/BMAL1 regulates human nocturnin transcription through binding to the E-box of nocturnin promoter - Mol Cell Biochem 317:169-77 - 2008 - - - - 9570564 - Campbell, EJ - Owen, CA - Pubmed - Angiotensin II generation at the cell surface of activated neutrophils: novel cathepsin G-mediated catalytic activity that is resistant to inhibition - J Immunol 160:1436-43 - 1998 - - - - - - Carbon dioxide - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule744 - Reactome DB_ID: 159751 - CO2 - - - - 159758 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159758 - - - - HGNC:2500 - HGNC - - - - EQUAL - 363 - - - - - - MOD_RES 670 670 Phosphoserine; by PKC/PRKCZ. - - - - RPS27A - HGNC - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite4649 - - - - NM_001190438 - RefSeq - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein5490 - Reactome DB_ID: 141412 - CDC20 - - - - - - MOD_RES 1033 1033 Phosphoserine. - - - - Q6GTH7 - UniProt - - - - Q96AD4 - UniProt - - - - - - - - - INHIBITION - - 'ramiprilat [extracellular region]' negatively regulates 'Secreted ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control312 - - - - - - Mediator of RNA polymerase II transcription subunit 29 - MED29_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6497 - Reactome DB_ID: 556821 - MED29 - - - - SMARCD3 - HGNC Symbol - - - - REACT_161173 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161173.2 - - - - A8K3G6 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5651 - - - - - - CUL1 - HGNC Symbol - - - - - - ANGT_HUMAN - AGT(34-42) - Ang-(1-9) - Angiotensin-(1-9) - - - - - Reactome DB_ID: 2022348 - http://www.reactome.org/biopax/46/48887#Protein12348 - AGT - - - - PPARG - HGNC - - - - NP_004255 - RefSeq - - - - - - MOD_RES 1560 1560 N6-acetyllysine; by autocatalysis. - - - - EQUAL - 46 - - - - ENST00000531439 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4770 - - - - - 612384 - omim - - - - ENST00000292035 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4781 - - - - MED13 - HGNC Symbol - - - - Q75MR8 - UniProt - - - - HGNC:7962 - HGNC - - - - EQUAL - 57 - http://www.reactome.org/biopax/46/48887#SequenceSite9999 - - - - NP_009220 - RefSeq - - - - 605667 - omim - - - - - - - - - - - - - - - - - Recruitment of Corepressors by PPARA:RXRA Heterodimer - Edited: May, B, 2009-06-08 - Edited: May, B, 2009-05-30 16:45:51 - In the absence of activating ligands of PPAR-alpha, the PPAR-alpha:RXR-alpha heterodimers recruit corepressors NCoR1, NCoR2(SMRT), and histone deacetylases (HDACs) to genes regulated by PPAR-alpha. The corepressors maintain chromatin at the gene in an inactive conformation and prevent expression of the gene. - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4674 - Authored: May, B, 2009-05-30 16:45:51 - - - - - EQUAL - 43 - http://www.reactome.org/biopax/46/48887#SequenceSite21733 - - - - Q4QZ40 - UniProt - - - - NP_001257450 - RefSeq - - - - - - MOD_RES 1741 1741 N6-acetyllysine. - - - - 11502696 - Richard, V - Thuillez, C - Lallemand, F - Scalbert, E - Ferry, G - Bessou, JP - Hurel-Merle, S - Pubmed - Functional evidence for a role of vascular chymase in the production of angiotensin II in isolated human arteries - Circulation 104:750-2 - 2001 - - - - Q6IB57 - UniProt - - - - EQUAL - 100 - http://www.reactome.org/biopax/46/48887#SequenceSite8670 - - - - EQUAL - 551 - - - - 400190 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400190 - - - - REACT_27096 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27096.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4784 - - - - P04150 - UniProt - - - - EQUAL - 70 - http://www.reactome.org/biopax/46/48887#SequenceSite21685 - - - - Q9NZL6 - UniProt - - - - ENSP00000389326 - Ensembl - - - - EQUAL - 80 - http://www.reactome.org/biopax/46/48887#SequenceSite9870 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10791 - - - - - - NP_009223 - RefSeq - - - - ENSP00000256495 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4745 - - - - - - MOD_RES 301 301 N6-acetyllysine. - - - - 138297 - omim - - - - EQUAL - 939 - - - - NM_001033930 - RefSeq - - - - 1989805 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989805 - - - - ENST00000536365 - Ensembl - - - - EQUAL - 504 - http://www.reactome.org/biopax/46/48887#SequenceSite25553 - - - - 381447 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381447 - - - - - - MED4_HUMAN - - - - - Reactome DB_ID: 350263 - http://www.reactome.org/biopax/46/48887#Protein6492 - MED4 - - - - Q16855 - UniProt - - - - 9575 - NCBI Gene - - - - NPAS2 - HGNC Symbol - - - - REACT_147720 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147720.2 - - - - NP_001136060 - RefSeq - - - - EQUAL - 38 - http://www.reactome.org/biopax/46/48887#SequenceSite25518 - - - - ENST00000262367 - Ensembl - - - - - - MOD_RES 680 680 Phosphothreonine (By similarity). - - - - Q9UGC8 - UniProt - - - - D3DX31 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12055 - - - - - - ENST00000225728 - Ensembl - - - - - - MOD_RES 668 668 Phosphothreonine. - - - - - - - - - - Retinoid X receptor alpha - RXRA - Nuclear receptor subfamily 2 group B member 1 - NR2B1 - - - - - - - - - - - - - - - - - - RXRA_HUMAN - Retinoic acid receptor RXR-alpha - FUNCTION: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. The high affinity ligand for RXRs is 9-cis retinoic acid. RXRA serves as a common heterodimeric partner for a number of nuclear receptors. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, the RXR-RAR heterodimers associate with a multiprotein complex containing transcription corepressors that induce histone acetylation, chromatin condensation and transcriptional suppression. On ligand binding, the corepressors dissociate from the receptors and associate with the coactivators leading to transcriptional activation. The RXRA/PPARA heterodimer is required for PPARA transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes.SUBUNIT: Homodimer. Heterodimer with RARA; required for ligand- dependent retinoic acid receptor transcriptional activity. Heterodimer with PPARA (via the leucine-like zipper in the LBD); the interaction is required for PPARA transcriptional activity. Also heterodimerizes with PPARG. Interacts with NCOA3 and NCOA6 coactivators. Interacts with FAM120B (By similarity). Interacts with PELP1, SENP6, SFPQ, DNTTIP2 and RNF8. Interacts (via the DNA binding domain) with HCV core protein; the interaction enhances the transcriptional activities of the RXRA/RARA and the RXRA/PPARA heterodimers. Interacts with PRMT2. Interacts with ASXL1 and NCOA1 (By similarity).SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Highly expressed in liver, also found in lung, kidney and heart.DOMAIN: Composed of three domains: a modulating N-terminal domain (AF1 domain), a DNA-binding domain and a C-terminal ligand-binding domain (AF2 domain).PTM: Phosphorylated on serine and threonine residues mainly in the N-terminal modulating domain. Constiutively phosphorylated on Ser- 21 in the presence or absence of ligand. Under stress conditions, hyperphosphorylated by activated JNK on Ser-56, Ser-70, Thr-82 and Ser-260 (By similarity). Phosphorylated on Ser-27, in vitro, by PKA. This phosphorylation is required for repression of cAMP- mediated transcriptional activity of RARA.PTM: Sumoylation negatively regulates transcriptional activity. Desumoylated specifically by SENP6.SIMILARITY: Belongs to the nuclear hormone receptor family. NR2 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rxra/";WEB RESOURCE: Name=Wikipedia; Note=Retinoid X receptor entry; URL="http://en.wikipedia.org/wiki/Retinoid_X_receptor"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - Mediator of RNA polymerase II transcription subunit 26 - MED26_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6473 - Reactome DB_ID: 556783 - MED26 - - - - REACT_26725 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26725.2 - - - - - - ubiquitin (UBB 2) - - - - - Reactome DB_ID: 939213 - http://www.reactome.org/biopax/46/48887#Protein1047 - UBB(77-152) - - - - ENSG00000158874 - Ensembl - - - - MED12 - HGNC Symbol - - - - HELZ2 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite20008 - - - - REACT_5363 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5363.2 - - - - NM_001901 - RefSeq - - - - GO:0005789 - Gene Ontology - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite5765 - - - - - - MOD_RES 234 234 N6-acetyllysine. - - - - plasma membrane - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8349 - - - - ATP6AP2 - HGNC - - - - NM_018849 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12418 - - - - InChI=1S/O2/c1-2 - InChI - - - - - - MOD_RES 266 266 Phosphoserine; by MAPK (By similarity). - - - - NM_001166598 - RefSeq - - - - - - Neuronal PAS domain-containing protein 2, phosphorylated - NPAS2_HUMAN, phosphorylated - p-S-NPAS2 - - - - - - Reactome DB_ID: 421309 - http://www.reactome.org/biopax/46/48887#Protein11502 - p-NPAS2 - - - - EQUAL - 354 - - - - REACT_26571 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26571.2 - - - - - - MOD_RES 977 977 N6-acetyllysine. - - - - NP_003583 - RefSeq - - - - NP_001248375 - RefSeq - - - - 171060 - omim - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21471 - - - - 15917222 - Harper, JW - Ang, XL - Jin, J - Shirogane, T - Pubmed - SCFbeta-TRCP controls clock-dependent transcription via casein kinase 1-dependent degradation of the mammalian period-1 (Per1) protein - J Biol Chem 280:26863-72 - 2005 - - - - ENSG00000149485 - Ensembl - - - - NP_001885 - RefSeq - - - - - - MOD_RES 558 558 Phosphoserine; by DYRK1A and MAPK (By similarity). - - - - 11267664 - Elder, GH - Roberts, AG - Pubmed - Alternative splicing and tissue-specific transcription of human and rodent ubiquitous 5-aminolevulinate synthase (ALAS1) genes - Biochim Biophys Acta 1518:95-105 - 2001 - - - - 163827 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163827 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The APOA2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction145 - Reviewed: Kersten, S, 2009-06-08 - Expression of APOA2 - - - - 2539258 - Toyoshima, K - Horiuchi, R - Fukushige, S - Miyajima, N - Shibuya, Y - Yamamoto, T - Matsubara, K - Pubmed - Two erbA homologs encoding proteins with different T3 binding capacities are transcribed from opposite DNA strands of the same genetic locus - Cell 57:31-9 - 1989 - - - - CURLTUGMZLYLDI-UHFFFAOYSA-N - InChIKey - - - - EQUAL - 69 - - - - - - MOD_RES 867 867 Phosphoserine. - - - - 939258 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939258 - - - - - - Nuclear transcription factor Y subunit gamma - NFYC_HUMAN - NF-YC - - - - - Reactome DB_ID: 981546 - http://www.reactome.org/biopax/46/48887#Protein12432 - NFYC - - - - 134650 - omim - - - - 1801587 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1801587 - - - - 879796 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879796 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13187 - - - - REACT_3588 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3588.3 - - - - ENST00000265162 - Ensembl - - - - D3DQ97 - UniProt - - - - 517931 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=517931 - - - - NM_001037335 - RefSeq - - - - EQUAL - 86 - http://www.reactome.org/biopax/46/48887#SequenceSite9868 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21459 - - - - 205877 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=205877 - - - - - - MOD_RES 79 79 N6-acetyllysine (By similarity). - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10130 - - - - ENSG00000105835 - Ensembl - - - - - - MOD_RES 75 75 4-carboxyglutamate. - - - - - - - - - - - - - Formation of BMAL1:CLOCK/NPAS2 Heterodimer - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - BMAL1 (ARNTL), CLOCK, and NPAS2 are basic helix-loop-helix transcription factors. In humans BMAL1 has been demonstrated to form a heterodimer with CLOCK. In mouse, BMAL1 can form a heterodimer with either CLOCK or NPAS2. By analogy with other basic helix-loop-helix proteins the basic domain binds DNA, in this case the E-box motif, and the helix-loop-helix domains interact to form the heterodimer. BMAL1 and CLOCK/NPAS2 are codependently phosphorylated by unknown kinases after dimerization. The phosphorylation enhances transactivation activity and is inhibited by PER:CRY complexes. Both CLOCK and NPAS2 are expressed in the suprachiasmatic nucleus of the hypothalamus and act redundantly there. The tissue distributions of CLOCK and NPAS2 do not entirely overlap, however. For example, NPAS2 but not CLOCK is found in forebrain. - Reviewed: Hirota, T, 2010-06-23 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3853 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - NM_001248005 - RefSeq - - - - HGNC:1046 - HGNC - - - - REACT_148059 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148059.2 - - - - REACT_18205 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18205.1 - - - - ENSP00000385897 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5606 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4726 - - - - NM_021724 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14050 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite21650 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite23168 - - - - NP_443200 - RefSeq - - - - BTRC - HGNC Symbol - - - - 1989784 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989784 - - - - REACT_12694 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12694.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry2652 - - - - ENSP00000345822 - Ensembl - - - - - - ubiquitin (UBC 2) - - - - - Reactome DB_ID: 939164 - http://www.reactome.org/biopax/46/48887#Protein1050 - UBC(77-152) - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CTGF' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation82 - - - - - - phospho-Emi1(Ser 145, Ser 149) - - - - - - - Reactome DB_ID: 174207 - http://www.reactome.org/biopax/46/48887#Protein6079 - p-S145,S149-FBXO5 - - - - Q9UML0 - UniProt - - - - 1592223 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592223 - - - - 8145194 - pubchem-substance - - - - ENSP00000444039 - Ensembl - - - - NP_037534 - RefSeq - - - - HGNC:1581 - HGNC - - - - EQUAL - 163 - http://www.reactome.org/biopax/46/48887#SequenceSite21645 - - - - NM_001018077 - RefSeq - - - - ENST00000310955 - Ensembl - - - - NP_001018087 - RefSeq - - - - 2065357 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065357 - - - - NM_005481 - RefSeq - - - - 1989826 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989826 - - - - EQUAL - 310 - - - - EQUAL - 41 - http://www.reactome.org/biopax/46/48887#SequenceSite21739 - - - - ENSP00000356163 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10112 - - - - D3DP57 - UniProt - - - - Q53H06 - UniProt - - - - 376497 - NCBI Gene - - - - ENST00000323441 - Ensembl - - - - EQUAL - 649 - http://www.reactome.org/biopax/46/48887#SequenceSite25583 - - - - EQUAL - 366 - http://www.reactome.org/biopax/46/48887#SequenceSite25323 - - - - 10969042 - Donoghue, M - Gosselin, M - Jeyaseelan, R - Donovan, M - Baronas, E - Breitbart, RE - Godbout, K - Hsieh, F - Robison, K - Acton, S - Woolf, B - Stagliano, N - Pubmed - A novel angiotensin-converting enzyme-related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9 - Circ Res 87:E1-9 - 2000 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10026 - - - - HGNC:4910 - HGNC - - - - ENST00000403750 - Ensembl - - - - - - MOD_RES 66 66 4-carboxyglutamate. - - - - 300556 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10012 - - - - ENSP00000396620 - Ensembl - - - - ENSP00000356969 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12834 - - - - REACT_4121 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4121.2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25562 - - - - - - MOD_RES 588 588 Phosphothreonine (By similarity). - - - - 15767263 - Pohnert, SC - Akimoto, T - Zhang, M - Yan, Z - Williams, RS - Li, P - Rosenberg, PB - Gumbs, C - Pubmed - Exercise stimulates Pgc-1alpha transcription in skeletal muscle through activation of the p38 MAPK pathway - J Biol Chem 280:19587-93 - 2005 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12420 - - - - EQUAL - 56 - - - - 1989747 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989747 - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4956 - - - - - - - - - - - - - SCF-associated multiubiquitinated Emi1complexes - http://www.reactome.org/biopax/46/48887#Complex2831 - Reactome DB_ID: 174061 - - - - 556797 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556797 - - - - ENSG00000042429 - Ensembl - - - - EQUAL - 1786 - - - - ENST00000269814 - Ensembl - - - - - - MOD_RES 89 89 Phosphoserine. - - - - ENSP00000402971 - Ensembl - - - - 52649 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=52649 - - - - EQUAL - 616 - - - - - - MOD_RES 79 79 4-carboxyglutamate. - - - - 2022380 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022380 - - - - ENST00000382070 - Ensembl - - - - D3DX32 - UniProt - - - - REACT_115677 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115677.1 - - - - - - MOD_RES 402 402 4-hydroxyproline. - - - - NM_001204260 - RefSeq - - - - NM_003598 - RefSeq - - - - REACT_46 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_46.2 - - - - - SERPINA8 - AGT - Ang III - Angiotensin 3-8 - Ang I - Angiotensin-3 - Angiotensin-2 - Angiotensin-4 - Angiotensin 2-8 - Angiotensin-1 - Angiotensin 1-9 - Angiotensin I - Angiotensin 1-5 - Angiotensin 1-7 - Serpin A8 - Ang II - Angiotensin 1-8 - Angiotensin II - Angiotensin 1-10 - Angiotensin III - Angiotensin 1-4 - Des-Asp[1]-angiotensin II - Angiotensin IV - Ang IV - - - - - - - - - - - - - - - - ANGT_HUMAN - Angiotensinogen - FUNCTION: Essential component of the renin-angiotensin system (RAS), a potent regulator of blood pressure, body fluid and electrolyte homeostasis.FUNCTION: Angiotensin-2: acts directly on vascular smooth muscle as a potent vasoconstrictor, affects cardiac contractility and heart rate through its action on the sympathetic nervous system, and alters renal sodium and water absorption through its ability to stimulate the zona glomerulosa cells of the adrenal cortex to synthesize and secrete aldosterone.FUNCTION: Angiotensin-3: stimulates aldosterone release.FUNCTION: Angiotensin 1-7: is a ligand for the G-protein coupled receptor MAS1 (By similarity). Has vasodilator and antidiuretic effects (By similarity). Has an antithrombotic effect that involves MAS1-mediated release of nitric oxide from platelets (By similarity).SUBUNIT: During pregnancy, exists as a disulfide-linked 2:2 heterotetramer with the proform of PRG2 and as a complex (probably a 2:2:2 heterohexamer) with pro-PRG2 and C3dg.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Expressed by the liver and secreted in plasma.PTM: Beta-decarboxylation of Asp-34 in angiotensin-2, by mononuclear leukocytes produces alanine. The resulting peptide form, angiotensin-A, has the same affinity for the AT1 receptor as angiotensin-2, but a higher affinity for the AT2 receptor.PTM: In response to low blood pressure, the enzyme renin/REN cleaves angiotensinogen to produce angiotensin-1. Angiotensin-1 is a substrate of ACE (angiotensin converting enzyme) that removes a dipeptide to yield the physiologically active peptide angiotensin- 2. Angiotensin-1 and angiotensin-2 can be further processed to generate angiotensin-3, angiotensin-4. Angiotensin 1-9 is cleaved from angiotensin-1 by ACE2 and can be further processed by ACE to produce angiotensin 1-7, angiotensin 1-5 and angiotensin 1-4. Angiotensin 1-7 has also been proposed to be cleaved from angiotensin-2 by ACE2 or from angiotensin-1 by MME (neprilysin).PTM: The disulfide bond is labile. Angiotensinogen is present in the circulation in a near 40:60 ratio with the oxidized disulfide- bonded form, which preferentially interacts with receptor-bound renin.DISEASE: Essential hypertension (EHT) [MIM:145500]: A condition in which blood pressure is consistently higher than normal with no identifiable cause. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Renal tubular dysgenesis (RTD) [MIM:267430]: Autosomal recessive severe disorder of renal tubular development characterized by persistent fetal anuria and perinatal death, probably due to pulmonary hypoplasia from early-onset oligohydramnios (the Potter phenotype). Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the serpin family.CAUTION: It is uncertain whether Met-1 or Met-10 is the initiator.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/AGT";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=AGT";WEB RESOURCE: Name=Wikipedia; Note=Angiotensin entry; URL="http://en.wikipedia.org/wiki/Angiotensin"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 84 84 Phosphotyrosine (By similarity). - - - - - - MOD_RES 70 70 4-carboxyglutamate. - - - - 1989804 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989804 - - - - F2 - HGNC - - - - - - - - - - - - - - - - - - - - pro-protein C, uncarboxylated + 8 CO2 + 8 O2 + 8 vitamin K hydroquinone -> pro-protein C + 8 H2O + 8 vitamin K epoxide - At the beginning of this reaction, 8 molecules of 'Oxygen', 8 molecules of 'vitamin K hydroquinone', 8 molecules of 'CO2', and 1 molecule of 'pro-protein C, uncarboxylated' are present. At the end of this reaction, 8 molecules of 'H2O', 8 molecules of 'vitamin K epoxide', and 1 molecule of 'pro-protein C' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3888 - - - - - - - HGNC:12468 - HGNC - - - - REACT_115953 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115953.1 - - - - HMGCR - HGNC - - - - EQUAL - 179 - http://www.reactome.org/biopax/46/48887#SequenceSite21702 - - - - NP_963849 - RefSeq - - - - - - carnitine O-palmitoyltransferase 2 - - - - - Reactome DB_ID: 200994 - http://www.reactome.org/biopax/46/48887#Protein13729 - CPT2 - - - - B2RMN5 - UniProt - - - - EQUAL - 303 - http://www.reactome.org/biopax/46/48887#SequenceSite23017 - - - - ENSP00000381963 - Ensembl - - - - - - MOD_RES 1321 1321 Phosphothreonine. - - - - ENST00000373842 - Ensembl - - - - 10731415 - Turunen, M - Gonzalez, FJ - Peters, JM - Schedin, S - Dallner, G - Pubmed - Influence of peroxisome proliferator-activated receptor alpha on ubiquinone biosynthesis - J Mol Biol 297:607-14 - 2000 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12006 - - - - - - MOD_RES 771 771 Phosphoserine (By similarity). - - - - Q7Z715 - UniProt - - - - HGNC:10258 - HGNC - - - - Q9H0J2 - UniProt - - - - A0AV01 - UniProt - - - - EQUAL - 82 - - - - NP_851397 - RefSeq - - - - - - MOD_RES 1479 1479 Phosphoserine. - - - - EQUAL - 103 - - - - ENSG00000134107 - Ensembl - - - - EQUAL - 113 - http://www.reactome.org/biopax/46/48887#SequenceSite10051 - - - - EQUAL - 1583 - - - - REACT_25321 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25321.1 - - - - A1A4S3 - UniProt - - - - A1L3Z2 - UniProt - - - - 151530 - omim - - - - ENST00000397015 - Ensembl - - - - lipid particle - - - - - NP_004821 - RefSeq - - - - APOA1 - HGNC - - - - ENSP00000290663 - Ensembl - - - - ENSP00000445836 - Ensembl - - - - REACT_115978 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115978.1 - - - - HGNC:2348 - HGNC - - - - EQUAL - 412 - http://www.reactome.org/biopax/46/48887#SequenceSite23007 - - - - ENSP00000441543 - Ensembl - - - - ENST00000327443 - Ensembl - - - - EQUAL - 1290 - http://www.reactome.org/biopax/46/48887#SequenceSite21452 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of APOA5' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation200 - - - - NFYA - HGNC Symbol - - - - REACT_27951 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27951.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2222 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5789 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9754 - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7592 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12952 - - - - - - MOD_RES 589 589 Phosphoserine; by GSK3-beta. - - - - NM_003078 - RefSeq - - - - EQUAL - 61 - http://www.reactome.org/biopax/46/48887#SequenceSite9681 - - - - ENSG00000183087 - Ensembl - - - - NFYB - HGNC - - - - NP_066307 - RefSeq - - - - REACT_19888 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19888.2 - - - - CHEBI:601027 - ChEBI - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite23014 - - - - 1989781 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989781 - - - - EQUAL - 26 - http://www.reactome.org/biopax/46/48887#SequenceSite25584 - - - - Q9GZV5 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12000 - - - - - - - - - - Reactome DB_ID: 1253322 - http://www.reactome.org/biopax/46/48887#Protein2833 - YAP1 - - - - - - Myocyte-specific enhancer factor 2C - MEFC_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein2602 - Reactome DB_ID: 199938 - MEF2C - - - - EQUAL - 67 - - - - - - ubiquitin (UBB 3) - - - - - Reactome DB_ID: 939230 - http://www.reactome.org/biopax/46/48887#Protein1048 - UBB(153-228) - - - - NP_001001683 - RefSeq - - - - REACT_27051 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27051.3 - - - - A4D7U5 - UniProt - - - - 113595 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113595 - - - - 1368175 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368175 - - - - EQUAL - 473 - http://www.reactome.org/biopax/46/48887#SequenceSite4906 - - - - A9IZ91 - UniProt - - - - - - MOD_RES 350 350 N6-acetyllysine (By similarity). - - - - 1989794 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989794 - - - - REACT_24880 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24880.2 - - - - - - - - - - Reactome DB_ID: 517830 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11540 - ub-p-PER1/2 - - - - ENSP00000352471 - Ensembl - - - - HGNC:7805 - HGNC - - - - REACT_27768 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27768.2 - - - - - C19H20N2O3S - (+-)-5-((4-(2-(5-ethyl-2-pyridinyl)ethoxy)phenyl)methyl)-2,4-thiazolidinedione - 5-{4-[2-(5-ethylpyridin-2-yl)ethoxy]benzyl}-1,3-thiazolidine-2,4-dione - Pioglitazone - - - - - 356.4398 - pioglitazone - pioglitazone - - - - Q3LIG1 - UniProt - - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction148 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The CYP1A1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of CYP1A1 - - - - 4330891 - Wolff, HP - Dahlheim, H - Weber, P - Rosenthal, J - Pubmed - Enzyme kinetic studies on human renin and its purified homologous substrate - Am J Physiol 221:1292-6 - 1971 - - - - 879834 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879834 - - - - EQUAL - 1185 - - - - Q8TDE4 - UniProt - - - - - - MOD_RES 57 57 4-carboxyglutamate. - - - - NM_001261445 - RefSeq - - - - EQUAL - 61 - http://www.reactome.org/biopax/46/48887#SequenceSite9915 - - - - ENSP00000408149 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5792 - - - - - - - - - - - - - - NF-Y - http://www.reactome.org/biopax/46/48887#Complex5130 - Reactome DB_ID: 381204 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5603 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5611 - - - - ENST00000394127 - Ensembl - - - - MOD_RES Phosphothreonine - - - - - - MOD_RES 873 873 Phosphoserine. - - - - 2908 - NCBI Gene - - - - Q15305 - UniProt - - - - NP_005509 - RefSeq - - - - 1LYB - PROTEIN DATA BANK - - - - B4DW63 - UniProt - - - - EQUAL - 80 - http://www.reactome.org/biopax/46/48887#SequenceSite21688 - - - - NM_003333 - RefSeq - - - - Q16358 - UniProt - - - - EQUAL - 34 - http://www.reactome.org/biopax/46/48887#SequenceSite22994 - - - - - C20H32O2 - ARA - AA - (5Z,8Z,11Z,14Z)-5,8,11,14-icosatetraenoic acid - cis-Delta(5,8,11,14)-eicosatetraenoic acid - (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoic acid - all-cis-5,8,11,14-eicosatetraenoic acid - Arachidonsaeure - - - - - - - - 304.4669 - arachidonic acid - arachidonic acid - A C<smallsub>20</smallsub>, polyunsaturated fatty acid having four (<stereo>Z</stereo>)-double bonds at positions 5, 8, 11 and 14. - - - - O00710 - UniProt - - - - Q9UQ45 - UniProt - - - - O76072 - UniProt - - - - Q5JUY4 - UniProt - - - - REACT_2045 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2045.3 - - - - REACT_4414 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4414.4 - - - - ENSP00000371988 - Ensembl - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction161 - Edited: May, B, 2011-11-08 - The Adipophilin (PLIN2) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - Expression of PLIN2 - - - - 2274 - NCBI Gene - - - - cytosol - - - - - NM_000688 - RefSeq - - - - - - - - - - - - Edited: May, B, 2011-06-22 - http://www.reactome.org/biopax/46/48887#TemplateReaction73 - The PPARGC1A (PGC-1alpha) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. PPARGC1A protein is located in the nucleus where it coactivates transcription. - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - Expression of PPARGC1A (PGC-1alpha) - - - - 10498 - NCBI Gene - - - - 11533194 - pubchem-substance - - - - ENSP00000282441 - Ensembl - - - - NP_001018661 - RefSeq - - - - NM_015335 - RefSeq - - - - - - - - - - SREBF1 - BHLHD1 - SREBP1 - Processed sterol regulatory element-binding protein 1 - bHLHd1 - Class D basic helix-loop-helix protein 1 - SREBP-1 - Sterol regulatory element-binding transcription factor 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - SRBP1_HUMAN - Sterol regulatory element-binding protein 1 - FUNCTION: Transcriptional activator required for lipid homeostasis. Regulates transcription of the LDL receptor gene as well as the fatty acid and to a lesser degree the cholesterol synthesis pathway (By similarity). Binds to the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3'). Has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').SUBUNIT: Forms a tight complex with SCAP in the ER membrane. Efficient DNA binding of the soluble transcription factor fragment requires dimerization with another bHLH protein. Interacts with LMNA.SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein. Cytoplasmic vesicle, COPII-coated vesicle membrane; Multi-pass membrane protein. Note=Moves from the endoplasmic reticulum to the Golgi in the absence of sterols.SUBCELLULAR LOCATION: Processed sterol regulatory element-binding protein 1: Nucleus.SUBCELLULAR LOCATION: Isoform SREBP-1aDelta: Nucleus.SUBCELLULAR LOCATION: Isoform SREBP-1cDelta: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Comment=Additional isoforms seem to exist; Name=SREBP-1A; IsoId=P36956-1; Sequence=Displayed; Name=SREBP-1B; IsoId=P36956-2; Sequence=VSP_002150; Name=SREBP-1C; IsoId=P36956-3; Sequence=VSP_002149, VSP_002150; Note=Predominantly expressed in liver and adipose tissues; Name=4; IsoId=P36956-4; Sequence=VSP_030859; Note=No experimental confirmation available; Name=SREBP-1aDelta; IsoId=P36956-5; Sequence=VSP_047598, VSP_047599; Note=The absence of Golgi proteolytic processing requirement makes this isoform constitutively active in transactivation of lipogenic gene promoters; Name=SREBP-1cDelta; IsoId=P36956-6; Sequence=VSP_002149, VSP_047598, VSP_047599; Note=The absence of Golgi proteolytic processing requirement makes this isoform constitutively active in transactivation of lipogenic gene promoters;TISSUE SPECIFICITY: Expressed in a wide variety of tissues, most abundant in liver and adrenal gland. In fetal tissues lung and liver shows highest expression. Isoform SREBP-1C predominates in liver, adrenal gland and ovary, whereas isoform SREBP-1A predominates in hepatoma cell lines. Isoform SREBP-1A and isoform SREBP-1C are found in kidney, brain, white fat, and muscle.PTM: At low cholesterol the SCAP/SREBP complex is recruited into COPII vesicles for export from the ER. In the Golgi complex SREBPs are cleaved sequentially by site-1 and site-2 protease. The first cleavage by site-1 protease occurs within the luminal loop, the second cleavage by site-2 protease occurs within the first transmembrane domain and releases the transcription factor from the Golgi membrane. Apoptosis triggers cleavage by the cysteine proteases caspase-3 and caspase-7.PTM: Phosphorylated by AMPK, leading to suppress protein processing and nuclear translocation, and repress target gene expression. Phosphorylation at Ser-402 by SIK1 represses activity possibly by inhibiting DNA-binding (By similarity).SIMILARITY: Belongs to the SREBP family.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SEQUENCE CAUTION: Sequence=AAB28522.2; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAD92846.1; Type=Miscellaneous discrepancy; Note=Intron retention;WEB RESOURCE: Name=Wikipedia; Note=Sterol regulatory element- binding protein entry; URL="http://en.wikipedia.org/wiki/Sterol_regulatory_element_binding_protein"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 57 - - - - EQUAL - 48 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite20834 - - - - SMARCD3 - HGNC - - - - Q14CD2 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10006 - - - - ACSL1 - HGNC Symbol - - - - EQUAL - 824 - http://www.reactome.org/biopax/46/48887#SequenceSite21424 - - - - NP_996560 - RefSeq - - - - ENSP00000430014 - Ensembl - - - - ENST00000288599 - Ensembl - - - - NP_000497 - RefSeq - - - - ENSP00000358414 - Ensembl - - - - HGNC:8800 - HGNC - - - - - - p-S-CRY1 - Phosphorylated Cryptochrome-1 - CRY1_HUMAN - - - - - - http://www.reactome.org/biopax/46/48887#Protein11522 - Reactome DB_ID: 400270 - p-CRY1 - - - - EQUAL - 204 - - - - EQUAL - 1977 - - - - 2033 - NCBI Gene - - - - ENST00000396441 - Ensembl - - - - YAP1 - HGNC - - - - EQUAL - 1269 - - - - ENSP00000429961 - Ensembl - - - - A8K6U6 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1811 - - - - - - REACT_26721 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26721.1 - - - - 400139 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400139 - - - - REACT_148411 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148411.1 - - - - Q9H8C0 - UniProt - - - - HGNC:1144 - HGNC - - - - NP_001132938 - RefSeq - - - - ENSP00000399402 - Ensembl - - - - REACT_24941 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24941.3 - - - - CHEBI:24541 - ChEBI - - - - ENST00000359492 - Ensembl - - - - O43793 - UniProt - - - - - - - - - - 60S ribosomal protein L40 - Ubiquitin A-52 residue ribosomal protein fusion product 1 - CEP52 - UBA52 - UBCEP2 - Ubiquitin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RL40_HUMAN - Ubiquitin-60S ribosomal protein L40 - FUNCTION: Ubiquitin: exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.FUNCTION: 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, and especially for cap-dependent translation of vesicular stomatitis virus mRNAs.SUBUNIT: Ribosomal protein L40 is part of the 60S ribosomal subunit (By similarity).SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).SUBCELLULAR LOCATION: 60S ribosomal protein L40: Cytoplasm (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: For a better understanding, features related to ubiquitin are only indicated for the first chain.SIMILARITY: In the N-terminal section; belongs to the ubiquitin family.SIMILARITY: In the C-terminal section; belongs to the ribosomal protein L40e family.SIMILARITY: Contains 1 ubiquitin-like domain.SEQUENCE CAUTION: Sequence=AAK31162.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_079107 - RefSeq - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - - Cathepsin Z (Cathepsin X) Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8) - - - - - - - Cathepsin Z (Cathepsin X) Hydrolyzes Angiotensin I to Yield Angiotensin II - Cathepsin Z (cathepsin X) hydrolyzes angiotensin-(1-10) (angiotensin I) to yield angiotensin-(1-8) (angiotensin II) (Nagler et al. 2010). - Authored: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4044 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - - - - - NP_001243021 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10045 - - - - - - 601112 - omim - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1775 - - - - 227500 - omim - - - - - - UDP-glucuronosyltransferase 1-9 - UD19_HUMAN - - - - - Reactome DB_ID: 400210 - http://www.reactome.org/biopax/46/48887#Protein13784 - UGT1A9 - - - - ENSP00000464810 - Ensembl - - - - NP_001005291 - RefSeq - - - - 159860 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159860 - - - - MOD_RES Sulfotyrosine (Potential) - - - - EQUAL - 61 - http://www.reactome.org/biopax/46/48887#SequenceSite21721 - - - - EQUAL - 609 - http://www.reactome.org/biopax/46/48887#SequenceSite1790 - - - - REACT_26816 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26816.3 - - - - - - MOD_RES 57 57 Phosphoserine (By similarity). - - - - EQUAL - 2069 - - - - 2022375 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022375 - - - - - - - 40S ribosomal protein S27a - UBA80 - Ubiquitin carboxyl extension protein 80 - RPS27A - Ubiquitin - UBCEP1 - - - - - - - - - - - - - - - - - - - - - - - RS27A_HUMAN - Ubiquitin-40S ribosomal protein S27a - FUNCTION: Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.FUNCTION: Ribosomal protein S27a is a component of the 40S subunit of the ribosome.SUBUNIT: Ribosomal protein S27a is part of the 40S ribosomal subunit (By similarity).SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: For a better understanding, features related to ubiquitin are only indicated for the first chain.SIMILARITY: In the N-terminal section; belongs to the ubiquitin family.SIMILARITY: In the C-terminal section; belongs to the ribosomal protein S27Ae family.SIMILARITY: Contains 1 ubiquitin-like domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 2022351 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022351 - - - - EQUAL - 123 - - - - 3EGI - PROTEIN DATA BANK - - - - RGL1 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5643 - - - - - - NP_001243591 - RefSeq - - - - Q06766 - UniProt - - - - NP_000303 - RefSeq - - - - 421287 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421287 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12070 - - - - - - ENSP00000216336 - Ensembl - - - - - - MOD_RES 142 142 Phosphoserine; by CaMK2 (By similarity). - - - - PEX11A - HGNC - - - - EQUAL - 246 - http://www.reactome.org/biopax/46/48887#SequenceSite12369 - - - - - - MOD_RES 1546 1546 N6-acetyllysine. - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of DEC1 (BHLHE40, BHLHB2)' - BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind E-boxes in the promoter of the DEC1 (BHLHE40, BHLHB2) gene and activate transcription of DEC1. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation93 - - - - NM_013261 - RefSeq - - - - ENST00000310638 - Ensembl - - - - ENSP00000378488 - Ensembl - - - - 16267379 - Guillaumond, F - Cermakian, N - Giguère, V - Dardente, H - Pubmed - Differential control of Bmal1 circadian transcription by REV-ERB and ROR nuclear receptors - J Biol Rhythms 20:391-403 - 2005 - - - - EQUAL - 203 - - - - Q8TAK9 - UniProt - - - - 7981125 - McDonnell, DP - Mukherjee, R - Noonan, D - Jow, L - Pubmed - Human and rat peroxisome proliferator activated receptors (PPARs) demonstrate similar tissue distribution but different responsiveness to PPAR activators - J Steroid Biochem Mol Biol 51:157-66 - 1994 - - - - 5972 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4679 - - - - - - NP_620693 - RefSeq - - - - ENSP00000272190 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2113 - - - - B2RTU2 - UniProt - - - - Q9BR49 - UniProt - - - - REACT_117941 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117941.1 - - - - 400150 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400150 - - - - A0AV35 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5630 - - - - NM_014071 - RefSeq - - - - ENSG00000157184 - Ensembl - - - - REACT_19482 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19482.3 - - - - REACT_26150 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26150.2 - - - - 199447 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=199447 - - - - ENSG00000132170 - Ensembl - - - - REACT_118004 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118004.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8331 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry2653 - - - - EQUAL - 400 - http://www.reactome.org/biopax/46/48887#SequenceSite21712 - - - - 2028287 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2028287 - - - - REACT_111118 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111118.3 - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12970 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10029 - - - - - - MOD_RES 59 59 Phosphoserine. - - - - MEF2D - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10059 - - - - - - - - - - - - - - pro-factor X - http://www.reactome.org/biopax/46/48887#Complex5016 - Reactome DB_ID: 159744 - - - - Q96IY4 - UniProt - - - - - - MOD_RES 9 9 Nitrated tyrosine (By similarity). - - - - Q16093 - UniProt - - - - 400230 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400230 - - - - EQUAL - 51 - http://www.reactome.org/biopax/46/48887#SequenceSite21678 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10123 - - - - REACT_25143 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25143.1 - - - - ENST00000526691 - Ensembl - - - - ENSP00000350846 - Ensembl - - - - - 12.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12927 - - - - 18006707 - Szwergold, NR - Curtin, JC - Lazar, MA - Reid, RA - Qatanani, M - Wu, N - Pearce, KH - Parks, DJ - Wisely, GB - Yin, L - Waitt, GM - Pubmed - Rev-erbalpha, a heme sensor that coordinates metabolic and circadian pathways - Science 318:1786-9 - 2007 - - - - F8W7V7 - UniProt - - - - RXRA - HGNC Symbol - - - - - - MOD_RES 1144 1144 Phosphoserine. - - - - ENSG00000148297 - Ensembl - - - - EQUAL - 798 - http://www.reactome.org/biopax/46/48887#SequenceSite21494 - - - - EQUAL - 1586 - - - - ENSP00000441257 - Ensembl - - - - Q9NSY9 - UniProt - - - - - - MOD_RES 2184 2184 Phosphoserine. - - - - EQUAL - 74 - - - - 108330 - omim - - - - - - SREBF1C cleaved by S2P - SRBP1_HUMAN - SREBF1C(1-466) - Sterol regulatory element-binding protein 1C - SREBP1C(1-466) - - - - - http://www.reactome.org/biopax/46/48887#Protein13771 - Reactome DB_ID: 1655716 - SREBF1-3 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12354 - - - - HGNC:22962 - HGNC - - - - Q6IBJ6 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10187 - - - - - - Q9UKT4 - UniProt - - - - Q9HD39 - UniProt - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1275 - - - - Q6VBP5 - UniProt - - - - 603810 - omim - - - - Q96BQ8 - UniProt - - - - 605042 - omim - - - - REACT_15625 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15625.3 - - - - ENSP00000295834 - Ensembl - - - - PGY3 - 3.6.3.44 - ATP-binding cassette sub-family B member 4 - MDR3 - P-glycoprotein 3 - ABCB4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MDR3_HUMAN - Multidrug resistance protein 3 - FUNCTION: Mediates ATP-dependent export of organic anions and drugs from the cytoplasm. Hydrolyzes ATP with low efficiency. Not capable of conferring drug resistance. Mediates the translocation of phosphatidylcholine across the canalicular membrane of the hepatocyte.CATALYTIC ACTIVITY: ATP + H(2)O + xenobiotic(In) = ADP + phosphate + xenobiotic(Out).SUBUNIT: Interacts with HAX1 (By similarity).SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P21439-1; Sequence=Displayed; Name=2; IsoId=P21439-2; Sequence=VSP_023263; Name=3; IsoId=P21439-3; Sequence=VSP_046258, VSP_023263; Note=No experimental confirmation available. Gene prediction based on EST data;DISEASE: Cholestasis, progressive familial intrahepatic, 3 (PFIC3) [MIM:602347]: A disorder characterized by early onset of cholestasis that progresses to hepatic fibrosis, cirrhosis, and end-stage liver disease before adulthood. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Cholestasis of pregnancy, intrahepatic 3 (ICP3) [MIM:614972]: A liver disorder of pregnancy. It presents during the second or, more commonly, the third trimester of pregnancy with intense pruritus which becomes more severe with advancing gestation and cholestasis. It causes fetal distress, spontaneous premature delivery and intrauterine death. Patients have spontaneous and progressive disappearance of cholestasis after delivery. Cholestasis results from abnormal biliary transport from the liver into the small intestine. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Gallbladder disease 1 (GBD1) [MIM:600803]: One of the major digestive diseases. Gallstones composed of cholesterol (cholelithiasis) are the common manifestations in western countries. Most people with gallstones, however, remain asymptomatic through their lifetimes. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the ABC transporter superfamily. ABCB family. Multidrug resistance exporter (TC 3.A.1.201) subfamily.SIMILARITY: Contains 2 ABC transmembrane type-1 domains.SIMILARITY: Contains 2 ABC transporter domains.SEQUENCE CAUTION: Sequence=CAA84542.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ABCB4";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/abcb4/";WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=P21439"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1248 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4965 - - - - - CHEBI:3283 - ChEBI - - - - Q8N8V7 - UniProt - - - - NM_002607 - RefSeq - - - - NM_001443 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4960 - - - - - - - pro-prothrombin (factor II) - - - - - http://www.reactome.org/biopax/46/48887#Protein11634 - Reactome DB_ID: 159739 - F2(25-622) - - - - - - Elongation of very long chain fatty acids protein 3 - - - - - Reactome DB_ID: 548785 - http://www.reactome.org/biopax/46/48887#Protein11516 - ELOVL3 - - - - FAKRSMQSSFJEIM-RQJHMYQMSA-N - InChIKey - - - - NP_068780 - RefSeq - - - - MOD_RES Phosphotyrosine (By similarity) - - - - EQUAL - 636 - - - - HGNC:11585 - HGNC - - - - Q68DN4 - UniProt - - - - ENSP00000377979 - Ensembl - - - - - - MOD_RES 1457 1457 Phosphothreonine; by MAPK1 or MAPK3. - - - - NCOA2 - HGNC Symbol - - - - - - - - - - - - ACTIVATION - - 'p-T69,T71-ATF2 [nucleoplasm]' positively regulates 'Expression of PPARGC1A (PGC-1alpha)' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation115 - As inferred from mouse, phosphorylated ATF2 binds the PGC-1alpha promoter and enhances expression (Cao et al. 2004, Akimoto et al. 2005, Wright et al. 2007, Akimoto et al. 2008). Intracellular calcium acting via p38 MAPK is believed to activate (phosphorylate) ATF2. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5632 - - - - - - EQUAL - 77 - - - - 1989785 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989785 - - - - 556779 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556779 - - - - MOD_RES Beta-decarboxylated aspartate - - - - ENST00000381527 - Ensembl - - - - Q5JVF1 - UniProt - - - - B1AKC2 - UniProt - - - - - - MOD_RES 832 832 Phosphoserine. - - - - - - MOD_RES 62 62 4-carboxyglutamate. - - - - CHEBI:25047 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11900 - - - - NM_001100816 - RefSeq - - - - Q99649 - UniProt - - - - 939870 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939870 - - - - EQUAL - 1038 - - - - HGNC:10477 - HGNC - - - - 83401 - NCBI Gene - - - - F10 - HGNC Symbol - - - - 939856 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939856 - - - - BHLHE41 - HGNC - - - - 12185597 - Liaudet-Coopman E - Vignon F - Glondu M - Berchem G - Garcia M - Gleizes M - Brouillet JP - PubMed - Cathepsin-D affects multiple tumor progression steps in vivo: proliferation, angiogenesis and apoptosis. - Oncogene 21(38);5951-5 - 2002 - - - - REACT_115946 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115946.1 - - - - NM_001178057 - RefSeq - - - - EQUAL - 684 - http://www.reactome.org/biopax/46/48887#SequenceSite4670 - - - - Q9UHL1 - UniProt - - - - 15130092 - Emmler, T - Schachtrup, C - Sandqvist, A - Bleck, B - Spener, F - Pubmed - Functional analysis of peroxisome-proliferator-responsive element motifs in genes of fatty acid-binding proteins - Biochem J 382:239-45 - 2004 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5666 - - - - - - Q53H68 - UniProt - - - - REACT_27325 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27325.3 - - - - HGNC:9958 - HGNC - - - - 556782 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556782 - - - - 14765176 - Sadler, JE - Pubmed - Medicine: K is for koagulation - Nature 427:493-4 - 2004 - - - - 11001805 - Boomsma C - Kuipers JR - Bartelds B - van der Leij FR - Huijkman NC - PubMed - Genomics of the human carnitine acyltransferase genes. - Mol Genet Metab 71(1-2);139-53 - - - - CHEBI:27432 - ChEBI - - - - REACT_12974 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12974.1 - - - - - - PRGC2_HUMAN - Peroxisome proliferator-activated receptor gamma coactivator 1-beta - - - - - http://www.reactome.org/biopax/46/48887#Protein13761 - Reactome DB_ID: 1592213 - PPARGC1B - - - - A7YET6 - UniProt - - - - - - MOD_RES 85 85 4-carboxyglutamate. - - - - EQUAL - 502 - http://www.reactome.org/biopax/46/48887#SequenceSite12373 - - - - REACT_111748 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111748.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite20060 - - - - A8KAA0 - UniProt - - - - 1989786 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989786 - - - - - - ubiquitin (UBB 3) - - - - - http://www.reactome.org/biopax/46/48887#Protein2476 - Reactome DB_ID: 939854 - UBB(153-228) - - - - - - MOD_RES 999 999 Phosphoserine. - - - - A6NIH2 - UniProt - - - - ENST00000492661 - Ensembl - - - - - - - - - - - - - - - - ROR-alpha:Coactivator - http://www.reactome.org/biopax/46/48887#Complex4974 - Reactome DB_ID: 1368124 - - - - Q9H9A1 - UniProt - - - - EQUAL - 2079 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4648 - - - - Q12834 - UniProt - - - - 5624 - NCBI Gene - - - - - - MOD_RES 1038 1038 Phosphoserine. - - - - 112950 - NCBI Gene - - - - NP_001138830 - RefSeq - - - - NP_001343 - RefSeq - - - - - - Cell division protein kinase 19 - CDK19_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6487 - Reactome DB_ID: 556782 - CDK19 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1836 - - - - Q4G136 - UniProt - - - - 2022398 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022398 - - - - ENST00000430215 - Ensembl - - - - CHEBI:41873 - ChEBI - - - - ENSP00000427672 - Ensembl - - - - EQUAL - 815 - - - - 400196 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400196 - - - - ENST00000394788 - Ensembl - - - - 14765195 - Chang, CY - Stafford, DW - Lin, PJ - Li, T - Jin, DY - Khvorova, A - Pubmed - Identification of the gene for vitamin K epoxide reductase - Nature 427:541-4 - 2004 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5669 - - - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The ACADM gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction139 - Reviewed: Kersten, S, 2009-06-08 - Expression of ACADM - - - - 14765194 - Muller, CR - Hortnagel, K - Strom, TM - Seifried, E - Scharrer, I - Rost, S - Pelz, HJ - Oldenburg, J - Fregin, A - Conzelmann, E - Lappegard, K - Ivaskevicius, V - Tuddenham, EG - Pubmed - Mutations in VKORC1 cause warfarin resistance and multiple coagulation factor deficiency type 2 - Nature 427:537-41 - 2004 - - - - NM_001130145 - RefSeq - - - - 2022384 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022384 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10022 - - - - 1655848 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655848 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8310 - - - - Q9UND7 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10804 - - - - - - 1989776 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989776 - - - - REACT_118042 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118042.3 - - - - 1989750 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989750 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7590 - - - - ENST00000422777 - Ensembl - - - - Q9ULK4 - UniProt - - - - EQUAL - 488 - http://www.reactome.org/biopax/46/48887#SequenceSite21655 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5600 - - - - ENSG00000100644 - Ensembl - - - - 939853 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939853 - - - - B0YJC8 - UniProt - - - - 1989796 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989796 - - - - 517935 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=517935 - - - - 10857746 - Hirose, M - Koike, N - Hida, A - Sakaki, Y - Hattori, M - Tei, H - Pubmed - The human and mouse Period1 genes: five well-conserved E-boxes additively contribute to the enhancement of mPer1 transcription - Genomics 65:224-33 - 2000 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10181 - - - - - - - - MOD_RES 1141 1141 Phosphoserine (By similarity). - - - - ENSG00000133997 - Ensembl - - - - Q01581 - UniProt - - - - - - CBPA3_HUMAN - Mast cell carboxypeptidase A - - - - - http://www.reactome.org/biopax/46/48887#Protein12357 - Reactome DB_ID: 2028289 - CPA3 - - - - EQUAL - 20 - http://www.reactome.org/biopax/46/48887#SequenceSite6430 - - - - A2I2N6 - UniProt - - - - EQUAL - 260 - - - - ENSP00000383981 - Ensembl - - - - NM_001093771 - RefSeq - - - - NM_198580 - RefSeq - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PPARA Activates Gene Expression - Authored: May, B, 2011-11-08 - The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include: <br>1) genes involved in fatty acid oxidation and ketogenesis (Acox1, Cyp4a, Acadm, Hmgcs2);<br>2) genes involved in fatty acid transport (Cd36, , Slc27a1, Fabp1, Cpt1a, Cpt2);<br>3) genes involved in producing fatty acids and very low density lipoproteins (Me1, Scd1);<br>4) genes encoding apolipoproteins (Apoa1, Apoa2, Apoa5);<br>5) genes involved in triglyceride clearance ( Angptl4);<br>6) genes involved in glycerol metabolism (Gpd1 in mouse);<br>7) genes involved in glucose metabolism (Pdk4);<br>8) genes involved in peroxisome proliferation (Pex11a);<br>9) genes involved in lipid storage (Plin, Adfp).<br>Many other genes are known to be regulated by PPAR-alpha but whether their regulation is direct or indirect remains to be found. These genes include: ACACA, FAS, SREBP1, FADS1, DGAT1, ABCA1, PLTP, ABCB4, UGT2B4, SULT2A1, Pnpla2, Acsl1, Slc27a4, many Acot genes, and others (reviewed in Rakhshandehroo et al. 2010). - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#Pathway1056 - - - - - REACT_17059 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17059.2 - - - - ACE2 - HGNC Symbol - - - - REACT_116136 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116136.1 - - - - HGNC:16617 - HGNC - - - - NP_061338 - RefSeq - - - - ENST00000596273 - Ensembl - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1765 - - - - Q9UD52 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5661 - - - - - - ENSP00000385216 - Ensembl - - - - EQUAL - 233 - http://www.reactome.org/biopax/46/48887#SequenceSite12389 - - - - REACT_117942 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117942.2 - - - - - - protein S propeptide - - - - - Reactome DB_ID: 159792 - http://www.reactome.org/biopax/46/48887#Protein11665 - PROS1(25-41) - - - - HDAC3 - HGNC Symbol - - - - Q4VXQ1 - UniProt - - - - - - MOD_RES 50 50 4-carboxyglutamate. - - - - HGNC:89 - HGNC - - - - REACT_118007 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118007.1 - - - - EAR-1 - NR1D1 - EAR1 - Rev-erbA-alpha - THRAL - V-erbA-related protein 1 - HREV - - - - - - - - - - - - - - - NR1D1_HUMAN - Nuclear receptor subfamily 1 group D member 1 - FUNCTION: Functions as a constitutive transcriptional repressor. In collaboration with SP1, activates GJA1 transcription (By similarity). Possible receptor for triiodothyronine.SUBUNIT: Interacts with C1D and NR2E3 (By similarity). Interacts with SP1 (By similarity).SUBCELLULAR LOCATION: Nucleus (Potential).TISSUE SPECIFICITY: Expressed in all tissues and cell lines examined. Expressed at high levels in some squamous carcinoma cell lines.DOMAIN: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - UBB - HGNC Symbol - - - - EQUAL - 36 - http://www.reactome.org/biopax/46/48887#SequenceSite23030 - - - - 1989812 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989812 - - - - ENST00000348332 - Ensembl - - - - - - - - - INHIBITION - - 'NR1D1 (REV-ERBA):heme:Corepressor [nucleoplasm]' negatively regulates 'Expression of CLOCK' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation87 - - - - NM_182743 - RefSeq - - - - 420931 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=420931 - - - - HGNC:500 - HGNC - - - - REACT_117985 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117985.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5585 - - - - - - EQUAL - 2649 - http://www.reactome.org/biopax/46/48887#SequenceSite12397 - - - - EQUAL - 63 - http://www.reactome.org/biopax/46/48887#SequenceSite9914 - - - - PTHR10625:SF59 - PANTHER Family - - - - - REACT_115878 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115878.1 - - - - - - - - - http://www.reactome.org/biopax/46/48887#Dna34 - Reactome DB_ID: 2393972 - HMGCS1 gene - - - - 549470 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549470 - - - - Q6P2C8 - UniProt - - - - FABP1 - HGNC Symbol - - - - EQUAL - 28 - http://www.reactome.org/biopax/46/48887#SequenceSite6431 - - - - EQUAL - 589 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21427 - - - - REACT_7621 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7621.1 - - - - 2159 - NCBI Gene - - - - EQUAL - 112 - - - - EQUAL - 1472 - - - - EQUAL - 2054 - - - - - - Transcriptional enhancer factor TEF-4 - - - - - Reactome DB_ID: 2032763 - http://www.reactome.org/biopax/46/48887#Protein11193 - TEAD2 - - - - REACT_1290 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1290.2 - - - - 23054 - NCBI Gene - - - - CREBBP - HGNC - - - - EQUAL - 530 - http://www.reactome.org/biopax/46/48887#SequenceSite25585 - - - - - - - - ACTIVATION - - 'Cl- [extracellular region]' positively regulates 'ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control305 - - - - EQUAL - 381 - http://www.reactome.org/biopax/46/48887#SequenceSite1784 - - - - - - PDGFA isoform 2 - Platelet-derived growth factor A chain precursor - - - - - Reactome DB_ID: 380742 - http://www.reactome.org/biopax/46/48887#Protein2632 - PDGFA-2 - - - - MED1 - HGNC Symbol - - - - - - MOD_RES 1147 1147 Phosphoserine (By similarity). - - - - - - - - - - - - INHIBITION - - 'enalaprilat [extracellular region]' negatively regulates 'Secreted ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control310 - - - - A2I2N9 - UniProt - - - - ENST00000395839 - Ensembl - - - - CMA1 - HGNC - - - - REACT_116437 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116437.4 - - - - Q8TAY2 - UniProt - - - - 2032783 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032783 - - - - O15516 - UniProt - - - - HGNC:8846 - HGNC - - - - EQUAL - 521 - http://www.reactome.org/biopax/46/48887#SequenceSite12228 - - - - 1989746 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989746 - - - - ENST00000567581 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1250 - - - - Q9NYR4 - UniProt - - - - 18775307 - Bass, J - Takahashi, JS - Green, CB - Pubmed - The meter of metabolism - Cell 134:728-42 - 2008 - - - - ENST00000295834 - Ensembl - - - - PTHR13844:SF0 - PANTHER Family - - - - - EQUAL - 670 - - - - 6822 - NCBI Gene - - - - 1I7G - PROTEIN DATA BANK - - - - - - MOD_RES 48 48 4-carboxyglutamate. - - - - ENST00000594882 - Ensembl - - - - ENST00000567032 - Ensembl - - - - EQUAL - 2 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of NPAS2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation88 - - - - REACT_118052 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118052.1 - - - - EQUAL - 533 - http://www.reactome.org/biopax/46/48887#SequenceSite1788 - - - - EQUAL - 33 - http://www.reactome.org/biopax/46/48887#SequenceSite21731 - - - - ENSP00000407183 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5660 - - - - - - PTHR11681:SF0 - PANTHER Family - - - - - ENST00000539743 - Ensembl - - - - 9691089 - Ruiter, JP - Gutman, A - Mandel, H - Oostheim, W - IJlst, L - Wanders, RJ - Pubmed - Molecular basis of hepatic carnitine palmitoyltransferase I deficiency - J Clin Invest 102:527-31 - 1998 - - - - EQUAL - 35 - http://www.reactome.org/biopax/46/48887#SequenceSite23026 - - - - Q99631 - UniProt - - - - REACT_148680 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148680.1 - - - - B2R6Z6 - UniProt - - - - 400154 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400154 - - - - MED6 - HGNC Symbol - - - - ENST00000524575 - Ensembl - - - - EQUAL - 331 - - - - NM_004380 - RefSeq - - - - REACT_3165 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3165.1 - - - - - - MOD_RES 117 117 Phosphoserine. - - - - ENST00000327064 - Ensembl - - - - EQUAL - 47 - http://www.reactome.org/biopax/46/48887#SequenceSite21676 - - - - NM_001429 - RefSeq - - - - NM_181054 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12064 - - - - - - O95821 - UniProt - - - - InChI=1S/C19H20N2O3S/c1-2-13-3-6-15(20-12-13)9-10-24-16-7-4-14(5-8-16)11-17-18(22)21-19(23)25-17/h3-8,12,17H,2,9-11H2,1H3,(H,21,22,23) - InChI - - - - REACT_26618 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26618.3 - - - - - - - - - - - - - - CRY:PER:Kinase - Reactome DB_ID: 421287 - http://www.reactome.org/biopax/46/48887#Complex4982 - - - - Q5VWA2 - UniProt - - - - EQUAL - 668 - - - - REACT_24310 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24310.2 - - - - REACT_118616 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118616.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12835 - - - - MED27 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4761 - - - - - - EQUAL - 75 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12830 - - - - 1592204 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592204 - - - - MED26 - HGNC Symbol - - - - EQUAL - 86 - - - - EQUAL - 1479 - - - - ENSG00000115966 - Ensembl - - - - EQUAL - 1542 - - - - ENSP00000231509 - Ensembl - - - - 159774 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159774 - - - - - - - - - - - - pro-protein C, uncarboxylated - Reactome DB_ID: 159852 - http://www.reactome.org/biopax/46/48887#Complex5014 - - - - 7896283 - Gellera C - Taroni F - Montermini L - Floridia G - Cavadini P - Zuffardi O - Verderio E - Finocchiaro G - PubMed - Assignment of the human carnitine palmitoyltransferase II gene (CPT1) to chromosome 1p32. - Genomics 24(1);195-7 - 1994 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10756 - - - - NP_001243588 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1057 - - - - NM_001204265 - RefSeq - - - - Q14DC3 - UniProt - - - - 8945 - NCBI Gene - - - - EQUAL - 551 - - - - 6720 - NCBI Gene - - - - Q5W142 - UniProt - - - - REACT_7808 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7808.1 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11533 - Converted from EntitySet in Reactome - Reactome DB_ID: 400237 - p-CRY1/2 - - - - 68524 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68524 - - - - 939871 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939871 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12019 - - - - HMGCS1 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12817 - - - - 6837 - NCBI Gene - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6484 - Reactome DB_ID: 212410 - MED10 - - - - REACT_148660 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148660.1 - - - - HGNC:19353 - HGNC - - - - REACT_26482 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26482.2 - - - - REACT_24503 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24503.2 - - - - 1592227 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592227 - - - - - - MOD_RES 1179 1179 Phosphothreonine. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1103 - - - - EQUAL - 238 - - - - C9JZV2 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14060 - - - - - - - - - - INHIBITION - - 'aliskiren [extracellular region]' negatively regulates 'Renin Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10)' - http://www.reactome.org/biopax/46/48887#Control300 - - - - - - MOD_RES 2026 2026 Phosphoserine. - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1306 - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry2650 - - - - NP_036586 - RefSeq - - - - 1LYW - PROTEIN DATA BANK - - - - Q9BTN5 - UniProt - - - - REACT_115967 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115967.1 - - - - PDGF subunit B - Proto-oncogene c-Sis - Becaplermin - SIS - PDGF2 - PDGFB - PDGF-2 - Platelet-derived growth factor beta polypeptide - Platelet-derived growth factor B chain - - - - - - - - - - - - - - - - - - - - - - PDGFB_HUMAN - Platelet-derived growth factor subunit B - FUNCTION: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).SUBUNIT: Homodimer; antiparallel disulfide-linked dimer. Heterodimer with PDGFA; antiparallel disulfide-linked dimer. The PDGFB homodimer interacts with PDGFRA and PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. The heterodimer composed of PDGFA and PDGFB interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. Interacts with XLKD1 (By similarity).SUBCELLULAR LOCATION: Secreted. Note=Released by platelets upon wounding.ALTERNATIVE PRODUCTS: Event=Alternative promoter usage; Named isoforms=2; Name=1; IsoId=P01127-1; Sequence=Displayed; Name=2; IsoId=P01127-2; Sequence=VSP_044913;TISSUE SPECIFICITY: Expressed at high levels in the heart, brain (sustantia nigra), placenta and fetal kidney. Expressed at moderate levels in the brain (hippocampus), skeletal muscle, kidney and lung.DISEASE: Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.PHARMACEUTICAL: Available under the name Regranex (Ortho-McNeil). Used to promote healing in diabetic neuropathic foot ulcers.SIMILARITY: Belongs to the PDGF/VEGF growth factor family.WEB RESOURCE: Name=R&D Systems' cytokine source book: PDGF; URL="http://www.rndsystems.com/molecule_detail.aspx?m=1967";WEB RESOURCE: Name=Regranex; Note=Clinical information on Regranex; URL="http://www.regranex.com/";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PDGFBID155.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 939863 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939863 - - - - EQUAL - 691 - http://www.reactome.org/biopax/46/48887#SequenceSite21714 - - - - ACOX1 - HGNC Symbol - - - - NM_016263 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1841 - - - - - - MOD_RES 499 499 N6-acetyllysine. - - - - EQUAL - 569 - - - - MED31 - Mediator complex subunit 31 - hSOH1 - SOH1 - Mediator complex subunit SOH1 - - - - - - - - - - - - - MED31_HUMAN - Mediator of RNA polymerase II transcription subunit 31 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 31 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_115721 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115721.1 - - - - Ramiprilat [PubChem Compound:5464096] - - Ramiprilat - http://www.reactome.org/biopax/46/48887#SmallMoleculeReference494 - - - - EQUAL - 681 - - - - 8553 - NCBI Gene - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8308 - - - - MOD_RES Dimethylated arginine (By similarity) - - - - REACT_3112 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3112.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14051 - - - - ENST00000415690 - Ensembl - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry2651 - - - - NP_001861 - RefSeq - - - - Q5T9K1 - UniProt - - - - - 13.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12967 - - - - ENST00000409807 - Ensembl - - - - HGNC:2378 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2095 - - - - ENSG00000175221 - Ensembl - - - - NP_001243589 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10005 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10801 - - - - - - ENST00000442744 - Ensembl - - - - Q56D06 - UniProt - - - - 1A7C - PROTEIN DATA BANK - - - - NM_001261446 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1774 - - - - KIAA0700 - SIN3B - Histone deacetylase complex subunit Sin3b - Transcriptional corepressor Sin3b - - - - - - - - - - - - - - - - - - - - - - SIN3B_HUMAN - Paired amphipathic helix protein Sin3b - FUNCTION: Acts as a transcriptional repressor. Interacts with MXI1 to repress MYC responsive genes and antagonize MYC oncogenic activities. Interacts with MAD-MAX heterodimers by binding to MAD. The heterodimer then represses transcription by tethering SIN3B to DNA. Also forms a complex with FOXK1 which represses transcription (By similarity).SUBUNIT: Interacts with FOXK1/MNF, MXI, MAD, NCOR1 and SAP30. Interaction with SUDS3 enhances the interaction with HDAC1 to form a complex. Interacts with MAD3, MAD4, MAEL, REST and SETDB1 (By similarity). Interacts with RNF220 (By similarity). Interacts with HCFC1.SUBCELLULAR LOCATION: Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=Long; IsoId=O75182-1; Sequence=Displayed; Note=No experimental confirmation available; Name=2; IsoId=O75182-2; Sequence=VSP_014186; Note=No experimental confirmation available; Name=3; IsoId=O75182-3; Sequence=VSP_014185; Note=No experimental confirmation available;PTM: Ubiquitinated by RNF220 that leads to proteasomal degradation (By similarity).SIMILARITY: Contains 3 PAH (paired amphipathic helix) domains.SEQUENCE CAUTION: Sequence=BAA31675.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14061 - - - - 351644 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=351644 - - - - EQUAL - 700 - - - - REACT_26034 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26034.3 - - - - REACT_25049 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25049.1 - - - - REACT_24088 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24088.2 - - - - EQUAL - 66 - http://www.reactome.org/biopax/46/48887#SequenceSite9884 - - - - Q9UDH5 - UniProt - - - - - C16H32O2 - CH3-[CH2]14-COOH - 1-Pentadecanecarboxylic acid - Hexaectylic acid - n-hexadecanoic acid - n-hexadecoic acid - hexadecanoic acid - Palmitinic acid - C16 fatty acid - Palmitinsaeure - hexadecoic acid - 1-hexyldecanoic acid - Hexadecylic acid - Palmitic acid - Pentadecanecarboxylic acid - cetylic acid - C16:0 - - - - - - - - - - - 256.4241 - palmitic acid - palmitic acid - A straight-chain, sixteen-carbon, saturated long-chain fatty acid. - - - - EQUAL - 1859 - - - - HGNC:3471 - HGNC - - - - NM_006540 - RefSeq - - - - HGNC:30021 - HGNC - - - - - - MOD_RES 36 36 Phosphoserine. - - - - NP_004220 - RefSeq - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1270 - - - - Q92811 - UniProt - - - - 1361 - NCBI GENE - - - - NP_003158 - RefSeq - - - - 212343 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212343 - - - - ENSP00000373506 - Ensembl - - - - NM_134260 - RefSeq - - - - 607000 - omim - - - - - - MED18_HUMAN - Mediator of RNA polymerase II transcription subunit 18 - - - - - http://www.reactome.org/biopax/46/48887#Protein6477 - Reactome DB_ID: 556826 - MED18 - - - - PEX11A - PEX11-alpha - HsPEX11p - Peroxisomal biogenesis factor 11A - PMP28 - Peroxin-11A - Protein PEX11 homolog alpha - 28 kDa peroxisomal integral membrane protein - PEX11 - - - - - - - - - - - - PX11A_HUMAN - Peroxisomal membrane protein 11A - FUNCTION: May be involved in peroxisomal proliferation and may regulate peroxisomes division. May mediate binding of coatomer proteins to the peroxisomal membrane.SUBUNIT: Probably interacts with COPB2 and COPA (By similarity). Interacts with PEX19.SUBCELLULAR LOCATION: Peroxisome membrane; Multi-pass membrane protein.PTM: Seems not to be N-glycosylated.SIMILARITY: Belongs to the peroxin-11 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 1312351 - Tan CP - Molowa DT - Chen WS - Cimis GM - PubMed - Transcriptional regulation of the human cholesterol 7 alpha-hydroxylase gene. - Biochemistry 31(9);2539-44 - 1992 - - - - REACT_160431 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160431.2 - - - - P07339 - UniProt - - - - InChI=1S/H2O/h1H2 - InChI - - - - 442501 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442501 - - - - 1856948 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1856948 - - - - B2RC40 - UniProt - - - - D6W5P3 - UniProt - - - - 381940 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381940 - - - - Q9UHV6 - UniProt - - - - - - Chymase - CMA1_HUMAN - - - - - Reactome DB_ID: 708327 - http://www.reactome.org/biopax/46/48887#Protein2761 - CMA1 - - - - 9606 - taxonomy - - - - Q96FQ4 - UniProt - - - - CCNC - HGNC Symbol - - - - REACT_160942 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160942.1 - - - - - - 12xCbxE-3D-F9(29-461) - - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11645 - Reactome DB_ID: 159726 - pro-factor IX - - - - EQUAL - 31 - http://www.reactome.org/biopax/46/48887#SequenceSite21713 - - - - REACT_17262 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17262.1 - - - - ENST00000236850 - Ensembl - - - - REACT_118050 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118050.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21463 - - - - REACT_115550 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115550.1 - - - - JAZBEHYOTPTENJ-JLNKQSITSA-N - InChIKey - - - - ME1 - HGNC Symbol - - - - ENSP00000357032 - Ensembl - - - - ENST00000393353 - Ensembl - - - - - ENPEP Hydrolyzes Angiotensin-(1-8) to Yield Angiotensin-(2-8) - - - - - - - ENPEP Hydrolyzes Angiotensin II to Yield Angiotensin III - Authored: May, B, 2011-11-19 - Aminopeptidase A (APA, ENPEP) hydrolyzes the N-terminal amino acid of angiotensin-(1-8) (angiotensin II) to yield angiotensin-(2-8) (angiotensin III) (Goto et al. 2006). The catalysis is more specific and efficient in the presence of calcium ions (Goto et al. 2006). - Edited: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4049 - Reviewed: Joseph, J, 2012-08-06 - - - - - 9572 - NCBI Gene - - - - Q6V963 - UniProt - - - - ENSG00000079459 - Ensembl - - - - EQUAL - 1179 - - - - ENST00000361204 - Ensembl - - - - 561165 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561165 - - - - ENST00000420607 - Ensembl - - - - 400253 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400253 - - - - NP_001001548 - RefSeq - - - - SREBF1 - HGNC - - - - ENSP00000396910 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12052 - - - - - - NP_647475 - RefSeq - - - - Q9UNQ1 - UniProt - - - - NM_004229 - RefSeq - - - - EQUAL - 1499 - - - - ENSP00000359022 - Ensembl - - - - ENSP00000337340 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12820 - - - - Q5T8J4 - UniProt - - - - 16380219 - Dean, NM - Koo, S - Kang, X - Kim, Y - White, N - Marcusson, EG - Perera, RJ - Pubmed - Identification of novel PPARgamma target genes in primary human adipocytes - Gene 369:90-9 - 2006 - - - - ENSG00000115641 - Ensembl - - - - HGNC:7895 - HGNC - - - - TBL1XR1 - HGNC Symbol - - - - Q9BW56 - UniProt - - - - - - MOD_RES 395 395 Phosphoserine. - - - - - - MOD_RES 71 71 Phosphoserine; by AMPK (By similarity). - - - - NP_001902 - RefSeq - - - - - - MOD_RES 274 274 Phosphoserine. - - - - REACT_148012 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148012.1 - - - - - - - - - - - ACTIVATION - - 'ROR-alpha:Coactivator [nucleoplasm]' positively regulates 'Expression of BMAL1 (ARNTL).' - Activation of BMAL1 (ARNTL) expression by ROR-alpha (RORA) is inferred from mouse. In mouse Rora together with coactivators Ep300 and Ppargc1a bind the promoter of Bmal1 and activate transcription. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation85 - - - - 8144345 - pubchem-substance - - - - 2032788 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032788 - - - - - - MOD_RES 123 123 (3R)-3-hydroxyaspartate. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2618 - - - - - - DBP - HGNC Symbol - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5280 - - - - P43490 - UniProt - - - - Q9Y5U0 - UniProt - - - - PROC - HGNC Symbol - - - - HGNC:3544 - HGNC - - - - REACT_147882 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147882.2 - - - - NP_001862 - RefSeq - - - - NM_002130 - RefSeq - - - - MED8 - HGNC - - - - Q8IVF5 - UniProt - - - - REACT_3818 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3818.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10077 - - - - - - 1655744 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655744 - - - - D3DTR3 - UniProt - - - - NM_001135592 - RefSeq - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1276 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10137 - - - - - - MOD_RES 383 383 Phosphoserine. - - - - ENSP00000379718 - Ensembl - - - - NP_001018085 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21445 - - - - REACT_115533 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115533.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4643 - - - - PTHR24278:SF2 - PANTHER Family - - - - - 19289416 - Hostetler, HA - Kier, AB - Storey, SM - McIntosh, AL - Atshaves, BP - Schroeder, F - Payne, HR - Pubmed - L-FABP directly interacts with PPARalpha in cultured primary hepatocytes - J Lipid Res 50:1663-75 - 2009 - - - - - - Apo-AI - APOA1 - Truncated apolipoprotein A-I - Apolipoprotein A-I(1-242) - ApoA-I - Apolipoprotein A1 - - - - - - - - - - - - - - - - - - - - - - - - APOA1_HUMAN - Apolipoprotein A-I - FUNCTION: Participates in the reverse transport of cholesterol from tissues to the liver for excretion by promoting cholesterol efflux from tissues and by acting as a cofactor for the lecithin cholesterol acyltransferase (LCAT). As part of the SPAP complex, activates spermatozoa motility.SUBUNIT: Interacts with APOA1BP and CLU. Component of a sperm activating protein complex (SPAP), consisting of APOA1, an immunoglobulin heavy chain, an immunoglobulin light chain and albumin. Interacts with NDRG1.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Major protein of plasma HDL, also found in chylomicrons. Synthesized in the liver and small intestine. The oxidized form at Met-110 and Met-136 is increased in individuals with increased risk for coronary artery disease, such as in carrier of the eNOSa/b genotype and exposure to cigarette smoking. It is also present in increased levels in aortic lesions relative to native ApoA-I and increased levels are seen with increasing severity of disease.PTM: Palmitoylated.PTM: Met-110 and Met-136 are oxidized to methionine sulfoxides.PTM: Phosphorylation sites are present in the extracellular medium.MASS SPECTROMETRY: Mass=28081; Method=Electrospray; Range=25-267; Note=Without methionine sulfoxide; Source=PubMed:12576517;MASS SPECTROMETRY: Mass=28098; Method=Electrospray; Range=25-267; Note=With 1 methionine sulfoxide, oxidation at Met-110; Source=PubMed:12576517;MASS SPECTROMETRY: Mass=28095; Method=Electrospray; Range=25-267; Note=With 1 methionine sulfoxide, oxidation at Met-136; Source=PubMed:12576517;MASS SPECTROMETRY: Mass=28114; Method=Electrospray; Range=25-267; Note=With 2 methionine sulfoxides, oxidation at Met-110 and Met- 136; Source=PubMed:12576517;POLYMORPHISM: Genetic variations in APOA1 can result in APOA1 deficiency and are associated with low levels of HDL cholesterol [MIM:107680].DISEASE: High density lipoprotein deficiency 2 (HDLD2) [MIM:604091]: Inherited as autosomal dominant trait. It is characterized by moderately low HDL cholesterol, predilection toward premature coronary artery disease (CAD) and a reduction in cellular cholesterol efflux. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: High density lipoprotein deficiency 1 (HDLD1) [MIM:205400]: Recessive disorder characterized by absence of high density lipoprotein (HDL) cholesterol from plasma, accumulation of cholesteryl esters, premature coronary artery disease (CAD), hepatosplenomegaly, recurrent peripheral neuropathy and progressive muscle wasting and weakness. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Note=APOA1 mutations may be involved in the pathogenesis of amyloid polyneuropathy-nephropathy Iowa type, also known as amyloidosis van Allen type or familial amyloid polyneuropathy type III (PubMed:3142462 and PubMed:2123470). The clinical picture is dominated by neuropathy in the early stages of the disease and nephropathy late in the course. Death is due in most cases to renal amyloidosis.DISEASE: Amyloidosis 8 (AMYL8) [MIM:105200]: A hereditary generalized amyloidosis due to deposition of apolipoprotein A1, fibrinogen and lysozyme amyloids. Viscera are particularly affected. There is no involvement of the nervous system. Clinical features include renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the apolipoprotein A1/A4/E family.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/APOA1";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=APOA1"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_001172698 - RefSeq - - - - NM_001127457 - RefSeq - - - - - - MOD_RES 913 913 Sulfotyrosine (Potential). - - - - NP_001137418 - RefSeq - - - - - - Class E basic helix-loop-helix protein 41 - BHE41_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein11505 - Reactome DB_ID: 879703 - BHLHE41 - - - - 1480011 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1480011 - - - - REACT_118038 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118038.1 - - - - F9 - HGNC Symbol - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8317 - - - - Q5VTA4 - UniProt - - - - REACT_15941 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15941.4 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2422 - - - - - - - - - CREB-1 - CREB1 - cAMP-responsive element-binding protein 1 - - - - - - - - - - - - - - - - - - - - - - - - CREB1_HUMAN - Cyclic AMP-responsive element-binding protein 1 - FUNCTION: Phosphorylation-dependent transcription factor that stimulates transcription upon binding to the DNA cAMP response element (CRE), a sequence present in many viral and cellular promoters. Transcription activation is enhanced by the TORC coactivators which act independently of Ser-133 phosphorylation. Involved in different cellular processes including the synchronization of circadian rhythmicity and the differentiation of adipose cells.SUBUNIT: Interacts with PPRC1. Binds DNA as a dimer. This dimer is stabilized by magnesium ions. Interacts, through the bZIP domain, with the coactivators TORC1/CRTC1, TORC2/CRTC2 and TORC3/CRTC3. When phosphorylated on Ser-133, binds CREBBP (By similarity). Interacts with CREBL2; regulates CREB1 phosphorylation, stability and transcriptional activity (By similarity). Interacts (phosphorylated form) with TOX3. Interacts with ARRB1. Binds to HIPK2. Interacts with SGK1.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=CREB-A; IsoId=P16220-1; Sequence=Displayed; Name=CREB-B; IsoId=P16220-2; Sequence=VSP_000596; Name=3; Synonyms=htCREB; IsoId=P16220-3; Sequence=VSP_043914; Note=Highly expressed in adult testis and sperm;PTM: Stimulated by phosphorylation. Phosphorylation of both Ser- 133 and Ser-142 in the SCN regulates the activity of CREB and participates in circadian rhythm generation. Phosphorylation of Ser-133 allows CREBBP binding (By similarity). CREBL2 positively regulates phosphorylation at Ser-133 thereby stimulating CREB1 transcriptional activity (By similarity). Phosphorylated upon calcium influx by CaMK4 and CaMK2 on Ser-133. CaMK4 is much more potent than CaMK2 in activating CREB. Phosphorylated by CaMK2 on Ser-142. Phosphorylation of Ser-142 blocks CREB-mediated transcription even when Ser-133 is phosphorylated. Phosphorylated by CaMK1 (By similarity). Phosphorylation of Ser-271 by HIPK2 in response to genotoxic stress promotes CREB1 activity, facilitating the recruitment of the coactivator CBP. Phosphorylated at Ser-133 by RPS6KA3, RPS6KA4 and RPS6KA5 in response to mitogenic or stress stimuli.PTM: Sumoylated with SUMO1. Sumoylation on Lys-304, but not on Lys-285, is required for nuclear localization of this protein. Sumoylation is enhanced under hypoxia, promoting nuclear localization and stabilization.DISEASE: Angiomatoid fibrous histiocytoma (AFH) [MIM:612160]: A distinct variant of malignant fibrous histiocytoma that typically occurs in children and adolescents and is manifest by nodular subcutaneous growth. Characteristic microscopic features include lobulated sheets of histiocyte-like cells intimately associated with areas of hemorrhage and cystic pseudovascular spaces, as well as a striking cuffing of inflammatory cells, mimicking a lymph node metastasis. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving CREB1 is found in a patient with angiomatoid fibrous histiocytoma. Translocation t(2;22)(q33;q12) with CREB1 generates a EWSR1/CREB1 fusion gene that is most common genetic abnormality in this tumor type.DISEASE: Note=A CREB1 mutation has been found in a patient with multiple congenital anomalies consisting of agenesis of the corpus callosum, cerebellar hypoplasia, severe neonatal respiratory distress refractory to surfactant, thymus hypoplasia, and thyroid follicular hypoplasia (PubMed:22267179).SIMILARITY: Belongs to the bZIP family.SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain.SIMILARITY: Contains 1 KID (kinase-inducible) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 48 48 N6-acetyllysine; alternate (By similarity). - - - - ENST00000375320 - Ensembl - - - - - - - APOA2 - ApoA-II - Apo-AII - Truncated apolipoprotein A-II - Apolipoprotein A2 - Apolipoprotein A-II(1-76) - - - - - - - - - - - - - - APOA2_HUMAN - Apolipoprotein A-II - FUNCTION: May stabilize HDL (high density lipoprotein) structure by its association with lipids, and affect the HDL metabolism.SUBUNIT: Homodimer; disulfide-linked. Also forms a disulfide- linked heterodimer with APOD. Interacts with HCV core protein. Interacts with APOA1BP and NDRG1.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Plasma; synthesized in the liver and intestine.PTM: Met-49 is oxidized to methionine sulfoxide.PTM: Phosphorylation sites are present in the extracellular medium.PTM: Apolipoprotein A-II is O-glycosylated.MASS SPECTROMETRY: Mass=17252; Method=Electrospray; Range=24-100; Note=Homodimer, without methionine sulfoxide; Source=PubMed:12576517;MASS SPECTROMETRY: Mass=17269; Method=Electrospray; Range=24-100; Note=Homodimer, with 1 methionine sulfoxide, oxidation at Met-49; Source=PubMed:12576517;MASS SPECTROMETRY: Mass=8701.2; Method=MALDI; Range=24-100; Source=PubMed:12562854;MASS SPECTROMETRY: Mass=8823.4; Method=MALDI; Range=24-100; Note=Cysteinylated ApoA-II; Source=PubMed:12562854;MASS SPECTROMETRY: Mass=17421.3; Method=MALDI; Range=24-100; Note=Homodimer; Source=PubMed:12562854;MASS SPECTROMETRY: Mass=17293.4; Method=MALDI; Range=24-100; Note=Heterodimer with truncated apolipoprotein A-II; Source=PubMed:12562854;MASS SPECTROMETRY: Mass=8578.3; Method=MALDI; Range=24-99; Source=PubMed:12562854;MASS SPECTROMETRY: Mass=17166.2; Method=MALDI; Range=24-99; Note=Homodimer; Source=PubMed:12562854;POLYMORPHISM: A homozygous transition at position 1 of intron 3 of APOA2 results in deficiency of apolipoprotein A-II, without significant influence either on lipid and lipoprotein profiles or on the occurrence of coronary artery disease [MIM:107670].SIMILARITY: Belongs to the apolipoprotein A2 family.WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=APOA2"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12001 - - - - - - MOD_RES 438 438 Phosphoserine. - - - - D3Y5K6 - UniProt - - - - Q9NZI5 - UniProt - - - - - Neprilysin Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-7) - - - - - - - Neprilysin Hydrolyzes Angiotensin I to Yield Angiotensin-(1-7) - Neprilysin hydrolyzes angiotensin-(1-10) (angiotensin I) directly to angiotensin-(1-7) (Rice et al. 2004). - Authored: May, B, 2011-11-19 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4048 - - - - - - - PRGC1_HUMAN - Peroxisome proliferator-activated receptor gamma coactivator 1-alpha - - - - - http://www.reactome.org/biopax/46/48887#Protein6468 - Reactome DB_ID: 442481 - PPARGC1A - - - - 15500444 - Ishida, N - Shirai, H - Oishi, K - Pubmed - CLOCK is involved in the circadian transactivation of peroxisome-proliferator-activated receptor alpha (PPARalpha) in mice - Biochem J 386:575-81 - 2005 - - - - EQUAL - 128 - - - - NM_033637 - RefSeq - - - - REACT_903 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_903.3 - - - - ENST00000282892 - Ensembl - - - - 159747 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159747 - - - - 1581 - NCBI Gene - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite4571 - - - - 879782 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879782 - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of DEC2 (BHLHE41, BHLHB3)' - As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind E-box elements in the promoter of the DEC2 gene and activate transcription of DEC2. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation94 - - - - ENSP00000349530 - Ensembl - - - - 1605570 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1605570 - - - - REACT_11810 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11810.2 - - - - CHEBI:10010 - ChEBI - - - - 4322712 - Gould, AB - Green, D - Pubmed - Kinetics of the human renin and human substrate reaction - Cardiovasc Res 5:86-9 - 1971 - - - - 159826 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159826 - - - - 12868535 - Baler, R - Muñoz, E - Pubmed - The circadian E-box: when perfect is not good enough - Chronobiol Int 20:371-88 - 2003 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10114 - - - - 400216 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400216 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4709 - - - - NM_001143945 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25528 - - - - InChI=1S/C18H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h6-7,9-10H,2-5,8,11-17H2,1H3,(H,19,20)/b7-6-,10-9- - InChI - - - - B7Z8R3 - UniProt - - - - - - MOD_RES 1473 1473 N6-acetyllysine. - - - - 10860550 - Kono T - Yasumoto R - Kusunose E - Sugimura K - Kishimoto T - Naganuma T - Kawashima H - PubMed - Human fatty acid omega-hydroxylase, CYP4A11: determination of complete genomic sequence and characterization of purified recombinant protein. - Arch Biochem Biophys 378(2);333-9 - 2000 - - - - ENST00000268712 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12051 - - - - - - NP_000122 - RefSeq - - - - NM_007292 - RefSeq - - - - EQUAL - 80 - - - - - - MOD_RES 1042 1042 Phosphoserine (By similarity). - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9713 - - - - Q6PFW7 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2730 - - - - - - MOD_RES 113 113 Phosphoserine (By similarity). - - - - EQUAL - 67 - - - - EQUAL - 640 - http://www.reactome.org/biopax/46/48887#SequenceSite25545 - - - - EQUAL - 190 - - - - NM_152310 - RefSeq - - - - HGNC:7806 - HGNC - - - - - - MOD_RES 331 331 Phosphoserine. - - - - EQUAL - 69 - http://www.reactome.org/biopax/46/48887#SequenceSite9883 - - - - 1BY4 - PROTEIN DATA BANK - - - - 879819 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879819 - - - - ENSP00000263390 - Ensembl - - - - EQUAL - 1299 - - - - CPA3 - HGNC Symbol - - - - 1237011 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1237011 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1080 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12336 - - - - 11535246 - Teubner W - Pabel U - Pomplun D - Engelke CE - Ma L - Kuhlow A - Meinl W - Boeing H - Glatt H - PubMed - Human cytosolic sulphotransferases: genetics, characteristics, toxicological aspects. - Mutat Res 482(1-2);27-40 - 2001 - - - - Q9UCE0 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10178 - - - - - - REACT_24504 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24504.2 - - - - ENSG00000169375 - Ensembl - - - - E9PEE1 - UniProt - - - - Q9BZN5 - UniProt - - - - FHL2 - HGNC - - - - ENST00000542506 - Ensembl - - - - NP_001892 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1764 - - - - Q5VSP8 - UniProt - - - - ME1 - HGNC - - - - Q06520 - UniProt - - - - ENSG00000065833 - Ensembl - - - - ENST00000380293 - Ensembl - - - - ENST00000371998 - Ensembl - - - - B3KWX4 - UniProt - - - - CHEBI:29097 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10188 - - - - - - REACT_117998 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117998.1 - - - - - - - - - - - SREBF1A/1C/2:NF-Y:HMGCS1 gene - - - - SREBP1A/1C/2:NF-Y:HMGCS1 gene - Reactome DB_ID: 2426129 - http://www.reactome.org/biopax/46/48887#Complex5485 - - - - - - SREBP1A(1-490) - SREBF1A(1-490) - Sterol regulatory element-binding protein 1A - SREBF1A cleaved by S2P - SREBF1-1(1-490) - - - - - http://www.reactome.org/biopax/46/48887#Protein6465 - Reactome DB_ID: 1655755 - SRBP1_HUMAN - - - - EQUAL - 396 - - - - - - - - - - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein2631 - Reactome DB_ID: 381929 - PDGF A isoforms - - - - 421312 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421312 - - - - 159734 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159734 - - - - ENST00000523799 - Ensembl - - - - ENSP00000358719 - Ensembl - - - - ENSP00000301455 - Ensembl - - - - ENST00000380961 - Ensembl - - - - Q9UQV6 - UniProt - - - - NP_690043 - RefSeq - - - - ENSP00000471622 - Ensembl - - - - A8K4J7 - UniProt - - - - FABP1 - HGNC - - - - - - MOD_RES 649 649 Phosphoserine (By similarity). - - - - REACT_968 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_968.2 - - - - 1989799 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989799 - - - - 177320 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=177320 - - - - EQUAL - 1306 - http://www.reactome.org/biopax/46/48887#SequenceSite23011 - - - - EQUAL - 90 - - - - EQUAL - 703 - - - - MED7 - HGNC Symbol - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1086 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10806 - - - - - - REACT_25061 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25061.1 - - - - NP_000769 - RefSeq - - - - EQUAL - 800 - - - - 939844 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939844 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7589 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8353 - - - - - - SREBP2(1-484) - SREBF2(1-484) - Sterol regulatory element-binding protein 2 - SREBF2 cleaved by S2P - - - - - http://www.reactome.org/biopax/46/48887#Protein6466 - Reactome DB_ID: 1655745 - SRBP2_HUMAN - - - - EQUAL - 1 - - - - Q6FGC8 - UniProt - - - - 2022348 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022348 - - - - EQUAL - 846 - http://www.reactome.org/biopax/46/48887#SequenceSite21428 - - - - Q14813 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12386 - - - - NFYA - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12018 - - - - ENSP00000225728 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4716 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTG repeat protein 26 - TRAC - Silencing mediator of retinoic acid and thyroid hormone receptor - T3 receptor-associating factor - CTG26 - N-CoR2 - Thyroid-, retinoic-acid-receptor-associated corepressor - NCOR2 - SMAP270 - SMRT - - - - - - - - - - - - - - - - - - - - - - - - NCOR2_HUMAN - Nuclear receptor corepressor 2 - FUNCTION: Transcriptional corepressor of NR4A2/NURR1 and acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state (By similarity). Mediates the transcriptional repression activity of some nuclear receptors by promoting chromatin condensation, thus preventing access of the basal transcription. Isoform 1 and isoform 5 have different affinities for different nuclear receptors.SUBUNIT: Interacts with BCL6, HDAC7 and C1D. Interacts with NR4A2; this interaction increases in the absence of PITX3 (By similarity). Forms a large corepressor complex that contains SIN3A/B and histone deacetylases HDAC1 and HDAC2. This complex associates with the thyroid (TR) and the retinoid acid receptors (RAR) in the absence of ligand, and may stabilize their interaction with TFIIB. Interacts directly with RARA in the absence of ligand; the interaction represses RARA activity. Interacts (isoform SRMT) with HDAC10. Interacts with MINT. Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1R, CORO2A and GPS2. Interacts with CBFA2T3 and ATXN1L. Interacts with RARB; the interaction is weak and does not repress RARB transactivational activity. May interact with DEAF1.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=5; Name=1; Synonyms=SMRT-alpha, TRAC-2; IsoId=Q9Y618-1; Sequence=Displayed; Name=2; Synonyms=TRAC-1; IsoId=Q9Y618-2; Sequence=VSP_003412, VSP_003413; Note=Contains only the C-terminal receptor-interacting domain and acts as an antirepressor; Name=3; Synonyms=h-SMRT; IsoId=Q9Y618-3; Sequence=VSP_036596; Name=4; Synonyms=SMRTe; IsoId=Q9Y618-4; Sequence=VSP_036595; Name=5; Synonyms=SMRT-tau; IsoId=Q9Y618-5; Sequence=VSP_036595, VSP_003413;TISSUE SPECIFICITY: Ubiquitous. High levels of expression are detected in lung, spleen and brain.INDUCTION: Regulated during cell cycle progression.DOMAIN: The N-terminal region contains repression functions that are divided into three independent repression domains (RD1, RD2 and RD3). The C-terminal region contains the nuclear receptor- interacting domains that are divided in two separate interaction domains (ID1 and ID2).DOMAIN: The two interaction domains (ID) contain a conserved sequence referred to as the CORNR box. This motif is required and sufficient to permit binding to unligated TR and RARS. Sequences flanking the CORNR box determine nuclear hormone receptor specificity.SIMILARITY: Belongs to the N-CoR nuclear receptor corepressors family.SIMILARITY: Contains 2 SANT domains.SEQUENCE CAUTION: Sequence=AAB91452.1; Type=Erroneous translation; Note=Wrong choice of CDS; Sequence=AAC50236.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part; Sequence=AAD20946.1; Type=Frameshift; Positions=787, 794; Sequence=BAD92326.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q9UI96 - UniProt - - - - ENST00000290863 - Ensembl - - - - EQUAL - 2463 - - - - ENST00000405692 - Ensembl - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - - - - - - - - - protein C - http://www.reactome.org/biopax/46/48887#Complex5019 - Reactome DB_ID: 159830 - - - - 12475254 - McNally BA - Hommema EL - Hallgren KW - Berkner KL - PubMed - Carboxylase overexpression effects full carboxylation but poor release and secretion of factor IX: implications for the release of vitamin K-dependent proteins. - Biochemistry 41(50);15045-55 - 2002 - - - - Q53FE3 - UniProt - - - - - - HIF1A_HUMAN - Hypoxia-inducible factor 1-alpha - - - - - Reactome DB_ID: 1234135 - http://www.reactome.org/biopax/46/48887#Protein3221 - HIF1A - - - - EQUAL - 1030 - - - - ENST00000539796 - Ensembl - - - - 603808 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10838 - - - - EQUAL - 48 - http://www.reactome.org/biopax/46/48887#SequenceSite9685 - - - - 11533194 - pubchem - - - - 9576906 - Bradfield, CA - Hogenesch, JB - Gu, YZ - Jain, S - Pubmed - The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors - Proc Natl Acad Sci U S A 95:5474-9 - 1998 - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite1770 - - - - HGNC:29600 - HGNC - - - - EQUAL - 593 - http://www.reactome.org/biopax/46/48887#SequenceSite21464 - - - - ENSP00000293777 - Ensembl - - - - MED21 - HGNC Symbol - - - - HGNC:28845 - HGNC - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - Q9BWX8 - UniProt - - - - ENSP00000419692 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12370 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval7309 - - - - - - CHEBI:13970 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10074 - - - - - - EQUAL - 183 - http://www.reactome.org/biopax/46/48887#SequenceSite21699 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10151 - - - - - - - - - - - - - - INHIBITION - - 'NR1D1 (REV-ERBA):heme:Corepressor [nucleoplasm]' negatively regulates 'Expression of BMAL1 (ARNTL).' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation86 - NR1D1 (REV-ERBA) binds to the same site in the promoter of the BMAL1 (ARNTL) gene as ROR-alpha (RORA). Whereas ROR-alpha activates transcription of BMAL1, REV-ERBA bound to heme recruits corepressors (NCoR and HDAC3) and inhibits transcription of BMAL1. Both REV-ERBA and ROR-alpha genes are targets of BMAL1:CLOCK/NPAS2 transactivation and they show alternating patterns of maximum protein levels, thus they give BMAL1 transcription circadian expression. - - - - ENST00000378586 - Ensembl - - - - EQUAL - 370 - - - - ENST00000357028 - Ensembl - - - - InChI=1S/C30H53N3O6/c1-19(2)22(14-21-10-11-26(38-8)27(15-21)39-13-9-12-37-7)16-24(31)25(34)17-23(20(3)4)28(35)33-18-30(5,6)29(32)36/h10-11,15,19-20,22-25,34H,9,12-14,16-18,31H2,1-8H3,(H2,32,36)(H,33,35)/t22-,23-,24-,25-/m0/s1 - InChI - - - - - - MOD_RES 52 52 Phosphoserine; by CK2. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8311 - - - - EQUAL - 1674 - - - - NM_001040110 - RefSeq - - - - 939203 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939203 - - - - Q16881 - UniProt - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12963 - - - - Q15528 - UniProt - - - - ENST00000266503 - Ensembl - - - - 2022354 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022354 - - - - NM_006312 - RefSeq - - - - NP_001138829 - RefSeq - - - - 508391 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=508391 - - - - EQUAL - 70 - http://www.reactome.org/biopax/46/48887#SequenceSite9678 - - - - REACT_148404 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148404.2 - - - - 549385 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549385 - - - - - - thioredoxin reductase 1 - Thioredoxin reductase, cytoplasmic precursor - TXNRD1 - TR1 - Thioredoxin reductase, cytoplasmic precursor (EC 1.8.1.9) (TR) - - - - - http://www.reactome.org/biopax/46/48887#Protein13783 - Reactome DB_ID: 73531 - TR - - - - ENST00000242728 - Ensembl - - - - - - MOD_RES 382 382 Phosphoserine (By similarity). - - - - - - MOD_RES 60 60 4-carboxyglutamate. - - - - - - MOD_RES 255 255 N6-acetyllysine. - - - - REACT_116020 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116020.1 - - - - - - MOD_RES 981 981 N6-acetyllysine. - - - - - - MOD_RES 389 389 Phosphoserine. - - - - ENSG00000167772 - Ensembl - - - - 7311 - NCBI Gene - - - - REACT_24765 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24765.2 - - - - Q9H5M8 - UniProt - - - - NM_002395 - RefSeq - - - - 14750904 - Ishida, N - Narukawa, J - Mesaki, M - Miyazaki, K - Ohara, O - Nagase, T - Pubmed - Phosphorylation of clock protein PER1 regulates its circadian degradation in normal human fibroblasts - Biochem J 380:95-103 - 2004 - - - - - - MOD_RES 6 6 N6-acetyllysine; alternate (By similarity). - - - - - - MOD_RES 56 56 Phosphoserine; by MAPK8 and MAPK9 (By similarity). - - - - EQUAL - 68 - http://www.reactome.org/biopax/46/48887#SequenceSite10044 - - - - - - MOD_RES 383 383 Phosphoserine (By similarity). - - - - - 8.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12955 - - - - EQUAL - 304 - http://www.reactome.org/biopax/46/48887#SequenceSite4660 - - - - ENSP00000379189 - Ensembl - - - - EQUAL - 104 - - - - ENSP00000435929 - Ensembl - - - - - - MOD_RES 493 493 Phosphoserine. - - - - - - MOD_RES 47 47 4-carboxyglutamate. - - - - EQUAL - 26 - http://www.reactome.org/biopax/46/48887#SequenceSite25476 - - - - EQUAL - 116 - - - - EQUAL - 194 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5613 - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21670 - - - - - - - - - - - - - - - - - - - - - Activation of PPARA by Fatty Acid Ligands - Edited: May, B, 2009-06-08 - PPAR-alpha is activated by binding polyunsaturated fatty acids especially those having 18-22 carbon groups and 2-6 double bonds. These ligands bind the C-terminal region of PPAR-alpha and include linoleic acid, linolenic acids, arachidonic acid, and eicosapentaenoic acid. The fibrate drugs are also agonists of PPAR-alpha.<br>Binding of a ligand causes a conformational change in PPAR-alpha so that it recruits coactivators. By analogy with the closely related receptor PPAR-gamma, PPAR-alpha probably binds TBL1 and TBLR1, which are responsible for recruiting the 19S proteasome to degrade corepressors during the exchange of corepressors for coactivators. The coactivators belong to the CBP-SRC-HAT complex (CBP/p300, SRC1, SRC2, SRC3, CARM1, SWI/SNF, BAF60C, PRIC320, and PRIC285), the ASC complex (PRIP/ASC2, PIMT), and the TRAP-DRIP-ARC-MEDIATOR complex (TRAP130, PBP/TRAP220). The coactivators contain LXXLL motifs (Nuclear Receptor Boxes) that interact with the AF-2 region in nuclear receptors such as PPAR-alpha. - Edited: May, B, 2009-05-30 16:45:51 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4675 - Authored: May, B, 2009-05-30 16:45:51 - - - - - - - - - PER1_HUMAN - Period circadian protein homolog 1 - - - - - Reactome DB_ID: 400373 - http://www.reactome.org/biopax/46/48887#Protein11513 - PER1 - - - - 981546 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=981546 - - - - NP_001161752 - RefSeq - - - - Q86YN4 - UniProt - - - - 1592205 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592205 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10066 - - - - - - 9801304 - Kanno, S - Kobayashi, K - Takao, M - Yasui, A - Smit, B - van der Horst, GT - Pubmed - Characterization of photolyase/blue-light receptor homologs in mouse and human cells - Nucleic Acids Res 26:5086-92 - 1998 - - - - InChI=1S/p+1 - InChI - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12971 - - - - REACT_118021 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118021.1 - - - - - - - - - - Cyclic AMP-responsive element-binding protein 2 - CREB-2 - CREB2 - Activating transcription factor 2 - CREBP1 - cAMP-dependent transcription factor ATF-2 - cAMP-responsive element-binding protein 2 - HB16 - cAMP response element-binding protein CRE-BP1 - ATF2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATF2_HUMAN - Cyclic AMP-dependent transcription factor ATF-2 - FUNCTION: Transcriptional activator, probably constitutive, which binds to the cAMP-responsive element (CRE) (consensus: 5'- GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Interaction with JUN redirects JUN to bind to CRES preferentially over the 12-O-tetradecanoylphorbol-13-acetate response elements (TRES) as part of an ATF2/JUN complex.SUBUNIT: Binds DNA as a dimer and can form a homodimer in the absence of DNA. Can form a heterodimer with JUN. Interacts with SMAD3 and SMAD4. Binds through its N-terminal region to UTF1 which acts as a coactivator of ATF2 transcriptional activity.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=7; Name=1; IsoId=P15336-1; Sequence=Displayed; Name=2; IsoId=P15336-2; Sequence=VSP_000587, VSP_000588; Name=3; IsoId=P15336-3; Sequence=VSP_045161; Name=4; IsoId=P15336-4; Sequence=VSP_046959; Name=5; IsoId=P15336-5; Sequence=VSP_046960; Name=6; IsoId=P15336-6; Sequence=VSP_046960, VSP_047593; Name=7; IsoId=P15336-7; Sequence=VSP_046960, VSP_047594, VSP_047595;TISSUE SPECIFICITY: Abundant expression seen in the brain.PTM: Phosphorylation of Thr-69 by MAPK14 and MAPK11, and at Thr-71 by MAPK1/ERK2, MAPK3/ERK1, MAPK11, MAPK12 and MAPK14 in response to external stimulus like insulin causes increased transcriptional activity. Phosphorylated by PLK3 following hyperosmotic stress. Also phosphorylated and activated by JNK and CaMK4.SIMILARITY: Belongs to the bZIP family. ATF subfamily.SIMILARITY: Contains 1 bZIP (basic-leucine zipper) domain.SIMILARITY: Contains 1 C2H2-type zinc finger.SEQUENCE CAUTION: Sequence=AAY17203.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAY17207.1; Type=Erroneous initiation; Note=Translation N-terminally extended;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/ATF2ID718ch2q31.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 400223 - http://www.reactome.org/biopax/46/48887#Protein11517 - CRY1/2 - - - - NM_001270521 - RefSeq - - - - 2022401 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022401 - - - - REACT_124 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124.3 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11040 - - - - 4199 - NCBI Gene - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21473 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10190 - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11521 - Converted from EntitySet in Reactome - Reactome DB_ID: 400287 - p-CRY1/2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12057 - - - - - - - - MOD_RES 68 68 4-carboxyglutamate. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1052 - - - - 29841 - NCBI Gene - - - - EQUAL - 68 - http://www.reactome.org/biopax/46/48887#SequenceSite9995 - - - - - - NPAS2_HUMAN - Neuronal PAS domain-containing protein 2 - - - - - http://www.reactome.org/biopax/46/48887#Protein11497 - Reactome DB_ID: 400314 - NPAS2 - - - - HGNC:23074 - HGNC - - - - O00317 - UniProt - - - - - - - - - - - - pro-factor X, uncarboxylated - http://www.reactome.org/biopax/46/48887#Complex5012 - Reactome DB_ID: 159754 - - - - PEX11A - HGNC Symbol - - - - ENSG00000105398 - Ensembl - - - - ENST00000403904 - Ensembl - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of AVP' - As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind an E-box enhancer in the AVP promoter and activate transcription of AVP. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation91 - - - - ENST00000233838 - Ensembl - - - - - - MOD_RES 226 226 Phosphoserine. - - - - EQUAL - 853 - http://www.reactome.org/biopax/46/48887#SequenceSite12419 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1055 - - - - ENST00000350997 - Ensembl - - - - NM_001001928 - RefSeq - - - - Q9NYF1 - UniProt - - - - 350263 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=350263 - - - - 549493 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549493 - - - - 1368124 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368124 - - - - nucleoplasm - - - - - D6W670 - UniProt - - - - NP_003324 - RefSeq - - - - ENSP00000396766 - Ensembl - - - - 374187 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=374187 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12422 - - - - 1BHI - PROTEIN DATA BANK - - - - EQUAL - 1273 - http://www.reactome.org/biopax/46/48887#SequenceSite10245 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12004 - - - - - - MOD_RES 32 32 Phosphoserine. - - - - 23097 - NCBI Gene - - - - HGNC:2345 - HGNC - - - - 11165242 - Keesler, GA - Yao, Z - Styren, S - Morse, B - Virshup, DM - Patel, K - Camacho, F - Cilio, M - Khorkova, O - Guo, Y - Pubmed - Human casein kinase Idelta phosphorylation of human circadian clock proteins period 1 and 2 - FEBS Lett 489:159-65 - 2001 - - - - 2393972 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2393972 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4954 - - - - 606461 - omim - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12374 - - - - - - - - - - - - phospho-Emi1(Ser 182):Cdc20/Cdh1:complexes - http://www.reactome.org/biopax/46/48887#Complex2828 - Reactome DB_ID: 177328 - - - - HGNC:11477 - HGNC - - - - EQUAL - 1207 - - - - 421295 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421295 - - - - CCN family member 2 - IGFBP-8 - IBP-8 - CTGF - IGFBP8 - Insulin-like growth factor-binding protein 8 - CCN2 - Hypertrophic chondrocyte-specific protein 24 - IGF-binding protein 8 - HCS24 - - - - - - - - - - - - - - - - - CTGF_HUMAN - Connective tissue growth factor - FUNCTION: Major connective tissue mitoattractant secreted by vascular endothelial cells. Promotes proliferation and differentiation of chondrocytes. Mediates heparin- and divalent cation-dependent cell adhesion in many cell types including fibroblasts, myofibroblasts, endothelial and epithelial cells. Enhances fibroblast growth factor-induced DNA synthesis.SUBUNIT: Monomer.SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix (By similarity). Secreted (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=Long; IsoId=P29279-1; Sequence=Displayed; Name=2; Synonyms=Short; IsoId=P29279-2; Sequence=VSP_002460; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in bone marrow and thymic cells. Also expressed one of two Wilms tumors tested.SIMILARITY: Belongs to the CCN family.SIMILARITY: Contains 1 CTCK (C-terminal cystine knot-like) domain.SIMILARITY: Contains 1 IGFBP N-terminal domain.SIMILARITY: Contains 1 TSP type-1 domain.SIMILARITY: Contains 1 VWFC domain.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CTGFID40192ch6q23.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12069 - - - - - - - - D site-binding protein - DBP_HUMAN - - - - - Reactome DB_ID: 879796 - http://www.reactome.org/biopax/46/48887#Protein11503 - DBP - - - - REACT_5060 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5060.2 - - - - REACT_2614 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2614.2 - - - - REACT_16041 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16041.2 - - - - 1989815 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989815 - - - - ENSG00000139278 - Ensembl - - - - CHEBI:43891 - ChEBI - - - - EQUAL - 197 - http://www.reactome.org/biopax/46/48887#SequenceSite21708 - - - - - - CP7A_HUMAN - Cytochrome P450 7A1 - - - - - Reactome DB_ID: 192169 - http://www.reactome.org/biopax/46/48887#Protein13767 - CYP7A1 - - - - P33121 - UniProt - - - - 1605560 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1605560 - - - - Q8WW95 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5644 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4782 - - - - 12045255 - Burcklé, C - Sraer, JD - Nguyen, G - Delarue, F - Bouzhir, L - Giller, T - Pubmed - Pivotal role of the renin/prorenin receptor in angiotensin II production and cellular responses to renin - J Clin Invest 109:1417-27 - 2002 - - - - ENST00000268711 - Ensembl - - - - ENST00000408995 - Ensembl - - - - 159779 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159779 - - - - EQUAL - 319 - http://www.reactome.org/biopax/46/48887#SequenceSite25547 - - - - 607777 - omim - - - - 561145 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561145 - - - - 2F73 - PROTEIN DATA BANK - - - - 7710689 - Aksoy S - Otterness DM - Weinshilboum RM - Her C - Kimura S - Wieben ED - PubMed - Human dehydroepiandrosterone sulfotransferase gene: molecular cloning and structural characterization. - DNA Cell Biol 14(4);331-41 - 1995 - - - - ENSP00000399968 - Ensembl - - - - - - MOD_RES 2054 2054 Phosphoserine; by PKA. - - - - 1989787 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989787 - - - - - ALAS3 - ALAS1 - 2.3.1.37 - Delta-ALA synthase 1 - Delta-aminolevulinate synthase 1 - ALASH - ALAS-H - 5-aminolevulinic acid synthase 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - HEM1_HUMAN - 5-aminolevulinate synthase, nonspecific, mitochondrial - CATALYTIC ACTIVITY: Succinyl-CoA + glycine = 5-aminolevulinate + CoA + CO(2).COFACTOR: Pyridoxal phosphate.PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin- IX biosynthesis; 5-aminolevulinate from glycine: step 1/1.SUBUNIT: Homodimer.SUBCELLULAR LOCATION: Mitochondrion matrix.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P13196-1; Sequence=Displayed; Name=2; IsoId=P13196-2; Sequence=VSP_025925, VSP_025924; Note=No experimental confirmation available;MISCELLANEOUS: There are two delta-ALA synthases in vertebrates: an erythroid- specific form and one (housekeeping) which is expressed in all tissues.SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.SEQUENCE CAUTION: Sequence=CAA68506.1; Type=Frameshift; Positions=Several; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 2065391 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065391 - - - - ENSG00000137693 - Ensembl - - - - ENSP00000275246 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5622 - - - - - - Active PDGF A-chain isoform 2 - PDGFA isoform 2 - Platelet-derived growth factor A chain isoform 2 - - - - - http://www.reactome.org/biopax/46/48887#Protein2127 - Reactome DB_ID: 380739 - PDGFA-2 - - - - PPARA - HGNC Symbol - - - - - - MOD_RES 57 57 4-carboxyglutamate. - - - - 939857 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939857 - - - - - - MOD_RES 85 85 Phosphoserine. - - - - A2I2P4 - UniProt - - - - EQUAL - 622 - http://www.reactome.org/biopax/46/48887#SequenceSite21704 - - - - ENST00000216336 - Ensembl - - - - Q2YD86 - UniProt - - - - NM_032286 - RefSeq - - - - Q9NTF4 - UniProt - - - - - - - - - ACTIVATION - - 'ROR-alpha:Coactivator [nucleoplasm]' positively regulates 'Expression of SREBF1 (SREBP1)' - As inferred from mouse, RORA (ROR-alpha) enhances expression of SREBP1 (SREBF1). - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation117 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4760 - - - - - - NM_170679 - RefSeq - - - - 56573 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=56573 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12021 - - - - - - MOD_RES 82 82 4-carboxyglutamate. - - - - REACT_5437 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5437.2 - - - - EQUAL - 47 - - - - Q0QJH8 - UniProt - - - - ENSP00000409543 - Ensembl - - - - EQUAL - 768 - http://www.reactome.org/biopax/46/48887#SequenceSite25577 - - - - Q16131 - UniProt - - - - NP_000528 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12372 - - - - - - MOD_RES 1136 1136 Phosphoserine. - - - - 159800 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159800 - - - - NM_001190440 - RefSeq - - - - EQUAL - 632 - - - - NP_004370 - RefSeq - - - - 15687497 - Suárez, MF - Quesada, V - Díaz-Perales, A - Fueyo, A - Ugalde, AP - López-Otin, C - Sánchez, LM - Pubmed - Identification of human aminopeptidase O, a novel metalloprotease with structural similarity to aminopeptidase B and leukotriene A4 hydrolase - J Biol Chem 280:14310-7 - 2005 - - - - FURIN - HGNC - - - - 193545 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193545 - - - - 549554 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549554 - - - - Q9BU57 - UniProt - - - - EQUAL - 27 - - - - - - p-T178,S539-PPARGC1A - p-T178-S539-PPARGC1A - PRGC1_HUMAN - Peroxisome proliferator-activated receptor gamma coactivator 1-alpha - p-S539,T178-PPARGC1A - - - - - - - Reactome DB_ID: 1592204 - http://www.reactome.org/biopax/46/48887#Protein11545 - PPARGC1A - - - - ENST00000394466 - Ensembl - - - - EQUAL - 76 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10017 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1266 - - - - Q9BQ26 - UniProt - - - - 188972 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=188972 - - - - REACT_117987 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117987.1 - - - - EQUAL - 1464 - http://www.reactome.org/biopax/46/48887#SequenceSite12399 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10148 - - - - EQUAL - 2442 - http://www.reactome.org/biopax/46/48887#SequenceSite3512 - - - - 159810 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159810 - - - - EQUAL - 47 - http://www.reactome.org/biopax/46/48887#SequenceSite9890 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10168 - - - - - - 159836 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159836 - - - - NM_001909 - RefSeq - - - - ENST00000300060 - Ensembl - - - - 601851 - omim - - - - NM_001024094 - RefSeq - - - - 1350662 - Holmes KV - Ashmun RA - Yeager CL - Shapiro LH - Williams RK - Cardellichio CB - Look AT - PubMed - Human aminopeptidase N is a receptor for human coronavirus 229E. - Nature 357(6377);420-2 - 1992 - - - - CHEBI:15379 - ChEBI - - - - EQUAL - 82 - - - - ENSP00000384673 - Ensembl - - - - - - MOD_RES 538 538 N6-acetyllysine (By similarity). - - - - MED14 - HGNC - - - - 1610352 - Chiang JY - Karam WG - PubMed - Polymorphisms of human cholesterol 7 alpha-hydroxylase. - Biochem Biophys Res Commun 185(2);588-95 - 1992 - - - - EQUAL - 1112 - - - - O00613 - UniProt - - - - EQUAL - 805 - - - - - - MOD_RES 49 49 4-carboxyglutamate. - - - - EQUAL - 32 - http://www.reactome.org/biopax/46/48887#SequenceSite21658 - - - - 2621 - NCBI Gene - - - - EQUAL - 47 - - - - 18037887 - Khorasanizadeh, S - Nosie, AK - McClure, DB - Huang, P - Burris, LL - Rastinejad, F - Stayrook, KR - Rogers, PM - Raghuram, S - Burris, TP - Pubmed - Identification of heme as the ligand for the orphan nuclear receptors REV-ERBalpha and REV-ERBbeta - Nat Struct Mol Biol 14:1207-13 - 2007 - - - - 159865 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159865 - - - - NP_001234931 - RefSeq - - - - ENST00000435819 - Ensembl - - - - - TBL1-related protein 1 - TBL1XR1 - IRA1 - Transducin beta-like 1X-related protein 1 - Nuclear receptor corepressor/HDAC3 complex subunit TBLR1 - TBLR1 - - - - - - - - - - - - - - - - - - - TBL1R_HUMAN - F-box-like/WD repeat-containing protein TBL1XR1 - FUNCTION: F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of the N-Cor corepressor complex that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of N-Cor complex, thereby allowing cofactor exchange, and transcription activation.SUBUNIT: Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1XR1, CORO2A and GPS2. Probable component of some E3 ubiquitin ligase complex. Interacts with histones H2B and H4.SUBCELLULAR LOCATION: Nucleus (Probable).TISSUE SPECIFICITY: Ubiquitous.DOMAIN: The F-box-like domain is related to the F-box domain, and apparently displays the same function as component of ubiquitin E3 ligase complexes (By similarity).SIMILARITY: Belongs to the WD repeat EBI family.SIMILARITY: Contains 1 F-box-like domain.SIMILARITY: Contains 1 LisH domain.SIMILARITY: Contains 8 WD repeats.SEQUENCE CAUTION: Sequence=AAH60320.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_133640 - RefSeq - - - - REACT_24956 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24956.1 - - - - ENSP00000417401 - Ensembl - - - - EQUAL - 641 - - - - EQUAL - 61 - http://www.reactome.org/biopax/46/48887#SequenceSite10047 - - - - 991 - NCBI Gene - - - - Q9NRA7 - UniProt - - - - EQUAL - 691 - http://www.reactome.org/biopax/46/48887#SequenceSite21694 - - - - - - MOD_RES 321 321 N6-acetyllysine (By similarity). - - - - 2266130 - Husain, A - Misono, KS - Kinoshita, A - Urata, H - Bumpus, FM - Pubmed - Identification of a highly specific chymase as the major angiotensin II-forming enzyme in the human heart - J Biol Chem 265:22348-57 - 1990 - - - - 2026077 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2026077 - - - - ENSP00000223190 - Ensembl - - - - GO:0005759 - Gene Ontology - - - - CHEBI:17996 - ChEBI - - - - B0YIV9 - UniProt - - - - 10198158 - Bowcock, AM - Sangoram, AM - Takahashi, JS - Du, F - Zhao, Y - King, DP - Moore, RY - Steeves, TD - Pubmed - Molecular cloning and characterization of the human CLOCK gene: expression in the suprachiasmatic nuclei - Genomics 57:189-200 - 1999 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8316 - - - - 1989811 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989811 - - - - 1386 - NCBI Gene - - - - PTHR24265:SF34 - PANTHER Family - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10037 - - - - ENST00000476080 - Ensembl - - - - 556823 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556823 - - - - ENST00000395048 - Ensembl - - - - - - - - - INHIBITION - - 'NR1D1 (REV-ERBA):heme:Corepressor [nucleoplasm]' negatively regulates 'Expression of PPARGC1A (PGC-1alpha)' - NR1D1 (REV-ERBA) binds heme and the promoter of the PGC-1alpha (PPARGC1A) gene. The REV-ERBA:heme complex recruits the corepressors NCoR and HDAC3 and represses transcription. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation111 - - - - - - MOD_RES 524 524 Phosphoserine. - - - - - - MOD_RES 47 47 Phosphoserine; by CK2. - - - - Q14336 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12059 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2118 - - - - - - 8262386 - Westley BR - Smith DJ - May FE - PubMed - The human cathepsin D-encoding gene is transcribed from an estrogen-regulated and a constitutive start point. - Gene 134(2);277-82 - 1993 - - - - 879837 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879837 - - - - ENSG00000137574 - Ensembl - - - - ENSP00000420276 - Ensembl - - - - 9748239 - Fruchart, JC - Staels, B - Laudet, V - Chopin-Delannoy, S - Bonnelye, E - Gervois, P - Martin, G - Vu-Dac, N - Pubmed - The nuclear receptors peroxisome proliferator-activated receptor alpha and Rev-erbalpha mediate the species-specific regulation of apolipoprotein A-I expression by fibrates - J Biol Chem 273:25713-20 - 1998 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature829 - - - - ENSP00000256379 - Ensembl - - - - HGNC:13584 - HGNC - - - - EQUAL - 112 - - - - REACT_1 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1.2 - - - - EQUAL - 805 - http://www.reactome.org/biopax/46/48887#SequenceSite23021 - - - - 3.4.18.1 - CTSZ - Cathepsin X - Cathepsin P - - - - - - - - - - - - - - - CATZ_HUMAN - Cathepsin Z - FUNCTION: Exhibits carboxy-monopeptidase as well as carboxy- dipeptidase activity.CATALYTIC ACTIVITY: Release of C-terminal amino acid residues with broad specificity, but lacks action on C-terminal proline. Shows weak endopeptidase activity.SUBCELLULAR LOCATION: Lysosome.TISSUE SPECIFICITY: Widely expressed.SIMILARITY: Belongs to the peptidase C1 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 2 - - - - 8086471 - DiDonato S - Wang H - Taroni F - Montermini L - Verderio E - Finocchiaro G - PubMed - Identification of 5' regulatory regions of the human carnitine palmitoyltransferase II gene. - Biochim Biophys Acta 1219(1);237-40 - 1994 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10154 - - - - - - - - - - Pro-GAS6 is transported from the endoplasmic reticulum to the Golgi apparatus - In this reaction, 1 molecule of 'pro-GAS6' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3899 - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10164 - - - - - - Q92793 - UniProt - - - - - - MOD_RES 1872 1872 Phosphoserine. - - - - O15055 - UniProt - - - - EQUAL - 603 - - - - - - MOD_RES 66 66 4-carboxyglutamate. - - - - REACT_10892 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10892.2 - - - - NP_219491 - RefSeq - - - - NP_599024 - RefSeq - - - - MOD_RES Asymmetric dimethylarginine - - - - 549551 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549551 - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - http://www.reactome.org/biopax/46/48887#TemplateReaction55 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - The BMAL1 (ARNTL) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The ROR-alpha transcription factor binds the RORE element of the BMAL1 (ARNTL) promoter and activates transcription of the BMAL1 gene. The REV-ERBA transcription factor binds the same RORE element and represses transcription of the BMAL1 gene. - Expression of BMAL1 (ARNTL). - - - - - - - - - - - - Prorenin-Prorenin Receptor - Reactome DB_ID: 2065393 - http://www.reactome.org/biopax/46/48887#Complex5110 - - - - Same Catalyst Activity - http://www.reactome.org/biopax/46/48887#RelationshipTypeVocabulary2 - - - - ENST00000301455 - Ensembl - - - - NP_002386 - RefSeq - - - - ENST00000395848 - Ensembl - - - - ENSP00000258648 - Ensembl - - - - 8144514 - pubchem-substance - - - - - - MOD_RES 864 864 Phosphoserine (By similarity). - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12371 - - - - - C34H32FeN4O4 - (protoporphyrinato)iron(1+) - ferriheme - (protoporphyrinato)iron(III) - ferriprotoheme - [Fe(ppIX)](+) - protoferriheme - - - - - 616.487 - ferriheme b - ferriheme b - Heme b in which the iron has oxidation state +3. - - - - - - apolipoprotein A-II - APOA2(24-100) - - - - - Reactome DB_ID: 174775 - http://www.reactome.org/biopax/46/48887#Protein4570 - apoA-II - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5615 - - - - REACT_115631 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115631.1 - - - - Q53GB4 - UniProt - - - - MOD:00041 - Protein Modification Ontology - - - - REACT_18208 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18208.2 - - - - 2903074 - Grzeschik KH - Sjostrom H - Bolund L - Noren O - Kruse TA - Ropers HH - Olsen J - PubMed - Assignment of the human aminopeptidase N (peptidase E) gene to chromosome 15q13-qter. - FEBS Lett 239(2);305-8 - 1988 - - - - EQUAL - 395 - - - - REACT_27173 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27173.2 - - - - NP_001129064 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5793 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12017 - - - - EQUAL - 60 - - - - CHEBI:10011 - ChEBI - - - - EQUAL - 520 - - - - 17003504 - Ferreyra, G - Anzulovich, A - Mir, A - Brewer, M - Baler, R - Vinson, C - Pubmed - Elovl3: a model gene to dissect homeostatic links between the circadian clock and nutritional status - J Lipid Res 47:2690-700 - 2006 - - - - ENSP00000419465 - Ensembl - - - - ENSG00000184634 - Ensembl - - - - CCRN4L - HGNC Symbol - - - - EQUAL - 396 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature121 - - - - 194209 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194209 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4763 - - - - - - REACT_117976 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117976.1 - - - - - - - AXL receptor tyrosine kinase ligand - GAS-6 - GAS6 - AXLLG - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAS6_HUMAN - Growth arrest-specific protein 6 - FUNCTION: Ligand for tyrosine-protein kinase receptors AXL, TYRO3 and MER whose signaling is implicated in cell growth and survival, cell adhesion and cell migration. GAS6/AXL signaling plays a role in various processes such as endothelial cell survival during acidification by preventing apoptosis, optimal cytokine signaling during human natural killer cell development, hepatic regeneration, gonadotropin-releasing hormone neuron survival and migration, platelet activation, or regulation of thrombotic responses.SUBUNIT: Heterodimer and heterotetramer with AXL.SUBCELLULAR LOCATION: Secreted.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=5; Name=1; Synonyms=gas6SV; IsoId=Q14393-1; Sequence=Displayed; Name=2; IsoId=Q14393-2; Sequence=VSP_010494; Name=3; IsoId=Q14393-3; Sequence=VSP_010492, VSP_010493, VSP_010494; Note=No experimental confirmation available; Name=4; IsoId=Q14393-4; Sequence=VSP_043832, VSP_010494; Name=5; IsoId=Q14393-5; Sequence=VSP_045685; Note=No experimental confirmation available;TISSUE SPECIFICITY: Plasma. Isoform 1 and isoform 2 are widely expressed. Isoform 1 is the predominant form in spleen.PTM: Isoform 1 is proteolytically processed after secretion to yield a N-terminal 36 kDa protein and a C-terminal 50 kDa protein including the laminin G-like domains which activates AXL.PTM: Gamma-carboxyglutamate residues are formed by vitamin K dependent carboxylation. These residues are essential for the binding of calcium (By similarity).SIMILARITY: Contains 4 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 2 laminin G-like domains.WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/gas6/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - - SCF-beta-TrCP1 complex - Reactome DB_ID: 174155 - http://www.reactome.org/biopax/46/48887#Complex1948 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10751 - - - - O43268 - UniProt - - - - EQUAL - 61 - http://www.reactome.org/biopax/46/48887#SequenceSite21682 - - - - 2022411 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022411 - - - - CG - 3.4.21.20 - CTSG - - - - - - - - - - - - - - - - CATG_HUMAN - Cathepsin G - FUNCTION: Serine protease with trypsin- and chymotrypsin-like specificity. Cleaves complement C3. Has antibacterial activity against the Gram-negative bacterium P.aeruginosa, antibacterial activity is inhibited by LPS from P.aeruginosa, Z-Gly-Leu-Phe- CH2Cl and phenylmethylsulfonyl fluoride.CATALYTIC ACTIVITY: Specificity similar to chymotrypsin C.ENZYME REGULATION: Inhibited by soybean trypsin inhibitor, benzamidine, the synthetic peptide R13K, Z-Gly-Leu-Phe-CH2Cl, phenylmethylsulfonyl fluoride, 3,4-dichloroisocoumarin, DFP, SBTI and alpha-1-antitrypsin. Inhibited by LPS from P.aeruginosa but not by LPS from S.minnesota. Not inhibited by elastinal, CMK, TLCK and ETDA.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=1.15 mM for Z-Lys-SBzl; KM=0.26 mM for Suc-Ala-Ala-Pro-Phe-SBzl;SUBCELLULAR LOCATION: Cell surface.SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 1 peptidase S1 domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 939232 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939232 - - - - EQUAL - 773 - http://www.reactome.org/biopax/46/48887#SequenceSite21503 - - - - PER2 - HGNC - - - - EQUAL - 285 - - - - Q9Y213 - UniProt - - - - - - - - - - - Binding of CRY:PER Heterodimer to the BMAL1:CLOCK/NPAS2 Heterodimer - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - CRY (CRY1 and CRY2) and PER (PER1, PER2, PER3) proteins form complex in the cytoplasm where they are phosphorylated by CSNK1D and CSNK1E kinases. CRY:PER complexes appear to form stable complexes with a kinase. Because of the nuclear localization signals of PER and CRY, the complexes are translocated to the nucleus where they bind BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimers and inhibit the transactivation activity of BMAL1:CLOCK/NPAS2.<br>CRY and PER proteins are themselves transcriptionally activated by BMAL1:CLOCK/NPAS2 thus they participate in a negative loop inhibiting their own synthesis and the synthesis of other targets of BMAL1:CLOCK/NPAS2.<br>Experiments with two-hybrid interactions and in vitro associations show that CRY1, CRY2, and PER2 bind BMAL1 at two different sites on BMAL1. PER2 but not CRY1 or CRY2 binds CLOCK. Different combinations of PER and CRY proteins in PER:CRY complexes have different inhibitory activities. - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3860 - - - - - CCRN4L - HGNC - - - - EQUAL - 747 - - - - ENSG00000072310 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2591 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10032 - - - - Q9BSC8 - UniProt - - - - ENSP00000377650 - Ensembl - - - - NM_002954 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25566 - - - - HGNC:9232 - HGNC - - - - ENSP00000236671 - Ensembl - - - - 2022340 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022340 - - - - ENSP00000408867 - Ensembl - - - - REACT_24675 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24675.2 - - - - 939214 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939214 - - - - EQUAL - 274 - - - - MED17 - HGNC - - - - EQUAL - 2234 - - - - EQUAL - 362 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1097 - - - - 400212 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400212 - - - - EQUAL - 1981 - - - - 2032772 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032772 - - - - Q7Z574 - UniProt - - - - NM_007288 - RefSeq - - - - - - MOD_RES 164 164 Phosphoserine; by LATS1 and LATS2. - - - - E9PBL7 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12384 - - - - ENST00000530819 - Ensembl - - - - 191308 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=191308 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval428 - - - - - - 159803 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159803 - - - - ENST00000394287 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10141 - - - - - 3.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7597 - - - - Q9UCZ5 - UniProt - - - - Q9UFG6 - UniProt - - - - EQUAL - 2414 - http://www.reactome.org/biopax/46/48887#SequenceSite887 - - - - EQUAL - 31 - http://www.reactome.org/biopax/46/48887#SequenceSite21691 - - - - CHEBI:28371 - ChEBI - - - - 9748295 - Brown, MS - Guryev, O - Goldstein, JL - Pai, JT - Pubmed - Differential stimulation of cholesterol and unsaturated fatty acid biosynthesis in cells expressing individual nuclear sterol regulatory element-binding proteins - J Biol Chem 273:26138-48 - 1998 - - - - Q96IH7 - UniProt - - - - ENSP00000329546 - Ensembl - - - - 1989757 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989757 - - - - - - - - - - - - - - - - ACTIVATION - - 'SREBP1A/2:NF-Y:HMGCR gene [nucleoplasm]' positively regulates 'Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR)' - SREBF1A (SREBP1A) and SREBF2 (SREBP2) bind the promoter of the Hydroxymethylglutaryl CoA Reductase gene (HMGCR) and enhance transcription (Shimano et al. 1996,Vallett et al. 1996, Shiman et al. 1997, Horton et al. 1998, Pai et al. 1998, Sakakura et al. 2001, Reed et al. 2008, reviewed in Horton et al. 2002). - http://www.reactome.org/biopax/46/48887#Control380 - - - - EQUAL - 1591 - - - - 400314 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400314 - - - - NM_001256658 - RefSeq - - - - P02647 - UniProt - - - - NP_001034756 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2116 - - - - - - REACT_19539 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19539.2 - - - - E1P578 - UniProt - - - - EQUAL - 411 - - - - 6604 - NCBI Gene - - - - O75331 - UniProt - - - - Q4ZFV9 - UniProt - - - - ENSP00000312247 - Ensembl - - - - NM_018850 - RefSeq - - - - NP_000593 - RefSeq - - - - 16476485 - Wahli, W - Gelman, L - Feige, JN - Desvergne, B - Michalik, L - Pubmed - From molecular action to physiological outputs: peroxisome proliferator-activated receptors are nuclear receptors at the crossroads of key cellular functions - Prog Lipid Res 45:120-59 - 2006 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12373 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10799 - - - - - - MOD_RES Phosphothreonine (By similarity) - - - - 400305 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400305 - - - - ENSP00000433425 - Ensembl - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of FABP1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation205 - - - - EQUAL - 82 - http://www.reactome.org/biopax/46/48887#SequenceSite9907 - - - - Thrombin-activable fibrinolysis inhibitor - pCPB - 3.4.17.20 - Plasma carboxypeptidase B - CPU - Carboxypeptidase U - TAFI - CPB2 - - - - - - - - - - - - - - - - - - - CBPB2_HUMAN - Carboxypeptidase B2 - FUNCTION: Cleaves C-terminal arginine or lysine residues from biologically active peptides such as kinins or anaphylatoxins in the circulation thereby regulating their activities. Down- regulates fibrinolysis by removing C-terminal lysine residues from fibrin that has already been partially degraded by plasmin.CATALYTIC ACTIVITY: Release of C-terminal Arg and Lys from a polypeptide.COFACTOR: Binds 1 zinc ion per subunit.ENZYME REGULATION: TAFI/CPB2 is unique among carboxypeptidases in that it spontaneously inactivates with a short half-life, a property that is crucial for its role in controlling blood clot lysis. The zymogen is stabilized by interactions with the activation peptide. Release of the activation peptide increases a dynamic flap mobility and in time this leads to conformational changes that disrupt the catalytic site and expose a cryptic thrombin-cleavage site present at Arg-324.SUBCELLULAR LOCATION: Secreted.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q96IY4-1; Sequence=Displayed; Name=2; IsoId=Q96IY4-2; Sequence=VSP_013446, VSP_013447;TISSUE SPECIFICITY: Plasma; synthesized in the liver.PTM: N-glycosylated. N-glycan at Asn-108: Hex5HexNAc4.SIMILARITY: Belongs to the peptidase M14 family.WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/cpb2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - PR285_HUMAN - Peroxisomal proliferator-activated receptor A-interacting complex 285 kDa protein - PRIC285 - - - - - http://www.reactome.org/biopax/46/48887#Protein6499 - Reactome DB_ID: 442499 - HELZ2 - - - - EQUAL - 89 - - - - HGNC:1663 - HGNC - - - - 400368 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400368 - - - - ENSP00000217964 - Ensembl - - - - 174207 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174207 - - - - - - MOD_RES 119 119 Phosphoserine. - - - - 400149 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400149 - - - - - - MOD_RES 640 640 Phosphothreonine; alternate. - - - - EQUAL - 57 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21449 - - - - HGNC:7996 - HGNC - - - - - - - - - Ubiquitination of CRY Proteins - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3863 - Edited: May, B, 2010-02-20 - Reviewed: Hirota, T, 2010-06-23 - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - Polyubiquitination of CRY proteins is directed by the FBXL3 component of SCF E3 ubiquitin ligase. The polyubiquitinated CRY proteins are recognized and degraded by the 26S proteasome. Degradation of CRY proteins occurs during the night and is necessary to allow new transcription of BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) targets in the morning during the circadian cycle. - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - - CREB1 - HGNC Symbol - - - - EQUAL - 41 - http://www.reactome.org/biopax/46/48887#SequenceSite23027 - - - - REACT_27087 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27087.2 - - - - 1605575 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1605575 - - - - ENSP00000370723 - Ensembl - - - - A4D0Q9 - UniProt - - - - - - MOD_RES 60 60 Phosphothreonine. - - - - REACT_118044 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118044.1 - - - - 2393991 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2393991 - - - - Q6N0A4 - UniProt - - - - 159762 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159762 - - - - NM_002397 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4653 - - - - ENST00000217233 - Ensembl - - - - EQUAL - 2184 - - - - CHEBI:34154 - ChEBI - - - - EQUAL - 178 - http://www.reactome.org/biopax/46/48887#SequenceSite12351 - - - - EQUAL - 1156 - - - - UXOWGYHJODZGMF-QORCZRPOSA-N - InChIKey - - - - REACT_3716 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3716.3 - - - - - 3.4.21 - - - - pro-protein S -> protein S + protein S propeptide - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3905 - At the beginning of this reaction, 1 molecule of 'pro-protein S' is present. At the end of this reaction, 1 molecule of 'protein S propeptide', and 1 molecule of 'protein S' are present.<br><br> This reaction takes place in the 'Golgi lumen' and is mediated by the 'furin activity' of 'furin'.<br> - - - - - - 381235 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381235 - - - - REACT_25415 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25415.1 - - - - CHEBI:22608 - ChEBI - - - - - - MOD_RES 2 2 N-acetylserine. - - - - - - MOD_RES 779 779 N6-acetyllysine (By similarity). - - - - EQUAL - 400 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5653 - - - - - - EQUAL - 215 - - - - NP_001018086 - RefSeq - - - - - UGT1I - UGT1*9 - UDPGT 1-9 - UGT1 - GNT1 - lugP4 - UGT1-09 - UGT1A9 - UDP-glucuronosyltransferase 1-I - UDP-glucuronosyltransferase 1A9 - 2.4.1.17 - UGT-1I - UGT1.9 - - - - - - - - - - - - - UD19_HUMAN - UDP-glucuronosyltransferase 1-9 - FUNCTION: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform has specificity for phenols.CATALYTIC ACTIVITY: UDP-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside.SUBCELLULAR LOCATION: Microsome. Endoplasmic reticulum membrane; Single-pass membrane protein (Potential).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=1; Comment=A number of isoforms may be produced. Isoforms have a different N-terminal domain and a common C-terminal domain of 245 residues; Name=1; IsoId=O60656-1; Sequence=Displayed;TISSUE SPECIFICITY: Liver.SIMILARITY: Belongs to the UDP-glycosyltransferase family.SEQUENCE CAUTION: Sequence=AAB19791.2; Type=Frameshift; Positions=59, 82; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 12377782 - Barbier, O - Fruchart, JC - Duez, H - Staels, B - Fruchart, J - Mautino, G - Raspè, E - Duval, C - Fontaine, C - Monte, D - Pubmed - Transcriptional regulation of human Rev-erbalpha gene expression by the orphan nuclear receptor retinoic acid-related orphan receptor alpha - J Biol Chem 277:49275-81 - 2002 - - - - REACT_4717 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4717.2 - - - - CHEBI:41879 - ChEBI - - - - - - MOD_RES 2037 2037 N6-acetyllysine. - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1835 - - - - NM_003214 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2089 - - - - 26697309 - pubchem - - - - HGNC:4247 - HGNC - - - - EQUAL - 71 - http://www.reactome.org/biopax/46/48887#SequenceSite10043 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2415 - - - - 1989773 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989773 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite23170 - - - - 1N9U - PROTEIN DATA BANK - - - - 12034728 - Lin PJ - Jin DY - Stafford DW - Tie JK - Presnell SR - Straight DL - PubMed - The putative vitamin K-dependent gamma-glutamyl carboxylase internal propeptide appears to be the propeptide binding site. - J Biol Chem 277(32);28584-91 - 2002 - - - - ENSP00000366419 - Ensembl - - - - REACT_17671 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17671.2 - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite21684 - - - - - - MOD_RES 1177 1177 N6-acetyllysine. - - - - NP_000850 - RefSeq - - - - ENST00000394128 - Ensembl - - - - REACT_117119 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117119.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8344 - - - - - - MOD_RES 129 129 N6-acetyllysine; by PCAF/KAT2B. - - - - NP_599022 - RefSeq - - - - REACT_5806 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5806.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5062 - - - - 11533283 - pubchem-substance - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2223 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4778 - - - - HGNC:11717 - HGNC - - - - ENSP00000262735 - Ensembl - - - - ENST00000256495 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12328 - - - - HGNC:9460 - HGNC - - - - REACT_19934 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19934.2 - - - - EQUAL - 211 - http://www.reactome.org/biopax/46/48887#SequenceSite3898 - - - - Q13503 - UniProt - - - - ENST00000311227 - Ensembl - - - - ENSP00000293217 - Ensembl - - - - - - - - - ACTIVATION - - 'ROR-alpha:Coactivator [nucleoplasm]' positively regulates 'Expression of NPAS2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation90 - As inferred from mouse, ROR-alpha binds the promoter of the NPAS2 gene and enhances transcription. - - - - - - - - - - - - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#SmallMolecule731 - Reactome DB_ID: 381235 - Ligands of PPARG - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7594 - - - - - - Peroxisome proliferator-activated receptor gamma - PPARG_HUMAN - - - - - Reactome DB_ID: 446172 - http://www.reactome.org/biopax/46/48887#Protein6462 - PPARG - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8337 - - - - ENSP00000417222 - Ensembl - - - - REACT_3316 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3316.3 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature3950 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4762 - - - - - - Q9P2Y6 - UniProt - - - - REACT_13171 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13171.1 - - - - 159853 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159853 - - - - UBC - HGNC Symbol - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 2990849 - http://www.reactome.org/biopax/46/48887#Protein12339 - Renin - - - - - - 13xCbxE-PROZ(24-400) - - - - - - - - - - - - - - - - - - Reactome DB_ID: 163827 - http://www.reactome.org/biopax/46/48887#Protein11653 - pro-protein Z - - - - REACT_164275 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164275.1 - - - - NP_001181974 - RefSeq - - - - 421342 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421342 - - - - CRY1 - HGNC Symbol - - - - - - Soluble ACE - Secreted ACE - ACE(30-1232) - Angiotensin-converting enzyme - - - - - Reactome DB_ID: 2065414 - http://www.reactome.org/biopax/46/48887#Protein12344 - ACE_HUMAN - - - - 1PDG - PROTEIN DATA BANK - - - - 174061 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174061 - - - - ANGPTL4 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10177 - - - - - - - - MOD_RES 527 527 Phosphoserine (By similarity). - - - - 10601301 - Nakamura, M - Cho, HP - Clarke, SD - Pubmed - Cloning, expression, and fatty acid regulation of the human delta-5 desaturase - J Biol Chem 274:37335-9 - 1999 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4733 - - - - EQUAL - 110 - - - - NP_006531 - RefSeq - - - - REACT_3946 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3946.2 - - - - EQUAL - 608 - http://www.reactome.org/biopax/46/48887#SequenceSite4668 - - - - ENST00000398997 - Ensembl - - - - ENSP00000323720 - Ensembl - - - - EQUAL - 113 - - - - REACT_147747 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147747.2 - - - - - - MOD_RES 26 26 Phosphoserine. - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4707 - - - - NP_619726 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5612 - - - - A8K645 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10752 - - - - 400167 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400167 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1102 - - - - ENST00000263253 - Ensembl - - - - ENST00000430157 - Ensembl - - - - 879813 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879813 - - - - - - - SREBF1A/1C/2 Dimer - - - - SREBP1A/1C/2 Dimer - http://www.reactome.org/biopax/46/48887#Complex5484 - Reactome DB_ID: 1655744 - - - - ENST00000258648 - Ensembl - - - - 939862 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939862 - - - - Q14514 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10119 - - - - 603800 - omim - - - - SP1 - HGNC Symbol - - - - EQUAL - 406 - http://www.reactome.org/biopax/46/48887#SequenceSite23009 - - - - - - ANG2-8 - AGT(35-41) - ANGT_HUMAN - Angiotensin-(2-8) - Angiotensin III - - - - - Reactome DB_ID: 2022354 - http://www.reactome.org/biopax/46/48887#Protein12352 - AGT - - - - EQUAL - 878 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4702 - - - - ENST00000381551 - Ensembl - - - - Q96ND3 - UniProt - - - - - - - - - Edited: May, B, 2011-06-22 - The ELOVL3 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction72 - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - Expression of ELOVL3 - - - - FHL2 - HGNC Symbol - - - - REACT_27129 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27129.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5658 - - - - - - EQUAL - 178 - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - http://www.reactome.org/biopax/46/48887#TemplateReaction63 - The NOCTURNIN gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The NOCTURNIN gene shows circadian expression because the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds an E-box element in the NOCTURNIN promoter and activates transcription. - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-03-19 - Reviewed: Delaunay, F, 2010-06-23 - Authored: May, B, 2010-03-19 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Expression of NOCTURNIN - - - - NM_018955 - RefSeq - - - - - - - Casein Kinase I delta or Casein kinase I epsilon - - - - http://www.reactome.org/biopax/46/48887#Protein11530 - Converted from EntitySet in Reactome - Reactome DB_ID: 421304 - CSNK1E/CSNK1D - - - - - - MOD_RES 604 604 Omega-N-methylated arginine; by CARM1. - - - - 174138 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174138 - - - - 1989810 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989810 - - - - ENSP00000216338 - Ensembl - - - - HGNC:2298 - HGNC - - - - - - MOD_RES 700 700 Phosphoserine (By similarity). - - - - NM_001142269 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10001 - - - - ENSG00000155111 - Ensembl - - - - Q86SU6 - UniProt - - - - ENSP00000255764 - Ensembl - - - - HGNC:10899 - HGNC - - - - ENST00000361003 - Ensembl - - - - 1368125 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368125 - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14058 - - - - TXNRD1 - HGNC - - - - 400122 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400122 - - - - NP_001191190 - RefSeq - - - - EQUAL - 56 - - - - Q6GT90 - UniProt - - - - EQUAL - 716 - - - - ENST00000311001 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5676 - - - - - - NP_001032412 - RefSeq - - - - - - MOD_RES 338 338 Phosphoserine; by SIK1 (By similarity). - - - - CHEBI:22462 - ChEBI - - - - EQUAL - 589 - - - - 184756 - omim - - - - - - MOD_RES 1590 1590 N6-acetyllysine. - - - - Q9H5V3 - UniProt - - - - EQUAL - 794 - http://www.reactome.org/biopax/46/48887#SequenceSite4971 - - - - - - MOD_RES 616 616 N6-acetyllysine; by CREBBP. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10149 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The ABCB4 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction138 - Expression of ABCB4 - - - - Q9UNB3 - UniProt - - - - MOD_RES Nitrated tyrosine (By similarity) - - - - REACT_25084 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25084.3 - - - - ENSP00000385246 - Ensembl - - - - Q8N6Y4 - UniProt - - - - 8145133 - pubchem-substance - - - - ENST00000302182 - Ensembl - - - - REACT_148647 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148647.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10028 - - - - REACT_12866 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12866.1 - - - - - - MOD_RES 267 267 Phosphoserine. - - - - NCOA2 - HGNC - - - - EQUAL - 44 - http://www.reactome.org/biopax/46/48887#SequenceSite21727 - - - - ENSP00000377685 - Ensembl - - - - EQUAL - 76 - - - - - - MOD_RES 1386 1386 Phosphoserine; by IKKA. - - - - ENSP00000354097 - Ensembl - - - - Q53S74 - UniProt - - - - Q2T9G5 - UniProt - - - - NM_206824 - RefSeq - - - - - - MOD_RES 1591 1591 N6-acetyllysine. - - - - 400207 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400207 - - - - GO:0005796 - Gene Ontology - - - - 517835 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=517835 - - - - EQUAL - 445 - - - - ENST00000465804 - Ensembl - - - - ENST00000310271 - Ensembl - - - - REACT_25657 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25657.2 - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite1777 - - - - 18654640 - Szekely, AM - Reed, BD - Weissman, SM - Charos, AE - Snyder, M - Pubmed - Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes - PLoS Genet 4:e1000133 - 2008 - - - - ENSEMBL:ENSG00000079459 FDFT1 - - FDFT1 - http://www.reactome.org/biopax/46/48887#DnaReference31 - - - - - B9ZVQ0 - UniProt - - - - Golgi lumen - - - - - Q0P5Z4 - UniProt - - - - 2065433 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065433 - - - - Q15354 - UniProt - - - - - - MOD_RES 1156 1156 Phosphoserine. - - - - HGNC:2385 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature827 - - - - REACT_27083 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27083.2 - - - - - - - - - - - - - - Circadian Repression of Expression by REV-ERBA - Edited: May, B, 2011-06-22 - http://www.reactome.org/biopax/46/48887#Pathway877 - REV-ERBA binds DNA elements very similar to those bound by the transcription activator RORA. RORAREV-ERBA bound to DNA and heme recruits the corepressors NCoR and HDAC3 to repress transcription. Thus REV-ERBA and RORA appear to compete to repress or activate genes, repectively. - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - - - - - 212331 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212331 - - - - - - - - - - Reactome DB_ID: 212441 - http://www.reactome.org/biopax/46/48887#Protein6490 - MED14 - - - - ENST00000376618 - Ensembl - - - - CHEBI:28364 - ChEBI - - - - endoplasmic reticulum lumen - - - - - MI:0355 - Molecular Interactions Ontology - - - - endoplasmic reticulum membrane - - - - - EQUAL - 1412 - - - - Q99475 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10010 - - - - peroxisomal matrix - - - - - EQUAL - 400 - http://www.reactome.org/biopax/46/48887#SequenceSite5742 - - - - 1L6L - PROTEIN DATA BANK - - - - - - - - ACTIVATION - - 'Cl- [extracellular region]' positively regulates 'Secreted ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control311 - - - - - - - - - http://www.reactome.org/biopax/46/48887#Dna33 - Reactome DB_ID: 2393991 - FDFT1 gene - - - - ENSG00000171720 - Ensembl - - - - - - MOD_RES 1463 1463 Phosphoserine. - - - - - - MOD_RES 2068 2068 Phosphoserine. - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1271 - - - - 9070950 - Foster DW - Burns DK - Esser V - Yarnall DP - Froguel P - Mackey DW - Britton CH - McGarry JD - PubMed - Fine chromosome mapping of the genes for human liver and muscle carnitine palmitoyltransferase I (CPT1A and CPT1B). - Genomics 40(1);209-11 - 1997 - - - - - - - - - - - - - - - - - - - PPARGC-1-alpha - PPARGC1 - PGC-1-alpha - LEM6 - Ligand effect modulator 6 - PGC1A - PGC1 - PPAR-gamma coactivator 1-alpha - PPARGC1A - - - - - - - - - - - - - - - - - - PRGC1_HUMAN - Peroxisome proliferator-activated receptor gamma coactivator 1-alpha - FUNCTION: Transcriptional coactivator for steroid receptors and nuclear receptors. Greatly increases the transcriptional activity of PPARG and thyroid hormone receptor on the uncoupling protein promoter. Can regulate key mitochondrial genes that contribute to the program of adaptive thermogenesis. Plays an essential role in metabolic reprogramming in response to dietary availability through coordination of the expression of a wide array of genes involved in glucose and fatty acid metabolism.SUBUNIT: Binds MYBBP1A, which inhibits transcriptional activation by this protein (By similarity). Interacts with PRDM16 (By similarity). Interacts with LRPPRC. Homooligomer. Interacts with LPIN1 (By similarity). Interacts with PML (By similarity).SUBCELLULAR LOCATION: Nucleus. Nucleus, PML body (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9UBK2-1; Sequence=Displayed; Name=2; IsoId=Q9UBK2-2; Sequence=VSP_047684, VSP_047685;TISSUE SPECIFICITY: Heart, skeletal muscle, liver and kidney. Expressed at lower levels in brain and pancreas and at very low levels in the intestine and white adipose tissue. In skeletal muscle, levels were lower in obese than in lean subjects and fasting induced a 2-fold increase in levels in the skeletal muscle in obese subjects.INDUCTION: Transcription is repressed by ZNF746 which binds to 'insulin response sequences' its promoter.PTM: Phosphorylation by AMPK in skeletal muscle increases activation of its own promoter (By similarity). Phosphorylated by CLK2 (By similarity).PTM: Heavily acetylated by GCN5 and biologically inactive under conditions of high nutrients. Deacetylated by SIRT1 in low nutrients/high NAD conditions.SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/ppargc1a/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1851 - - - - EQUAL - 1124 - - - - 603347 - omim - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - B3KVL4 - UniProt - - - - EQUAL - 145 - http://www.reactome.org/biopax/46/48887#SequenceSite11620 - - - - EQUAL - 281 - - - - ENST00000360632 - Ensembl - - - - ENSG00000112282 - Ensembl - - - - peroxisomal membrane - - - - - ENST00000343975 - Ensembl - - - - G0S2 - HGNC Symbol - - - - EQUAL - 496 - http://www.reactome.org/biopax/46/48887#SequenceSite11627 - - - - Q9Y3C6 - uniprot - - - - REACT_19283 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19283.1 - - - - EQUAL - 586 - http://www.reactome.org/biopax/46/48887#SequenceSite21448 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6485 - Reactome DB_ID: 212359 - MED6 - - - - 1989816 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989816 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4772 - - - - - ENST00000312865 - Ensembl - - - - CHEBI:123355 - ChEBI - - - - EQUAL - 2058 - - - - Q96F91 - UniProt - - - - ENSP00000314420 - Ensembl - - - - - - - - - - PDGF A homodimer - Reactome DB_ID: 380761 - http://www.reactome.org/biopax/46/48887#Complex892 - - - - ENSG00000170485 - Ensembl - - - - ENST00000392544 - Ensembl - - - - Q9HA81 - UniProt - - - - mitochondrial matrix - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval824 - - - - - - InChI=1S/C18H24N2O5/c1-12(16(21)20-11-5-8-15(20)18(24)25)19-14(17(22)23)10-9-13-6-3-2-4-7-13/h2-4,6-7,12,14-15,19H,5,8-11H2,1H3,(H,22,23)(H,24,25)/t12-,14-,15-/m0/s1 - InChI - - - - EQUAL - 739 - - - - 1989809 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989809 - - - - EQUAL - 472 - http://www.reactome.org/biopax/46/48887#SequenceSite1307 - - - - - - MOD_RES 1499 1499 N6-acetyllysine; by autocatalysis. - - - - - - MOD_RES 66 66 4-carboxyglutamate. - - - - ENST00000409469 - Ensembl - - - - EQUAL - 3 - http://www.reactome.org/biopax/46/48887#SequenceSite1302 - - - - HDAC3 - HGNC - - - - NP_003204 - RefSeq - - - - ENSP00000361066 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite11120 - - - - NP_001243022 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature7276 - - - - 300335 - omim - - - - mitochondrial inner membrane - - - - - ENST00000286317 - Ensembl - - - - 1360 - NCBI Gene - - - - mitochondrial outer membrane - - - - - - - MOD_RES 1403 1403 Phosphoserine. - - - - 14718224 - pubchem-substance - - - - Q4LE28 - UniProt - - - - ENST00000368911 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5314 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9753 - - - - - - RGL1 - HGNC Symbol - - - - EQUAL - 1051 - - - - NM_001256094 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1842 - - - - ENST00000354289 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21423 - - - - EQUAL - 34 - http://www.reactome.org/biopax/46/48887#SequenceSite23022 - - - - - - Platelet-derived growth factor subunit A - PDGFA_HUMAN - - - - - Reactome DB_ID: 3009039 - http://www.reactome.org/biopax/46/48887#Protein2639 - PDGFA - - - - - - MOD_RES 203 203 Phosphoserine. - - - - REACT_1969 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1969.3 - - - - EQUAL - 216 - - - - NP_001123617 - RefSeq - - - - ENST00000394949 - Ensembl - - - - 141412 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=141412 - - - - - - - - - - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11537 - Reactome DB_ID: 517938 - ub-p-CRY1/2 - - - - REACT_5471 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5471.2 - - - - EQUAL - 57 - http://www.reactome.org/biopax/46/48887#SequenceSite9683 - - - - - - MOD_RES 238 238 Phosphoserine. - - - - EQUAL - 593 - http://www.reactome.org/biopax/46/48887#SequenceSite21480 - - - - 380751 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380751 - - - - NFYC - HGNC - - - - - - - - - - Edited: May, B, 2011-06-22 - The NPAS2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. Transcription of NPAS2 is enhanced by the RORA:Coactivator complex and repressed by the REV-ERBA:Corepressor complex. - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction57 - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - Expression of NPAS2 - - - - - - MOD_RES 2058 2058 Phosphoserine. - - - - EQUAL - 1595 - - - - - - p-S-CRY2 - Phosphorylated Cryptochrome-2 - CRY2_HUMAN - - - - - - Reactome DB_ID: 400328 - http://www.reactome.org/biopax/46/48887#Protein11535 - p-CRY2 - - - - NM_003891 - RefSeq - - - - ENST00000309576 - Ensembl - - - - REACT_147889 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147889.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8330 - - - - - - - - - - CKI-delta - CKId - HCKID - CSNK1D - Tau-protein kinase CSNK1D - 2.7.11.1 - 2.7.11.26 - - - - - - - - - - - - - - - - - - - - KC1D_HUMAN - Casein kinase I isoform delta - FUNCTION: Essential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. It can phosphorylate a large number of proteins. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Phosphorylates connexin-43/GJA1, MAP1A, SNAPIN, MAPT/TAU, TOP2A, DCK, HIF1A, EIF6, p53/TP53, DVL2, DVL3, ESR1, AIB1/NCOA3, DNMT1, PKD2, YAP1, PER1 and PER2. Central component of the circadian clock. May act as a negative regulator of circadian rhythmicity by phosphorylating PER1 and PER2, leading to retain PER1 in the cytoplasm. YAP1 phosphorylation promotes its SCF(beta-TRCP) E3 ubiquitin ligase-mediated ubiquitination and subsequent degradation. DNMT1 phosphorylation reduces its DNA- binding activity. Phosphorylation of ESR1 and AIB1/NCOA3 stimulates their activity and coactivation. Phosphorylation of DVL2 and DVL3 regulates WNT3A signaling pathway that controls neurite outgrowth. EIF6 phosphorylation promotes its nuclear export. Triggers down-regulation of dopamine receptors in the forebrain. Activates DCK in vitro by phosphorylation. TOP2A phosphorylation favors DNA cleavable complex formation. May regulate the formation of the mitotic spindle apparatus in extravillous trophoblast. Modulates connexin-43/GJA1 gap junction assembly by phosphorylation. Probably involved in lymphocyte physiology. Regulates fast synaptic transmission mediated by glutamate.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.CATALYTIC ACTIVITY: ATP + [tau protein] = ADP + [tau protein] phosphate.ENZYME REGULATION: Exhibits substrate-dependent heparin activation. Drug-mediated inhibition leads to a delay of the oscillations with the magnitude of this effect dependent upon the timing of drug administration. Inhibited by phosphorylation. Repressed by 3-[(2,4,6-trimethoxyphenyl)methylidenyl]-indolin-2- one (IC261), N-(2-aminoethyl)-5-chloroisoquinoline-8-sulfonamide (CKI-7), 4-[4-(2,3-dihydro-benzo[1,4]dioxin-6-yl)-5-pyridin-2-yl- 1H-imidazol-2-yl]benzamide (D4476), 3,4-diaryl-isoxazoles and -imidazoles, and 4-(3-cyclohexyl-5-(4-fluoro-phenyl)-3H-imidazol- 4-yl) pyrimidin-2-ylamine (PF670462, PF670).BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=36.5 uM for alpha-casein; KM=635.8 uM for PER2 peptide; KM=180.6 uM for ATP; Note=Maximal velocity nearly identical for the reactions with alpha-casein and PER2 peptide;SUBUNIT: Binds to DNMT1 and MAP1A (By similarity). Monomer. Component of the circadian core oscillator, which includes the CRY proteins, CLOCK, or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Interacts directly with PER1 and PER2 which may lead to their degradation. Interacts with MAPT/TAU, SNAPIN, DBNDD2, AIB1/NCOA3 and ESR1. AKAP9/AKAP450 binding promotes centrosomal subcellular location. Binds to tubulins in mitotic cells upon DNA damage.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cytoplasm, perinuclear region. Cell membrane. Cytoplasm, cytoskeleton, spindle. Golgi apparatus. Note=Localized at mitotic spindle microtubules, and at the centrosomes and interphase in interphase cells. Recruited to the spindle apparatus and the centrosomes in response to DNA- damage. Correct subcellular localization requires kinase activity.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P48730-1; Sequence=Displayed; Name=2; IsoId=P48730-2; Sequence=VSP_010253;TISSUE SPECIFICITY: Expressed in all tissues examined, including brain, heart, lung, liver, pancreas, kidney, placenta and skeletal muscle. However, kinase activity is not uniform, with highest kinase activity in splenocytes. In blood, highly expressed in hemopoietic cells and mature granulocytes. Also found in monocytes and lymphocytes.DEVELOPMENTAL STAGE: Highly present in extravillous trophoblast cells, which are present at the placenta implantation site and invade the decidua and decidual vessels.PTM: Autophosphorylated on serine and threonine residues; this autophosphorylation represses activity. Reactivated by phosphatase-mediated dephosphorylation.DISEASE: Advanced sleep phase syndrome, familial, 2 (FASPS2) [MIM:615224]: A disorder characterized by very early sleep onset and offset. Individuals are 'morning larks' with a 4 hours advance of the sleep, temperature and melatonin rhythms. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: May be involved in Alzheimer disease by phosphorylating MAPT/TAU (PubMed:17562708).SIMILARITY: Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. Casein kinase I subfamily.SIMILARITY: Contains 1 protein kinase domain.CAUTION: Was shown to phosphorylate and activate DCK in vitro but probably not in vivo (PubMed:20637175). COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000536769 - Ensembl - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite10045 - - - - - - MOD_RES 664 664 Phosphothreonine (By similarity). - - - - ENST00000430624 - Ensembl - - - - 19800993 - Feierler, J - Jochum, M - Nägler, DK - Lottspeich, F - Mentele, R - Faussner, A - Kraus, S - Pubmed - A cysteine-type carboxypeptidase, cathepsin X, generates peptide receptor agonists - Int Immunopharmacol 10:134-9 - 2010 - - - - CHD9 - HGNC - - - - NP_001257710 - RefSeq - - - - NP_056953 - RefSeq - - - - O00150 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4710 - - - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21672 - - - - Q9UKW0 - UniProt - - - - - - - - - - - Neprilysin Hydrolyzes Angiotensin-(1-9) to Yield Angiotensin-(1-7) - Neprilysin hydrolyzes angiotensin-(1-9) to yield angiotensin-(1-7) (Rice et al. 2004). The hydrolysis of angiotensin-(1-9) catalyzed by neprilysin is more efficient than that catalyzed by angiotensin-converting enzyme (ACE) (Rice et al. 2004). - Authored: May, B, 2011-11-19 - Edited: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4047 - Reviewed: Joseph, J, 2012-08-06 - - - - - ENSP00000340934 - Ensembl - - - - REACT_118036 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118036.1 - - - - - - protein C light chain propeptide - - - - - http://www.reactome.org/biopax/46/48887#Protein11663 - Reactome DB_ID: 159779 - PROC(33-42) - - - - Mediator complex subunit CDK8 - CDK8 - Cell division protein kinase 8 - Mediator of RNA polymerase II transcription subunit CDK8 - Protein kinase K35 - 2.7.11.23 - 2.7.11.22 - - - - - - - - - - - - - - CDK8_HUMAN - Cyclin-dependent kinase 8 - FUNCTION: Component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Phosphorylates the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAp II), which may inhibit the formation of a transcription initiation complex. Phosphorylates CCNH leading to down-regulation of the TFIIH complex and transcriptional repression. Recruited through interaction with MAML1 to hyperphosphorylate the intracellular domain of NOTCH, leading to its degradation.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.CATALYTIC ACTIVITY: ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.COFACTOR: Magnesium (By similarity).SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The cylin/CDK pair formed by CCNC/CDK8 also associates with the large subunit of RNA polymerase II. Interacts with CTNNB1, GLI3 and MAML1.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P49336-1; Sequence=Displayed; Name=2; IsoId=P49336-2; Sequence=VSP_029970;SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.SIMILARITY: Contains 1 protein kinase domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000325464 - Ensembl - - - - EQUAL - 416 - http://www.reactome.org/biopax/46/48887#SequenceSite21474 - - - - 170998 - omim - - - - ENST00000433297 - Ensembl - - - - - - MOD_RES 1857 1857 Phosphothreonine. - - - - PTHR13808:SF0 - PANTHER Family - - - - ENSP00000325690 - Ensembl - - - - Q0D2P5 - UniProt - - - - 6256 - NCBI Gene - - - - ENST00000395851 - Ensembl - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1267 - - - - - - - - - - - - - - p-CRY:p-PER:Kinase - http://www.reactome.org/biopax/46/48887#Complex4983 - Reactome DB_ID: 421296 - - - - ENST00000379803 - Ensembl - - - - Q9UQI9 - UniProt - - - - NP_001193583 - RefSeq - - - - 879724 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879724 - - - - - - MOD_RES 2059 2059 Phosphoserine. - - - - - - CYPIA1 - Cytochrome P450 1A1 - P450 form 6 - P450-P1 - P450-C - - - - - Reactome DB_ID: 52623 - http://www.reactome.org/biopax/46/48887#Protein13765 - CYP1A1 - - - - ENSP00000361737 - Ensembl - - - - RORA - HGNC Symbol - - - - REACT_27698 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27698.3 - - - - EQUAL - 1248 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5315 - - - - - - A0A2V7 - UniProt - - - - 2393990 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2393990 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4714 - - - - - 1592238 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592238 - - - - - - - - - - - - - - PPARA:RXRA Heterodimer - http://www.reactome.org/biopax/46/48887#Complex5477 - Reactome DB_ID: 400138 - - - - 5244 - NCBI Gene - - - - NM_000313 - RefSeq - - - - - - - - - 2.3.3.10 - HMGCS - HMGCS1 - HMG-CoA synthase - 3-hydroxy-3-methylglutaryl coenzyme A synthase - - - - - - - - - - - - - - - - - HMCS1_HUMAN - Hydroxymethylglutaryl-CoA synthase, cytoplasmic - FUNCTION: This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.CATALYTIC ACTIVITY: Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3- hydroxy-3-methylglutaryl-CoA + CoA.PATHWAY: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step 2/3.SUBCELLULAR LOCATION: Cytoplasm.SIMILARITY: Belongs to the HMG-CoA synthase family.SEQUENCE CAUTION: Sequence=AAH00297.2; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - HGNC:18984 - HGNC - - - - 604062 - omim - - - - - - MOD_RES 384 384 Phosphoserine. - - - - Q6FHE7 - UniProt - - - - 1989825 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989825 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2224 - - - - EQUAL - 57 - - - - - - - - - - Reactome DB_ID: 212445 - http://www.reactome.org/biopax/46/48887#Protein6488 - MED1 - - - - 51645 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=51645 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1265 - - - - NP_001191188 - RefSeq - - - - NP_001001928 - RefSeq - - - - NM_003109 - RefSeq - - - - CRSP34 - CRSP8 - Transcriptional coactivator CRSP34 - MED27 - P37 TRAP/SMCC/PC2 subunit - Cofactor required for Sp1 transcriptional activation subunit 8 - CRSP complex subunit 8 - Mediator complex subunit 27 - - - - - - - - - - - - - - - - - - - - - - - - MED27_HUMAN - Mediator of RNA polymerase II transcription subunit 27 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q6P2C8-1; Sequence=Displayed; Name=2; IsoId=Q6P2C8-2; Sequence=VSP_051869;SIMILARITY: Belongs to the Mediator complex subunit 27 family.SEQUENCE CAUTION: Sequence=AAH02878.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH02878.1; Type=Erroneous termination; Positions=109; Note=Translated as Gln; Sequence=CAH72530.1; Type=Erroneous initiation; Sequence=CAH72547.1; Type=Erroneous initiation; Sequence=CAI13387.1; Type=Erroneous initiation; Sequence=CAI17284.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q504U2 - UniProt - - - - REACT_26910 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26910.2 - - - - ENSG00000100393 - Ensembl - - - - - - MOD_RES 208 208 Phosphothreonine (By similarity). - - - - ACSL1 - HGNC - - - - - 3.4.21 - - - - pro-protein Z -> protein Z + protein Z propeptide - At the beginning of this reaction, 1 molecule of 'pro-protein Z' is present. At the end of this reaction, 1 molecule of 'protein Z propeptide', and 1 molecule of 'protein Z' are present.<br><br> This reaction takes place in the 'Golgi lumen' and is mediated by the 'furin activity' of 'furin'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3906 - - - - - - 2999 - NCBI Gene - - - - REACT_15085 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15085.4 - - - - - - MOD_RES 214 214 Phosphoserine. - - - - Q6P9H6 - UniProt - - - - CTGF - HGNC Symbol - - - - EQUAL - 110 - http://www.reactome.org/biopax/46/48887#SequenceSite23034 - - - - NM_015076 - RefSeq - - - - NP_671756 - RefSeq - - - - CYP1A1 - HGNC Symbol - - - - - - MOD_RES 407 407 Phosphotyrosine; by ABL1. - - - - ENST00000392811 - Ensembl - - - - 2022379 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022379 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7593 - - - - EQUAL - 41 - http://www.reactome.org/biopax/46/48887#SequenceSite6201 - - - - EQUAL - 402 - http://www.reactome.org/biopax/46/48887#SequenceSite9718 - - - - REACT_117983 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117983.1 - - - - HGNC:19338 - HGNC - - - - ENSP00000262188 - Ensembl - - - - Q9UD31 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2428 - - - - - - Q4ZFU9 - UniProt - - - - O95783 - UniProt - - - - - - MOD_RES 4 4 N6-acetyllysine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval604 - - - - - - Q96I35 - UniProt - - - - 17803194 - Taylor, H - Wallis, JA - Axton, R - Hanks, M - Forrester, LM - Pubmed - Aminopeptidase O contains a functional nucleolar localization signal and is implicated in vascular biology - J Cell Biochem 103:1171-82 - 2008 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4645 - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite1776 - - - - REACT_26715 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26715.3 - - - - 2990853 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2990853 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14056 - - - - REACT_24496 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24496.2 - - - - Q6UXN0 - UniProt - - - - NP_001420 - RefSeq - - - - - - Steroid hormone receptor ERR1 - ERR1_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein10802 - Reactome DB_ID: 446159 - ESRRA - - - - ENST00000537812 - Ensembl - - - - - - MOD_RES 260 260 Phosphoserine; by MAPK8 and MAPK9 (By similarity). - - - - NP_542382 - RefSeq - - - - ENST00000394464 - Ensembl - - - - EQUAL - 608 - http://www.reactome.org/biopax/46/48887#SequenceSite12413 - - - - NM_005037 - RefSeq - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1273 - - - - HGNC:12541 - HGNC - - - - REACT_2305 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2305.2 - - - - 159756 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159756 - - - - 2990877 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2990877 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of UGT1A9' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation222 - - - - - - MOD_RES 851 851 Phosphoserine. - - - - 55588 - NCBI Gene - - - - REACT_7631 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7631.1 - - - - EQUAL - 68 - http://www.reactome.org/biopax/46/48887#SequenceSite9874 - - - - - - MOD_RES 2 2 N-acetylserine. - - - - EQUAL - 55 - http://www.reactome.org/biopax/46/48887#SequenceSite9684 - - - - EQUAL - 371 - - - - Q7Z3W5 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature123 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12825 - - - - NM_147233 - RefSeq - - - - NM_138712 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12838 - - - - HIF1A - HGNC - - - - 549578 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549578 - - - - REACT_7889 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7889.2 - - - - ENSP00000268711 - Ensembl - - - - GO:0008237 - GENE ONTOLOGY - - - - - - - MOD_RES 439 439 N6-acetyllysine; alternate. - - - - - - MOD_RES 247 247 Phosphoserine; by MAPK (By similarity). - - - - ENSP00000364709 - Ensembl - - - - EQUAL - 484 - http://www.reactome.org/biopax/46/48887#SequenceSite12331 - - - - NAMPT - HGNC - - - - REACT_27926 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27926.2 - - - - ENST00000301645 - Ensembl - - - - REACT_26754 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26754.3 - - - - REACT_18197 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18197.1 - - - - 6233 - NCBI Gene - - - - EQUAL - 197 - http://www.reactome.org/biopax/46/48887#SequenceSite21665 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite886 - - - - P28347 - UniProt - - - - - - MOD_RES 857 857 Phosphoserine. - - - - ENSG00000005471 - Ensembl - - - - Q9H944 - UniProt - - - - EQUAL - 41 - http://www.reactome.org/biopax/46/48887#SequenceSite21725 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12816 - - - - 3017438 - Maeder, DL - Ehlers, MR - Kirsch, RE - Pubmed - Rapid affinity chromatographic purification of human lung and kidney angiotensin-converting enzyme with the novel N-carboxyalkyl dipeptide inhibitor N-[1(S)-carboxy-5-aminopentyl]glycylglycine - Biochim Biophys Acta 883:361-72 - 1986 - - - - CHEBI:28433 - ChEBI - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21485 - - - - NM_001450 - RefSeq - - - - D3DWG3 - UniProt - - - - REACT_15128 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15128.5 - - - - CHEBI:4461 - ChEBI - - - - ENST00000360439 - Ensembl - - - - - - presqualene-di-diphosphate synthase - farnesyltransferase - Farnesyl-diphosphate farnesyltransferase - squalene synthase - - - - - http://www.reactome.org/biopax/46/48887#Protein13772 - Reactome DB_ID: 191369 - FDFT1 - - - - Q9BS95 - UniProt - - - - EQUAL - 533 - http://www.reactome.org/biopax/46/48887#SequenceSite4667 - - - - ENSG00000221983 - Ensembl - - - - Q13952 - UniProt - - - - BHLHE40 - HGNC Symbol - - - - InChI=1S/C18H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h3-4,6-7,9-10H,2,5,8,11-17H2,1H3,(H,19,20)/b4-3-,7-6-,10-9- - InChI - - - - ENSP00000370963 - Ensembl - - - - A8K464 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1088 - - - - CTSD - HGNC - - - - 163816 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163816 - - - - - - MOD_RES 7 7 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10139 - - - - NM_005036 - RefSeq - - - - 138040 - omim - - - - PER1 - HGNC Symbol - - - - 7005 - NCBI Gene - - - - 8454 - NCBI Gene - - - - ENSP00000408315 - Ensembl - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of NAMPT (NamPRT, PBEF, Visfatin)' - As inferred from mouse, the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds an E-box element in the promoter of the NAMPT gene and enhances transcription. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation102 - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry3485 - - - - O15379 - UniProt - - - - NM_000133 - RefSeq - - - - ENSP00000456585 - Ensembl - - - - Q93074 - UniProt - - - - 1SP1 - PROTEIN DATA BANK - - - - REACT_3690 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3690.2 - - - - EQUAL - 121 - - - - - - MOD_RES 22 22 Phosphoserine (By similarity). - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1081 - - - - - - MOD_RES 551 551 Phosphoserine; by GSK3-beta. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10145 - - - - REACT_161260 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161260.1 - - - - - - MOD_RES 72 72 4-carboxyglutamate. - - - - F2 - HGNC Symbol - - - - 605043 - omim - - - - ENSP00000397593 - Ensembl - - - - ENSP00000386633 - Ensembl - - - - 9110174 - Lennon G - Andersson B - Yu W - Ding Y - Wentland MA - Gibbs RA - Worley KC - Liu W - Muzny DM - Ricafrente JY - PubMed - Large-scale concatenation cDNA sequencing. - Genome Res 7(4);353-8 - 1997 - - - - P04035 - UniProt - - - - 29079 - NCBI Gene - - - - Q6FI31 - UniProt - - - - REACT_25092 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25092.1 - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12947 - - - - REACT_119773 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119773.1 - - - - - - - - - - Reactome DB_ID: 176559 - http://www.reactome.org/biopax/46/48887#Protein13781 - SULT2A1 - - - - 173360 - omim - - - - EQUAL - 406 - http://www.reactome.org/biopax/46/48887#SequenceSite22999 - - - - Q86U60 - UniProt - - - - EQUAL - 26 - http://www.reactome.org/biopax/46/48887#SequenceSite12410 - - - - 2263504 - Bishop DF - PubMed - Two different genes encode delta-aminolevulinate synthase in humans: nucleotide sequences of cDNAs for the housekeeping and erythroid genes. - Nucleic Acids Res 18(23);7187-8 - 1990 - - - - NP_003838 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite18498 - - - - REACT_1065 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1065.3 - - - - ENSP00000470419 - Ensembl - - - - EQUAL - 967 - http://www.reactome.org/biopax/46/48887#SequenceSite23033 - - - - MOD_RES N6-succinyllysine (By similarity) - - - - - - MOD_RES 293 293 Phosphothreonine; by MAPK14. - - - - ENST00000420343 - Ensembl - - - - - - MOD_RES 400 400 Phosphoserine; by CK1. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12060 - - - - - - REACT_18738 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18738.2 - - - - - - MOD_RES 702 702 Phosphoserine; alternate. - - - - - - - - - - - - pro-protein C - http://www.reactome.org/biopax/46/48887#Complex5017 - Reactome DB_ID: 159731 - - - - ENST00000370841 - Ensembl - - - - NM_004462 - RefSeq - - - - NP_004889 - RefSeq - - - - REACT_118740 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118740.2 - - - - EQUAL - 662 - - - - 600662 - omim - - - - ENSP00000379153 - Ensembl - - - - Q9NZU4 - UniProt - - - - - - MOD_RES 645 645 Phosphotyrosine (By similarity). - - - - ENST00000432329 - Ensembl - - - - REACT_8829 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_8829.2 - - - - P0CG48 - UniProt - - - - EQUAL - 860 - - - - ENST00000393352 - Ensembl - - - - 2022356 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022356 - - - - 2026984 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2026984 - - - - - - - - - - INHIBITION - - 'aliskiren [extracellular region]' negatively regulates 'Renin:Prorenin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10)' - http://www.reactome.org/biopax/46/48887#Control301 - - - - - - - - - - - - pro-factor X - http://www.reactome.org/biopax/46/48887#Complex5013 - Reactome DB_ID: 159734 - - - - ENST00000396832 - Ensembl - - - - REACT_19814 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19814.1 - - - - - - - - - - - - Formation of CRY:PER:Kinase Complex - Reviewed: Kay, SA, 2010-06-23 - Authored: May, B, 2011-10-29 - CRYPTOCHROME, PERIOD, and a kinase (CKIepsilon or CKIdelta) form a ternary complex in the cytosol. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3857 - Edited: May, B, 2011-10-29 - Reviewed: Hirota, T, 2010-06-23 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - - - - - EQUAL - 2026 - - - - 300188 - omim - - - - EQUAL - 412 - http://www.reactome.org/biopax/46/48887#SequenceSite23001 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10767 - - - - - - p-S-CRY2 - Phosphorylated Cryptochrome-2 - CRY2_HUMAN - - - - - - http://www.reactome.org/biopax/46/48887#Protein11523 - Reactome DB_ID: 400305 - p-CRY2 - - - - EQUAL - 1032 - - - - REACT_151863 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_151863.1 - - - - ENST00000356219 - Ensembl - - - - HGNC:2453 - HGNC - - - - ENST00000542499 - Ensembl - - - - ENST00000520429 - Ensembl - - - - EQUAL - 1121 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12977 - - - - - - MOD_RES 2 2 Phosphoserine. - - - - O43513 - UniProt - - - - EQUAL - 989 - http://www.reactome.org/biopax/46/48887#SequenceSite12341 - - - - ENSG00000120837 - Ensembl - - - - NM_002569 - RefSeq - - - - 9968 - NCBI Gene - - - - 10882719 - Norlin M - Andersson U - Bjorkhem I - Wikvall K - PubMed - Oxysterol 7 alpha-hydroxylase activity by cholesterol 7 alpha-hydroxylase (CYP7A). - J Biol Chem 275(44);34046-53 - 2000 - - - - ENST00000268171 - Ensembl - - - - UBC - Ubiquitin - - - - - - - - - - UBC_HUMAN - Polyubiquitin-C - FUNCTION: Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: For the sake of clarity sequence features are annotated only for the first chain, and are not repeated for each of the following chains.SIMILARITY: Belongs to the ubiquitin family.SIMILARITY: Contains 9 ubiquitin-like domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 2222 - NCBI Gene - - - - CHEBI:14730 - ChEBI - - - - UBB - Ubiquitin - - - - - - - - - - - - - - - UBB_HUMAN - Polyubiquitin-B - FUNCTION: Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: The mRNA encoding variant UBB(+1) is produced by an unknown mechanism involving the deletion of a GT dinucleotide in the close proximity of a GAGAG motif (PubMed:9422699). This variant mRNA is found in normal brain, but the encoded protein accumulates only in brain neurofibrillary tangles and neuritic plaques in Alzheimer disease and other tauopathies, as well as polyglutaminopathies (PubMed:14597671). UBB(+1) variant cannot be used for polyubiquitination, is not effectively degraded by the proteasome when ubiquitinated and ubiquitinated UBB(+1) is refractory to disassembly by deubiquitinating enzymes (DUBs). In healthy brain, UBB(+1) C-terminus can be cleaved by UCHL3 (PubMed:21762696).MISCELLANEOUS: For a better understanding, features related to ubiquitin are only indicated for the first chain.SIMILARITY: Belongs to the ubiquitin family.SIMILARITY: Contains 3 ubiquitin-like domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2413 - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21660 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10800 - - - - - - NM_007287 - RefSeq - - - - gene ontology term for cellular function - - - - - REACT_4498 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4498.2 - - - - ENSP00000320940 - Ensembl - - - - gene ontology term for cellular process - - - - - EQUAL - 66 - - - - - - HDAC3_HUMAN - Histone deacetylase 3 - - - - - Reactome DB_ID: 442464 - http://www.reactome.org/biopax/46/48887#Protein2499 - HDAC3 - - - - NP_001003801 - RefSeq - - - - EQUAL - 310 - - - - NP_001120800 - RefSeq - - - - NM_021804 - RefSeq - - - - REACT_3830 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3830.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21421 - - - - ENSP00000312649 - Ensembl - - - - 20936127 - Kersten, S - Knoch, B - Rakhshandehroo, M - Müller, M - Pubmed - Peroxisome proliferator-activated receptor alpha target genes - PPAR Res 2010: - 2010 - - - - - 8.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12954 - - - - D7F7N5 - UniProt - - - - - - MOD_RES 956 956 Phosphoserine. - - - - NCOA1 - HGNC - - - - EQUAL - 1290 - http://www.reactome.org/biopax/46/48887#SequenceSite21488 - - - - EQUAL - 887 - - - - REACT_20142 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20142.1 - - - - 1989788 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989788 - - - - GO:0004252 - GENE ONTOLOGY - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10131 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1855 - - - - 20380117 - Buksa, M - Loza, V - Gerc, V - Kulic, M - Pubmed - Is aliskiren superior to inhibitors of angiotensin-converting enzyme and angiotensin receptor blockers in renin-angiotensin system blockade? - Med Arh 63:343-9 - 2009 - - - - ENSG00000110243 - Ensembl - - - - EQUAL - 539 - http://www.reactome.org/biopax/46/48887#SequenceSite21492 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8324 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10144 - - - - A4D0R0 - UniProt - - - - 400143 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400143 - - - - - - UBC(1-76) - ubiquitin (UBC 1) - - - - - Reactome DB_ID: 939188 - http://www.reactome.org/biopax/46/48887#Protein1049 - UBC - - - - NP_877420 - RefSeq - - - - CHEBI:4764 - ChEBI - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12973 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12071 - - - - - - 174155 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174155 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5607 - - - - EQUAL - 138 - - - - ENST00000439329 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10046 - - - - - - EQUAL - 41 - http://www.reactome.org/biopax/46/48887#SequenceSite23031 - - - - REACT_4145 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4145.2 - - - - - - - - Pro-protein Z is transported from the endoplasmic reticulum to the Golgi apparatus - In this reaction, 1 molecule of 'pro-protein Z' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3898 - - - - - ENSP00000329357 - Ensembl - - - - ENSP00000356210 - Ensembl - - - - 556761 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556761 - - - - ENST00000395095 - Ensembl - - - - 1GWQ - PROTEIN DATA BANK - - - - 184201 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=184201 - - - - Q9UNP7 - UniProt - - - - REACT_1535 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1535.3 - - - - Q5JYJ8 - UniProt - - - - 300746 - omim - - - - EQUAL - 604 - - - - - - MOD_RES 1472 1472 Phosphoserine. - - - - A6NMB4 - UniProt - - - - PPARA - HGNC - - - - ENST00000397010 - Ensembl - - - - SREBF1 - HGNC Symbol - - - - 18317514 - Katayama, S - Inoue, I - Takahashi, S - Nakamura, K - Komoda, T - Pubmed - Cryptochrome and Period Proteins Are Regulated by the CLOCK/BMAL1 Gene: Crosstalk between the PPARs/RXRalpha-Regulated and CLOCK/BMAL1-Regulated Systems - PPAR Res 2008:348610 - 2008 - - - - 1453 - NCBI Gene - - - - ANKRD1 - HGNC - - - - ENSP00000222122 - Ensembl - - - - 1592257 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592257 - - - - A8K9N4 - UniProt - - - - CYP1A1 - HGNC - - - - Q8N1N9 - UniProt - - - - 1588921 - Watson WG - Madden BJ - Wood TC - Otterness DM - Weinshilboum RM - McCormick DJ - Wieben ED - PubMed - Human liver dehydroepiandrosterone sulfotransferase: molecular cloning and expression of cDNA. - Mol Pharmacol 41(5);865-72 - 1992 - - - - 212410 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212410 - - - - 2466373 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2466373 - - - - EQUAL - 79 - - - - NP_055206 - RefSeq - - - - CREBBP - HGNC Symbol - - - - EQUAL - 48 - - - - REACT_3279 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3279.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10792 - - - - - - GO:0008488 - GENE ONTOLOGY - - - - - NP_001238754 - RefSeq - - - - 2990850 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2990850 - - - - 400163 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400163 - - - - ARNTL2 - HGNC - - - - HGNC:32687 - HGNC - - - - EQUAL - 1057 - - - - MOD_RES Phosphotyrosine - - - - - - - - - - - - - - - - - - - - - - - - - - PPARG:Fatty Acid:RXRA:Mediator:Coactivator Complex - http://www.reactome.org/biopax/46/48887#Complex3136 - Reactome DB_ID: 381367 - - - - B2RDL8 - UniProt - - - - - - Ub-p-S-CRY2 - CRY2_HUMAN - Ubiquitinated Phosphorylated Cryptochrome-2 - - - - - - - Reactome DB_ID: 517935 - http://www.reactome.org/biopax/46/48887#Protein11539 - ub-p-CRY2 - - - - REACT_27102 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27102.3 - - - - - MED30 - Mediator complex subunit 30 - Trap25 - Thyroid hormone receptor-associated protein 6 - THRAP6 - TRAP25 - TRAP/Mediator complex component TRAP25 - Thyroid hormone receptor-associated protein complex 25 kDa component - - - - - - - - - - - - MED30_HUMAN - Mediator of RNA polymerase II transcription subunit 30 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).TISSUE SPECIFICITY: Expressed in brain, heart, kidney, liver, lung, pancreas, placenta and skeletal muscle.SIMILARITY: Belongs to the Mediator complex subunit 30 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - FURIN - HGNC Symbol - - - - - - MOD_RES 664 664 Phosphoserine. - - - - - - MOD_RES 1412 1412 N6-acetyllysine. - - - - 8864 - NCBI Gene - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - NM_001255 - RefSeq - - - - F9 - HGNC - - - - 11929048 - Furuyama K - Sassa S - PubMed - Multiple mechanisms for hereditary sideroblastic anemia. - Cell Mol Biol (Noisy-le-grand) 48(1);5-10 - 2002 - - - - NP_037393 - RefSeq - - - - EQUAL - 182 - http://www.reactome.org/biopax/46/48887#SequenceSite11617 - - - - P0CG47 - UniProt - - - - ENST00000340208 - Ensembl - - - - NM_014815 - RefSeq - - - - - - MOD_RES 278 278 N6-acetyllysine (By similarity). - - - - - - MOD_RES 1583 1583 N6-acetyllysine. - - - - 11929042 - Cheltsov AV - Ferreira GC - PubMed - Circular permutation of 5-aminolevulinate synthase as a tool to evaluate folding, structure and function. - Cell Mol Biol (Noisy-le-grand) 48(1);11-6 - 2002 - - - - ENST00000272317 - Ensembl - - - - PAS IV - Thrombospondin receptor - Fatty acid translocase - PAS-4 - GP3B - GPIV - GPIIIB - Leukocyte differentiation antigen CD36 - Glycoprotein IIIb - CD36 - GP4 - Platelet collagen receptor - FAT - Platelet glycoprotein IV - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CD36_HUMAN - Platelet glycoprotein 4 - FUNCTION: Seems to have numerous potential physiological functions. Binds to collagen, thrombospondin, anionic phospholipids and oxidized LDL. May function as a cell adhesion molecule. Directly mediates cytoadherence of Plasmodium falciparum parasitized erythrocytes. Binds long chain fatty acids and may function in the transport and/or as a regulator of fatty acid transport. Receptor for thombospondins, THBS1 AND THBS2, mediating their antiangiogenic effects.SUBUNIT: Interacts with THBS1 and THBS2; the interactions mediate the THBS antiangiogenic activity.SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.PTM: N-glycosylated and O-glycosylated with a ratio of 2:1.POLYMORPHISM: Genetic variations in CD36 are involved in susceptibility to malaria and influence the severity and outcome of malaria infection [MIM:611162].DISEASE: Platelet glycoprotein IV deficiency (PG4D) [MIM:608404]: A disorder characterized by macrothrombocytopenia without notable hemostatic problems and bleeding tendency. Platelet glycoprotein IV deficiency can be divided into 2 subgroups. The type I phenotype is characterized by platelets and monocytes/macrophages exhibiting complete CD36 deficiency. The type II phenotype lacks the surface expression of CD36 in platelets, but expression in monocytes/macrophages is near normal. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Coronary heart disease 7 (CHDS7) [MIM:610938]: A multifactorial disease characterized by an imbalance between myocardial functional requirements and the capacity of the coronary vessels to supply sufficient blood flow. Decreased capacity of the coronary vessels is often associated with thickening and loss of elasticity of the coronary arteries. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.SIMILARITY: Belongs to the CD36 family.SEQUENCE CAUTION: Sequence=AAM14636.2; Type=Frameshift; Positions=53;WEB RESOURCE: Name=Wikipedia; Note=CD36 entry; URL="http://en.wikipedia.org/wiki/CD36";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CD36";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/cd36/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_26190 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26190.3 - - - - - - 3-hydroxy-3-methylglutaryl-coenzyme A reductase-1 - HMDH_HUMAN - HMGCR isoform 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein13757 - Reactome DB_ID: 191308 - HMGCR-1 - - - - P16220 - UniProt - - - - ENSP00000405539 - Ensembl - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21729 - - - - ENSP00000356954 - Ensembl - - - - ENSP00000346768 - Ensembl - - - - MED22 - HGNC - - - - 893505 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=893505 - - - - ENST00000374080 - Ensembl - - - - EQUAL - 72 - - - - - - MOD_RES 371 371 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4718 - - - - HGNC:22474 - HGNC - - - - MOD_RES Glycine amide - - - - - - MOD_RES 54 54 Phosphoserine. - - - - - - - CRY2 - KIAA0658 - - - - - - - - - - - - - - - - - CRY2_HUMAN - Cryptochrome-2 - FUNCTION: Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.COFACTOR: Binds 1 FAD per subunit (By similarity).COFACTOR: Binds 1 5,10-methenyltetrahydrofolate non-covalently per subunit (By similarity).SUBUNIT: Component of the circadian core oscillator, which includes the CRY proteins, CLOCK or NPAS2, ARNTL or ARNTL2, CSNK1D and/or CSNK1E, TIMELESS, and the PER proteins. Interacts directly with PER1 and PER2 C-terminal domains. Interaction with PER2 inhibits its ubiquitination and vice versa. Interacts with NFIL3. Interacts with FBXL3 and FBXL21.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Translocated to the nucleus through interaction with other Clock proteins such as PER2 or ARNTL.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q49AN0-1; Sequence=Displayed; Name=2; IsoId=Q49AN0-2; Sequence=VSP_038970; Note=No experimental confirmation available. Ref.2 (BAG57993) sequence is in conflict in position: 9:H->L;TISSUE SPECIFICITY: Expressed in all tissues examined including fetal brain, fibroblasts, heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon and leukocytes. Highest levels in heart and skeletal muscle.PTM: Phosphorylation on Ser-266 by MAPK is important for the inhibition of CLOCK-ARNTL-mediated transcriptional activity. Phosphorylation by CSKNE requires interaction with PER1 or PER2. Phosphorylated in a circadian manner at Ser-554 and Ser-558 in the suprachiasmatic nucleus (SCN) and liver. Phosphorylation at Ser- 558 by DYRK1A promotes subsequent phosphorylation at Ser-554 by GSK3-beta: the two-step phosphorylation at the neighboring Ser residues leads to its proteasomal degradation (By similarity).PTM: Ubiquitinated by the SCF(FBXL3) and SCF(FBXL21) complexes, regulating the balance between degradation and stabilization. The SCF(FBXL3) complex is mainly nuclear and mediates ubiquitination and subsequent degradation of CRY2. In contrast, cytoplasmic SCF(FBXL21) complex-mediated ubiquitination leads to stabilize CRY2 and counteract the activity of the SCF(FBXL3) complex. The SCF(FBXL3) and SCF(FBXL21) complexes probably mediate ubiquitination at different Lys residues. The SCF(FBXL3) complex recognizes and binds CRY2 phosphorylated at Ser-554 and Ser-558 (Probable).SIMILARITY: Belongs to the DNA photolyase class-1 family.SIMILARITY: Contains 1 photolyase/cryptochrome alpha/beta domain.SEQUENCE CAUTION: Sequence=AAH35161.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact. Aberrant splice sites; Sequence=BAG57993.1; Type=Erroneous termination; Positions=110; Note=Translated as Trp; Sequence=BAG57993.1; Type=Erroneous translation; Note=Wrong choice of CDS;WEB RESOURCE: Name=Wikipedia; Note=Cryptochrome entry; URL="http://en.wikipedia.org/wiki/Cryptochrome"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 251 251 Phosphoserine. - - - - - - - - - - - - - - - - Activated factor Xa heavy chain - Stuart factor - F10 - Factor X light chain - 3.4.21.6 - Factor X heavy chain - Stuart-Prower factor - - - - - - - - - - - - - - - FA10_HUMAN - Coagulation factor X - FUNCTION: Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.CATALYTIC ACTIVITY: Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.ENZYME REGULATION: Inhibited by SERPINA5 and SERPINA10.SUBUNIT: The two chains are formed from a single-chain precursor by the excision of two Arg residues and are held together by 1 or more disulfide bonds. Forms a heterodimer with SERPINA5.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Plasma; synthesized in the liver.PTM: The vitamin K-dependent, enzymatic carboxylation of some glutamate residues allows the modified protein to bind calcium.PTM: N- and O-glycosylated. O-glycosylated with core 1 or possibly core 8 glycans.PTM: The activation peptide is cleaved by factor IXa (in the intrinsic pathway), or by factor VIIa (in the extrinsic pathway).PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains.DISEASE: Factor X deficiency (FA10D) [MIM:227600]: A hemorrhagic disease with variable presentation. Affected individuals can manifest prolonged nasal and mucosal hemorrhage, menorrhagia, hematuria, and occasionally hemarthrosis. Some patients do not have clinical bleeding diathesis. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 2 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 1 peptidase S1 domain.WEB RESOURCE: Name=Wikipedia; Note=Factor X entry; URL="http://en.wikipedia.org/wiki/Factor_X";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/f10/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 1749935 - Cheung WF - Frazier D - Wu SM - Stafford DW - PubMed - Cloning and expression of the cDNA for human gamma-glutamyl carboxylase. - Science 254(5038);1634-6 - 1991 - - - - D3DUC9 - UniProt - - - - - - - - - - - - - - - - - - - - Christmas factor - Coagulation factor IXa light chain - Coagulation factor IXa heavy chain - 3.4.21.22 - Plasma thromboplastin component - F9 - PTC - - - - - - - - - - - - - - - - - - - - FA9_HUMAN - Coagulation factor IX - FUNCTION: Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.CATALYTIC ACTIVITY: Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.SUBUNIT: Heterodimer of a light chain and a heavy chain; disulfide-linked.SUBCELLULAR LOCATION: Secreted.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P00740-1; Sequence=Displayed; Name=2; IsoId=P00740-2; Sequence=VSP_047689;TISSUE SPECIFICITY: Synthesized primarily in the liver and secreted in plasma.DOMAIN: Calcium binds to the gamma-carboxyglutamic acid (Gla) residues and, with stronger affinity, to another site, beyond the Gla domain.PTM: Activated by factor XIa, which excises the activation peptide.PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains.DISEASE: Hemophilia B (HEMB) [MIM:306900]: An X-linked blood coagulation disorder characterized by a permanent tendency to hemorrhage, due to factor IX deficiency. It is phenotypically similar to hemophilia A, but patients present with fewer symptoms. Many patients are asymptomatic until the hemostatic system is stressed by surgery or trauma. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide.DISEASE: Thrombophilia, X-linked, due to factor IX defect (THPH8) [MIM:300807]: A hemostatic disorder characterized by a tendency to thrombosis. Note=The disease is caused by mutations affecting the gene represented in this entry.PHARMACEUTICAL: Available under the name BeneFix (Baxter and American Home Products). Used to treat hemophilia B.MISCELLANEOUS: In 1952, one of the earliest researchers of the disease, Dr. R.G. Macfarlane used the patient's surname, Christmas, to refer to the disease and also to refer to the clotting factor which he called the 'Christmas Factor' At the time Stephen Christmas was a 5-year-old boy. He died in 1993 at the age of 46 from acquired immunodeficiency syndrome contracted through treatment with blood products.SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 2 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 1 peptidase S1 domain.WEB RESOURCE: Name=Wikipedia; Note=Factor IX entry; URL="http://en.wikipedia.org/wiki/Factor_IX";WEB RESOURCE: Name=Factor IX Mutation Database; URL="http://www.factorix.org/";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/F9";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/f9/";WEB RESOURCE: Name=BeneFix; Note=Clinical information on BeneFix; URL="http://www.pfizer.com/products/rx/rx_product_benefix.jsp";WEB RESOURCE: Name=Protein Spotlight; Note=The Christmas Factor - Issue 41 of December 2003; URL="http://web.expasy.org/spotlight/back_issues/sptlt041.shtml"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - B2RNS5 - UniProt - - - - - - - - - http://www.reactome.org/biopax/46/48887#Dna31 - Reactome DB_ID: 2393990 - HMGCR gene - - - - - - - - - - - - - - Activation peptide fragment 1 - Activation peptide fragment 2 - Thrombin heavy chain - Coagulation factor II - Thrombin light chain - F2 - 3.4.21.5 - - - - - - - - - - - - - - - - - - - - - THRB_HUMAN - Prothrombin - FUNCTION: Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.CATALYTIC ACTIVITY: Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.ENZYME REGULATION: Inhibited by SERPINA5.SUBUNIT: Heterodimer (named alpha-thrombin) of a light and a heavy chain; disulfide-linked. Forms a heterodimer with SERPINA5.SUBCELLULAR LOCATION: Secreted, extracellular space.TISSUE SPECIFICITY: Expressed by the liver and secreted in plasma.PTM: The gamma-carboxyglutamyl residues, which bind calcium ions, result from the carboxylation of glutamyl residues by a microsomal enzyme, the vitamin K-dependent carboxylase. The modified residues are necessary for the calcium-dependent interaction with a negatively charged phospholipid surface, which is essential for the conversion of prothrombin to thrombin.PTM: N-glycosylated. N-glycan heterogeneity at Asn-121: Hex3HexNAc3 (minor), Hex4HexNAc3 (minor) and Hex5HexNAc4 (major). At Asn-143: Hex4HexNAc3 (minor) and Hex5HexNAc4 (major).DISEASE: Factor II deficiency (FA2D) [MIM:613679]: A very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Ischemic stroke (ISCHSTR) [MIM:601367]: A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Thrombophilia due to thrombin defect (THPH1) [MIM:188050]: A multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=The disease is caused by mutations affecting the gene represented in this entry. A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis.DISEASE: Pregnancy loss, recurrent, 2 (RPRGL2) [MIM:614390]: A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.PHARMACEUTICAL: The peptide TP508 also known as Chrysalin (Orthologic) could be used to accelerate repair of both soft and hard tissues.MISCELLANEOUS: Prothrombin is activated on the surface of a phospholipid membrane that binds the amino end of prothrombin and factors Va and Xa in Ca-dependent interactions; factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. The activation process starts slowly because factor V itself has to be activated by the initial, small amounts of thrombin.MISCELLANEOUS: It is not known whether 1 or 2 smaller activation peptides, with additional cleavage after Arg-314, are released in natural blood clotting.MISCELLANEOUS: Thrombin can itself cleave the N-terminal fragment (fragment 1) of the prothrombin, prior to its activation by factor Xa.MISCELLANEOUS: The cleavage after Arg-198, observed in vitro, does not occur in plasma.SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 2 kringle domains.SIMILARITY: Contains 1 peptidase S1 domain.WEB RESOURCE: Name=Wikipedia; Note=Thrombin entry; URL="http://en.wikipedia.org/wiki/Thrombin";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/F2";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/f2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10024 - - - - REACT_7434 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7434.2 - - - - EQUAL - 1554 - - - - 2846041 - Ehlers, MR - Kirsch, RE - Pubmed - Catalysis of angiotensin I hydrolysis by human angiotensin-converting enzyme: effect of chloride and pH - Biochemistry 27:5538-44 - 1988 - - - - GO:0004190 - GENE ONTOLOGY - - - - - NM_001267797 - RefSeq - - - - 1989766 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989766 - - - - GO:0005654 - Gene Ontology - - - - HGNC:2097 - HGNC - - - - CHEBI:42328 - ChEBI - - - - NP_001018084 - RefSeq - - - - REACT_148550 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148550.1 - - - - - - MOD_RES 805 805 Phosphothreonine. - - - - EQUAL - 447 - http://www.reactome.org/biopax/46/48887#SequenceSite11625 - - - - ENSG00000159479 - Ensembl - - - - - - pro-factor X light chain - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11633 - Reactome DB_ID: 159786 - 11xCbxE-3D-F10(32-179) - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12027 - - - - NP_073728 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1056 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1834 - - - - 2022391 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022391 - - - - 15469984 - Loktev, AV - Ban, KH - Hansen, DV - Pubmed - Plk1 regulates activation of the anaphase promoting complex by phosphorylating and triggering SCFbetaTrCP-dependent destruction of the APC Inhibitor Emi1 - Mol Biol Cell 15:5623-34 - 2004 - - - - 2032780 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032780 - - - - NM_001131005 - RefSeq - - - - GRHL1 - HGNC - - - - - - MOD_RES 354 354 Phosphoserine. - - - - CHEBI:13416 - ChEBI - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite9909 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10878 - - - - - - 380759 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380759 - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite4652 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10773 - - - - - - MOD_RES 617 617 Phosphoserine. - - - - A6NLF1 - UniProt - - - - B0G0X3 - UniProt - - - - ENSP00000361734 - Ensembl - - - - EQUAL - 461 - http://www.reactome.org/biopax/46/48887#SequenceSite21667 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2094 - - - - ENSP00000386665 - Ensembl - - - - - - - - - Reactome DB_ID: 2022365 - http://www.reactome.org/biopax/46/48887#SmallMolecule1077 - lisinopril - - - - REACT_25234 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25234.1 - - - - 1989758 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989758 - - - - EQUAL - 134 - - - - ENST00000312090 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12013 - - - - D6W5P4 - UniProt - - - - EQUAL - 266 - http://www.reactome.org/biopax/46/48887#SequenceSite25565 - - - - 1675638 - Ashmun RA - Shapiro LH - Roberts WM - Look AT - PubMed - Separate promoters control transcription of the human aminopeptidase N gene in myeloid and intestinal epithelial cells. - J Biol Chem 266(18);11999-2007 - 1991 - - - - 400351 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400351 - - - - 2022381 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022381 - - - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of PERIOD-1' - The phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds E-boxes in the promoter of the PER1 gene and activates transcription of PER1. NPAS2 is predicted to act redundantly with CLOCK. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation104 - - - - NM_013402 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8338 - - - - ENSP00000348013 - Ensembl - - - - 174150 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174150 - - - - ENSP00000322229 - Ensembl - - - - ENST00000319788 - Ensembl - - - - - H - H(+) - hydrogen(1+) - - - - - - - - 1.00794 - hydron - hydron - The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes). - - - - - O2 - dioxygene - [OO] - Disauerstoff - O2 - - - - - - - - - - - - - 31.9988 - dioxygen - dioxygen - - - - 556784 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556784 - - - - - H2O - acqua - [OH2] - agua - HOH - dihydrogen oxide - Wasser - oxidane - hydrogen hydroxide - H2O - dihydridooxygen - eau - aqua - - - - - - - - - - - - - - - 18.0153 - water - water - - - - EQUAL - 7 - - - - 1387 - NCBI Gene - - - - Q9HBV4 - UniProt - - - - 381319 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381319 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2119 - - - - - - O75586 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2755 - - - - SERPINE1 - HGNC - - - - EQUAL - 2065 - - - - PPARA - PPAR-alpha - NR1C1 - PPAR - Nuclear receptor subfamily 1 group C member 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PPARA_HUMAN - Peroxisome proliferator-activated receptor alpha - FUNCTION: Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl- 2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.SUBUNIT: Heterodimer; with RXRA. This heterodimerization is required for DNA binding and transactivation activity. Interacts with AKAP13, LPIN1 and PRDM16. Also interacts with PPARBP coactivator in vitro. Interacts with CITED2; the interaction stimulates its transcriptional activity (By similarity). Interacts with NCOA3 and NCOA6 coactivators. Interacts with ASXL1 AND ASXL2.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q07869-1; Sequence=Displayed; Name=2; IsoId=Q07869-2; Sequence=VSP_047571, VSP_047572;TISSUE SPECIFICITY: Skeletal muscle, liver, heart and kidney.SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.WEB RESOURCE: Name=Wikipedia; Note=Peroxisome proliferator- activated receptor entry; URL="http://en.wikipedia.org/wiki/Peroxisome_proliferator-activated_receptor";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/ppara/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - - - - INHIBITION - - 'captopril [extracellular region]' negatively regulates 'Secreted ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control309 - - - - REACT_25820 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25820.3 - - - - HGNC:5007 - HGNC - - - - ENSG00000166167 - Ensembl - - - - - - MOD_RES 1487 1487 Phosphoserine. - - - - 116840 - omim - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 177320 - http://www.reactome.org/biopax/46/48887#Protein6077 - Cdc20/Cdh1 - - - - E1P5P7 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5634 - - - - - - REACT_119064 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119064.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2101 - - - - EQUAL - 747 - http://www.reactome.org/biopax/46/48887#SequenceSite12385 - - - - 400353 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400353 - - - - REACT_160842 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160842.2 - - - - EQUAL - 775 - - - - ENST00000222122 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1048 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The ACSL1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction141 - Expression of ACSL1 - - - - EQUAL - 2 - - - - Q13229 - UniProt - - - - P24863 - UniProt - - - - Q9NYQ4 - UniProt - - - - 400256 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400256 - - - - ENSP00000282957 - Ensembl - - - - CHEBI:27313 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2414 - - - - - - MOD_RES 277 277 Phosphoserine. - - - - EQUAL - 358 - http://www.reactome.org/biopax/46/48887#SequenceSite4032 - - - - ENST00000409635 - Ensembl - - - - ENSP00000385659 - Ensembl - - - - 1JSP - PROTEIN DATA BANK - - - - - CDK19 - CDC2-related protein kinase 6 - Cyclin-dependent kinase 11 - Cell division cycle 2-like protein kinase 6 - KIAA1028 - CDC2L6 - CDK11 - Cell division protein kinase 19 - 2.7.11.22 - Death-preventing kinase - - - - - - - - - - - - - - - - - - CDK19_HUMAN - Cyclin-dependent kinase 19 - CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9BWU1-1; Sequence=Displayed; Name=2; IsoId=Q9BWU1-2; Sequence=VSP_015857; Note=No experimental confirmation available;SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.SIMILARITY: Contains 1 protein kinase domain.SEQUENCE CAUTION: Sequence=AAH24247.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 657 - - - - 191369 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=191369 - - - - 15024092 - Floering, LM - Puigserver, P - Medvedev, AV - Robidoux, J - Spiegelman, BM - Bai, X - Cao, W - Daniel, KW - Collins, S - Pubmed - p38 mitogen-activated protein kinase is the central regulator of cyclic AMP-dependent transcription of the brown fat uncoupling protein 1 gene - Mol Cell Biol 24:3057-67 - 2004 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4722 - - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of PEX11A' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation214 - - - - - - MOD_RES 1595 1595 N6-acetyllysine. - - - - CYP7A1 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10174 - - - - - - - - Pre-B cell enhancing factor - NamPRT - PBEF_HUMAN - PBEF1 - - - - - Reactome DB_ID: 197188 - http://www.reactome.org/biopax/46/48887#Protein11510 - NAMPT - - - - 5468 - NCBI Gene - - - - EQUAL - 241 - - - - - - MOD_RES 47 47 4-carboxyglutamate. - - - - REACT_4816 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4816.2 - - - - EQUAL - 423 - http://www.reactome.org/biopax/46/48887#SequenceSite20061 - - - - EQUAL - 461 - http://www.reactome.org/biopax/46/48887#SequenceSite21718 - - - - EQUAL - 402 - - - - - - - - gp150 - 3.4.11.2 - AP-M - hAPN - ANPEP - Microsomal aminopeptidase - APN - Aminopeptidase M - AP-N - PEPN - CD13 - Myeloid plasma membrane glycoprotein CD13 - Alanyl aminopeptidase - - - - - - - - - - - - - - - - - - - - - - - - - - - AMPN_HUMAN - Aminopeptidase N - FUNCTION: Broad specificity aminopeptidase. Plays a role in the final digestion of peptides generated from hydrolysis of proteins by gastric and pancreatic proteases. May play a critical role in the pathogenesis of cholesterol gallstone disease. May be involved in the metabolism of regulatory peptides of diverse cell types, responsible for the processing of peptide hormones, such as angiotensin III and IV, neuropeptides, and chemokines. Found to cleave antigen peptides bound to major histocompatibility complex class II molecules of presenting cells and to degrade neurotransmitters at synaptic junctions. Is also implicated as a regulator of IL-8 bioavailability in the endometrium, and therefore may contribute to the regulation of angiogenesis. Is used as a marker for acute myeloid leukemia and plays a role in tumor invasion. In case of human coronavirus 229E (HCoV-229E) infection, serves as receptor for HCoV-229E spike glycoprotein. Mediates as well human cytomegalovirus (HCMV) infection.CATALYTIC ACTIVITY: Release of an N-terminal amino acid, Xaa-|- Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.COFACTOR: Binds 1 zinc ion per subunit.SUBUNIT: Homodimer. Interacts with the S1 domain of HCoV-229E spike protein.SUBCELLULAR LOCATION: Cell membrane; Single-pass type II membrane protein. Cytoplasm, cytosol (Potential). Note=A soluble form has also been detected.TISSUE SPECIFICITY: Expressed in epithelial cells of the kidney, intestine, and respiratory tract; granulocytes, monocytes, fibroblasts, endothelial cells, cerebral pericytes at the blood- brain barrier, synaptic membranes of cells in the CNS. Also expressed in endometrial stromal cells, but not in the endometrial glandular cells. Found in the vasculature of tissues that undergo angiogenesis and in malignant gliomas and lymph node metastases from multiple tumor types but not in blood vessels of normal tissues. A soluble form has been found in plasma. It is found to be elevated in plasma and effusions of cancer patients.INDUCTION: Estradiol and IL8/interleukin-8 decrease enzymatic activity in vitro in endometrial stromal cells by 40% and 30%, respectively.DOMAIN: Amino acids 260-353 are essential to mediate susceptibility to infection with HCoV-229E (in porcine/human chimeric studies) and more specifically amino acids 288-295 (mutagenesis studies).PTM: Sulfated (By similarity).PTM: N- and O-glycosylated.PTM: May undergo proteolysis and give rise to a soluble form.MISCELLANEOUS: Found to serve as a receptor for tumor-homing peptides, more specifically NGR peptides. It could serve thus as a target for delivering drugs into tumors. Concentration in human hepatic bile, varies from 17.3 to 57.6 micrograms/ml.SIMILARITY: Belongs to the peptidase M1 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000322909 - Ensembl - - - - - - MOD_RES 113 113 N6-acetyllysine. - - - - 1AU8 - PROTEIN DATA BANK - - - - ENSG00000186951 - Ensembl - - - - Q3L8U1 - UniProt - - - - - - Skp1 - - - - - Reactome DB_ID: 174150 - http://www.reactome.org/biopax/46/48887#Protein2846 - SKP1 - - - - MOD:00115 - Protein Modification Ontology - - - - PROZ - HGNC - - - - ENST00000377214 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry5025 - - - - Q15788 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2230 - - - - EQUAL - 491 - http://www.reactome.org/biopax/46/48887#SequenceSite21446 - - - - Q14393 - UniProt - - - - - 8.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12957 - - - - Q6ZUP9 - UniProt - - - - PTHR12346:SF0 - PANTHER Family - - - - - - - MOD_RES 543 543 N6-acetyllysine (By similarity). - - - - EQUAL - 1042 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11915 - - - - ENSP00000346508 - Ensembl - - - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of PAI-1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation99 - The phosphorylated BMAL1:CLOCK (ARNTL) heterodimer binds an E-box in the promoter of the PAI-1 gene and activate transcription of PAI-1. NPAS2 is predicted to act redundantly with CLOCK. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10184 - - - - - - EQUAL - 626 - http://www.reactome.org/biopax/46/48887#SequenceSite21426 - - - - 2028289 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2028289 - - - - REACT_160849 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160849.1 - - - - 109276 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109276 - - - - NM_005121 - RefSeq - - - - Q6Q788 - UniProt - - - - EQUAL - 10 - - - - - - - - - - - SREBF1A/2:NF-Y:HMGCR gene - - - - SREBP1A/2:NF-Y:HMGCR gene - Reactome DB_ID: 2426128 - http://www.reactome.org/biopax/46/48887#Complex5480 - - - - - - - - - - - - FABP1:Ligands of PPARA - Reactome DB_ID: 2026984 - http://www.reactome.org/biopax/46/48887#Complex5479 - - - - NM_001010927 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25568 - - - - - - MOD_RES 252 252 N6-acetyllysine. - - - - O60656 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12823 - - - - MOD_RES Phosphoserine (By similarity) - - - - ENST00000335670 - Ensembl - - - - REACT_147872 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147872.2 - - - - EQUAL - 65 - - - - NP_001136062 - RefSeq - - - - 11780226 - Gao Y - Yu G - Peng X - PubMed - [The expression of cathepsin-D in salivary adenoid cystic carcinoma] - Zhonghua Kou Qiang Yi Xue Za Zhi 35(3);206-8 - 2000 - - - - NP_619725 - RefSeq - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite4658 - - - - 336 - NCBI Gene - - - - NM_002957 - RefSeq - - - - - C18H32O3 - (9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid - (9S)-Hydroxyoctadecadinoiec acid - (10E,12Z)-(9S)-9-Hydroxyoctadeca-10,12-dienoic acid - - - - - 296.4449 - 9(S)-HODE - 9(S)-HODE - - - - ENSP00000242728 - Ensembl - - - - 2022383 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022383 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2630 - - - - - - B7Z4S0 - UniProt - - - - 1989751 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989751 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5643 - - - - NP_000063 - RefSeq - - - - SP1 - HGNC - - - - REACT_7311 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7311.2 - - - - Q8NA25 - UniProt - - - - NM_000499 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1850 - - - - HGNC:600 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10180 - - - - - - ENSG00000133398 - Ensembl - - - - - - - - - - - - - - - - - - - - - - - - CREBBP - 2.3.1.48 - CBP - - - - - - - - - - - - - - - - - - - - - - CBP_HUMAN - CREB-binding protein - FUNCTION: Acetylates histones, giving a specific tag for transcriptional activation. Also acetylates non-histone proteins, like NCOA3 and FOXO1. Binds specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes. Acts as a coactivator of ALX1 in the presence of EP300.CATALYTIC ACTIVITY: Acetyl-CoA + [histone] = CoA + acetyl- [histone].SUBUNIT: Found in a complex containing NCOA2; NCOA3; IKKA; IKKB and IKBKG. Probably part of a complex with HIF1A and EP300. Interacts with GATA1; the interaction results in acetylation and enhancement of transcriptional activity of GATA1. Interacts with MAF AND ZCCHC12. Interacts with DAXX; the interaction is dependent on CBP sumoylation and results in suppression of the transcriptional activiy via recruitment of HDAC2 to DAAX (By similarity). Interacts with phosphorylated CREB1. Interacts with CITED4 (C-terminal region). Interacts (via the TAZ-type 1 domain) with HIF1A. Interacts with SRCAP, CARM1, ELF3, MLLT7/FOXO4, N4BP2, NCOA1, NCOA3, NCOA6, PCAF, DDX5, DDX17, PELP1, PML, SMAD1, SMAD2, SMAD3, SPIB and TRERF1. Interacts with HTLV-1 Tax and p30II. Interacts with HIV-1 Tat. Interacts with KLF1; the interaction results in acetylation of KLF1 and enhancement of its transcriptional activity. Interacts with MTDH. Interacts with NFATC4. Interacts with MAFG; the interaction acetylates MAFG in the basic region and stimulates NFE2 transcriptional activity through increasing its DNA-binding activity. Interacts with IRF2; the interaction acetylates IRF2 and regulates its activity on the H4 promoter. Interacts (via N-terminus) with SS18L1/CREST (via C- terminus). Interacts with MECOM. Interacts with CITED1 (via C- terminus). Interacts with FOXO1; the interaction acetylates FOXO1 and inhibits its transcriptional activity.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Recruited to nuclear bodies by SS18L1/CREST. In the presence of ALX1 relocalizes from the cytoplasm to the nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q92793-1; Sequence=Displayed; Name=2; IsoId=Q92793-2; Sequence=VSP_045700; Note=No experimental confirmation available;DOMAIN: The KIX domain mediates binding to HIV-1 Tat.PTM: Methylation of the KIX domain by CARM1 blocks association with CREB. This results in the blockade of CREB signaling, and in activation of apoptotic response (By similarity).PTM: Phosphorylated by CHUK/IKKA at Ser-1382 and Ser-1386; these phosphorylations promote cell growth by switching the binding preference of CREBBP from TP53 to NF-kappa-B.PTM: Sumoylation negatively regulates transcriptional activity via the recruitment of DAAX (By similarity).DISEASE: Note=Chromosomal aberrations involving CREBBP may be a cause of acute myeloid leukemias. Translocation t(8;16)(p11;p13) with KAT6A; translocation t(11;16)(q23;p13.3) with KMT2A/MLL1; translocation t(10;16)(q22;p13) with KAT6B. KAT6A-CREBBP may induce leukemia by inhibiting RUNX1-mediated transcription.DISEASE: Rubinstein-Taybi syndrome 1 (RSTS1) [MIM:180849]: A disorder characterized by craniofacial abnormalities, postnatal growth deficiency, broad thumbs, broad big toes, mental retardation and a propensity for development of malignancies. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Contains 1 bromo domain.SIMILARITY: Contains 1 KIX domain.SIMILARITY: Contains 2 TAZ-type zinc fingers.SIMILARITY: Contains 1 ZZ-type zinc finger.SEQUENCE CAUTION: Sequence=BAE06125.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CBPID42.html";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CREBBP";WEB RESOURCE: Name=Wikipedia; Note=P300/CBP entry; URL="http://en.wikipedia.org/wiki/P300/CBP"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 1655734 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655734 - - - - REN - 3.4.23.15 - Angiotensinogenase - - - - - - - - - - - - - - - - - RENI_HUMAN - Renin - FUNCTION: Renin is a highly specific endopeptidase, whose only known function is to generate angiotensin I from angiotensinogen in the plasma, initiating a cascade of reactions that produce an elevation of blood pressure and increased sodium retention by the kidney.CATALYTIC ACTIVITY: Cleavage of Leu-|-Xaa bond in angiotensinogen to generate angiotensin I.ENZYME REGULATION: Interaction with ATP6AP2 results in a 5-fold increased efficiency in angiotensinogen processing.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=1 uM for angiotensinogen (in absence of ATP6AP2); KM=0.15 uM for angiotensinogen (in presence of membrane-bound ATP6AP2);SUBUNIT: Interacts with ATP6AP2.SUBCELLULAR LOCATION: Secreted. Membrane. Note=Associated to membranes via binding to ATP6AP2.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P00797-1; Sequence=Displayed; Name=2; IsoId=P00797-2; Sequence=VSP_012899;DISEASE: Renal tubular dysgenesis (RTD) [MIM:267430]: Autosomal recessive severe disorder of renal tubular development characterized by persistent fetal anuria and perinatal death, probably due to pulmonary hypoplasia from early-onset oligohydramnios (the Potter phenotype). Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Familial juvenile hyperuricemic nephropathy 2 (HNFJ2) [MIM:613092]: A renal disease characterized by juvenile onset of hyperuricemia, slowly progressive renal failure and anemia. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the peptidase A1 family.WEB RESOURCE: Name=Wikipedia; Note=Renin entry; URL="http://en.wikipedia.org/wiki/Renin"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 176 176 Sulfotyrosine (Potential). - - - - - C30H53N3O6 - SPP 100 - (2S,4S,5S,7S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-4-hydroxy-7-[4-methoxy-3-(3-methoxypropoxy)benzyl]-8-methyl-2-(propan-2-yl)nonanamide - - - - - - - aliskiren - aliskiren - A monomethoxybenzene compound having a 3-methoxypropoxy group at the 2-position and a multi-substituted branched alkyl substituent at the 4-position. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1039 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The TRIB3 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction166 - Expression of TRIB3 - - - - Q6XGZ1 - UniProt - - - - EQUAL - 1433 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25530 - - - - ENSG00000186350 - Ensembl - - - - EQUAL - 2059 - - - - EQUAL - 503 - http://www.reactome.org/biopax/46/48887#SequenceSite25543 - - - - REACT_5085 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5085.2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21441 - - - - 561160 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561160 - - - - REACT_118034 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118034.1 - - - - GO:0004181 - GENE ONTOLOGY - - - - - ENSG00000057593 - Ensembl - - - - REACT_111385 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111385.2 - - - - - - - - - - Reactome DB_ID: 212428 - http://www.reactome.org/biopax/46/48887#Protein6483 - MED20 - - - - 2065405 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065405 - - - - NM_000778 - RefSeq - - - - 1989798 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989798 - - - - Q8IYW1 - UniProt - - - - 605718 - omim - - - - 18719978 - Bonkovsky, HL - Donohue, SE - Shan, Y - Lambrecht, RW - Zheng, J - Pubmed - Differential regulation of human ALAS1 mRNA and protein levels by heme and cobalt protoporphyrin - Mol Cell Biochem 319:153-61 - 2008 - - - - - - - - - - - - - - - RORA Activates Circadian Expression - Edited: May, B, 2011-06-22 - http://www.reactome.org/biopax/46/48887#Pathway878 - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - As inferred from mouse, RORA binds ROR elements (ROREs) in DNA and recruits the coactivators PPARGC1A (PGC-1alpha) and p300 (EP300, a histone acetylase) to activate transcription. - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1037 - - - - Q9NVC6 - UniProt - - - - ENSP00000413251 - Ensembl - - - - NM_001911 - RefSeq - - - - NM_001018074 - RefSeq - - - - Q16865 - UniProt - - - - ENSP00000353803 - Ensembl - - - - REACT_27351 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27351.2 - - - - EQUAL - 514 - http://www.reactome.org/biopax/46/48887#SequenceSite6153 - - - - ENSG00000213923 - Ensembl - - - - ENSP00000377686 - Ensembl - - - - EQUAL - 457 - http://www.reactome.org/biopax/46/48887#SequenceSite4665 - - - - 10713165 - Knutti, D - Kaul, A - Kralli, A - Pubmed - A tissue-specific coactivator of steroid receptors, identified in a functional genetic screen - Mol Cell Biol 20:2411-22 - 2000 - - - - - NTEF-1 - Transcription factor 13 - TEAD-1 - TEF1 - TEAD1 - TEA domain family member 1 - TCF-13 - TCF13 - Protein GT-IIC - - - - - - - - - - - - - TEAD1_HUMAN - Transcriptional enhancer factor TEF-1 - FUNCTION: Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein MST1/MST2, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Acts by mediating gene expression of YAP1 and WWTR1/TAZ, thereby regulating cell proliferation, migration and epithelial mesenchymal transition (EMT) induction. Binds specifically and cooperatively to the SPH and GT-IIC 'enhansons' (5'-GTGGAATGT-3') and activates transcription in vivo in a cell-specific manner. The activation function appears to be mediated by a limiting cell-specific transcriptional intermediary factor (TIF). Involved in cardiac development. Binds to the M-CAT motif.SUBUNIT: Interacts with YAP1 and WWTR1/TAZ.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Preferentially expressed in skeletal muscle. Lower levels in pancreas, placenta, and heart.DISEASE: Sveinsson chorioretinal atrophy (SCRA) [MIM:108985]: Characterized by symmetrical lesions radiating from the optic disk involving the retina and the choroid. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Contains 1 TEA DNA-binding domain.CAUTION: It is uncertain whether Met-1 or Met-16 is the initiator.SEQUENCE CAUTION: Sequence=AAB00791.1; Type=Miscellaneous discrepancy; Note=Unusual initiator. The initiator methionine is coded by a non-canonical ATT isoleucine codon; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000261646 - Ensembl - - - - Q2NL91 - UniProt - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4644 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9714 - - - - EQUAL - 415 - http://www.reactome.org/biopax/46/48887#SequenceSite21460 - - - - ENSG00000146426 - Ensembl - - - - - - MOD_RES 1549 1549 N6-acetyllysine; by autocatalysis. - - - - GO:0070573 - GENE ONTOLOGY - - - - - ENSP00000446392 - Ensembl - - - - - - FHL2_HUMAN - Four and a half LIM domains protein 2 - - - - - Reactome DB_ID: 561161 - http://www.reactome.org/biopax/46/48887#Protein13769 - FHL2 - - - - ENST00000394320 - Ensembl - - - - NM_001260 - RefSeq - - - - InChI=1S/C22H29FO5/c1-12-8-16-15-5-4-13-9-14(25)6-7-19(13,2)21(15,23)17(26)10-20(16,3)22(12,28)18(27)11-24/h6-7,9,12,15-17,24,26,28H,4-5,8,10-11H2,1-3H3/t12-,15+,16+,17+,19+,20+,21+,22+/m1/s1 - InChI - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1067 - - - - EQUAL - 564 - - - - 9559267 - Russell DW - Schwarz M - Lund EG - PubMed - Two 7 alpha-hydroxylase enzymes in bile acid biosynthesis. - Curr Opin Lipidol 9(2);113-8 - 1998 - - - - EQUAL - 162 - - - - 2022372 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022372 - - - - 609786 - omim - - - - Q9HBY4 - UniProt - - - - ALAS1 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12344 - - - - - - - - - - Reactome DB_ID: 212398 - http://www.reactome.org/biopax/46/48887#Protein6476 - MED30 - - - - REACT_25237 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25237.1 - - - - EQUAL - 179 - http://www.reactome.org/biopax/46/48887#SequenceSite21657 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10163 - - - - - - 1989807 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989807 - - - - - - MOD_RES 544 544 N6-acetyllysine (By similarity). - - - - P15336 - UniProt - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite25559 - - - - EQUAL - 576 - - - - - - MOD_RES 65 65 4-carboxyglutamate. - - - - ENSP00000418275 - Ensembl - - - - 2022357 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022357 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1065 - - - - REACT_111923 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111923.3 - - - - CDC20 - HGNC - - - - EQUAL - 1024 - - - - 219541 - NCBI Gene - - - - REACT_118789 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118789.2 - - - - 600481 - omim - - - - - - MOD_RES 82 82 Phosphoserine. - - - - - DRAL - Skeletal muscle LIM-protein 3 - SLIM-3 - LIM domain protein DRAL - FHL2 - SLIM3 - FHL-2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FHL2_HUMAN - Four and a half LIM domains protein 2 - FUNCTION: May function as a molecular transmitter linking various signaling pathways to transcriptional regulation. Negatively regulates the transcriptional repressor E4F1 and may function in cell growth. Inhibits the transcriptional activity of FOXO1 and its apoptotic function by enhancing the interaction of FOXO1 with SIRT1 and FOXO1 deacetylation.SUBUNIT: Interacts with ZNF638 and TTN/titin. Interacts with E4F1. Interacts with GRB7. Interacts with SIRT1 and FOXO1.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.TISSUE SPECIFICITY: Expressed in skeletal muscle and heart.DOMAIN: The third LIM zinc-binding mediates interaction with E4F1.SIMILARITY: Contains 4 LIM zinc-binding domains.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/FHL2ID44092ch2q12.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 90 90 Phosphoserine. - - - - REACT_5288 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5288.1 - - - - Q9BWU1 - UniProt - - - - REACT_1117 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1117.2 - - - - CHEBI:40501 - ChEBI - - - - EQUAL - 1215 - - - - - - MOD_RES 1583 1583 N6-acetyllysine. - - - - EQUAL - 49 - http://www.reactome.org/biopax/46/48887#SequenceSite10050 - - - - 9611 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval835 - - - - - - 400325 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400325 - - - - 603184 - omim - - - - Q9NYX1 - UniProt - - - - ENST00000484952 - Ensembl - - - - - 12.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12930 - - - - - - BMAL1_HUMAN - Aryl hydrocarbon receptor nuclear translocator-like protein 1 - BMAL1 - - - - - Reactome DB_ID: 400353 - http://www.reactome.org/biopax/46/48887#Protein11494 - ARNTL - - - - ENSP00000363215 - Ensembl - - - - EQUAL - 72 - - - - 376414 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=376414 - - - - - - MOD_RES 657 657 Phosphoserine; by PLK3. - - - - NM_001204263 - RefSeq - - - - EQUAL - 179 - http://www.reactome.org/biopax/46/48887#SequenceSite21726 - - - - EQUAL - 43 - http://www.reactome.org/biopax/46/48887#SequenceSite21730 - - - - 609599 - omim - - - - ENST00000434345 - Ensembl - - - - 15283675 - Thomas, DA - Rice, GI - Turner, AJ - Hooper, NM - Grant, PJ - Pubmed - Evaluation of angiotensin-converting enzyme (ACE), its homologue ACE2 and neprilysin in angiotensin peptide metabolism - Biochem J 383:45-51 - 2004 - - - - REACT_7461 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7461.1 - - - - ENST00000296046 - Ensembl - - - - - - - - ACTIVATION - - 'TEAD:WWTR1(TAZ) [nucleoplasm]' positively regulates 'Expression of CTGF' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation83 - - - - 159785 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159785 - - - - - - - - - - ACTIVATION - - 'PPARG:Fatty Acid:RXRA:Mediator:Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CD36 (platelet glycoprotein IV, FAT)' - The PPARG:RXRA heterodimer bound to fatty acids activates transcription of the Platelet glycoprotein IV (CD36, PAS IV, GPIV) gene. In mouse the Pparg:Rxra heterodimer binds the promoter of the Platelet glycoprotein IV gene (Lefterova et al. 2008). - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation71 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval823 - - - - - - ENST00000297347 - Ensembl - - - - Q14415 - UniProt - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite1773 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1767 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4728 - - - - - 51129 - NCBI Gene - - - - REACT_27550 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27550.3 - - - - - - MOD_RES 1336 1336 N6-acetyllysine. - - - - ENSP00000377783 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10004 - - - - 8800 - NCBI Gene - - - - Q9UKV9 - UniProt - - - - 604517 - omim - - - - NM_012118 - RefSeq - - - - EQUAL - 2083 - - - - Q53XP6 - UniProt - - - - - - - - - - Reactome DB_ID: 212401 - http://www.reactome.org/biopax/46/48887#Protein6472 - MED17 - - - - HGNC:2697 - HGNC - - - - ENSG00000140396 - Ensembl - - - - ENST00000353868 - Ensembl - - - - EQUAL - 538 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10118 - - - - ENST00000596802 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10007 - - - - HGNC:17843 - HGNC - - - - Q5T4U4 - UniProt - - - - EQUAL - 490 - http://www.reactome.org/biopax/46/48887#SequenceSite12329 - - - - - - pro-factor X light chain - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11648 - Reactome DB_ID: 159774 - 11xCbxE-3D-F10(32-179) - - - - ENST00000000442 - Ensembl - - - - REACT_147744 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147744.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10771 - - - - 16987893 - Takahashi, JS - Ko, CH - Pubmed - Molecular components of the mammalian circadian clock - Hum Mol Genet 15:R271-7 - 2006 - - - - EQUAL - 600 - http://www.reactome.org/biopax/46/48887#SequenceSite12345 - - - - EQUAL - 447 - http://www.reactome.org/biopax/46/48887#SequenceSite11629 - - - - - - - - - - - - PDGF A/B-chain precursor hetero dimer - Reactome DB_ID: 380751 - http://www.reactome.org/biopax/46/48887#Complex1212 - - - - GO:0047057 - GENE ONTOLOGY - - - - - - - MOD_RES 487 487 Phosphoserine. - - - - 212456 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212456 - - - - - - MOD_RES 68 68 4-carboxyglutamate. - - - - 9441 - NCBI Gene - - - - Q5JYD9 - UniProt - - - - - - - - - - - - - - p-CRY:p-PER:Kinase - http://www.reactome.org/biopax/46/48887#Complex4984 - Reactome DB_ID: 400277 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5646 - - - - ENST00000356800 - Ensembl - - - - ENSP00000379197 - Ensembl - - - - 1253322 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1253322 - - - - - - MOD_RES 271 271 N6-acetyllysine (By similarity). - - - - 159783 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159783 - - - - MED16 - HGNC - - - - - - MOD_RES 1051 1051 Phosphothreonine. - - - - 879829 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879829 - - - - P37231 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25532 - - - - REACT_22727 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22727.3 - - - - EQUAL - 553 - - - - P35397 - UniProt - - - - 421309 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421309 - - - - REACT_148673 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148673.1 - - - - ENSP00000376327 - Ensembl - - - - PTHR11877:SF10 - PANTHER Family - - - - - REACT_3086 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3086.2 - - - - Q8N3A6 - UniProt - - - - EQUAL - 953 - - - - 400141 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400141 - - - - NM_001267843 - RefSeq - - - - - - Fatty acid desaturase 1 - FADS1_HUMAN - - - - - Reactome DB_ID: 400122 - http://www.reactome.org/biopax/46/48887#Protein13768 - FADS1 - - - - B7Z429 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1061 - - - - ENST00000338854 - Ensembl - - - - Q96PT9 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature828 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval11080 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1796 - - - - F10 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12075 - - - - - - HGNC:4710 - HGNC - - - - 8463 - NCBI Gene - - - - REACT_20029 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20029.1 - - - - Q8NBP3 - UniProt - - - - Q6NWN8 - UniProt - - - - Q15068 - UniProt - - - - NM_003883 - RefSeq - - - - EQUAL - 79 - - - - HGNC:2595 - HGNC - - - - B3DLF8 - UniProt - - - - - - MOD_RES 1391 1391 Phosphothreonine. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite23166 - - - - - - vitamin K hydroquinone - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule972 - Reactome DB_ID: 159853 - VKHQ - - - - - - MOD_RES 128 128 Phosphoserine (By similarity). - - - - EQUAL - 680 - - - - ENSP00000396345 - Ensembl - - - - ENST00000254658 - Ensembl - - - - ENST00000375547 - Ensembl - - - - ENST00000428043 - Ensembl - - - - ENSP00000351894 - Ensembl - - - - - - - - - - Authored: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction162 - Edited: May, B, 2011-11-08 - The RGL1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - Expression of RGL1 - - - - HGNC:11714 - HGNC - - - - REACT_5179 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5179.2 - - - - REACT_19792 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19792.2 - - - - REACT_13055 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13055.1 - - - - REACT_117937 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117937.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2250 - - - - - - 556826 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556826 - - - - 159761 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159761 - - - - 26230 - NCBI Gene - - - - Q53HJ3 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10154 - - - - - - MOD_RES 34 34 Beta-decarboxylated aspartate; in form angiotensin-A. - - - - PTHR11633:SF3 - PANTHER Family - - - - - - Chloride - - - - Reactome DB_ID: 188972 - http://www.reactome.org/biopax/46/48887#SmallMolecule48 - Cl- - - - - EQUAL - 87 - http://www.reactome.org/biopax/46/48887#SequenceSite3897 - - - - - - 3.4.21.75 - PACE - FUR - Dibasic-processing enzyme - FURIN - Paired basic amino acid residue-cleaving enzyme - PCSK3 - - - - - - - - - - - - - - - - FURIN_HUMAN - Furin - FUNCTION: Furin is likely to represent the ubiquitous endoprotease activity within constitutive secretory pathways and capable of cleavage at the RX(K/R)R consensus motif.CATALYTIC ACTIVITY: Release of mature proteins from their proproteins by cleavage of -Arg-Xaa-Yaa-Arg-|-Zaa- bonds, where Xaa can be any amino acid and Yaa is Arg or Lys. Releases albumin, complement component C3 and vWF from their respective precursors.COFACTOR: Calcium.ENZYME REGULATION: Could be inhibited by the not secondly cleaved propeptide.SUBUNIT: Interacts with FLNA (By similarity). Binds to PACS1 which mediates TGN localization and connection to clathrin adapters.SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane; Single-pass type I membrane protein. Cell membrane; Single-pass type I membrane protein. Note=Shuttles between the trans-Golgi network and the cell surface. Propeptide cleavage is a prerequisite for exit of furin molecules out of the endoplasmic reticulum (ER). A second cleavage within the propeptide occurs in the trans Golgi network (TGN), followed by the release of the propeptide and the activation of furin.TISSUE SPECIFICITY: Seems to be expressed ubiquitously.DOMAIN: Contains a cytoplasmic domain responsible for its TGN localization and recycling from the cell surface.PTM: The inhibition peptide, which plays the role of an intramolecular chaperone, is autocatalytically removed in the endoplasmic reticulum (ER) and remains non-covalently bound to furin as a potent autoinhibitor. Following transport to the trans Golgi, a second cleavage within the inhibition propeptide results in propeptide dissociation and furin activation.PTM: Phosphorylation is required for TGN localization of the endoprotease. In vivo, exists as di-, mono- and non-phosphorylated forms.SIMILARITY: Belongs to the peptidase S8 family. Furin subfamily.SIMILARITY: Contains 1 homo B/P domain.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/FURINID40646ch15q26.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P50416 - UniProt - - - - NM_021158 - RefSeq - - - - - - ferriprotoheme IX - - - - Reactome DB_ID: 1368125 - http://www.reactome.org/biopax/46/48887#SmallMolecule967 - ferriheme b - - - - EQUAL - 62 - http://www.reactome.org/biopax/46/48887#SequenceSite23016 - - - - NP_001120916 - RefSeq - - - - 20581824 - Williams, SP - Hu, X - Bynum, J - Lambert, MH - Lazar, MA - Nolte, RT - Broderick, TM - Gampe RT, Jr - Parks, DJ - Phelan, CA - Montana, V - Pubmed - Structure of Rev-erbalpha bound to N-CoR reveals a unique mechanism of nuclear receptor-co-repressor interaction - Nat Struct Mol Biol 17:808-14 - 2010 - - - - EQUAL - 146 - - - - - - - - - - - - - - - Amplified in breast cancer 1 protein - RAC-3 - Thyroid hormone receptor activator molecule 1 - CBP-interacting protein - AIB1 - bHLHe42 - Receptor-associated coactivator 3 - NCoA-3 - pCIP - AIB-1 - SRC-3 - ACTR - Class E basic helix-loop-helix protein 42 - NCOA3 - RAC3 - Steroid receptor coactivator protein 3 - 2.3.1.48 - TRAM-1 - BHLHE42 - TRAM1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NCOA3_HUMAN - Nuclear receptor coactivator 3 - FUNCTION: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Plays a central role in creating a multisubunit coactivator complex, which probably acts via remodeling of chromatin. Involved in the coactivation of different nuclear receptors, such as for steroids (GR and ER), retinoids (RARs and RXRs), thyroid hormone (TRs), vitamin D3 (VDR) and prostanoids (PPARs). Displays histone acetyltransferase activity. Also involved in the coactivation of the NF-kappa-B pathway via its interaction with the NFKB1 subunit. Interacts with PSMB9.CATALYTIC ACTIVITY: Acetyl-CoA + [histone] = CoA + acetyl- [histone].ENZYME REGULATION: Coactivator activity on nuclear receptors and NF-kappa-B pathways is enhanced by various hormones, and the TNF cytokine, respectively. TNF stimulation probably enhances phosphorylation, which in turn activates coactivator function. In contrast, acetylation by CREBBP apparently suppresses coactivation of target genes by disrupting its association with nuclear receptors. Binds to CSNK1D.SUBUNIT: Interacts with CARM1 (By similarity). Present in a complex containing NCOA2, IKKA, IKKB, IKBKG and the histone acetyltransferase protein CREBBP. Interacts with CASP8AP2, NR3C1 and PCAF. Interacts with ATAD2 and this interaction is enhanced by estradiol. Found in a complex containing NCOA3, AR and MAK. Interacts with DDX5.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Mainly cytoplasmic and weakly nuclear. Upon TNF activation and subsequent phosphorylation, it translocates from the cytoplasm to the nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=5; Comment=Additional isoforms seem to exist; Name=1; IsoId=Q9Y6Q9-1; Sequence=Displayed; Name=2; IsoId=Q9Y6Q9-2; Sequence=VSP_003407; Name=3; IsoId=Q9Y6Q9-3; Sequence=VSP_003405, VSP_003407, VSP_003408; Name=4; IsoId=Q9Y6Q9-4; Sequence=VSP_003405, VSP_003406, VSP_003407, VSP_003408; Name=5; IsoId=Q9Y6Q9-5; Sequence=VSP_003408;TISSUE SPECIFICITY: Widely expressed. High expression in heart, skeletal muscle, pancreas and placenta. Low expression in brain, and very low in lung, liver and kidney.DOMAIN: Contains three Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs. Motifs 1 and 2 are essential for the association with nuclear receptors, and constitute the RID domain (Receptor-interacting domain).PTM: Acetylated by CREBBP. Acetylation occurs in the RID domain, and disrupts the interaction with nuclear receptors and regulates its function.PTM: Methylated by CARM1 (By similarity).PTM: Phosphorylated by IKK complex. Regulated its function. Phosphorylation at Ser-601 by CK1 promotes coactivator function.POLYMORPHISM: The length of the poly-Gln region is polymorphic in the normal population.MISCELLANEOUS: NCOA3 is frequently amplified or overexpressed in breast and ovarian cancers.SIMILARITY: Belongs to the SRC/p160 nuclear receptor coactivator family.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAS (PER-ARNT-SIM) domain.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/NCOA3ID505ch20q13.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ncoa3/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21457 - - - - ABCB4 - HGNC Symbol - - - - REACT_27081 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27081.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10151 - - - - EQUAL - 66 - http://www.reactome.org/biopax/46/48887#SequenceSite21683 - - - - InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18) - InChI - - - - CHEBI:16526 - ChEBI - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4963 - - - - EQUAL - 58 - http://www.reactome.org/biopax/46/48887#SequenceSite10048 - - - - EQUAL - 48 - http://www.reactome.org/biopax/46/48887#SequenceSite21677 - - - - B3KN07 - UniProt - - - - NM_001204264 - RefSeq - - - - EQUAL - 1331 - - - - CPB2 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12348 - - - - ENST00000388854 - Ensembl - - - - CUL1 - HGNC - - - - - - MOD_RES 741 741 Phosphoserine (By similarity). - - - - NP_066981 - RefSeq - - - - Q75MJ2 - UniProt - - - - - - Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor - - - - - http://www.reactome.org/biopax/46/48887#Protein13739 - Reactome DB_ID: 49491 - ACADM - - - - - - - - - - - - Activated PPARG:RXRA - http://www.reactome.org/biopax/46/48887#Complex3137 - Reactome DB_ID: 2026078 - - - - REACT_3685 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3685.2 - - - - Q16241 - UniProt - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite21674 - - - - EQUAL - 89 - - - - 517938 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=517938 - - - - - - MOD_RES 310 310 Phosphoserine (By similarity). - - - - - - MOD_RES 402 402 Phosphoserine; by SIK1 (By similarity). - - - - PTHR11269:SF8 - PANTHER Family - - - - - 1368065 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368065 - - - - P04070 - UniProt - - - - EQUAL - 67 - - - - EQUAL - 146 - http://www.reactome.org/biopax/46/48887#SequenceSite12349 - - - - EQUAL - 85 - - - - ENST00000260129 - Ensembl - - - - 1989822 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989822 - - - - Q9H2I1 - UniProt - - - - CHEBI:43755 - ChEBI - - - - EQUAL - 645 - - - - EQUAL - 1549 - - - - NM_001001653 - RefSeq - - - - - - MOD_RES 106 106 Phosphothreonine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12023 - - - - EQUAL - 1558 - - - - - - vitamin K epoxide reductase 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein11626 - Reactome DB_ID: 159746 - VKORC1 - - - - 10531061 - Staknis, D - Weitz, CJ - Griffin EA, Jr - Pubmed - Light-independent role of CRY1 and CRY2 in the mammalian circadian clock - Science 286:768-71 - 1999 - - - - GO:0005778 - Gene Ontology - - - - - - MOD_RES 104 104 (3R)-3-hydroxyaspartate (By similarity). - - - - REACT_120065 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120065.1 - - - - 605166 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5677 - - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1853 - - - - 600849 - omim - - - - - 3.4.21 - - - - pro-protein C -> protein C + protein C propeptide - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3904 - At the beginning of this reaction, 1 molecule of 'pro-protein C' is present. At the end of this reaction, 1 molecule of 'protein C', and 1 molecule of 'protein C light chain propeptide' are present.<br><br> This reaction takes place in the 'Golgi lumen' and is mediated by the 'furin activity' of 'furin'.<br> - - - - - - ENST00000539791 - Ensembl - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12945 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8325 - - - - CGL2 - Cytotoxic T-lymphocyte proteinase - 3.4.21.- - CSP-C - Cathepsin G-like 2 - GZMH - CCP-X - Cytotoxic serine protease C - CTSGL2 - - - - - - - - - - - - - - - - - - - - GRAH_HUMAN - Granzyme H - FUNCTION: Cytotoxic chymotrypsin-like serine protease with preference for bulky and aromatic residues at the P1 position and acidic residues at the P3' and P4' sites. Probably necessary for target cell lysis in cell-mediated immune responses. Participates in the antiviral response via direct cleavage of several proteins essential for viral replication.ENZYME REGULATION: Inhibited by SERPINB1.SUBCELLULAR LOCATION: Cytoplasmic granule. Note=Cytoplasmic granules of cytolytic T-lymphocytes.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P20718-1; Sequence=Displayed; Name=2; IsoId=P20718-2; Sequence=VSP_047073; Name=3; IsoId=P20718-3; Sequence=VSP_047573;TISSUE SPECIFICITY: Constituvely expressed in NK cells.SIMILARITY: Belongs to the peptidase S1 family. Granzyme subfamily.SIMILARITY: Contains 1 peptidase S1 domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 380760 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380760 - - - - - - MOD_RES 77 77 4-carboxyglutamate. - - - - O75869 - UniProt - - - - - - MOD_RES 1444 1444 Phosphothreonine (By similarity). - - - - FADSD5 - D5D - Delta(5) desaturase - FADS1 - 1.14.19.- - Delta-5 desaturase - Delta(5) fatty acid desaturase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FADS1_HUMAN - Fatty acid desaturase 1 - FUNCTION: Isoform 1: Component of a lipid metabolic pathway that catalyzes biosynthesis of highly unsaturated fatty acids (HUFA) from precursor essential polyunsaturated fatty acids (PUFA) linoleic acid (LA) (18:2n-6) and alpha-linolenic acid (ALA) (18:3n-3). Catalyzes the desaturation of dihomo-gamma-linoleic acid (DHGLA) (20:3n-6) and eicosatetraenoic acid (20:4n-3) to generate arachidonic acid (AA) (20:4n-6) and eicosapentaenoic acid (EPA)(20:5n-3) respectively.FUNCTION: Isoform 2: Enhances desaturation of FADS2, leading to increased production of eicosanoid precursors.PATHWAY: Lipid metabolism; polyunsaturated fatty acid biosynthesis.SUBCELLULAR LOCATION: Isoform 1: Endoplasmic reticulum membrane; Multi-pass membrane protein. Mitochondrion.SUBCELLULAR LOCATION: Isoform 2: Endoplasmic reticulum membrane; Multi-pass membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=FADS1CS; IsoId=O60427-1; Sequence=Displayed; Name=2; Synonyms=FADS1AT1; IsoId=O60427-2; Sequence=VSP_047521;TISSUE SPECIFICITY: Expressed in many tissues, it is most abundant in the liver, brain, adrenal gland and heart. Found as well in skeletal muscle, lung, placenta, kidney, pancreas and retina.DEVELOPMENTAL STAGE: Highly expressed in fetal liver and fetal brain.DOMAIN: The histidine box domains may contain the active site and/or be involved in metal ion binding.SIMILARITY: Belongs to the fatty acid desaturase family.SIMILARITY: Contains 1 cytochrome b5 heme-binding domain.CAUTION: It is uncertain whether Met-1 or Met-58 is the initiator.SEQUENCE CAUTION: Sequence=AAC23397.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAG23120.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH07846.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB55103.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB55173.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAD96626.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAG36877.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAC21679.1; Type=Erroneous initiation; Note=Translation N-terminally extended; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q16359 - UniProt - - - - 11135616 - Torra, IP - Fruchart, JC - Neve, B - Staels, B - Chinetti, G - Remaley, AT - Duverger, N - Lestavel, S - Jaye, M - Brewer, HB - Teissier, E - Clavey, V - Minnich, A - Bocher, V - Pubmed - PPAR-alpha and PPAR-gamma activators induce cholesterol removal from human macrophage foam cells through stimulation of the ABCA1 pathway - Nat Med 7:53-8 - 2001 - - - - REACT_26599 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26599.2 - - - - HGNC:15936 - HGNC - - - - B9TX30 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4731 - - - - Q6NXN9 - UniProt - - - - 159852 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159852 - - - - 189903 - omim - - - - ENSP00000308450 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4420 - - - - EQUAL - 156 - - - - EQUAL - 524 - - - - CARM1 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval11955 - - - - - - P16671 - UniProt - - - - REACT_22597 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22597.3 - - - - ENSP00000266503 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10143 - - - - EQUAL - 442 - - - - EQUAL - 728 - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of FHL2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation208 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10069 - - - - - - REACT_2320 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2320.2 - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite4656 - - - - MED13 - HGNC - - - - - - Nuclear receptor coactivator 3 - NCOA3_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6469 - Reactome DB_ID: 442488 - NCOA3 - - - - NM_000072 - RefSeq - - - - UBB - HGNC - - - - NP_002607 - RefSeq - - - - ENST00000246672 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12352 - - - - NP_001120822 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5678 - - - - - - - - - - - - - - - - - - - - - - - SP1 - TSFP1 - - - - - - - - - - - - - - - - - - - - - - SP1_HUMAN - Transcription factor Sp1 - FUNCTION: Transcription factor that can activate or repress transcription in response to physiological and pathological stimuli. Binds with high affinity to GC-rich motifs and regulates the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses. Highly regulated by post-translational modifications (phosphorylations, sumoylation, proteolytic cleavage, glycosylation and acetylation). Binds also the PDGFR- alpha G-box promoter. May have a role in modulating the cellular response to DNA damage. Implicated in chromatin remodeling. Plays a role in the recruitment of SMARCA4/BRG1 on the c-FOS promoter. Plays an essential role in the regulation of FE65 gene expression. In complex with ATF7IP, maintains telomerase activity in cancer cells by inducing TERT and TERC gene expression.SUBUNIT: Interacts with ATF7IP, ATF7IP2, BAHD1, POGZ, HCFC1, AATF and PHC2. Interacts with varicella-zoster virus IE62 protein. Interacts with HIV-1 Vpr; the interaction is inhibited by SP1 O- glycosylation. Interacts with SV40 VP2/3 proteins. Interacts with SV40 major capsid protein VP1; this interaction leads to a cooperativity between the 2 proteins in DNA binding. Interacts with HLTF; the interaction may be required for basal transcriptional activity of HLTF. Interacts (deacetylated form) with EP300; the interaction enhances gene expression. Interacts with HDAC1 and JUN. Interacts with ELF1; the interaction is inhibited by glycosylation of SP1. Interaction with NFYA; the interaction is inhibited by glycosylation of SP1. Interacts with SMARCA4/BRG1 (By similarity). Interacts with ATF7IP and TBP. Interacts with MEIS2 isoform 4 and PBX1 isoform PBX1a. Interacts with EGR1.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Nuclear location is governed by glycosylated/phosphorylated states. Insulin promotes nuclear location, while glucagon favors cytoplasmic location.TISSUE SPECIFICITY: Up-regulated in adenocarcinomas of the stomach (at protein level).INDUCTION: By insulin.PTM: Phosphorylated on multiple serine and threonine residues. Phosphorylation is coupled to ubiquitination, sumoylation and proteolytic processing. Phosphorylation on Ser-59 enhances proteolytic cleavage. Phosphorylation on Ser-7 enhances ubiquitination and protein degradation. Hyperphosphorylation on Ser-101 in response to DNA damage has no effect on transcriptional activity. MAPK1/MAPK3-mediated phosphorylation on Thr-453 and Thr- 739 enhances VEGF transcription but, represses FGF2-triggered PDGFR-alpha transcription. Also implicated in the repression of RECK by ERBB2. Hyperphosphorylated on Thr-278 and Thr-739 during mitosis by MAPK8 shielding SP1 from degradation by the ubiquitin- dependent pathway. Phosphorylated in the zinc-finger domain by calmodulin-activated PKCzeta. Phosphorylation on Ser-641 by PKCzeta is critical for TSA-activated LHR gene expression through release of its repressor, p107. Phosphorylation on Thr-668, Ser- 670 and Thr-681 is stimulated by angiotensin II via the AT1 receptor inducing increased binding to the PDGF-D promoter. This phosphorylation is increased in injured artey wall. Ser-59 and Thr-681 can both be dephosphorylated by PP2A during cell-cycle interphase. Dephosphorylation on Ser-59 leads to increased chromatin association during interphase and increases the transcriptional activity. On insulin stimulation, sequentially glycosylated and phosphorylated on several C-terminal serine and threonine residues.PTM: Acetylated. Acetylation/deacetylation events affect transcriptional activity. Deacetylation leads to an increase in the expression the 12(s)-lipooxygenase gene though recruitment of p300 to the promoter.PTM: Ubiquitinated. Ubiquitination occurs on the C-terminal proteolytically-cleaved peptide and is triggered by phosphorylation.PTM: Sumoylated with SUMO1. Sumoylation modulates proteolytic cleavage of the N-terminal repressor domain. Sumoylation levels are attenuated during tumorigenesis. Phosphorylation mediates SP1 desumoylation.PTM: Proteolytic cleavage in the N-terminal repressor domain is prevented by sumoylation. The C-terminal cleaved product is susceptible to degradation.PTM: O-glycosylated; Contains 8 N-acetylglucosamine side chains. Levels are controlled by insulin and the SP1 phosphorylation states. Insulin-mediated O-glycosylation locates SP1 to the nucleus, where it is sequentially deglycosylated and phosphorylated. O-glycosylation affects transcriptional activity through disrupting the interaction with a number of transcription factors including ELF1 and NFYA. Also inhibits interaction with the HIV1 promoter. Inhibited by peroxisomome proliferator receptor gamma (PPARgamma).MISCELLANEOUS: In the hepatoma cell line Hep-G2, SP1 precursor mRNA may undergo homotype trans-splicing leading to the duplication of exons 2 and 3.SIMILARITY: Belongs to the Sp1 C2H2-type zinc-finger protein family.SIMILARITY: Contains 3 C2H2-type zinc fingers.SEQUENCE CAUTION: Sequence=AAH43224.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q9BY76 - UniProt - - - - CTSZ - HGNC - - - - REACT_118691 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118691.2 - - - - ENSP00000399421 - Ensembl - - - - EQUAL - 32 - http://www.reactome.org/biopax/46/48887#SequenceSite21701 - - - - NM_138473 - RefSeq - - - - 600825 - omim - - - - NP_006842 - RefSeq - - - - NP_005737 - RefSeq - - - - EQUAL - 69 - - - - Q8NCC7 - UniProt - - - - - - pro-protein C light chain - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11638 - Reactome DB_ID: 159730 - 8xCbxE-3D-PROC(33-197) - - - - ENSEMBL:ENSG00000112972 HMGCS1 - - HMGCS1 - http://www.reactome.org/biopax/46/48887#DnaReference32 - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12841 - - - - 189967 - omim - - - - - - MOD_RES 110 110 (3R)-3-hydroxyaspartate. - - - - REACT_5873 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5873.2 - - - - VKORC1 - HGNC Symbol - - - - ENST00000445463 - Ensembl - - - - ENSP00000455307 - Ensembl - - - - NM_001039492 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval11940 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5638 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5679 - - - - - - MED19 - HGNC Symbol - - - - - - - - - CKI-epsilon - CKIe - CSNK1E - 2.7.11.1 - - - - - - - - - - - - - - - - - - - - - KC1E_HUMAN - Casein kinase I isoform epsilon - FUNCTION: Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Can phosphorylate a large number of proteins. Participates in Wnt signaling. Phosphorylates DVL1. Central component of the circadian clock. May act as a negative regulator of circadian rhythmicity by phosphorylating PER1 and PER2. Retains PER1 in the cytoplasm. Inhibits cytokine-induced granuloytic differentiation.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.SUBUNIT: Monomer. Component of the circadian core oscillator, which includes the CRY proteins, CLOCK, or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Interacts directly with PER1 and PER2 which may lead to their degradation. Interacts with ANKRD6, DBNDD2, LRP5, LRP6 and SOCS3. Interacts with SNAI1 (via zinc fingers).SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).TISSUE SPECIFICITY: Expressed in all tissues examined, including brain, heart, lung, liver, pancreas, kidney, placenta and skeletal muscle. Expressed in monocytes and lymphocytes but not in granulocytes.INDUCTION: Down-regulated during granulocytic differentiation.PTM: Autophosphorylated (By similarity).SIMILARITY: Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. Casein kinase I subfamily.SIMILARITY: Contains 1 protein kinase domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 981 - - - - 2002063 - van der Velde-Koerts T - Lincke CR - Smit JJ - Borst P - PubMed - Structure of the human MDR3 gene and physical mapping of the human MDR locus. - J Biol Chem 266(8);5303-10 - 1991 - - - - 400277 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400277 - - - - REACT_111380 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111380.1 - - - - P00740 - UniProt - - - - ELOVL fatty acid elongase 3 - Cold-inducible glycoprotein of 30 kDa - 2.3.1.199 - 3-keto acyl-CoA synthase ELOVL3 - ELOVL FA elongase 3 - ELOVL3 - CIG30 - Very-long-chain 3-oxoacyl-CoA synthase 3 - - - - - - - - - - - - - ELOV3_HUMAN - Elongation of very long chain fatty acids protein 3 - FUNCTION: Condensing enzyme that elongates saturated and monounsaturated very long chain fatty acids (VLCFAs). Highest activity toward C18 acyl-CoAs, especially C18:0 acyl-CoAs.CATALYTIC ACTIVITY: A very-long-chain acyl-CoA + malonyl-CoA = CoA + a very-long-chain 3-oxoacyl-CoA + CO(2).SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.TISSUE SPECIFICITY: Testis.DOMAIN: The di-lysine motif may confer endoplasmic reticulum localization (By similarity).PTM: N-Glycosylated.SIMILARITY: Belongs to the ELO family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000370938 - Ensembl - - - - - - Renin - RENI_HUMAN - - - - - Reactome DB_ID: 2022343 - http://www.reactome.org/biopax/46/48887#Protein12336 - REN - - - - 1LDJ - PROTEIN DATA BANK - - - - - - pro-growth-arrest-specific protein 6 - 11xCbxE-GAS6(31-691) - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11644 - Reactome DB_ID: 163795 - pro-GAS6 - - - - 420841 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=420841 - - - - NP_001027017 - RefSeq - - - - FADS1 - HGNC - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite1772 - - - - REACT_17367 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17367.2 - - - - REACT_27435 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27435.2 - - - - ENSP00000353679 - Ensembl - - - - - - 5-aminolevulinate synthase, non-specific - 5-aminolevulinate synthase, non-specific, mitochondrial - HEM1_HUMAN - - - - - Reactome DB_ID: 189438 - http://www.reactome.org/biopax/46/48887#Protein13763 - ALAS1 - - - - 400119 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400119 - - - - EQUAL - 229 - http://www.reactome.org/biopax/46/48887#SequenceSite4659 - - - - 8833906 - Brown, MS - Horton, JD - Shimano, H - Hammer, RE - Goldstein, JL - Shimomura, I - Pubmed - Overproduction of cholesterol and fatty acids causes massive liver enlargement in transgenic mice expressing truncated SREBP-1a - J Clin Invest 98:1575-84 - 1996 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8321 - - - - 1989771 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989771 - - - - HGNC:16262 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval836 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10044 - - - - - - HGNC:3535 - HGNC - - - - B2RPA8 - UniProt - - - - O95402 - UniProt - - - - ENSP00000349254 - Ensembl - - - - 3157 - NCBI Gene - - - - O60907 - UniProt - - - - Q08AL6 - UniProt - - - - Q9UFD8 - UniProt - - - - ENST00000345739 - Ensembl - - - - MOD:00046 - Protein Modification Ontology - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12937 - - - - ENST00000450766 - Ensembl - - - - EQUAL - 651 - http://www.reactome.org/biopax/46/48887#SequenceSite12343 - - - - REACT_160583 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160583.2 - - - - REACT_120346 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120346.1 - - - - 421306 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421306 - - - - GLIPR1 - HGNC - - - - extracellular region - - - - - NM_024006 - RefSeq - - - - ENSG00000106459 - Ensembl - - - - - - MOD_RES 328 328 Phosphoserine. - - - - Q9NNY5 - UniProt - - - - - C31H46O3 - 1a-methyl-7a-(-3,7,11,15-tetramethylhexadec-2-en-1-yl)-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione - - - - - - - 466.69513 - vitamin K epoxide - vitamin K epoxide - - - - ENST00000309241 - Ensembl - - - - EQUAL - 117 - - - - DBP - HGNC - - - - NM_000039 - RefSeq - - - - 10135 - NCBI Gene - - - - - 3.4.23 - Prorenin Bound to Renin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin I - - - - - - - - - Prorenin:Prorenin Receptor Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10) - The binding of prorenin to the (pro)renin receptor activates the protease activity of prorenin, which can then hydrolyze angiotensinogen to yield angiotensin-(1-10) (angiotensin I) (Nguyen et al. 2002). Prorenin is inactive when not bound to the (pro)renin receptor. Aliskiren, a drug used clinically to treat hypertension, inhibits the cleavage of angiotensinogen by renin (Gossas et al. 2011, Wood et al. 2003, reviewed in Gerc et al. 2009). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4039 - Authored: May, B, 2011-11-19 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - - - - - - - MOD_RES 469 469 N6-acetyllysine. - - - - 9604010 - Inoue, J - Sato, R - Maeda, M - Pubmed - Multiple DNA elements for sterol regulatory element-binding protein and NF-Y are responsible for sterol-regulated transcription of the genes for human 3-hydroxy-3-methylglutaryl coenzyme A synthase and squalene synthase - J Biochem 123:1191-8 - 1998 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1078 - - - - NM_001643 - RefSeq - - - - NP_006302 - RefSeq - - - - EQUAL - 1290 - http://www.reactome.org/biopax/46/48887#SequenceSite21470 - - - - Q15327 - UniProt - - - - 1FM6 - PROTEIN DATA BANK - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12812 - - - - 6807977 - Travis, J - Schechter, NM - Tewksbury, DA - Reilly, CF - Pubmed - Rapid conversion of angiotensin I to angiotensin II by neutrophil and mast cell proteinases - J Biol Chem 257:8619-22 - 1982 - - - - NP_001177367 - RefSeq - - - - 159850 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159850 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2607 - - - - Hepatic fibrinogen/angiopoietin-related protein - HFARP - PGAR - ARP4 - Angiopoietin-like protein 4 - ANGPTL4 - - - - - - - - - - - - - - - - - - - - - - - - - ANGL4_HUMAN - Angiopoietin-related protein 4 - FUNCTION: Protein with hypoxia-induced expression in endothelial cells. May act as a regulator of angiogenesis and modulate tumorigenesis. Inhibits proliferation, migration, and tubule formation of endothelial cells and reduces vascular leakage. May exert a protective function on endothelial cells through an endocrine action. It is directly involved in regulating glucose homeostasis, lipid metabolism, and insulin sensitivity. In response to hypoxia, the unprocessed form of the protein accumulates in the subendothelial extracellular matrix (ECM). The matrix-associated and immobilized unprocessed form limits the formation of actin stress fibers and focal contacts in the adhering endothelial cells and inhibits their adhesion. It also decreases motility of endothelial cells and inhibits the sprouting and tube formation (By similarity).SUBUNIT: Homooligomer. The homooligomer undergoes proteolytic processing to release its carboxyl fibrinogen-like domain, which circulates as a monomer. The homooligomer unprocessed form is able to interact with the extracellular matrix (By similarity).SUBCELLULAR LOCATION: Secreted. Secreted, extracellular space, extracellular matrix (By similarity). Note=The unprocessed form interacts with the extracellular matrix. This may constitute a dynamic reservoir, a regulatory mechanism of the bioavailability of ANGPTL4 (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9BY76-1; Sequence=Displayed; Name=2; IsoId=Q9BY76-2; Sequence=VSP_047045; Note=Gene prediction based on EST data;TISSUE SPECIFICITY: Expressed at high levels in the placenta, heart, liver, muscle, pancreas and lung but expressed poorly in the brain and kidney.PTM: N-glycosylated.SIMILARITY: Contains 1 fibrinogen C-terminal domain.SEQUENCE CAUTION: Sequence=AAQ88642.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1195 - - - - 7547509 - Troen BR - Atkins KB - PubMed - Regulation of cathepsin D gene expression in HL-60 cells by retinoic acid and calcitriol. - Cell Growth Differ 6(7);871-7 - 1995 - - - - 2892668 - Kooiman PM - Baas F - Van der Velde-Koerts T - Van der Bliek AM - Ten Houte de Lange T - Borst P - PubMed - The human mdr3 gene encodes a novel P-glycoprotein homologue and gives rise to alternatively spliced mRNAs in liver. - EMBO J 6(11);3325-31 - 1987 - - - - EQUAL - 325 - http://www.reactome.org/biopax/46/48887#SequenceSite21432 - - - - - C20H30O2 - 5,8,11,14,17-EICOSAPENTAENOIC ACID - (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoic acid - cis-Delta(5,8,11,14,17)-eicosapentaenoic acid - cis-5,8,11,14,17-eicosapentaenoic acid - EPA - (5Z,8Z,11Z,14Z,17Z)-5,8,11,14,17-eicosapentaenoic acid - all-cis-icosa-5,8,11,14,17-pentaenoic acid - cis-5,8,11,14,17-EPA - Timnodonic acid - all-cis-5,8,11,14,17-eicosapentaenoic acid - cis, cis, cis, cis, cis-eicosa-5,8,11,14,17-pentaenoic acid - (all-Z)-5,8,11,14,17-eicosapentaenoic acid - - - - - - - - 302.451 - all-cis-5,8,11,14,17-icosapentaenoic acid - all-cis-5,8,11,14,17-icosapentaenoic acid - An icosapentaenoic acid having <stereo>cis</stereo> double bonds at positions 5, 8, 11, 14 and 17. - - - - 605299 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10770 - - - - MME - HGNC Symbol - - - - NM_001248002 - RefSeq - - - - ENST00000309881 - Ensembl - - - - CHEBI:13284 - ChEBI - - - - - - MOD_RES 2142 2142 Citrulline; by PADI4; alternate. - - - - EQUAL - 1 - - - - 612385 - omim - - - - - - MOD_RES 154 154 Phosphoserine. - - - - EQUAL - 1141 - - - - REACT_148624 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148624.2 - - - - 879762 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879762 - - - - - - - - - ACTIVATION - - 'HIF1A [nucleoplasm]' positively regulates 'Expression of RORA (ROR-alpha)' - HIF1A binds the RORA promoter and enhances transcription. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation116 - - - - A8K6X8 - UniProt - - - - REACT_27524 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27524.3 - - - - EQUAL - 530 - - - - 9144434 - Nomura, M - Ikeda, M - Pubmed - cDNA cloning and tissue-specific expression of a novel basic helix-loop-helix/PAS protein (BMAL1) and identification of alternatively spliced variants with alternative translation initiation site usage - Biochem Biophys Res Commun 233:258-64 - 1997 - - - - NP_001254726 - RefSeq - - - - - - 10xCbxE-F7(21-466) - - - - - - - - - - - - - - Reactome DB_ID: 159722 - http://www.reactome.org/biopax/46/48887#Protein11630 - pro-factor VII - - - - ENSP00000353622 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite6150 - - - - ENST00000281928 - Ensembl - - - - EQUAL - 254 - - - - EQUAL - 108 - http://www.reactome.org/biopax/46/48887#SequenceSite4970 - - - - B4DPZ1 - UniProt - - - - - - MOD_RES 194 194 Phosphoserine. - - - - 12388190 - Deeley RG - Oleschuk CJ - Cole SP - PubMed - Substitution of Trp1242 of TM17 alters substrate specificity of human multidrug resistance protein 3. - Am J Physiol Gastrointest Liver Physiol 284(2);G280-9 - 2003 - - - - EQUAL - 462 - http://www.reactome.org/biopax/46/48887#SequenceSite12333 - - - - EQUAL - 1033 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1858 - - - - HGNC:2642 - HGNC - - - - ENSP00000380888 - Ensembl - - - - CHEBI:24540 - ChEBI - - - - REACT_115847 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115847.1 - - - - HGNC:11458 - HGNC - - - - NP_001161750 - RefSeq - - - - REACT_19775 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19775.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5617 - - - - REACT_2869 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2869.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8315 - - - - 400342 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400342 - - - - ENSP00000369050 - Ensembl - - - - NM_001005291 - RefSeq - - - - 17084382 - Jedidi, I - Barouki, R - Gardès-Albert, M - Aggerbeck, M - Bonnefont-Rousselot, D - Thérond, P - Couturier, M - Legrand, A - Pubmed - Cholesteryl ester hydroperoxides increase macrophage CD36 gene expression via PPARalpha - Biochem Biophys Res Commun 351:733-8 - 2006 - - - - 606200 - omim - - - - Q14814 - UniProt - - - - REACT_120029 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120029.1 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1034 - - - - EQUAL - 464 - http://www.reactome.org/biopax/46/48887#SequenceSite5738 - - - - - KIAA1769 - HELZ2 - PPAR-gamma DNA-binding domain-interacting protein 1 - Peroxisomal proliferator-activated receptor A-interacting complex 285 kDa protein - ATP-dependent helicase PRIC285 - PPAR-alpha-interacting complex protein 285 - PPAR-gamma DBD-interacting protein 1 - PDIP1 - Helicase with zinc finger 2, transcriptional coactivator - 3.6.4.- - PRIC285 - - - - - - - - - - - - - - - - - - - - - HELZ2_HUMAN - Helicase with zinc finger domain 2 - FUNCTION: Helicase that acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA.SUBUNIT: Interacts with PPARA (via DNA-binding domain); the interaction stimulates the transcriptional activity of PPARA. It is probably part of the peroxisome proliferator activated receptor alpha interacting complex (PRIC).SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=PDIP1-alpha; IsoId=Q9BYK8-1; Sequence=Displayed; Name=2; Synonyms=PDIP1-beta; IsoId=Q9BYK8-2; Sequence=VSP_007297, VSP_007298; Name=3; IsoId=Q9BYK8-4; Sequence=VSP_017377, VSP_017378; Note=Incomplete sequence. No experimental confirmation available;TISSUE SPECIFICITY: Expressed in various tissues including heart, pancreas, skeletal muscle, colon, spleen, liver, kidney, lung, peripheral blood and placenta.DOMAIN: Contains 5 Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs. These motifs are not required for interaction with PPARG.SIMILARITY: Belongs to the DNA2/NAM7 helicase family.SIMILARITY: Contains 1 C2H2-type zinc finger.CAUTION: PubMed:12189208 experiments have been carried out partly in rat and partly in human.SEQUENCE CAUTION: Sequence=BAB70969.1; Type=Frameshift; Positions=2206; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 940 - - - - REACT_148408 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148408.2 - - - - NP_001170884 - RefSeq - - - - 8289818 - Sun, Y - Suggs, S - McNiece, I - Xie, C - Samal, B - Stearns, G - Pubmed - Cloning and characterization of the cDNA encoding a novel human pre-B-cell colony-enhancing factor - Mol Cell Biol 14:1431-7 - 1994 - - - - ENSP00000263253 - Ensembl - - - - Q8N8N4 - UniProt - - - - 174237 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174237 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of FADS1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation206 - - - - Q71F56 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13185 - - - - 49836649 - pubchem - - - - 7935485 - Miralles F - Augereau P - Parker M - Gaudelet C - Cavailles V - Rochefort H - PubMed - Characterization of the proximal estrogen-responsive element of human cathepsin D gene. - Mol Endocrinol 8(6);693-703 - 1994 - - - - - - MOD_RES 611 611 Phosphoserine. - - - - 163810 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163810 - - - - NP_056150 - RefSeq - - - - ENSP00000438545 - Ensembl - - - - ENST00000356271 - Ensembl - - - - ENST00000265350 - Ensembl - - - - O75376 - UniProt - - - - EQUAL - 702 - - - - ENST00000358400 - Ensembl - - - - EQUAL - 1020 - - - - - - MOD_RES 1020 1020 N6-acetyllysine; alternate. - - - - 388474 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=388474 - - - - MOD_RES Sulfotyrosine - - - - - - REV-ERB-alpha - NR1D1_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein10776 - Reactome DB_ID: 375499 - NR1D1 - - - - NM_001243084 - RefSeq - - - - NP_877419 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4715 - - - - EQUAL - 417 - http://www.reactome.org/biopax/46/48887#SequenceSite23037 - - - - ENSP00000236995 - Ensembl - - - - EQUAL - 1103 - - - - EQUAL - 280 - - - - - C31H48O2 - 2-methyl-3-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]naphthalene-1,4-diol - vitamin K1 hydroquinone - Phytonadiol - - - - - - - 452.7116 - phyllohydroquinone - phyllohydroquinone - - - - - 3.4.21 - - - - pro-factor IX -> factor IX + factor IX propeptide - At the beginning of this reaction, 1 molecule of 'pro-factor IX' is present. At the end of this reaction, 1 molecule of 'factor IX', and 1 molecule of 'factor IX propeptide' are present.<br><br> This reaction takes place in the 'Golgi membrane' and is mediated by the 'furin activity' of 'furin'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3900 - - - - - - REACT_117965 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117965.1 - - - - - 11.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12962 - - - - ENSG00000143839 - Ensembl - - - - ENSP00000314343 - Ensembl - - - - EQUAL - 5 - http://www.reactome.org/biopax/46/48887#SequenceSite25550 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1859 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10803 - - - - - - - - MOD_RES 32 32 Phosphothreonine. - - - - NM_004264 - RefSeq - - - - EQUAL - 138 - - - - 1368071 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368071 - - - - REACT_27098 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27098.2 - - - - NM_052968 - RefSeq - - - - 1989770 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989770 - - - - Q9H2P8 - UniProt - - - - REACT_148054 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148054.2 - - - - - - MOD_RES 80 80 4-carboxyglutamate. - - - - EQUAL - 1441 - http://www.reactome.org/biopax/46/48887#SequenceSite12403 - - - - NP_003321 - RefSeq - - - - - - NF-YA - - - - - http://www.reactome.org/biopax/46/48887#Protein12431 - Reactome DB_ID: 420841 - NFYA - - - - REACT_12664 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12664.2 - - - - ENST00000339647 - Ensembl - - - - 1592224 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592224 - - - - REACT_148221 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148221.2 - - - - ENSG00000123066 - Ensembl - - - - 6907 - NCBI Gene - - - - 1655870 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655870 - - - - HGNC:7978 - HGNC - - - - EQUAL - 977 - - - - REACT_147762 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147762.2 - - - - ENSP00000383067 - Ensembl - - - - ENSP00000311095 - Ensembl - - - - ENST00000222002 - Ensembl - - - - EQUAL - 437 - http://www.reactome.org/biopax/46/48887#SequenceSite25575 - - - - 380761 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380761 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein6479 - Reactome DB_ID: 212456 - MED21 - - - - 18441015 - Lau, P - Fitzsimmons, RL - Raichur, S - Muscat, GE - Lechtken, A - Wang, SC - Pubmed - The orphan nuclear receptor, RORalpha, regulates gene expression that controls lipid metabolism: staggerer (SG/SG) mice are resistant to diet-induced obesity - J Biol Chem 283:18411-21 - 2008 - - - - EQUAL - 214 - - - - REACT_115739 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115739.2 - - - - EQUAL - 1368 - http://www.reactome.org/biopax/46/48887#SequenceSite12339 - - - - EQUAL - 267 - - - - EQUAL - 417 - http://www.reactome.org/biopax/46/48887#SequenceSite25561 - - - - - - MOD_RES 854 854 Phosphothreonine. - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5801 - - - - - - - - Translocation of CRY:PER:Kinase Ternary Complex into the Nucleus - Reviewed: Kay, SA, 2010-06-23 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3859 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-03-19 - Reviewed: Delaunay, F, 2010-06-23 - Authored: May, B, 2010-03-19 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - The ternary complex containing phosphorylated CRY and PER proteins with a kinase (CSNK1D or CSNK1E) is translocated to the nucleus. Phosphorylation controls transfer to the nucleus and retention in the nucleus. - - - - - - - Cleaved fragment of PDGF B-chain - - - - - - http://www.reactome.org/biopax/46/48887#Protein2638 - Reactome DB_ID: 389058 - PDGFB(1-81) - - - - 16484495 - Klein, PS - Wang, J - Lazar, MA - Yin, L - Pubmed - Nuclear receptor Rev-erbalpha is a critical lithium-sensitive component of the circadian clock - Science 311:1002-5 - 2006 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5281 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14065 - - - - CHEBI:580746 - ChEBI - - - - REACT_115547 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115547.1 - - - - NCOR2 - HGNC - - - - EQUAL - 532 - http://www.reactome.org/biopax/46/48887#SequenceSite4666 - - - - EQUAL - 61 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5618 - - - - 212359 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212359 - - - - ENST00000467148 - Ensembl - - - - EQUAL - 980 - - - - REACT_116576 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116576.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature492 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite23028 - - - - Q7LA96 - UniProt - - - - - - pro-factor IX, uncarboxylated - - - - - - http://www.reactome.org/biopax/46/48887#Protein11627 - Reactome DB_ID: 159765 - 3D-F9(29-461) - - - - P00797 - UniProt - - - - REACT_3534 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3534.1 - - - - NM_005011 - RefSeq - - - - HGNC:19354 - HGNC - - - - EQUAL - 469 - - - - NP_003100 - RefSeq - - - - - - 8xCbxE-3D-PROC(43-197) - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11664 - Reactome DB_ID: 159756 - protein C light chain - - - - ENSP00000341761 - Ensembl - - - - - - MOD_RES 44 44 Phosphoserine; by CK2. - - - - 10536878 - Baudin, B - Bénéteau-Burnat, B - Pubmed - Mixed-type inhibition of pulmonary angiotensin I-converting enzyme by captopril, enalaprilat and ramiprilat - J Enzyme Inhib 14:447-56 - 1999 - - - - - - - - - - - - - - - - - ACTIVATION - - 'SREBP1A/1C/2:NF-Y:SP1:FDFT1 gene [nucleoplasm]' positively regulates 'Expression of Farnesyldiphosphate Farnesyltransferase (FDFT1, Squalene Synthase)' - http://www.reactome.org/biopax/46/48887#Control386 - SREBF1A/1C/2 (SREBP1A/1C/2) and NF-Y bind the promoter of the Farnesyldiphosphate Farnesyltransferase (FDFT1, Squalene Synthase) gene and enhance transcription (Shimano et al. 1996, Shimano et al. 1997, Guan et al. 1998, Horton et al. 1998, Inoue et al. 1998, Pai et al. 1998, Sakakura et al. 2001, Reed et al. 2008, reviewed in Reed et al. 2002). - - - - NP_004442 - RefSeq - - - - 400137 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400137 - - - - EQUAL - 406 - http://www.reactome.org/biopax/46/48887#SequenceSite23005 - - - - Q5TZR6 - UniProt - - - - REACT_25404 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25404.2 - - - - NP_877393 - RefSeq - - - - Q8IZD1 - UniProt - - - - 10860662 - Weber BH - Stohr H - White K - Marquardt A - PubMed - cDNA cloning, genomic structure, and chromosomal localization of three members of the human fatty acid desaturase family. - Genomics 66(2);175-83 - 2000 - - - - F5H402 - UniProt - - - - - - - - - - - - pro-protein C - Reactome DB_ID: 159772 - http://www.reactome.org/biopax/46/48887#Complex5015 - - - - PDGFA - HGNC - - - - ENSP00000369647 - Ensembl - - - - NM_001195045 - RefSeq - - - - NM_004451 - RefSeq - - - - REACT_3225 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3225.1 - - - - 159726 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159726 - - - - 606608 - omim - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12358 - - - - TEAD4 - HGNC Symbol - - - - - - MOD_RES 632 632 N6-acetyllysine (By similarity). - - - - EQUAL - 82 - - - - 400186 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400186 - - - - ENSP00000385581 - Ensembl - - - - MED9 - HGNC - - - - ENSP00000292035 - Ensembl - - - - - - PPAR-alpha - Peroxisome proliferator-activated receptor alpha - - - - - Reactome DB_ID: 400186 - http://www.reactome.org/biopax/46/48887#Protein6513 - PPARA - - - - EQUAL - 49 - - - - NM_001136197 - RefSeq - - - - PLIN2 - HGNC - - - - - 3.4.23 - Renin Hydrolyzes Angiotensinogen to Yield Angiotensin-(1-10) - - - - - - - - - - - - - - Renin Hydrolyzes Angiotensinogen to Yield Angiotensin I - Renin in the bloodstream hydrolyzes angiotensinogen to yield angiotensin-(1-10) (angiotensin I). Renin is produced in the juxtaglomerular cells of the kidney in response to reduced blood pressure. Aliskiren, a drug used clinically to treat hypertension, inhibits this reaction (Gossas et al. 2011, Wood et al. 2003, reviewed in Gerc et al. 2009). - Authored: May, B, 2011-11-19 - Edited: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4037 - Reviewed: Joseph, J, 2012-08-06 - - - - - 17007889 - Suruga, K - Goda, T - Kiso, Y - Fukami, H - Takase, S - Mochizuki, K - Pubmed - Selectivity of fatty acid ligands for PPARalpha which correlates both with binding to cis-element and DNA binding-independent transactivity in Caco-2 cells - Life Sci 80:140-5 - 2006 - - - - NM_006311 - RefSeq - - - - ENSP00000326135 - Ensembl - - - - - - MOD_RES 601 601 Phosphoserine; by CK1. - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12950 - - - - ENSP00000393257 - Ensembl - - - - - - - - - - - - - AOX - ACOX1 - Straight-chain acyl-CoA oxidase - ACOX - SCOX - 1.3.3.6 - Palmitoyl-CoA oxidase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACOX1_HUMAN - Peroxisomal acyl-coenzyme A oxidase 1 - FUNCTION: Catalyzes the desaturation of acyl-CoAs to 2-trans- enoyl-CoAs. Isoform 1 shows highest activity against medium-chain fatty acyl-CoAs and activity decreases with increasing chain length. Isoform 2 is active against a much broader range of substrates and shows activity towards very long-chain acyl-CoAs. Isoform 2 is twice as active as isoform 1 against 16-hydroxy- palmitoyl-CoA and is 25% more active against 1,16-hexadecanodioyl- CoA.CATALYTIC ACTIVITY: Acyl-CoA + O(2) = trans-2,3-dehydroacyl-CoA + H(2)O(2).COFACTOR: FAD.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=73 uM for palmitoyl-CoA (isoform 1); KM=90 uM for palmitoyl-CoA (isoform 2); pH dependence: Optimum pH is 8.5 for isoform 1 and 7.5-8.5 for isoform 2; Temperature dependence: Optimum temperature for isoform 1 at pH 7.5 is 40 degrees Celsius with no activity at 50 degrees Celsius. Optimum temperature for isoform 2 at pH 7.5 is 47.5 degrees Celsius with 57% activity retained at 50 degrees Celsius;PATHWAY: Lipid metabolism; peroxisomal fatty acid beta-oxidation.SUBCELLULAR LOCATION: Peroxisome.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=ACOX1a, SCOX-exon 3I; IsoId=Q15067-1; Sequence=Displayed; Name=2; Synonyms=ACOX1b, SCOX-exon 3II; IsoId=Q15067-2; Sequence=VSP_000146; Name=3; IsoId=Q15067-3; Sequence=VSP_046129, VSP_000146; Note=No experimental confirmation available;TISSUE SPECIFICITY: Widely expressed with highest levels of isoform 1 and isoform 2 detected in testis. Isoform 1 is expressed at higher levels than isoform 2 in liver and kidney while isoform 2 levels are higher in brain, lung, muscle, white adipose tissue and testis. Levels are almost equal in heart.DISEASE: Adrenoleukodystrophy, pseudoneonatal (Pseudo-NALD) [MIM:264470]: A peroxisomal single-enzyme disorder of fatty acid beta-oxidation, resulting in clinical manifestations that remind neonatal adrenoleukodystrophy. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly, hearing deficit. Pseudo-NALD is characterized by increased plasma levels of very-long chain fatty acids, due to decreased or absent peroxisome acyl-CoA oxidase activity. Peroxisomes are intact and functioning. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: Isoform 1 and isoform 2 can reverse the Acox1 null phenotype in mouse which is characterized by severe microvesicular hepatic steatosis, sustained activation of Ppara, spontaneous massive peroxisome proliferation and eventual development of hepatocellular carcinomas. Isoform 2 is more effective in reversal of the phenotype than isoform 1 (PubMed:20195242).SIMILARITY: Belongs to the acyl-CoA oxidase family.SEQUENCE CAUTION: Sequence=CAD97622.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ACOX1"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 65 - http://www.reactome.org/biopax/46/48887#SequenceSite23000 - - - - Q6FHQ4 - UniProt - - - - D3DX10 - UniProt - - - - NP_001243023 - RefSeq - - - - - 12.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12931 - - - - REACT_5058 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5058.2 - - - - - - - - - Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR) - Authored: May, B, 2011-09-28 - Reviewed: Liang, Guosheng, 2012-08-25 - Edited: May, B, 2011-09-28 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4676 - The HMGCR gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - - - - - ENSG00000155846 - Ensembl - - - - ENST00000374397 - Ensembl - - - - ENSG00000105325 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1840 - - - - NP_378663 - RefSeq - - - - ENSG00000074219 - Ensembl - - - - ENST00000564120 - Ensembl - - - - NM_001256090 - RefSeq - - - - Q53EP5 - UniProt - - - - REACT_5618 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5618.1 - - - - - - - PHLL1 - CRY1 - - - - - - - - - - - - - CRY1_HUMAN - Cryptochrome-1 - FUNCTION: Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.COFACTOR: Binds 1 FAD per subunit.COFACTOR: Binds 1 5,10-methenyltetrahydrofolate non-covalently per subunit.SUBUNIT: Component of the circadian core oscillator, which includes the CRY proteins, CLOCK or NPAS2, ARNTL or ARNTL2, CSNK1D and/or CSNK1E, TIMELESS, and the PER proteins. Interacts directly with TIMELESS and the PER proteins. Interacts directly with PER1 and PER2 C-terminal domains. Interaction with PER2 inhibits its ubiquitination and vice versa. Binds MAPK. Interacts with FBXL21 (By similarity). Interacts with FBXL3.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Translocated to the nucleus through interaction with other Clock proteins such as PER2 or ARNTL (By similarity).INDUCTION: Expression is regulated by light and circadian rhythms. Peak expression in the suprachiasma nucleus (SCN) and eye at the day/night transition (CT12). Levels decrease with ARNTL-CLOCK inhibition as part of the autoregulatory feedback loop.PTM: Phosphorylation on Ser-247 by MAPK is important for the inhibition of CLOCK-ARNTL-mediated transcriptional activity. Phosphorylation by CSNK1E requires interaction with PER1 or PER2. Phosphorylation at Ser-71 and Ser-280 by AMPK destabilizes it (By similarity).PTM: Ubiquitinated by the SCF(FBXL3) and SCF(FBXL21) complexes, regulating the balance between degradation and stabilization. The SCF(FBXL3) complex is mainly nuclear and mediates ubiquitination and subsequent degradation of CRY1. In contrast, cytoplasmic SCF(FBXL21) complex-mediated ubiquitination leads to stabilize CRY1 and counteract the activity of the SCF(FBXL3) complex. The SCF(FBXL3) and SCF(FBXL21) complexes probably mediate ubiquitination at different Lys residues. Ubiquitination at Lys-11 and Lys-107 are specifically ubiquitinated by the SCF(FBXL21) complex but not by the SCF(FBXL3) complex (Probable).SIMILARITY: Belongs to the DNA photolyase class-1 family.SIMILARITY: Contains 1 photolyase/cryptochrome alpha/beta domain.WEB RESOURCE: Name=Wikipedia; Note=Cryptochrome entry; URL="http://en.wikipedia.org/wiki/Cryptochrome"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of GRHL1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation211 - - - - NM_001145358 - RefSeq - - - - ENSP00000268712 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12416 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10047 - - - - - - EQUAL - 1128 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10179 - - - - - - EQUAL - 86 - http://www.reactome.org/biopax/46/48887#SequenceSite9906 - - - - ENSG00000112972 - Ensembl - - - - - - MOD_RES 580 580 Omega-N-methylated arginine; by CARM1. - - - - P11474 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12840 - - - - - - MOD_RES 216 216 Phosphoserine. - - - - CHEBI:27303 - ChEBI - - - - NR1D1 - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5665 - - - - - - EQUAL - 424 - - - - EQUAL - 508 - http://www.reactome.org/biopax/46/48887#SequenceSite25519 - - - - - - hydroxymethylglutaryl-CoA synthase - Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor - 3-hydroxy-3-methylglutaryl coenzyme A synthase - HMG-CoA synthase - - - - - Reactome DB_ID: 56573 - http://www.reactome.org/biopax/46/48887#Protein13749 - HMGCS2 - - - - 1801583 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1801583 - - - - EQUAL - 2063 - - - - Q9BTT4 - UniProt - - - - - Homo sapiens - Homo sapiens - - - - D3DQE1 - UniProt - - - - 15761026 - Lazar, MA - Yin, L - Pubmed - The orphan nuclear receptor Rev-erbalpha recruits the N-CoR/histone deacetylase 3 corepressor to regulate the circadian Bmal1 gene - Mol Endocrinol 19:1452-9 - 2005 - - - - EQUAL - 62 - - - - 556808 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556808 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12340 - - - - B3KW83 - UniProt - - - - Q9UCT8 - UniProt - - - - 2028 - NCBI Gene - - - - REACT_7558 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7558.2 - - - - NM_198182 - RefSeq - - - - REACT_116040 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116040.1 - - - - - - MOD_RES 363 363 Phosphoserine. - - - - 556819 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556819 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12005 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5601 - - - - EQUAL - 456 - http://www.reactome.org/biopax/46/48887#SequenceSite1785 - - - - ENSG00000135744 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval833 - - - - - - NP_003734 - RefSeq - - - - ENSP00000361533 - Ensembl - - - - 163795 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163795 - - - - - - - - - - - - - - - - - - PROZ - - - - - - - - - - - - - - - - - - - - - PROZ_HUMAN - Vitamin K-dependent protein Z - FUNCTION: Appears to assist hemostasis by binding thrombin and promoting its association with phospholipid vesicles. Inhibits activity of the coagulation protease factor Xa in the presence of SERPINA10, calcium and phospholipids.SUBUNIT: Interacts with SERPINA10.SUBCELLULAR LOCATION: Secreted.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P22891-1; Sequence=Displayed; Name=2; IsoId=P22891-2; Sequence=VSP_005415;TISSUE SPECIFICITY: Plasma.PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains (By similarity).SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 2 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 1 peptidase S1 domain.CAUTION: Although related to peptidase S1 family vitamin K- dependent clotting factors, it has lost two of the essential catalytic residues and therefore lacks protease activity.WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/proz/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000367976 - Ensembl - - - - - - p-S-CRY1 - Phosphorylated Cryptochrome-1 - CRY1_HUMAN - - - - - - Reactome DB_ID: 400340 - http://www.reactome.org/biopax/46/48887#Protein11534 - p-CRY1 - - - - ENST00000453593 - Ensembl - - - - Q6VBP3 - UniProt - - - - ENSP00000446042 - Ensembl - - - - EQUAL - 69 - http://www.reactome.org/biopax/46/48887#SequenceSite9994 - - - - - - MOD_RES 72 72 4-carboxyglutamate. - - - - ENST00000447388 - Ensembl - - - - EQUAL - 201 - - - - HGNC:12463 - HGNC - - - - - - - - - - - - BMAL2:CLOCK - Reactome DB_ID: 879827 - http://www.reactome.org/biopax/46/48887#Complex4979 - - - - 389066 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389066 - - - - EQUAL - 75 - - - - ACE-related carboxypeptidase - 3.4.17.23 - ACEH - Metalloprotease MPROT15 - Processed angiotensin-converting enzyme 2 - ACE2 - Angiotensin-converting enzyme homolog - - - - - - - - - - - - - - - - - - - - ACE2_HUMAN - Angiotensin-converting enzyme 2 - FUNCTION: Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin- 13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. In case of human coronaviruses SARS and HCoV-NL63 infections, serve as functional receptor for the spike glycoprotein of both coronaviruses.CATALYTIC ACTIVITY: Angiotensin II + H(2)O = angiotensin-(1-7) + L-phenylalanine.COFACTOR: Binds 1 zinc ion per subunit.COFACTOR: Binds 1 chloride ion per subunit.ENZYME REGULATION: Activated by chloride and fluoride, but not bromide. Inhibited by MLN-4760, cFP_Leu, and EDTA, but not by the ACE inhibitors linosipril, captopril and enalaprilat.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=6.9 uM for angiotensin I; KM=2 uM for angiotensin II; KM=6.8 uM for apelin-13; KM=5.5 uM for dynorphin-13; pH dependence: Optimum pH is 6.5 in the presence of 1 M NaCl. Active from pH 6 to 9;SUBUNIT: Interacts with ITGB1. Interacts with SARS-CoV and HCoV- NL63 spike glycoprotein.SUBCELLULAR LOCATION: Processed angiotensin-converting enzyme 2: Secreted.SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9BYF1-1; Sequence=Displayed; Name=2; IsoId=Q9BYF1-2; Sequence=VSP_014901, VSP_014902; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in endothelial cells from small and large arteries, and in arterial smooth muscle cells. Expressed in lung alveolar epithelial cells, enterocytes of the small intestine, Leydig cells and Sertoli cells (at protein level). Expressed in heart, kidney, testis, and gastrointestinal system.INDUCTION: Up-regulated in failing heart.PTM: N-glycosylation on Asn-90 may limit SARS infectivity.PTM: Proteolytic cleavage by ADAM17 generates a secreted form.SIMILARITY: Belongs to the peptidase M2 family.WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/ace2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001087240 - RefSeq - - - - ENST00000379727 - Ensembl - - - - 106150 - omim - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12932 - - - - TNFRSF21 - HGNC - - - - NP_055891 - RefSeq - - - - 406 - NCBI Gene - - - - ENSG00000185591 - Ensembl - - - - ENST00000355768 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10175 - - - - - - ENST00000338863 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21417 - - - - EQUAL - 593 - http://www.reactome.org/biopax/46/48887#SequenceSite21450 - - - - NCOR1 - HGNC - - - - NP_004026 - RefSeq - - - - 1Z6C - PROTEIN DATA BANK - - - - - - MOD_RES 70 70 Phosphothreonine. - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite1039 - - - - ARNTL - HGNC - - - - 1655863 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655863 - - - - NM_022817 - RefSeq - - - - Q8TA99 - UniProt - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ACSL1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation195 - - - - - - SLC27A1 - S27A1_HUMAN - Long-chain fatty acid transport protein 1 - - - - - Reactome DB_ID: 400190 - http://www.reactome.org/biopax/46/48887#Protein12671 - FATP1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1795 - - - - - - - - - - - - MEF2D - - - - - - - - - - - - - - - - - - - - - - - - - - MEF2D_HUMAN - Myocyte-specific enhancer factor 2D - FUNCTION: Transcriptional activator which binds specifically to the MEF2 element, 5'-YTA[AT](4)TAR-3', found in numerous muscle- specific, growth factor- and stress-induced genes. Mediates cellular functions not only in skeletal and cardiac muscle development, but also in neuronal differentiation and survival. Plays diverse roles in the control of cell growth, survival and apoptosis via p38 MAPK signaling in muscle-specific and/or growth factor-related transcription. Plays a critical role in the regulation of neuronal apoptosis (By similarity).SUBUNIT: Forms a complex with class II HDACs in undifferentiating cells. On myogenic differentiation, HDACs are released into the cytoplasm allowing MEF2s to interact with other proteins for activation. Interacts with HDAC4 (in undifferentiating cells); the interaction translocates MEF2D to nuclear dots. Forms a heterodimer with MEF2A.SUBCELLULAR LOCATION: Nucleus. Note=Translocated by HDAC4 to nuclear dots.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Name=MEF2DAB; IsoId=Q14814-1; Sequence=Displayed; Name=MEF2DA'B; IsoId=Q14814-2; Sequence=VSP_006250; Name=MEF2D0B; IsoId=Q14814-3; Sequence=VSP_006251; Name=MEF2DA0; IsoId=Q14814-4; Sequence=VSP_006252; Name=MEF2DA'0; IsoId=Q14814-5; Sequence=VSP_006250, VSP_006252; Name=MEF2D00; IsoId=Q14814-6; Sequence=VSP_006251, VSP_006252;DEVELOPMENTAL STAGE: Present in myotubes and also in undifferentiated myoblasts.DOMAIN: The beta domain, missing in a number of isoforms, is required for enhancement of transcriptional activity.PTM: Phosphorylated on Ser-444 by CDK5 is required for Lys-439 sumoylation and inhibits transcriptional activity. In neurons, enhanced CDK5 activity induced by neurotoxins promotes caspase 3- mediated cleavage leading to neuron apoptosis. Phosphorylation on Ser-180 can be enhanced by EGF. Phosphorylated and activated by CaMK4.PTM: Acetylated on Lys-439 by CREBBP. Deacetylated by SIRT1.PTM: Sumoylated on Lys-439 with SUMO2 but not SUMO1; which inhibits transcriptional activity and myogenic activity. Desumoylated by SENP3.PTM: Proteolytically cleaved in cerebellar granule neurons on several sites by caspase 7 following neurotoxicity. Preferentially cleaves the CDK5-mediated hyperphosphorylated form which leads to neuron apoptosis and transcriptional inactivation (By similarity).SIMILARITY: Belongs to the MEF2 family.SIMILARITY: Contains 1 MADS-box domain.SIMILARITY: Contains 1 Mef2-type DNA-binding domain.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/MEF2DID43636ch1q22.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 7314 - NCBI Gene - - - - EQUAL - 95 - http://www.reactome.org/biopax/46/48887#SequenceSite9866 - - - - REACT_17286 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17286.1 - - - - NP_001867 - RefSeq - - - - 400331 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400331 - - - - HGNC:8583 - HGNC - - - - 8294001 - Charles AD - Karst F - Summers C - PubMed - Cloning, expression and characterisation of the cDNA encoding human hepatic squalene synthase, and its relationship to phytoene synthase. - Gene 136(1-2Che);185-92 - 1993 - - - - EQUAL - 1583 - - - - EQUAL - 2076 - - - - - - MOD_RES 69 69 4-carboxyglutamate. - - - - NM_003743 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5626 - - - - ENST00000354728 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10125 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12959 - - - - NM_000131 - RefSeq - - - - REACT_148644 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148644.1 - - - - ENSP00000296046 - Ensembl - - - - EQUAL - 766 - - - - BHLHE40 - HGNC - - - - - RNA polymerase II elongation factor-like protein - EMC19 - SKP1 - SKP1A - TCEB1L - OCP2 - OCP-2 - SIII - Cyclin-A/CDK2-associated protein p19 - p19skp1 - Organ of Corti protein 2 - Organ of Corti protein II - OCP-II - Transcription elongation factor B - p19A - - - - - - - - - - - - - - - - - - - - - - - - - SKP1_HUMAN - S-phase kinase-associated protein 1 - FUNCTION: Essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. In the SCF complex, serves as an adapter that links the F-box protein to CUL1. The functional specificity of the SCF complex depends on the F-box protein as substrate recognition component. SCF(BTRC) and SCF(FBXW11) direct ubiquitination of CTNNB1 and participate in Wnt signaling. SCF(FBXW11) directs ubiquitination of phosphorylated NFKBIA. SCF(BTRC) directs ubiquitination of NFKBIB, NFKBIE, ATF4, SMAD3, SMAD4, CDC25A, FBXO5 and probably NFKB2. SCF(SKP2) directs ubiquitination of phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. SCF(SKP2) directs ubiquitination of ORC1, CDT1, RBL2, ELF4, CDKN1A, RAG2, FOXO1A, and probably MYC and TAL1. SCF(FBXW7) directs ubiquitination of cyclin E, NOTCH1 released notch intracellular domain (NICD), and probably PSEN1. SCF(FBXW2) directs ubiquitination of GCM1. SCF(FBXO32) directs ubiquitination of MYOD1. SCF(FBXO7) directs ubiquitination of BIRC2 and DLGAP5. SCF(FBXO33) directs ubiquitination of YBX1. SCF(FBXO11) does not seem to direct ubiquitination of TP53. SCF(BTRC) mediates the ubiquitination of NFKBIA at 'Lys-21' and 'Lys-22'; the degradation frees the associated NFKB1-RELA dimer to translocate into the nucleus and to activate transcription. SCF(CCNF) directs ubiquitination of CCP110. SCF(FBXL3) and SCF(FBXL21) direct ubiquitination of CRY1 and CRY2. SCF(FBXO9) direct ubiquitination of TTI1 and TELO2.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: Component of multiple SCF (SKP1-CUL1-F-box) E3 ubiquitin- protein ligase complexes formed of CUL1, SKP1, RBX1 and a variable F-box domain-containing protein as substrate-specific subunit. Component of the SCF(FBXW11) complex containing FBXW11. Component of the SCF(SKP2) complex containing SKP2, in which it interacts directly with SKP1, SKP2 and RBX1. Component of the SCF(FBXW2) complex containing FBXw2. Component of the SCF(FBXO32) complex containing FBXO32. Component of the probable SCF(FBXO7) complex containing FBXO7. Component of the SCF(FBXO11) complex containing FBXO11. Component of the SCF(FBXO25) complex containing FBXO25. Component of the SCF(FBXO33) complex containing FBXO33. Component of the probable SCF(FBXO4) complex containing FBXO4. Component of the SCF(FBXO44) complex, composed of SKP1, CUL1 and FBXO44. Component of the SCF(BTRC) complex, composed of SKP1, CUL1 and BTRC. This complex binds phosphorylated NFKBIA. Part of a SCF complex consisting of CUL1, RBX1, SKP1 and FBXO2. Component of a SCF(SKP2)-like complex containing CUL1, SKP1, TRIM21 and SKP2. Component of the SCF(FBXO17) complex, composed of SKP1, CUL1 and FBXO17. Component of the SCF(FBXO27) complex, composed of SKP1, CUL1 and FBXO27. Component of the SCF(CCNF) complex consisting of CUL1, RBX1, SKP1 and CCNF. Component of the SCF(FBXL3) complex composed of CUL1, SKP1, RBX1 and FBXL3. Component of the SCF(FBXL21) complex composed of CUL1, SKP1, RBX1 and FBXL21. Component of the SCF(FBXO9) composed of CUL1, SKP1, RBX1 and FBXO9. Component of the SCF(FBXW7) composed of CUL1, SKP1, RBX1 and FBXW7.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P63208-1, P34991-1; Sequence=Displayed; Name=2; IsoId=P63208-2, P34991-2; Sequence=VSP_007555; Note=No experimental confirmation available;SIMILARITY: Belongs to the SKP1 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q86WT0 - UniProt - - - - EQUAL - 79 - - - - EQUAL - 888 - http://www.reactome.org/biopax/46/48887#SequenceSite25533 - - - - NP_001634 - RefSeq - - - - ENSP00000282892 - Ensembl - - - - EQUAL - 1857 - - - - EQUAL - 1744 - - - - EQUAL - 17 - http://www.reactome.org/biopax/46/48887#SequenceSite23002 - - - - NP_001243590 - RefSeq - - - - P62979 - UniProt - - - - 177324 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=177324 - - - - ENSP00000469672 - Ensembl - - - - 608771 - omim - - - - Q6FHC4 - UniProt - - - - ENSG00000101160 - Ensembl - - - - NM_001206654 - RefSeq - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry3484 - - - - - - MOD_RES 62 62 4-carboxyglutamate. - - - - - - MOD_RES 437 437 N6-acetyllysine (By similarity). - - - - Q15213 - UniProt - - - - 607898 - omim - - - - MOD_RES 4-hydroxyproline - - - - REACT_25378 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25378.1 - - - - O60719 - UniProt - - - - - - MOD_RES 442 442 N6-acetyllysine (By similarity). - - - - ENSG00000141027 - Ensembl - - - - ENSP00000300651 - Ensembl - - - - EQUAL - 676 - http://www.reactome.org/biopax/46/48887#SequenceSite21671 - - - - MOD_RES (3R)-3-hydroxyaspartate (By similarity) - - - - 1629775 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1629775 - - - - 2022409 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022409 - - - - ENSG00000008838 - Ensembl - - - - InChI=1S/C21H31N3O5/c22-13-5-4-9-16(19(25)24-14-6-10-18(24)21(28)29)23-17(20(26)27)12-11-15-7-2-1-3-8-15/h1-3,7-8,16-18,23H,4-6,9-14,22H2,(H,26,27)(H,28,29)/t16-,17-,18-/m0/s1 - InChI - - - - EQUAL - 59 - http://www.reactome.org/biopax/46/48887#SequenceSite9887 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8336 - - - - C9JMZ0 - UniProt - - - - NM_001893 - RefSeq - - - - - - MOD_RES 1124 1124 Phosphoserine (By similarity). - - - - 1989818 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989818 - - - - ENSP00000354476 - Ensembl - - - - ENSP00000472551 - Ensembl - - - - REACT_26570 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26570.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval495 - - - - - - - Stimulated by retinoic acid gene 13 protein - DEC1 - Class B basic helix-loop-helix protein 2 - bHLHb2 - Enhancer-of-split and hairy-related protein 2 - STRA13 - SHARP2 - bHLHe40 - SHARP-2 - Differentially expressed in chondrocytes protein 1 - BHLHE40 - BHLHB2 - - - - - - - - - - - - - BHE40_HUMAN - Class E basic helix-loop-helix protein 40 - FUNCTION: May function as a transcriptional factor to modulate chondrogenesis in response to the cAMP pathway.SUBUNIT: Able to homodimerize or heterodimerize with TCF3/E47. Interacts with ubiquitin-conjugating enzyme UBE2I/UBC9.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Expressed in cartilage, spleen, intestine, lung, and to a lesser extent in heart, brain, liver, muscle and stomach.PTM: Ubiquitinated; which may lead to proteasomal degradation.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 Orange domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 1989753 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989753 - - - - 1339389 - Taroni F - Colombo I - Martin AL - Di Donato S - Minoletti F - Pandolfo M - Finocchiaro G - PubMed - Localization of the human gene for carnitine palmitoyltransferase to 1p13-p11 by nonradioactive in situ hybridization. - Genomics 13(4);1372-4 - 1992 - - - - EQUAL - 42 - http://www.reactome.org/biopax/46/48887#SequenceSite23019 - - - - ENSP00000385339 - Ensembl - - - - ENST00000222553 - Ensembl - - - - ENSG00000001167 - Ensembl - - - - 17218255 - Ptácek, LJ - Xu, Y - Fu, YH - Shin, JY - Jones, CR - Toh, KL - Pubmed - Modeling of a human circadian mutation yields insights into clock regulation by PER2 - Cell 128:59-70 - 2007 - - - - ENST00000218099 - Ensembl - - - - REACT_164631 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164631.1 - - - - ENSP00000372434 - Ensembl - - - - CPB2 - HGNC Symbol - - - - - - MOD_RES 747 747 Phosphoserine (By similarity). - - - - MED11 - Mediator complex subunit 11 - - - - - - - - - - - - - MED11_HUMAN - Mediator of RNA polymerase II transcription subunit 11 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 11 family.SEQUENCE CAUTION: Sequence=AAF28974.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4765 - - - - - - EQUAL - 73 - http://www.reactome.org/biopax/46/48887#SequenceSite10125 - - - - ENSP00000364469 - Ensembl - - - - EQUAL - 86 - - - - ENST00000375581 - Ensembl - - - - NM_000504 - RefSeq - - - - HGNC:11290 - HGNC - - - - ENSP00000361540 - Ensembl - - - - NM_001142589 - RefSeq - - - - Q13071 - UniProt - - - - B5ME11 - UniProt - - - - ENST00000397012 - Ensembl - - - - ENST00000381322 - Ensembl - - - - ENSG00000198431 - Ensembl - - - - SREBF2 - HGNC Symbol - - - - - - pro-prothrombin (factor II) - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11635 - Reactome DB_ID: 159800 - 10xCbxE-F2(25-622) - - - - - - - - - - - - Reactome DB_ID: 2032773 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11191 - TEAD - - - - REACT_120306 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120306.1 - - - - B2R7F7 - UniProt - - - - EQUAL - 80 - - - - Q6XGZ0 - UniProt - - - - REACT_24649 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24649.2 - - - - ENST00000514028 - Ensembl - - - - ENSG00000116604 - Ensembl - - - - EQUAL - 277 - - - - ENST00000345877 - Ensembl - - - - EQUAL - 622 - http://www.reactome.org/biopax/46/48887#SequenceSite21663 - - - - - - factor IX propeptide - - - - - http://www.reactome.org/biopax/46/48887#Protein11655 - Reactome DB_ID: 159735 - F9(29-46) - - - - APOA5 - HGNC Symbol - - - - EQUAL - 34 - - - - 879843 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879843 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5634 - - - - 450243 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=450243 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10811 - - - - - - - - CARM1_HUMAN - Histone-arginine methyltransferase CARM1 - - - - - http://www.reactome.org/biopax/46/48887#Protein6508 - Reactome DB_ID: 400139 - CARM1 - - - - REACT_148657 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148657.1 - - - - EQUAL - 649 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval187 - - - - - - 612383 - omim - - - - REACT_115994 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115994.1 - - - - ENSG00000159640 - Ensembl - - - - NP_000089 - RefSeq - - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction151 - The FABP1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of FABP1 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1861 - - - - - - MOD_RES 986 986 Phosphoserine. - - - - - - - - Pro-factor IX is transported from the endoplasmic reticulum to the Golgi apparatus - In this reaction, 1 molecule of 'pro-factor IX' is translocated from endoplasmic reticulum lumen to Golgi lumen.<br><br>This reaction takes place in the 'ER to Golgi transport vesicle'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3892 - - - - - 2147 - NCBI Gene - - - - ATF2 - HGNC Symbol - - - - MED18 - HGNC Symbol - - - - EQUAL - 61 - - - - - - Mediator of RNA polymerase II transcription subunit 11 - MED11_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6474 - Reactome DB_ID: 556808 - MED11 - - - - 12011083 - Rudling M - Araya Z - Bjorkhem I - Wikvall K - Einarsson C - Angelin B - PubMed - Differences in the regulation of the classical and the alternative pathway for bile acid synthesis in human liver. No coordinate regulation of CYP7A1 and CYP27A1. - J Biol Chem 277(30);26804-7 - 2002 - - - - 1DL9 - PROTEIN DATA BANK - - - - - - pro-prothrombin (factor II) - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11649 - Reactome DB_ID: 159841 - 10xCbxE-F2(25-622) - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10142 - - - - EQUAL - 1006 - - - - - - 11xCbxE-PROS1 - - - - - - - - - - - - - - - Reactome DB_ID: 159865 - http://www.reactome.org/biopax/46/48887#Protein11666 - protein S - - - - 1989820 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989820 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12332 - - - - REACT_4725 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4725.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10063 - - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1084 - - - - REACT_26089 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26089.2 - - - - CLIF - PASD9 - Basic-helix-loop-helix-PAS protein MOP9 - Class E basic helix-loop-helix protein 6 - PAS domain-containing protein 9 - BMAL2 - Brain and muscle ARNT-like 2 - bHLHe6 - BHLHE6 - ARNTL2 - MOP9 - CYCLE-like factor - Member of PAS protein 9 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BMAL2_HUMAN - Aryl hydrocarbon receptor nuclear translocator-like protein 2 - FUNCTION: ARNTL2-CLOCK heterodimers activate E-box element (5'- CACGTG-5') transcription. Also, in umbilical vein endothelial cells, activates SERPINE1 through E-box sites. This transactivation is inhibited by PER2 and CRY1.SUBUNIT: Component of the circadian core oscillator, which includes the CRY proteins, CLOCK, or NPAS2, ARNTL or ARNTL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Interacts directly with CLOCK to form the ARNTL2-CLOCK transactivator. Can form heterodimers or homodimers which interact directly with CLOCK to form the transcription activator. Also interacts with NPAS2 and HIF1A.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=9; Name=1; Synonyms=BMAL2a; IsoId=Q8WYA1-1; Sequence=Displayed; Name=2; Synonyms=BMAL2b; IsoId=Q8WYA1-2; Sequence=VSP_022584; Name=3; Synonyms=BMAL2c; IsoId=Q8WYA1-3; Sequence=VSP_022585, VSP_022581, VSP_022584; Name=4; Synonyms=BMAL2d; IsoId=Q8WYA1-4; Sequence=VSP_022581, VSP_022584; Name=5; Synonyms=CLIF; IsoId=Q8WYA1-5; Sequence=VSP_022581; Name=6; IsoId=Q8WYA1-6; Sequence=VSP_022580, VSP_022581, VSP_022584; Name=7; Synonyms=MOP9 long form; IsoId=Q8WYA1-7; Sequence=VSP_022580, VSP_022584; Name=8; Synonyms=MOP9 short form; IsoId=Q8WYA1-8; Sequence=VSP_022580, VSP_022582, VSP_022583, VSP_022584; Note=No experimental confirmation available; Name=9; IsoId=Q8WYA1-9; Sequence=VSP_022585, VSP_022581, VSP_022584, VSP_044773; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in fetal brain. Highly expressed in brain and placenta. Lower levels in heart, liver, thymus, kidney and lung. Located to endothelial cells and neuronal cells of the suprachiasmatic nucleus (SCN). Also detected in endothelial cells of the heart, lung and kidney. In the brain, specifically expressed in the thalamus, hippocampus and amygdala.INDUCTION: Constitutively expressed. Has no circadian rhythm expression pattern.SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - GO:0008236 - GENE ONTOLOGY - - - - - REACT_24844 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24844.2 - - - - NP_001191194 - RefSeq - - - - EQUAL - 42 - http://www.reactome.org/biopax/46/48887#SequenceSite21732 - - - - 1989743 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989743 - - - - - - MOD_RES 69 69 Phosphothreonine; by MAPK11 and MAPK14. - - - - 1368133 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368133 - - - - NM_001001547 - RefSeq - - - - - - MOD_RES 1248 1248 N6-acetyllysine. - - - - EQUAL - 2151 - - - - DTOSIQBPPRVQHS-PDBXOOCHSA-N - InChIKey - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10758 - - - - ARNTL2 - HGNC Symbol - - - - ENST00000266659 - Ensembl - - - - CHEBI:34496 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12058 - - - - - - ENSP00000324693 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1071 - - - - REACT_11899 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11899.3 - - - - 159796 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159796 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10182 - - - - - - - - MOD_RES 82 82 Phosphothreonine; by MAPK8 and MAPK9 (By similarity). - - - - EQUAL - 1290 - http://www.reactome.org/biopax/46/48887#SequenceSite21466 - - - - CDK8 - HGNC - - - - EQUAL - 73 - - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction154 - Reviewed: Kersten, S, 2009-06-08 - The FHL2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of FHL2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25572 - - - - MOD:01148 - Protein Modification Ontology - - - - EQUAL - 1321 - - - - A6NN38 - UniProt - - - - - - MOD_RES 815 815 Phosphoserine. - - - - B3KVW0 - UniProt - - - - REACT_26466 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26466.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5785 - - - - NM_001256660 - RefSeq - - - - Q9UBR2 - UniProt - - - - NP_003069 - RefSeq - - - - 608886 - omim - - - - - SMARCD3 - 60 kDa BRG-1/Brm-associated factor subunit C - BAF60C - BRG1-associated factor 60C - - - - - - - - - - - - - - - - - - - - - - - - - - - SMRD3_HUMAN - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 - FUNCTION: Plays a role in ATP dependent nucleosome remodeling by SMARCA4 containing complexes. Stimulates nuclear receptor mediated transcription. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron- specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post- mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity).SUBUNIT: Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Interacts with SMARCA4/BRG1/BAF190A, the catalytic subunit of the SWI/SNF related nucleosome-remodeling complexes BRG1(I) and BRG1(II). The precise distribution of the related SMARCD1, SMARCD2 and SMARCD3 proteins among these and other SWI/SNF nucleosome-remodeling complexes is not fully known. Also interacts with several nuclear receptors including PPARG/NR1C3, RXRA/NR1F1, ESR1, NR5A1, NR5A2/LRH1 and other transcriptional activators including the HLH protein SREBF1/SREBP1 and the homeobox protein PBX1. May allow recruitment of Swi/SNF containing complexes specifically to promoters where these factors are located. Component of neural progenitors- specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron- specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin (By similarity).SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=BAF60C2; IsoId=Q6STE5-1; Sequence=Displayed; Name=2; Synonyms=BAF60C1; IsoId=Q6STE5-2; Sequence=VSP_012498;TISSUE SPECIFICITY: Isoform 2 and isoform 1 are expressed in brain, heart, kidney, placenta, prostate, salivary gland, spleen, testis, thyroid, trachea and uterus. Isoform 1 is also expressed in skeletal muscle and adipose tissue.SIMILARITY: Belongs to the SMARCD family.SIMILARITY: Contains 1 SWIB domain.SEQUENCE CAUTION: Sequence=AAC50697.1; Type=Frameshift; Positions=41, 65, 78; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q96HR3 - UniProt - - - - - - MOD_RES 1859 1859 Phosphothreonine. - - - - A4D1D4 - UniProt - - - - - - MOD_RES 72 72 Phosphoserine. - - - - ENSP00000396219 - Ensembl - - - - 8187880 - Loeber G - Ahorn H - Infante A - Dworkin MB - PubMed - Characterization of cytosolic malic enzyme in human tumor cells. - FEBS Lett 344(2-3);181-6 - 1994 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10795 - - - - - - Q9UH04 - UniProt - - - - 51 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5627 - - - - - - MOD_RES 138 138 Phosphoserine. - - - - HGNC:701 - HGNC - - - - REACT_25125 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25125.2 - - - - REACT_117365 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117365.1 - - - - ENSP00000338018 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9758 - - - - - - ENSG00000163586 - Ensembl - - - - REACT_117950 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117950.1 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction137 - Reviewed: Kersten, S, 2009-06-08 - The ABCA1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of ABCA1 - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite22998 - - - - ENST00000374102 - Ensembl - - - - O95401 - UniProt - - - - 1655745 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655745 - - - - GGCX - HGNC - - - - 9412 - NCBI Gene - - - - ENSP00000322706 - Ensembl - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14063 - - - - 1989765 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989765 - - - - NM_199166 - RefSeq - - - - ENST00000248054 - Ensembl - - - - REACT_111904 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111904.1 - - - - EQUAL - 57 - http://www.reactome.org/biopax/46/48887#SequenceSite21680 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12022 - - - - - - - 3.4.17 - ACE2 Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-9) - - - - - - - - - - ACE2 Hydrolyzes Angiotensin I to Yield Angiotensin-(1-9) - Authored: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4045 - Edited: May, B, 2011-11-19 - Angiotensin-converting enzyme 2 (ACE2) hydrolyzes angiotensin-(1-10) (angiotensin I) to yield angiotensin-(1-9) (Donoghue et al. 2000, Tipnis et al. 2000, Vickers et al. 2002, Rice t al. 2004). The activity of ACE2 on angiotensin I is weak (Rice et al. 2004), being 400-fold lower than the activity of ACE2 on angiotensin II (Vickers et al. 2002). - Reviewed: Joseph, J, 2012-08-06 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4719 - - - - EQUAL - 977 - - - - KUTXFBIHPWIDJQ-UHFFFAOYSA-N - InChIKey - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1768 - - - - REACT_27432 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27432.1 - - - - B5MD49 - UniProt - - - - ENST00000372652 - Ensembl - - - - HGNC:3569 - HGNC - - - - C6G491 - UniProt - - - - SIN3B - HGNC - - - - - - MOD_RES 76 76 4-carboxyglutamate. - - - - ENSP00000271555 - Ensembl - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of FACTOR VII (F7)' - Activation of FACTOR VII expression by phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) is inferred from mouse. NPAS2 is predicted to act redundantly with CLOCK. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation96 - - - - 1KBH - PROTEIN DATA BANK - - - - REACT_8281 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_8281.2 - - - - NM_001030273 - RefSeq - - - - NP_004066 - RefSeq - - - - REACT_5486 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5486.2 - - - - EQUAL - 68 - - - - EQUAL - 110 - http://www.reactome.org/biopax/46/48887#SequenceSite9917 - - - - 1655755 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1655755 - - - - ENST00000344150 - Ensembl - - - - F7 - HGNC - - - - Q4KMR7 - UniProt - - - - By Homology - - - - - ENSP00000348003 - Ensembl - - - - EQUAL - 431 - http://www.reactome.org/biopax/46/48887#SequenceSite21440 - - - - A0ZXF9 - UniProt - - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ACSL1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation194 - - - - NM_182729 - RefSeq - - - - ENST00000223095 - Ensembl - - - - 1JMQ - PROTEIN DATA BANK - - - - NM_000312 - RefSeq - - - - NM_004269 - RefSeq - - - - EQUAL - 54 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1072 - - - - REACT_19740 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19740.2 - - - - FBXO5 - HGNC - - - - ENST00000491148 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8341 - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of APOA1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation198 - - - - EQUAL - 149 - - - - ENSG00000179094 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10055 - - - - - - - - - - - - ACTIVATION - - 'p-S133-CREB1 [nucleoplasm]' positively regulates 'Expression of PPARGC1A (PGC-1alpha)' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation112 - As inferred from mouse, phosphorylated CREB enhances expression of PPARGC1A (PGC-1alpha). - - - - - 2.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12832 - - - - - - MOD_RES 2399 2399 Phosphothreonine. - - - - ENST00000282957 - Ensembl - - - - ENSP00000240055 - Ensembl - - - - ENSG00000100448 - Ensembl - - - - A2RUM8 - UniProt - - - - Q9BZN4 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5735 - - - - ENSP00000263205 - Ensembl - - - - EQUAL - 66 - http://www.reactome.org/biopax/46/48887#SequenceSite9680 - - - - EQUAL - 1218 - - - - REACT_27123 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27123.3 - - - - - - MOD_RES 24 24 Pyrrolidone carboxylic acid. - - - - NM_004270 - RefSeq - - - - A5YM69 - uniprot - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12414 - - - - ENST00000315588 - Ensembl - - - - ENST00000304685 - Ensembl - - - - Q9UMT7 - UniProt - - - - REACT_120255 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120255.1 - - - - EQUAL - 487 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12370 - - - - EQUAL - 867 - - - - MED10 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1079 - - - - - - - - - - - Authored: May, B, 2011-11-08 - The ACOX1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction140 - Expression of ACOX1 - - - - ENST00000424279 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2228 - - - - - - MOD_RES 282 282 Nitrated tyrosine (By similarity). - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1073 - - - - EQUAL - 279 - - - - EQUAL - 66 - http://www.reactome.org/biopax/46/48887#SequenceSite9913 - - - - 939854 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939854 - - - - CARM1 - HGNC Symbol - - - - Q9NUD2 - UniProt - - - - ENSP00000380205 - Ensembl - - - - CHEBI:27302 - ChEBI - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite1779 - - - - NP_689407 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8319 - - - - - - MOD_RES 224 224 Phosphoserine. - - - - Q96KZ6 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10192 - - - - - - NP_054885 - RefSeq - - - - O00684 - UniProt - - - - 10734069 - Cescato R - Beuret N - Spiess M - Fiedler K - Renold A - Brown JL - Vogel LK - Wahlberg JM - PubMed - Basolateral sorting signals differ in their ability to redirect apical proteins to the basolateral cell surface. - J Biol Chem 275(13);9290-5 - 2000 - - - - Q9P086 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12388 - - - - EQUAL - 1386 - - - - REACT_115624 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115624.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9712 - - - - - - Plasminogen activator inhibitor-1 - SERPINE1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5124 - Reactome DB_ID: 158797 - PAI1 - - - - Q9H543 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5662 - - - - - - Q96H83 - UniProt - - - - HGNC:248 - HGNC - - - - NP_001251 - RefSeq - - - - EQUAL - 92 - - - - Q5JQZ7 - UniProt - - - - 15635043 - Strom, SC - Runge-Morris, M - Falany, CN - Cai, H - Kocarek, TA - Fang, HL - Pubmed - Regulation of human hepatic hydroxysteroid sulfotransferase gene expression by the peroxisome proliferator-activated receptor alpha transcription factor - Mol Pharmacol 67:1257-67 - 2005 - - - - P48163 - UniProt - - - - ENSP00000471062 - Ensembl - - - - P23786 - UniProt - - - - NP_001129670 - RefSeq - - - - 5469 - NCBI Gene - - - - - - - - - - - - FBXL3:CRY - http://www.reactome.org/biopax/46/48887#Complex4987 - Reactome DB_ID: 400351 - - - - 1368889 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368889 - - - - ENST00000359003 - Ensembl - - - - CHEBI:50122 - ChEBI - - - - 2026078 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2026078 - - - - CHEBI:6479 - ChEBI - - - - Q8WV18 - UniProt - - - - 156540 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=156540 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2098 - - - - - - - - - - - - - - - - INHIBITION - - 'captopril [extracellular region]' negatively regulates 'ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8)' - http://www.reactome.org/biopax/46/48887#Control304 - - - - NP_002496 - RefSeq - - - - Q13966 - UniProt - - - - ENSP00000423075 - Ensembl - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4698 - - - - - ENSG00000132964 - Ensembl - - - - CHEBI:5584 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2114 - - - - - - EQUAL - 212 - http://www.reactome.org/biopax/46/48887#SequenceSite12365 - - - - 15199055 - Lau, P - Parton, RG - Nixon, SJ - Muscat, GE - Pubmed - RORalpha regulates the expression of genes involved in lipid homeostasis in skeletal muscle cells: caveolin-3 and CPT-1 are direct targets of ROR - J Biol Chem 279:36828-40 - 2004 - - - - P07148 - UniProt - - - - 10917896 - Berkner, KL - Pubmed - The vitamin K-dependent carboxylase - J Nutr 130:1877-80 - 2000 - - - - ENSP00000450576 - Ensembl - - - - REACT_26632 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26632.3 - - - - ENST00000337138 - Ensembl - - - - ENSG00000184500 - Ensembl - - - - - - MOD_RES 74 74 4-carboxyglutamate. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12073 - - - - - - 400223 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400223 - - - - ENSP00000265641 - Ensembl - - - - HGNC:7668 - HGNC - - - - - - MOD_RES 54 54 4-carboxyglutamate. - - - - REACT_12834 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12834.1 - - - - ENST00000263205 - Ensembl - - - - EQUAL - 423 - http://www.reactome.org/biopax/46/48887#SequenceSite23039 - - - - EQUAL - 53 - - - - 5155 - NCBI Gene - - - - Q9HB34 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite23574 - - - - HST - SULT2A1 - Dehydroepiandrosterone sulfotransferase - DHEA-ST - STD - 2.8.2.14 - ST2A3 - Sulfotransferase 2A1 - ST2A1 - ST2 - Hydroxysteroid Sulfotransferase - - - - - - - - - - - - - - - - - - - - - - - - - ST2A1_HUMAN - Bile salt sulfotransferase - FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfonation of steroids and bile acids in the liver and adrenal glands.CATALYTIC ACTIVITY: 3'-phosphoadenylyl sulfate + glycolithocholate = adenosine 3',5'-bisphosphate + glycolithocholate 3-sulfate.CATALYTIC ACTIVITY: 3'-phosphoadenylyl sulfate + taurolithocholate = adenosine 3',5'-bisphosphate + taurolithocholate sulfate.SUBUNIT: Homodimer.SUBCELLULAR LOCATION: Cytoplasm.TISSUE SPECIFICITY: Liver, adrenal and at lower level in the kidney. Is present in human fetus in higher level in the adrenal than the liver and the kidney.PTM: The N-terminus is blocked.MISCELLANEOUS: Estrogens present in maternal circulation is predominantly derived from fetal dehydroepiandosterone sulfate which is hydrolyzed and metabolized to estrogens in placenta.SIMILARITY: Belongs to the sulfotransferase 1 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 138 138 Phosphoserine; by MAPK8 and MAPK9. - - - - - - RXRA_HUMAN - Retinoic acid receptor RXR-alpha - - - - - http://www.reactome.org/biopax/46/48887#Protein6467 - Reactome DB_ID: 381319 - RXRA - - - - 380740 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380740 - - - - 939866 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939866 - - - - ENST00000327773 - Ensembl - - - - - - PDGF A-chain - Platelet-derived growth factor, A chain isoform 1 - PDGFA isoform 1 - Platelet-derived growth factor alpha polypeptide - - - - - Reactome DB_ID: 184199 - http://www.reactome.org/biopax/46/48887#Protein2126 - PDGFA-1 - - - - P15144 - UniProt - - - - 12433930 - Canepa ET - Scassa ME - Varone CL - Giono LE - Guberman AS - PubMed - Inhibitory effect of AP-1 complex on 5-aminolevulinate synthase gene expression through sequestration of cAMP-response element protein (CRE)-binding protein (CBP) coactivator. - J Biol Chem 278(4);2317-26 - 2003 - - - - Q9UN32 - UniProt - - - - ENSP00000360762 - Ensembl - - - - 9034160 - Her, C - Wood, TC - Otterness, DM - Aksoy, IA - Weinshilboum, RM - Raftogianis, RB - Pubmed - Sulfation and sulfotransferases 1: Sulfotransferase molecular biology: cDNAs and genes - FASEB J 11:3-14 - 1997 - - - - YAP1 - HGNC Symbol - - - - - - MOD_RES 178 178 Phosphoserine. - - - - ENST00000522552 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10073 - - - - - - 7622060 - Ferrer M - Ayuso MS - Gonzalez-Manchon C - Parrilla R - PubMed - Cloning, sequencing and functional expression of a cDNA encoding a NADP-dependent malic enzyme from human liver. - Gene 159(2);255-60 - 1995 - - - - ENST00000354895 - Ensembl - - - - ENST00000393962 - Ensembl - - - - Q96L98 - UniProt - - - - A8K7B9 - UniProt - - - - ENST00000366667 - Ensembl - - - - HGNC:333 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2247 - - - - - - Q16062 - UniProt - - - - 1989748 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989748 - - - - GGCX - HGNC Symbol - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5804 - - - - Q16665 - UniProt - - - - 96764 - NCBI Gene - - - - EQUAL - 415 - http://www.reactome.org/biopax/46/48887#SequenceSite21476 - - - - - - MED6 - hMed6 - ARC33 - Mediator complex subunit 6 - Activator-recruited cofactor 33 kDa component - Renal carcinoma antigen NY-REN-28 - - - - - - - - - - - - - - - - - - MED6_HUMAN - Mediator of RNA polymerase II transcription subunit 6 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with CTNNB1 and GLI3.SUBCELLULAR LOCATION: Nucleus.SIMILARITY: Belongs to the Mediator complex subunit 6 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - CTSZ - HGNC Symbol - - - - ENST00000263390 - Ensembl - - - - REACT_24888 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24888.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1666 - - - - - - 212441 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212441 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21498 - - - - HGNC:14254 - HGNC - - - - ENSG00000142453 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8312 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12845 - - - - 26224 - NCBI Gene - - - - NP_036290 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12048 - - - - - - PDGFB - HGNC Symbol - - - - NP_001166169 - RefSeq - - - - EQUAL - 279 - http://www.reactome.org/biopax/46/48887#SequenceSite25557 - - - - 176559 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176559 - - - - 14718417 - pubchem-substance - - - - NM_005120 - RefSeq - - - - HGNC:25487 - HGNC - - - - REACT_115644 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115644.2 - - - - D3DNH7 - UniProt - - - - NP_733779 - RefSeq - - - - - - MOD_RES 48 48 4-carboxyglutamate. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1066 - - - - 159780 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159780 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21493 - - - - EQUAL - 142 - - - - ENSP00000401046 - Ensembl - - - - REACT_19898 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19898.3 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12822 - - - - - - - - - - - - TEAD:WWTR1(TAZ) - http://www.reactome.org/biopax/46/48887#Complex4780 - Reactome DB_ID: 2032762 - - - - REACT_9625 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9625.3 - - - - NP_001243587 - RefSeq - - - - - - - - - - phospho-Emi1:Cdc20/Cdh1 complexes - Converted from EntitySet in Reactome - Reactome DB_ID: 177332 - http://www.reactome.org/biopax/46/48887#Complex2827 - - - - 1628 - NCBI Gene - - - - EQUAL - 979 - - - - Q6ISB5 - UniProt - - - - - - - - - - - - - - - Proconvertin - Factor VII light chain - Factor VII heavy chain - Eptacog alfa - 3.4.21.21 - F7 - SPCA - Serum prothrombin conversion accelerator - - - - - - - - - - - - - - - - - - - - - - - - - FA7_HUMAN - Coagulation factor VII - FUNCTION: Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium.CATALYTIC ACTIVITY: Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.SUBUNIT: Heterodimer of a light chain and a heavy chain linked by a disulfide bond.SUBCELLULAR LOCATION: Secreted.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=A; IsoId=P08709-1; Sequence=Displayed; Name=B; IsoId=P08709-2; Sequence=VSP_005387;TISSUE SPECIFICITY: Plasma.PTM: The vitamin K-dependent, enzymatic carboxylation of some glutamate residues allows the modified protein to bind calcium.PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains.PTM: O- and N-glycosylated. N-glycosylation at Asn-205 occurs cotranslationally and is mediated by STT3A-containing complexes, while glycosylation at Asn-382 is post-translational and is mediated STT3B-containing complexes before folding. O-fucosylated by POFUT1 on a conserved serine or threonine residue found in the consensus sequence C2-X(4,5)-[S/T]-C3 of EGF domains, where C2 and C3 are the second and third conserved cysteines.DISEASE: Factor VII deficiency (FA7D) [MIM:227500]: A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels. Note=The disease is caused by mutations affecting the gene represented in this entry.PHARMACEUTICAL: Available under the names Niastase or Novoseven (Novo Nordisk). Used for the treatment of bleeding episodes in hemophilia A or B patients with antibodies to coagulation factors VIII or IX.SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 2 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 1 peptidase S1 domain.WEB RESOURCE: Name=Wikipedia; Note=Factor VII entry; URL="http://en.wikipedia.org/wiki/Factor_VII";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/F7";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/f7/";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=F7"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_005911 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13224 - - - - - - MOD_RES 71 71 4-carboxyglutamate. - - - - 11907135 - Spann NJ - Hui TY - Miyake JH - Davis RA - PubMed - Regulation of cholesterol-7alpha-hydroxylase: BAREly missing a SHP. - J Lipid Res 43(4);533-43 - 2002 - - - - EQUAL - 29 - http://www.reactome.org/biopax/46/48887#SequenceSite21715 - - - - ENSP00000286317 - Ensembl - - - - 601714 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12024 - - - - NP_054790 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4776 - - - - - 8504159 - Williams S - Hayes LS - Lira ME - Elsenboss L - Lloyd DB - Thompson JF - PubMed - Cholesterol 7 alpha hydroxylase promoter separated from cyclophilin pseudogene by Alu sequence. - Biochim Biophys Acta 1168(2);239-42 - 1993 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10008 - - - - 939164 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939164 - - - - 2428842 - Peiper SC - Lemons RS - Rubin CM - Ashmun RA - Sherr CJ - Look AT - Roussel MF - Le Beau MM - Rebentisch MB - PubMed - Molecular cloning, expression, and chromosomal localization of the gene encoding a human myeloid membrane antigen (gp150). - J Clin Invest 78(4);914-21 - 1986 - - - - REACT_26444 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26444.3 - - - - - - Transcriptional enhancer factor TEF-1 - - - - - Reactome DB_ID: 2032774 - http://www.reactome.org/biopax/46/48887#Protein11192 - TEAD1 - - - - 1368141 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368141 - - - - - - MOD_RES 166 166 Phosphotyrosine. - - - - ENST00000570094 - Ensembl - - - - Q8TB55 - UniProt - - - - EQUAL - 66 - - - - Q5TF47 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10134 - - - - - - MOD_RES 98 98 N6,N6,N6-trimethyllysine (By similarity). - - - - - - Hydroxymethylglutaryl-CoA synthase - - - - - Reactome DB_ID: 191329 - http://www.reactome.org/biopax/46/48887#Protein13776 - HMGCS1 - - - - Q6QMH5 - UniProt - - - - 508496 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=508496 - - - - 2022360 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022360 - - - - NM_001193348 - RefSeq - - - - 1989774 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989774 - - - - EQUAL - 22 - http://www.reactome.org/biopax/46/48887#SequenceSite25564 - - - - Q96IG3 - UniProt - - - - NCOR2 - HGNC Symbol - - - - - - MOD_RES 517 517 Phosphoserine. - - - - - - MOD_RES 2463 2463 Phosphoserine (By similarity). - - - - 2GUT - PROTEIN DATA BANK - - - - REACT_25365 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25365.1 - - - - HMGCS2 - HGNC - - - - - - MOD_RES 280 280 Phosphoserine; by AMPK (By similarity). - - - - P07225 - UniProt - - - - EQUAL - 197 - http://www.reactome.org/biopax/46/48887#SequenceSite21669 - - - - 600140 - omim - - - - Mediator complex subunit 29 - MED29 - IXL - Intersex-like protein - - - - - - - - - - - - - - MED29_HUMAN - Mediator of RNA polymerase II transcription subunit 29 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Associates with the MED18/MED20 heteromer.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Widely expressed in embryo and adult.SIMILARITY: Belongs to the Mediator complex subunit 29 family.SEQUENCE CAUTION: Sequence=AAU43732.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_001139468 - RefSeq - - - - EQUAL - 59 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7591 - - - - 20817722 - Wang, Y - Crumbley, C - Kojetin, DJ - Burris, TP - Pubmed - Characterization of the core mammalian clock component, NPAS2, as a REV-ERBalpha/RORalpha target gene - J Biol Chem 285:35386-92 - 2010 - - - - ENSG00000182220 - Ensembl - - - - 445328 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=445328 - - - - B3KRQ7 - UniProt - - - - NP_001001547 - RefSeq - - - - - - MOD_RES 119 119 Phosphothreonine; by MAPK8 and MAPK9. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1105 - - - - - - MOD_RES 136 136 (3R)-3-hydroxyaspartate (By similarity). - - - - Q96FV6 - UniProt - - - - EQUAL - 438 - - - - REACT_115625 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115625.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10802 - - - - - - Q969K2 - UniProt - - - - 1C5M - PROTEIN DATA BANK - - - - Q707U4 - UniProt - - - - - - - - - - - - - - - - PROS - PROS1 - - - - - - - - - - - - - - - - - - - PROS_HUMAN - Vitamin K-dependent protein S - FUNCTION: Anticoagulant plasma protein; it is a cofactor to activated protein C in the degradation of coagulation factors Va and VIIIa. It helps to prevent coagulation and stimulating fibrinolysis.SUBCELLULAR LOCATION: Secreted.TISSUE SPECIFICITY: Plasma.PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains (By similarity).DISEASE: Thrombophilia due to protein S deficiency, autosomal dominant (THPH5) [MIM:612336]: A hemostatic disorder characterized by impaired regulation of blood coagulation and a tendency to recurrent venous thrombosis. Based on the plasma levels of total and free PROS1 as well as the serine protease-activated protein C cofactor activity, three types of THPH5 have been described: type I, characterized by reduced total and free PROS1 levels together with reduced anticoagulant activity; type III, in which only free PROS1 antigen and PROS1 activity levels are reduced; and the rare type II which is characterized by normal concentrations of both total and free PROS1 antigen, but low cofactor activity. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Thrombophilia due to protein S deficiency, autosomal recessive (THPH6) [MIM:614514]: A very rare and severe hematologic disorder resulting in thrombosis and secondary hemorrhage usually beginning in early infancy. Some affected individuals develop neonatal purpura fulminans, multifocal thrombosis, or intracranial hemorrhage. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Contains 4 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 2 laminin G-like domains.SEQUENCE CAUTION: Sequence=AAP45054.1; Type=Erroneous gene model prediction;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PROS1";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/pros1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P46937 - UniProt - - - - ENSP00000471464 - Ensembl - - - - P25208 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10016 - - - - 601487 - omim - - - - ENSP00000419653 - Ensembl - - - - P00742 - UniProt - - - - CSNK1D - HGNC Symbol - - - - NP_001025443 - RefSeq - - - - HGNC:23663 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2093 - - - - NM_201555 - RefSeq - - - - NCOA1 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21481 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10171 - - - - - - B4DTJ6 - UniProt - - - - REACT_25460 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25460.2 - - - - NM_001127350 - RefSeq - - - - NP_079410 - RefSeq - - - - EQUAL - 61 - - - - Q6PJ36 - UniProt - - - - Q9BZK7 - UniProt - - - - 879798 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879798 - - - - 421296 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421296 - - - - REACT_117910 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117910.1 - - - - B2R4L9 - UniProt - - - - Q96LB5 - UniProt - - - - Q9UMA7 - UniProt - - - - ENSG00000008405 - Ensembl - - - - reactome - Reactome - Source type: BIOPAX, Reactome v46 (using only 'Homo sapiens.owl') 23-SEP-2013 - - - - EQUAL - 458 - http://www.reactome.org/biopax/46/48887#SequenceSite23169 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9325 - - - - - - Cryptochrome-1 - CRY1_HUMAN - - - - - Reactome DB_ID: 400247 - http://www.reactome.org/biopax/46/48887#Protein11511 - CRY1 - - - - EQUAL - 57 - - - - ENST00000395808 - Ensembl - - - - ENSP00000312472 - Ensembl - - - - EQUAL - 1741 - - - - ENSP00000433348 - Ensembl - - - - EQUAL - 1255 - http://www.reactome.org/biopax/46/48887#SequenceSite21468 - - - - 400219 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400219 - - - - EQUAL - 72 - - - - Q7Z7P3 - UniProt - - - - MED7 - HGNC - - - - REACT_25395 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25395.1 - - - - 14672706 - Kawamoto, T - Iwata, T - Furukawa, M - Honma, K - Miyazaki, K - Fujimoto, K - Sato, F - Maemura, K - Nagai, R - Noshiro, M - Takeda, N - Kato, Yoichi - Honma, S - Pubmed - A novel autofeedback loop of Dec1 transcription involved in circadian rhythm regulation - Biochem Biophys Res Commun 313:117-24 - 2004 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10194 - - - - - - 212428 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212428 - - - - ENSP00000344458 - Ensembl - - - - ENST00000360595 - Ensembl - - - - O15534 - UniProt - - - - 6270633 - Weare, JA - Stewart, TA - Erdös, EG - Pubmed - Purification and characterization of human converting enzyme (kininase II) - Peptides 2:145-52 - 1981 - - - - 157049 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=157049 - - - - 177328 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=177328 - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4696 - - - - - - - Dexamethasone - - - - Reactome DB_ID: 879813 - http://www.reactome.org/biopax/46/48887#SmallMolecule968 - DEXA - - - - NM_002505 - RefSeq - - - - 1490 - NCBI Gene - - - - - - MOD_RES 860 860 Phosphoserine. - - - - ENSG00000165029 - Ensembl - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21662 - - - - Q76P53 - UniProt - - - - 12093884 - Young SG - Hofmann AF - Beigneux A - PubMed - Human CYP7A1 deficiency: progress and enigmas. - J Clin Invest 110(1);29-31 - 2002 - - - - Q16018 - UniProt - - - - - - MOD_RES 625 625 Omega-N-methylated arginine (By similarity). - - - - CHEBI:25366 - ChEBI - - - - REACT_26322 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26322.3 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5786 - - - - Nuclear transcription factor Y subunit B - HAP3 - NFYB - NF-YB - CAAT box DNA-binding protein subunit B - - - - - - - - - - - - - - - - - NFYB_HUMAN - Nuclear transcription factor Y subunit beta - FUNCTION: Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters, for example in type 1 collagen, albumin and beta-actin genes.SUBUNIT: Heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. Interacts with C1QBP.SUBCELLULAR LOCATION: Nucleus.DOMAIN: Can be divided into 3 domains: the weakly conserved A domain, the highly conserved B domain thought to be involved in subunit interaction and DNA binding, and the Glu-rich C domain.PTM: Monoubiquitination at Lys-140 plays an important role in transcriptional activation by allowing the deposition of histone H3 methylations as well as histone H2B monoubiquitination at 'Lys- 121'.SIMILARITY: Belongs to the NFYB/HAP3 subunit family.SEQUENCE CAUTION: Sequence=CAA42230.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_26768 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26768.2 - - - - NM_001894 - RefSeq - - - - HYAFETHFCAUJAY-UHFFFAOYSA-N - InChIKey - - - - - - MOD_RES 67 67 Phosphoserine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12939 - - - - Q0VF45 - UniProt - - - - NM_014223 - RefSeq - - - - NM_033405 - RefSeq - - - - HGNC:2651 - HGNC - - - - B3KNX5 - UniProt - - - - EQUAL - 224 - - - - HGNC:23032 - HGNC - - - - EQUAL - 461 - http://www.reactome.org/biopax/46/48887#SequenceSite21696 - - - - MED23 - HGNC Symbol - - - - ENST00000523985 - Ensembl - - - - O00313 - UniProt - - - - 34 - NCBI Gene - - - - NM_015869 - RefSeq - - - - EQUAL - 149 - http://www.reactome.org/biopax/46/48887#SequenceSite11621 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1063 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9752 - - - - - - REACT_26312 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26312.2 - - - - ENSP00000365803 - Ensembl - - - - - - MOD_RES 424 424 Phosphoserine. - - - - 10068650 - Furie, B - Bouchard, BA - Furie, BC - Pubmed - Vitamin K-dependent biosynthesis of gamma-carboxyglutamic acid - Blood 93:1798-808 - 1999 - - - - - - - - - - Estrogen-related receptor alpha - ESRRA - Nuclear receptor subfamily 3 group B member 1 - ERR-alpha - NR3B1 - ESRL1 - Estrogen receptor-like 1 - ERR1 - - - - - - - - - - - - - - - - - - ERR1_HUMAN - Steroid hormone receptor ERR1 - FUNCTION: Binds to an ERR-alpha response element (ERRE) containing a single consensus half-site, 5'-TNAAGGTCA-3'. Can bind to the medium-chain acyl coenzyme A dehydrogenase (MCAD) response element NRRE-1 and may act as an important regulator of MCAD promoter. Binds to the C1 region of the lactoferrin gene promoter. Requires dimerization and the coactivator, PGC-1A, for full activity. The ERRalpha/PGC1alpha complex is a regulator of energy metabolism.SUBUNIT: Binds DNA as a monomer or a homodimer. Interacts (via the AF2 domain) with coactivator PPARGC1A (via the L3 motif); the interaction greatly enhances transriptional activity of genes involved in energy metabolism. Interacts with PIAS4; the interaction enhances sumoylation.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P11474-1; Sequence=Displayed; Name=2; IsoId=P11474-2; Sequence=VSP_035756; Note=No experimental confirmation available;INDUCTION: Induced by PGC1alpha in a number of specific cell types including heart, kidney and muscle.PTM: Phosphorylation on Ser-19 enhances sumoylation on Lys-14 increasing repression of transcriptional activity.PTM: Sumoylated with SUMO2. Main site is Lys-14 which is enhanced by phosphorylation on Ser-19, cofactor activation, and by interaction with PIAS4. Sumoylation enhances repression of transcriptional activiy, but has no effect on subcellular location nor on DNA binding.PTM: Reversibly acetylated. Acetylation by PCAF/KAT2 at Lys-129, Lys-138, Lys-160 and Lys-162 and PCAF/KAT2 decreases transcriptional activity probably by inhibiting DNA-binding activity; deacetylation involves SIRT1 and HDAC8 and increases DNA-binding.SIMILARITY: Belongs to the nuclear hormone receptor family. NR3 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.SEQUENCE CAUTION: Sequence=AAB17015.1; Type=Erroneous initiation; Sequence=CAA35778.1; Type=Frameshift; Positions=345, 354;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/ESRRAID44408ch11q13.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - Rosiglitazone - - - - Reactome DB_ID: 420931 - http://www.reactome.org/biopax/46/48887#SmallMolecule734 - RGZ - - - - ENSG00000108510 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1074 - - - - NM_001185039 - RefSeq - - - - - - MOD_RES 604 604 Phosphothreonine (By similarity). - - - - ENSP00000357039 - Ensembl - - - - NP_055038 - RefSeq - - - - NP_078941 - RefSeq - - - - ENST00000280614 - Ensembl - - - - 8145132 - pubchem-substance - - - - EQUAL - 39 - - - - EQUAL - 798 - http://www.reactome.org/biopax/46/48887#SequenceSite21499 - - - - Q9UES8 - UniProt - - - - A0JLT2 - UniProt - - - - NM_000016 - RefSeq - - - - ENST00000369406 - Ensembl - - - - 18292238 - Tai, ES - Husna, B - Shen, P - Yong, EL - Liu, MH - Li, J - Pubmed - A natural polymorphism in peroxisome proliferator-activated receptor-alpha hinge region attenuates transcription due to defective release of nuclear receptor corepressor from chromatin - Mol Endocrinol 22:1078-92 - 2008 - - - - EQUAL - 208 - - - - - - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule1079 - Reactome DB_ID: 2065405 - ramiprilat - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5636 - - - - - - NM_134442 - RefSeq - - - - MED9 - MED25 - Mediator complex subunit 9 - - - - - - - - - - - - MED9_HUMAN - Mediator of RNA polymerase II transcription subunit 9 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 9 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 400399 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400399 - - - - ACADM - HGNC Symbol - - - - HGNC:11473 - HGNC - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - The PERIOD-2 (PER2) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The promoter of the PER2 gene contains an E-box which binds the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer (and probably also the BMAL1:NPAS2 (ARNTL:NPAS2) heterodimer). The BMAL1:CLOCK heterodimer activates transcription of PER2. - Authored: May, B, 2010-03-11 - Reviewed: Hirota, T, 2010-06-23 - http://www.reactome.org/biopax/46/48887#TemplateReaction70 - Reviewed: Delaunay, F, 2010-06-23 - Edited: May, B, 2010-03-11 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Expression of PERIOD-2 - - - - ENSP00000418779 - Ensembl - - - - EQUAL - 178 - http://www.reactome.org/biopax/46/48887#SequenceSite21491 - - - - 1592213 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1592213 - - - - 442464 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=442464 - - - - NP_004261 - RefSeq - - - - 400176 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400176 - - - - ENST00000360453 - Ensembl - - - - REACT_118766 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118766.2 - - - - REACT_199 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_199.2 - - - - ENST00000231509 - Ensembl - - - - - FABPL - L-FABP - Fatty acid-binding protein 1 - Liver-type fatty acid-binding protein - FABP1 - - - - - - - - - - - - - FABPL_HUMAN - Fatty acid-binding protein, liver - FUNCTION: Binds free fatty acids and their coenzyme A derivatives, bilirubin, and some other small molecules in the cytoplasm. May be involved in intracellular lipid transport.SUBCELLULAR LOCATION: Cytoplasm.DOMAIN: Forms a beta-barrel structure that accommodates hydrophobic ligands in its interior.SIMILARITY: Belongs to the calycin superfamily. Fatty-acid binding protein (FABP) family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - HGNC:29529 - HGNC - - - - - - - - - - Reactome DB_ID: 400346 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11524 - p-PER1/2 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of TIAM2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation218 - - - - - - 9xCbxE-F7(61-466) - - - - - - - - - - - - - - Reactome DB_ID: 159808 - http://www.reactome.org/biopax/46/48887#Protein11658 - factor VII - - - - EQUAL - 60 - http://www.reactome.org/biopax/46/48887#SequenceSite21681 - - - - Q6P4R7 - UniProt - - - - ENST00000370005 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12846 - - - - ENSG00000143344 - Ensembl - - - - GO:0005829 - Gene Ontology - - - - PPARGC1A - HGNC Symbol - - - - - - MOD_RES 2069 2069 Phosphoserine. - - - - 176895 - omim - - - - 2065426 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065426 - - - - ENST00000506055 - Ensembl - - - - REACT_7438 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7438.2 - - - - 7589785 - Hagen M - Coughtrie MW - Forbes KJ - Hume R - Glatt H - PubMed - Human fetal adrenal hydroxysteroid sulphotransferase: cDNA cloning, stable expression in V79 cells and functional characterisation of the expressed enzyme. - Mol Cell Endocrinol 112(1);53-60 - 1995 - - - - - MED7 - CRSP9 - RNA polymerase transcriptional regulation mediator subunit 7 homolog - hMED7 - ARC34 - Activator-recruited cofactor 34 kDa component - Transcriptional coactivator CRSP33 - Mediator complex subunit 7 - Cofactor required for Sp1 transcriptional activation subunit 9 - CRSP complex subunit 9 - - - - - - - - - - - - - - - - MED7_HUMAN - Mediator of RNA polymerase II transcription subunit 7 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus.PTM: Constitutively sumoylated.SIMILARITY: Belongs to the Mediator complex subunit 7 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_201443 - RefSeq - - - - REACT_24885 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24885.2 - - - - ENST00000403290 - Ensembl - - - - HGNC:3555 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10057 - - - - - - 400392 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400392 - - - - Q9UM11 - UniProt - - - - 142910 - omim - - - - HGNC:5006 - HGNC - - - - - - MOD_RES 57 57 4-carboxyglutamate. - - - - FZR1 - HGNC - - - - EQUAL - 1 - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite23004 - - - - ENSP00000394097 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5788 - - - - P08311 - UniProt - - - - - - - SREBP1A,2 - - - - Reactome DB_ID: 1655734 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein6464 - SREBF1A,2 - - - - - - - - - - Reactome DB_ID: 212440 - http://www.reactome.org/biopax/46/48887#Protein3050 - CDK8 - - - - NM_001077261 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature9718 - - - - ENSG00000113558 - Ensembl - - - - ENST00000407597 - Ensembl - - - - EQUAL - 64 - http://www.reactome.org/biopax/46/48887#SequenceSite10122 - - - - 9439 - NCBI Gene - - - - REACT_24326 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24326.2 - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite10127 - - - - Q53ZW7 - UniProt - - - - ENST00000447544 - Ensembl - - - - Q6I9S0 - UniProt - - - - - - MOD_RES 945 945 Phosphoserine (By similarity). - - - - 12464674 - Paddon-Jones D - Morio-Liondore B - Rasmussen BB - Holmback UC - Wolfe RR - Volpi E - PubMed - Malonyl coenzyme A and the regulation of functional carnitine palmitoyltransferase-1 activity and fat oxidation in human skeletal muscle. - J Clin Invest 110(11);1687-93 - 2002 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12360 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14066 - - - - ENSP00000302967 - Ensembl - - - - 159843 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159843 - - - - Q8IUT4 - UniProt - - - - ENST00000353267 - Ensembl - - - - 59272 - NCBI Gene - - - - 9477 - NCBI Gene - - - - 1AUT - PROTEIN DATA BANK - - - - EQUAL - 60 - http://www.reactome.org/biopax/46/48887#SequenceSite9682 - - - - - - Nuclear receptor corepressor 1 - NCOR1_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein2827 - Reactome DB_ID: 442501 - NCOR1 - - - - EQUAL - 247 - - - - EQUAL - 817 - - - - Q02928 - UniProt - - - - EQUAL - 1590 - - - - CHEBI:48829 - ChEBI - - - - MED15 - HGNC - - - - TGS1 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1649 - - - - NP_005111 - RefSeq - - - - EQUAL - 32 - - - - MED10 - HGNC Symbol - - - - EQUAL - 382 - - - - - - Transcriptional enhancer factor TEF-3 - - - - - Reactome DB_ID: 2032780 - http://www.reactome.org/biopax/46/48887#Protein11195 - TEAD4 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2133 - - - - - - EQUAL - 2 - - - - NM_003939 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1856 - - - - - - MOD_RES 1382 1382 Phosphoserine; by IKKA. - - - - EQUAL - 1177 - - - - ENSP00000363193 - Ensembl - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - http://www.reactome.org/biopax/46/48887#TemplateReaction62 - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-03-19 - The FACTOR VII (F7) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. In mouse the F7 gene shows circadian expression due to activation by the Bmal1:Clock (Arntl:Clock) heterodimer. - Reviewed: Delaunay, F, 2010-06-23 - Authored: May, B, 2010-03-19 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Expression of FACTOR VII (F7) - - - - Q5T6K8 - UniProt - - - - P22966 - UniProt - - - - ENST00000442725 - Ensembl - - - - 605044 - omim - - - - 381067 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381067 - - - - REACT_148271 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148271.1 - - - - - - MOD_RES 73 73 4-carboxyglutamate. - - - - ENSG00000156603 - Ensembl - - - - 400569 - NCBI Gene - - - - ENSP00000378426 - Ensembl - - - - A8K0I7 - UniProt - - - - - - - - - - - - factor X - http://www.reactome.org/biopax/46/48887#Complex5018 - Reactome DB_ID: 159785 - - - - ENST00000481739 - Ensembl - - - - ENST00000524698 - Ensembl - - - - P04085 - UniProt - - - - ENSG00000166821 - Ensembl - - - - REACT_5612 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5612.2 - - - - Q96T85 - UniProt - - - - - - MOD_RES 55 55 4-carboxyglutamate. - - - - ENSP00000417719 - Ensembl - - - - 163809 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163809 - - - - ENST00000402285 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12827 - - - - CHEBI:10743 - ChEBI - - - - ENST00000250378 - Ensembl - - - - REACT_22795 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22795.3 - - - - NM_004275 - RefSeq - - - - NP_963836 - RefSeq - - - - EQUAL - 88 - - - - - - MOD_RES 1259 1259 Phosphoserine. - - - - Q9UCA1 - UniProt - - - - 381271 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381271 - - - - - - - - - - - - - - - - - - - - pro-protein Z, uncarboxylated + 13 CO2 + 13 O2 + 13 vitamin K hydroquinone -> pro-protein Z + 13 H2O + 13 vitamin K epoxide - At the beginning of this reaction, 1 molecule of 'pro-protein Z, uncarboxylated', 13 molecules of 'Oxygen', 13 molecules of 'vitamin K hydroquinone', and 13 molecules of 'CO2' are present. At the end of this reaction, 1 molecule of 'pro-protein Z', 13 molecules of 'H2O', and 13 molecules of 'vitamin K epoxide' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3890 - - - - - - - - - CLOCK_HUMAN - Circadian locomoter output cycles protein kaput - - - - - Reactome DB_ID: 879828 - http://www.reactome.org/biopax/46/48887#Protein11509 - CLOCK - - - - EQUAL - 41 - http://www.reactome.org/biopax/46/48887#SequenceSite21736 - - - - 400270 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400270 - - - - REACT_148676 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148676.1 - - - - 9174159 - Butta N - Ferrer M - Ayuso MS - Gonzalez-Manchon C - Parrilla R - PubMed - Molecular cloning and functional characterization of the human cytosolic malic enzyme promoter: thyroid hormone responsiveness. - DNA Cell Biol 16(5);533-44 - 1997 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10000 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12398 - - - - EQUAL - 62 - http://www.reactome.org/biopax/46/48887#SequenceSite10121 - - - - EQUAL - 785 - - - - - - MOD_RES 201 201 Sulfotyrosine. - - - - PTHR24265:SF21 - PANTHER Family - - - - - 2901990 - Hansen OC - Hunziker W - Laustsen L - Konigshofer E - Danielsen EM - Moller J - Welinder KG - Olsen J - Engberg J - Cowell GM - PubMed - Complete amino acid sequence of human intestinal aminopeptidase N as deduced from cloned cDNA. - FEBS Lett 238(2);307-14 - 1988 - - - - 556802 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556802 - - - - - - MOD_RES 131 131 Phosphoserine. - - - - ENSG00000151726 - Ensembl - - - - 2022343 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022343 - - - - Q96RU7 - UniProt - - - - NP_001160070 - RefSeq - - - - - - MOD_RES 146 146 N6-acetyllysine (By similarity). - - - - NP_852468 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1094 - - - - B5BUA1 - UniProt - - - - 1989772 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989772 - - - - Q92689 - UniProt - - - - 549581 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549581 - - - - VEXZGXHMUGYJMC-UHFFFAOYSA-M - InChIKey - - - - - - MOD_RES 27 27 Phosphoserine. - - - - 561138 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=561138 - - - - 400204 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400204 - - - - EQUAL - 1444 - - - - 420932 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=420932 - - - - NM_001098272 - RefSeq - - - - EQUAL - 163 - http://www.reactome.org/biopax/46/48887#SequenceSite5363 - - - - HGNC:2529 - HGNC - - - - Q5T9U5 - UniProt - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein2128 - Converted from EntitySet in Reactome - Reactome DB_ID: 381935 - Processed PDGF-B - - - - 163838 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163838 - - - - 163840 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163840 - - - - REACT_2966 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2966.2 - - - - EQUAL - 49 - - - - 49836665 - pubchem-substance - - - - HGNC:7154 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5644 - - - - EQUAL - 154 - - - - ENST00000503201 - Ensembl - - - - REACT_4548 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4548.2 - - - - 80205 - NCBI Gene - - - - - - ubiquitin (UBB 2) - - - - - Reactome DB_ID: 939870 - http://www.reactome.org/biopax/46/48887#Protein2475 - UBB(77-152) - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4704 - - - - EQUAL - 46 - - - - Q15561 - UniProt - - - - NM_001256092 - RefSeq - - - - - - - - - - - NRF1:PGC-1beta:ALAS1 gene - - - - ALAS1 gene:NRF1:PPARGC1B - http://www.reactome.org/biopax/46/48887#Complex5482 - Reactome DB_ID: 2466384 - - - - NP_001019265 - RefSeq - - - - 11010 - NCBI Gene - - - - EQUAL - 1255 - http://www.reactome.org/biopax/46/48887#SequenceSite21490 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10113 - - - - ENST00000462745 - Ensembl - - - - - - MOD_RES 520 520 Phosphoserine (By similarity). - - - - ENSP00000340576 - Ensembl - - - - - - MOD_RES 683 683 Phosphotyrosine (By similarity). - - - - EQUAL - 1472 - - - - REACT_117514 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117514.2 - - - - EQUAL - 34 - http://www.reactome.org/biopax/46/48887#SequenceSite23018 - - - - 197188 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=197188 - - - - 1989819 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989819 - - - - 9612 - NCBI Gene - - - - Q9BQC2 - UniProt - - - - EQUAL - 2174 - http://www.reactome.org/biopax/46/48887#SequenceSite12363 - - - - NP_940982 - RefSeq - - - - NM_153450 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10807 - - - - - - ENST00000281455 - Ensembl - - - - 173430 - omim - - - - NP_055630 - RefSeq - - - - Q12772 - UniProt - - - - NM_001270629 - RefSeq - - - - - - MOD_RES 92 92 Phosphoserine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14052 - - - - TNFRSF21 - CD358 - Death receptor 6 - DR6 - - - - - - - - - - - - - - - - TNR21_HUMAN - Tumor necrosis factor receptor superfamily member 21 - FUNCTION: May activate NF-kappa-B and promote apoptosis. May activate JNK and be involved in T-cell differentiation. Required for both normal cell body death and axonal pruning. Trophic-factor deprivation triggers the cleavage of surface APP by beta-secretase to release sAPP-beta which is further cleaved to release an N- terminal fragment of APP (N-APP). N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6).SUBUNIT: Associates with TRADD. Interacts with N-APP (By similarity).SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Probable).TISSUE SPECIFICITY: Highly expressed in heart, brain, placenta, pancreas, lymph node, thymus and prostate. Detected at lower levels in lung, skeletal muscle, kidney, testis, uterus, small intestine, colon, spleen, bone marrow and fetal liver. Very low levels were found in adult liver and peripheral blood leukocytes.SIMILARITY: Contains 1 death domain.SIMILARITY: Contains 4 TNFR-Cys repeats.CAUTION: It is uncertain whether Met-1 or Met-25 is the initiator.SEQUENCE CAUTION: Sequence=AAH10241.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 7759116 - Kuo WL - Gray J - Solera J - Stafford DW - Cruces J - PubMed - Chromosomal localization of the gamma-glutamyl carboxylase gene at 2p12. - Genomics 25(3);746-8 - 1995 - - - - NM_001142522 - RefSeq - - - - 879703 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879703 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12938 - - - - 400287 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400287 - - - - NP_076869 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5778 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10054 - - - - - - 5187 - NCBI Gene - - - - REACT_119652 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119652.1 - - - - ENSG00000126231 - Ensembl - - - - MOD_RES Omega-N-methylated arginine (By similarity) - - - - EQUAL - 271 - - - - - - MOD_RES 1481 1481 Phosphoserine. - - - - NR3C1 - HGNC Symbol - - - - 11513608 - Berkner, KL - McNally, BA - Pudota, BN - Hommema, EL - Stenina, O - Pubmed - Tethered processivity of the vitamin K-dependent carboxylase: factor IX is efficiently modified in a mechanism which distinguishes Gla's from Glu's and which accounts for comprehensive carboxylation in vivo - Biochemistry 40:10301-9 - 2001 - - - - 2022344 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022344 - - - - 20346956 - Yue WW - Zschocke J - Shafqat N - Turnbull A - Oppermann U - PubMed - Crystal structures of human HMG-CoA synthase isoforms provide insights into inherited ketogenesis disorders and inhibitor design. - J Mol Biol 398(4);497-506 - 2010 - - - - NP_068351 - RefSeq - - - - ENSG00000134852 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval9339 - - - - - - CDK19 - HGNC Symbol - - - - - - MOD_RES 69 69 4-carboxyglutamate. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1099 - - - - EQUAL - 347 - http://www.reactome.org/biopax/46/48887#SequenceSite23167 - - - - Q8TC78 - UniProt - - - - 12093894 - Salen, G - Erickson, SK - Eng, C - Pullinger, CR - Mulvihill, SJ - Rivera, CR - Batta, AK - Malloy, MJ - Shefer, S - Kane, JP - Verhagen, A - Pubmed - Human cholesterol 7alpha-hydroxylase (CYP7A1) deficiency has a hypercholesterolemic phenotype - J Clin Invest 110:109-17 - 2002 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5609 - - - - REACT_21954 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21954.2 - - - - NP_001141 - RefSeq - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction156 - The GLIPR1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of GLIPR1 - - - - Q9UPB1 - UniProt - - - - EQUAL - 60 - http://www.reactome.org/biopax/46/48887#SequenceSite9886 - - - - D3DPM1 - UniProt - - - - NP_001171528 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1064 - - - - EQUAL - 554 - - - - NM_201557 - RefSeq - - - - ENSP00000379192 - Ensembl - - - - Q9Y2T8 - UniProt - - - - ENST00000456393 - Ensembl - - - - NP_055964 - RefSeq - - - - EQUAL - 544 - - - - Q8N180 - UniProt - - - - EQUAL - 617 - - - - MED26 - HGNC - - - - NM_201441 - RefSeq - - - - Q5SW68 - UniProt - - - - MED19 - HGNC - - - - D3DNY5 - UniProt - - - - MED20 - HGNC Symbol - - - - EQUAL - 144 - http://www.reactome.org/biopax/46/48887#SequenceSite12357 - - - - 10001 - NCBI Gene - - - - REACT_118016 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118016.1 - - - - CHEBI:48804 - ChEBI - - - - EQUAL - 495 - - - - CHEBI:42395 - ChEBI - - - - ENST00000374736 - Ensembl - - - - EQUAL - 110 - - - - CYP7A1 - 1.14.13.17 - CYPVII - CYP7 - Cytochrome P450 7A1 - Cholesterol 7-alpha-hydroxylase - - - - - - - - - - - - - - - - - - - - - - - - - - - - CP7A1_HUMAN - Cholesterol 7-alpha-monooxygenase - FUNCTION: Catalyzes a rate-limiting step in cholesterol catabolism and bile acid biosynthesis by introducing a hydrophilic moiety at position 7 of cholesterol. Important for cholesterol homeostasis.CATALYTIC ACTIVITY: Cholesterol + NADPH + O(2) = 7-alpha- hydroxycholesterol + NADP(+) + H(2)O.COFACTOR: Heme group.PATHWAY: Lipid metabolism; bile acid biosynthesis.SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Peripheral membrane protein. Microsome membrane; Peripheral membrane protein.TISSUE SPECIFICITY: Detected in liver.INDUCTION: Up-regulated by glucose and by cholestyramine. Down- regulated by chenodeoxycholic acid.SIMILARITY: Belongs to the cytochrome P450 family.WEB RESOURCE: Name=Wikipedia; Note=Cholesterol-7 alpha-hydroxylase entry; URL="http://en.wikipedia.org/wiki/Cholesterol_7_alpha-hydroxylase";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CYP7A1ID40254ch8q12.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 538738 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=538738 - - - - NP_004260 - RefSeq - - - - ENSG00000197461 - Ensembl - - - - 4801 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5631 - - - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 400149 - http://www.reactome.org/biopax/46/48887#SmallMolecule736 - Ligands of PPARA - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13222 - - - - Q9UEI5 - UniProt - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12933 - - - - Q8IVH3 - UniProt - - - - 1368960 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368960 - - - - 7003 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10161 - - - - - - ENSG00000152944 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21447 - - - - Q9Y618 - UniProt - - - - ENST00000367990 - Ensembl - - - - MED18 - HGNC - - - - ENSP00000252519 - Ensembl - - - - UGT1A9 - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2897 - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14053 - - - - REACT_119871 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119871.2 - - - - Q8TDG9 - UniProt - - - - ENSP00000344705 - Ensembl - - - - 1989741 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989741 - - - - 3992 - NCBI Gene - - - - 2101 - NCBI Gene - - - - EQUAL - 33 - http://www.reactome.org/biopax/46/48887#SequenceSite21668 - - - - EQUAL - 270 - http://www.reactome.org/biopax/46/48887#SequenceSite12383 - - - - CTGF - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12020 - - - - ENSP00000287936 - Ensembl - - - - REACT_26101 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26101.2 - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite21741 - - - - 120520 - omim - - - - - - - - - - Reactome DB_ID: 1605563 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11543 - MEF2C/D - - - - NP_004167 - RefSeq - - - - EQUAL - 72 - http://www.reactome.org/biopax/46/48887#SequenceSite9882 - - - - 51003 - NCBI Gene - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction164 - Reviewed: Kersten, S, 2009-06-08 - The TIAM2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of TIAM2 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1093 - - - - EQUAL - 81 - http://www.reactome.org/biopax/46/48887#SequenceSite4965 - - - - NM_003167 - RefSeq - - - - EQUAL - 1468 - - - - NR1D1 - HGNC - - - - HGNC:30022 - HGNC - - - - - - MOD_RES 1542 1542 N6-acetyllysine. - - - - EQUAL - 25 - http://www.reactome.org/biopax/46/48887#SequenceSite21709 - - - - REACT_164154 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164154.1 - - - - REACT_148380 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148380.1 - - - - CHEBI:23833 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2589 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CPT2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation201 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5620 - - - - - - MOD_RES 136 136 Methionine sulfoxide. - - - - ENST00000300651 - Ensembl - - - - - - ANG1-8 - Angiotensin-(1-8) - ANGT_HUMAN - AGT(34-41) - Angiotensin II - Angiotensin-2 - - - - - Reactome DB_ID: 374187 - http://www.reactome.org/biopax/46/48887#Protein3228 - AGT - - - - - - Trap100 - Thyroid hormone receptor-associated protein 4 - CRSP4 - Activator-recruited cofactor 100 kDa component - MED24 - KIAA0130 - ARC100 - Mediator complex subunit 24 - DRIP100 - Thyroid hormone receptor-associated protein complex 100 kDa component - THRAP4 - CRSP complex subunit 4 - hTRAP100 - Vitamin D3 receptor-interacting protein complex 100 kDa component - TRAP100 - Cofactor required for Sp1 transcriptional activation subunit 4 - - - - - - - - - - - - - - - - - - - - - - - - MED24_HUMAN - Mediator of RNA polymerase II transcription subunit 24 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with AR.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O75448-1; Sequence=Displayed; Name=2; IsoId=O75448-2; Sequence=VSP_041125;TISSUE SPECIFICITY: Ubiquitous. Abundant in skeletal muscle, heart and placenta.SIMILARITY: Belongs to the Mediator complex subunit 24 family.SEQUENCE CAUTION: Sequence=BAA09479.2; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1089 - - - - EQUAL - 777 - http://www.reactome.org/biopax/46/48887#SequenceSite21456 - - - - 12130638 - Brewer, M - Baler, R - Muñoz, E - Pubmed - Circadian Transcription. Thinking outside the E-Box - J Biol Chem 277:36009-17 - 2002 - - - - REACT_4182 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4182.1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval3977 - - - - - - 163812 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163812 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1070 - - - - EQUAL - 79 - http://www.reactome.org/biopax/46/48887#SequenceSite9908 - - - - NM_003330 - RefSeq - - - - MOD_RES N-acetylalanine (By similarity) - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5771 - - - - EQUAL - 532 - http://www.reactome.org/biopax/46/48887#SequenceSite1787 - - - - B2RB04 - UniProt - - - - NM_001127328 - RefSeq - - - - EQUAL - 704 - - - - - - Water - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule973 - Reactome DB_ID: 113519 - H2O - - - - O14503 - UniProt - - - - Q5T8U0 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5779 - - - - MED9 - HGNC Symbol - - - - REACT_5867 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5867.2 - - - - - Expression of 5-aminolevulinate synthase 1 - - - - - - Expression of ALAS1 - The ALAS1 gene is transcribed to yield mRNA and the mRNA is translated in the cytosol to yield precursor protein. The ALAS1 precursor is imported into the mitochodrial matrix where it catalyzes the synthesis of 5-aminolevulinate from glycine and succinyl-CoA as part of heme biosynthesis. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4677 - Reviewed: Kersten, S, 2009-06-08 - Authored: May, B, 2011-08-20 - Edited: May, B, 2011-08-20 - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10014 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12380 - - - - EQUAL - 500 - - - - CHEBI:30491 - ChEBI - - - - 8619474 - Andersson B - Wentland MA - Gibbs RA - Liu W - Ricafrente JY - PubMed - A "double adaptor" method for improved shotgun library construction. - Anal Biochem 236(1);107-13 - 1996 - - - - EQUAL - 533 - - - - Q9C0J9 - UniProt - - - - 5045 - NCBI Gene - - - - - - MOD_RES 1042 1042 Phosphoserine; by PKA. - - - - Q9UPG4 - UniProt - - - - ENST00000529824 - Ensembl - - - - 4800 - NCBI Gene - - - - REACT_25029 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25029.1 - - - - 123810 - omim - - - - - - - - - - - - - - - - MEF2C - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MEF2C_HUMAN - Myocyte-specific enhancer factor 2C - FUNCTION: Transcription activator which binds specifically to the MEF2 element present in the regulatory regions of many muscle- specific genes. Controls cardiac morphogenesis and myogenesis, and is also involved in vascular development. Plays an essential role in hippocampal-dependent learning and memory by suppressing the number of excitatory synapses and thus regulating basal and evoked synaptic transmission. Crucial for normal neuronal development, distribution, and electrical activity in the neocortex. Necessary for proper development of megakaryocytes and platelets and for bone marrow B-lymphopoiesis. Required for B-cell survival and proliferation in response to BCR stimulation, efficient IgG1 antibody responses to T-cell-dependent antigens and for normal induction of germinal center B-cells. May also be involved in neurogenesis and in the development of cortical architecture (By similarity). Isoform 3 and isoform 4, which lack the repressor domain, are more active than isoform 1 and isoform 2.SUBUNIT: Forms a complex with class II HDACs in undifferentiating cells. On myogenic differentiation, HDACs are released into the cytoplasm allowing MEF2s to interact with other proteins for activation. Interacts with EP300 in differentiating cells; the interaction acetylates MEF2C leading to increased DNA binding and activation. Interacts with HDAC7 and CARM1 (By similarity). Interacts with HDAC4, HDAC7 AND HDAC9; the interaction WITH HDACs represses transcriptional activity. Interacts with MYOCD (By similarity).SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Comment=Additional isoforms seem to exist; Name=1; IsoId=Q06413-1; Sequence=Displayed; Name=2; Synonyms=Muscle; IsoId=Q06413-2; Sequence=VSP_006248; Name=3; Synonyms=hMEF2C-delta32, Brain; IsoId=Q06413-3; Sequence=VSP_006249; Name=4; IsoId=Q06413-4; Sequence=VSP_043339, VSP_006248; Name=5; IsoId=Q06413-5; Sequence=VSP_045478, VSP_006248; Note=No experimental confirmation available; Name=6; IsoId=Q06413-6; Sequence=VSP_046251, VSP_006248; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in brain and skeletal muscle.DEVELOPMENTAL STAGE: Expression is highest during the early stages of postnatal development, at later stages levels greatly decrease.DOMAIN: The beta domain, missing in a number of isoforms, is required for enhancement of transcriptional activity (By similarity).PTM: Phosphorylation on Ser-59 enhances DNA binding activity (By similarity). Phosphorylation on Ser-396 is required for Lys-391 sumoylation and inhibits transcriptional activity.PTM: Acetylated by p300 on several sites in diffentiating myocytes. Acetylation on Lys-4 increases DNA binding and transactivation.PTM: Sumoylated on Lys-391 with SUMO2 but not by SUMO1 represses transcriptional activity.PTM: Proteolytically cleaved in cerebellar granule neurons, probably by caspase 7, following neurotoxicity. Preferentially cleaves the CDK5-mediated hyperphosphorylated form which leads to neuron apoptosis and transcriptional inactivation.DISEASE: Mental retardation, autosomal dominant 20 (MRD20) [MIM:613443]: A disorder characterized by severe mental retardation, absent speech, hypotonia, poor eye contact and stereotypic movements. Dysmorphic features include high broad forehead with variable small chin, short nose with anteverted nares, large open mouth, upslanted palpebral fissures and prominent eyebrows. Some patients have seizures. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the MEF2 family.SIMILARITY: Contains 1 MADS-box domain.SIMILARITY: Contains 1 Mef2-type DNA-binding domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 71 - - - - CCNC - HGNC - - - - - - - - - - - - PDGF A/B heterodimer - http://www.reactome.org/biopax/46/48887#Complex894 - Reactome DB_ID: 380759 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry13184 - - - - - C21H31N3O5 - N(2)-[(1S)-1-carboxy-3-phenylpropyl]-L-lysyl-L-proline - (S)-1-(N(2)-(1-carboxy-3-phenylpropyl)-L-lysyl)-L-proline - lisinopril anhydrous - - - - - - 405.4879 - lisinopril - lisinopril - - - - 1989779 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989779 - - - - EQUAL - 263 - http://www.reactome.org/biopax/46/48887#SequenceSite21495 - - - - NM_001271629 - RefSeq - - - - - - MOD_RES 1014 1014 N6-acetyllysine. - - - - B2R6S0 - UniProt - - - - - - MOD_RES 1433 1433 Phosphoserine. - - - - ENSP00000345772 - Ensembl - - - - - - MOD_RES 687 687 N6-acetyllysine. - - - - EQUAL - 73 - http://www.reactome.org/biopax/46/48887#SequenceSite9677 - - - - ENSP00000361073 - Ensembl - - - - REACT_147891 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147891.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8309 - - - - ELOVL3 - HGNC Symbol - - - - Q99629 - UniProt - - - - ENSP00000379238 - Ensembl - - - - EQUAL - 236 - - - - EQUAL - 79 - http://www.reactome.org/biopax/46/48887#SequenceSite9881 - - - - 159718 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159718 - - - - NM_201542 - RefSeq - - - - REACT_27090 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27090.2 - - - - NCOA3 - HGNC - - - - HGNC:9236 - HGNC - - - - - - MOD_RES 63 63 Phosphothreonine. - - - - - - MOD_RES 61 61 4-carboxyglutamate. - - - - ENST00000456877 - Ensembl - - - - InChI=1S/C9H15NO3S/c1-6(5-14)8(11)10-4-2-3-7(10)9(12)13/h6-7,14H,2-5H2,1H3,(H,12,13)/t6-,7+/m1/s1 - InChI - - - - - - MOD_RES 22 22 Phosphoserine. - - - - EQUAL - 70 - - - - - - Nuclear receptor coactivator RAP250 - RAP250 - PPAR-interacting protein - KIAA0181 - AIB3 - PRIP - Thyroid hormone receptor-binding protein - NRC RAP250 - Peroxisome proliferator-activated receptor-interacting protein - ASC-2 - Amplified in breast cancer protein 3 - Activating signal cointegrator 2 - Nuclear receptor-activating protein, 250 kDa - NCOA6 - Cancer-amplified transcriptional coactivator ASC-2 - TRBP - - - - - - - - - - - - - - - - - - - - - - NCOA6_HUMAN - Nuclear receptor coactivator 6 - FUNCTION: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Coactivates expression in an agonist- and AF2-dependent manner. Involved in the coactivation of different nuclear receptors, such as for steroids (GR and ERs), retinoids (RARs and RXRs), thyroid hormone (TRs), vitamin D3 (VDR) and prostanoids (PPARs). Probably functions as a general coactivator, rather than just a nuclear receptor coactivator. May also be involved in the coactivation of the NF-kappa-B pathway. May coactivate expression via a remodeling of chromatin and its interaction with histone acetyltransferase proteins.SUBUNIT: Monomer and homodimer. Interacts with RBM39 (By similarity). Interacts in vitro with the basal transcription factors GTF2A and TBP, suggesting an autonomous transactivation function. Interacts with NCOA1, CRSP3, RBM14, the histone acetyltransferases EP300 and CREBBP, and with the methyltransferases NCOA6IP and PRMT2/HRMT1L1. Component of the MLL2/3 complex (also named ASCOM complex), at least composed of KMT2D/MLL2 or KMT2C/MLL3, ASH2L, RBBP5, WDR5, NCOA6, DPY30, KDM6A, PAXIP1/PTIP, PAGR1 and alpha- and beta-tubulin. Interacts with ZNF335; may enhance ligand-dependent transcriptional activation by nuclear hormone receptors.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Ubiquitous. Highly expressed in brain, prostate, testis and ovary; weakly expressed in lung, thymus and small intestine.DOMAIN: Contains two Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs. Only motif 1 is essential for the association with nuclear receptors, while adjacent Ser-884 displays selectivity for nuclear receptors.PTM: Phosphorylated by PRKDC.PTM: Phosphorylation on Ser-884 leads to a strong decrease in binding to ESR1 and ESR2.MISCELLANEOUS: Frequently amplified or overexpressed in colon, breast and lung cancers.SEQUENCE CAUTION: Sequence=AAF16403.1; Type=Frameshift; Positions=88; Sequence=BAA11498.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000359867 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10058 - - - - - - Q6UWP0 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4450 - - - - - - REACT_25088 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25088.1 - - - - P20718 - UniProt - - - - P19793 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10169 - - - - - - EQUAL - 278 - - - - 612382 - omim - - - - Q99594 - UniProt - - - - - Carnitine palmitoyltransferase II - CPT1 - CPT2 - 2.3.1.21 - CPT II - - - - - - - - - - - - - - - - - - - - - - - - - - - CPT2_HUMAN - Carnitine O-palmitoyltransferase 2, mitochondrial - CATALYTIC ACTIVITY: Palmitoyl-CoA + L-carnitine = CoA + L- palmitoylcarnitine.PATHWAY: Lipid metabolism; fatty acid beta-oxidation.SUBCELLULAR LOCATION: Mitochondrion inner membrane; Peripheral membrane protein; Matrix side.DISEASE: Carnitine palmitoyltransferase 2 deficiency late-onset (CPT2D) [MIM:255110]: Autosomal recessive disorder characterized by recurrent myoglobinuria, episodes of muscle pain, stiffness, and rhabdomyolysis. These symptoms are triggered by prolonged exercise, fasting or viral infection and patients are usually young adults. In addition to this classical, late-onset, muscular type, a hepatic or hepatocardiomuscular form has been reported in infants. Clinical pictures in these children or neonates include hypoketotic hypoglycemia, liver dysfunction, cardiomyopathy and sudden death. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Carnitine palmitoyltransferase 2 deficiency infantile (CPT2DI) [MIM:600649]: A disorder of mitochondrial long-chain fatty acid oxidation characterized by hepatic or hepato-cardio- muscular manifestations with onset in infancy. Clinical features include hypoketotic hypoglycemia, lethargy, seizures, hepatomegaly, liver dysfunction, cardiomegaly and dilated cardiomyopathy. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Carnitine palmitoyltransferase 2 deficiency lethal neonatal (CPT2D-LN) [MIM:608836]: Lethal neonatal form of CPT2D. This rarely presentation is antenatal with cerebral periventricular cysts and cystic dysplastic kidneys. The clinical variability of the disease is likely attributed to the variable residual enzymatic activity. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Encephalopathy, acute, infection-induced, 4 (IIAE4) [MIM:614212]: A severe neurologic complication of an infection. It manifests within days in otherwise healthy children after common viral infections, without evidence of viral infection of the brain or inflammatory cell infiltration. In affected children, high- grade fever is accompanied within 12 to 48 hours by febrile convulsions, often leading to coma, multiple-organ failure, brain edema, and high morbidity and mortality. The infections are usually viral, particularly influenza, although other viruses and even mycoplasma have been found to cause the disorder. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. CPT2 polymorphic variants do not cause classical carnitine palmitoyltransferase 2 deficiency, and patients harboring any of them are asymptomatic most of the time. However, they are prone to viral infection (high fever)-related encephalopathy (PubMed:21697855).SIMILARITY: Belongs to the carnitine/choline acetyltransferase family.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CPT2"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 40 - http://www.reactome.org/biopax/46/48887#SequenceSite21742 - - - - Q53HQ6 - UniProt - - - - Q5T9U6 - UniProt - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5775 - - - - - - - - - - - - - - - - PPARA:RXRA Coactivator Complex - http://www.reactome.org/biopax/46/48887#Complex3139 - Reactome DB_ID: 400154 - - - - 879826 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879826 - - - - ENSP00000296861 - Ensembl - - - - ENSG00000147872 - Ensembl - - - - ENST00000382548 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10166 - - - - - - CREB1 - HGNC - - - - REACT_13284 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13284.1 - - - - 600528 - omim - - - - 10499 - NCBI Gene - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1845 - - - - Q3MIK6 - UniProt - - - - ENSP00000422607 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12049 - - - - - - - - MOD_RES 1482 1482 Phosphoserine. - - - - REACT_117924 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117924.1 - - - - ENSG00000115718 - Ensembl - - - - ENST00000355761 - Ensembl - - - - EQUAL - 435 - http://www.reactome.org/biopax/46/48887#SequenceSite20839 - - - - ENSP00000378403 - Ensembl - - - - - - - - - - Edited: May, B, 2011-06-22 - The CLOCK gene is transcribed to yield mRNA and the mRNA is translated to yield protein. Transcription of CLOCK is repressed by REV-ERBA. - http://www.reactome.org/biopax/46/48887#TemplateReaction56 - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - Expression of CLOCK - - - - ENSP00000261523 - Ensembl - - - - ENSP00000335087 - Ensembl - - - - ANKRD1 - HGNC Symbol - - - - - - MOD_RES 67 67 4-carboxyglutamate. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14055 - - - - ENSP00000218099 - Ensembl - - - - HMGCR - HGNC Symbol - - - - NM_001530 - RefSeq - - - - 375499 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=375499 - - - - A2I2P7 - UniProt - - - - ENST00000370187 - Ensembl - - - - EQUAL - 517 - - - - 1989782 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989782 - - - - EQUAL - 68 - - - - 549449 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549449 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite20840 - - - - ENST00000217964 - Ensembl - - - - ENST00000290866 - Ensembl - - - - NP_002598 - RefSeq - - - - 612283 - omim - - - - REACT_23231 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23231.3 - - - - - - TNR21_HUMAN - Tumor necrosis factor receptor superfamily member 21 - - - - - http://www.reactome.org/biopax/46/48887#Protein13782 - Reactome DB_ID: 561169 - TNFRSF21 - - - - ENSP00000330382 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4701 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10040 - - - - - - REACT_6827 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6827.1 - - - - ENSG00000180182 - Ensembl - - - - D3DQW6 - UniProt - - - - ENSG00000029153 - Ensembl - - - - EQUAL - 47 - - - - - - - - - - - Reviewed: Kay, SA, 2010-06-23 - The NR1D1 (REV-ERBA) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. In mouse the Rev-erba gene shows circadian expression due to transactivation by the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer. REV-ERBA binds the promoter of its own gene and represses its own expression (Adelmont et al. 1996). - Reviewed: Hirota, T, 2010-06-23 - Edited: May, B, 2010-03-19 - http://www.reactome.org/biopax/46/48887#TemplateReaction71 - Reviewed: Delaunay, F, 2010-06-23 - Authored: May, B, 2010-03-19 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - Expression of NR1D1 (REV-ERBA) - - - - - - MOD_RES 160 160 N6-acetyllysine; by PCAF/KAT2B. - - - - PER2 - HGNC Symbol - - - - REACT_117986 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117986.1 - - - - Q9BYK8 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1839 - - - - ENSG00000092009 - Ensembl - - - - - - MOD_RES 785 785 N6-acetyllysine. - - - - - - MOD_RES 10 10 Phosphoserine. - - - - REACT_12956 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12956.1 - - - - 20889553 - Craik, CS - Makarova, A - Raymond, WW - Caughey, GH - Ray, M - Trivedi, NN - Pubmed - How immune peptidases change specificity: cathepsin G gained tryptic function but lost efficiency during primate evolution - J Immunol 185:5360-8 - 2010 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10041 - - - - - - ENST00000368240 - Ensembl - - - - CSNK1D - HGNC - - - - EQUAL - 252 - - - - NM_004268 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4958 - - - - - EQUAL - 1648 - - - - EQUAL - 229 - http://www.reactome.org/biopax/46/48887#SequenceSite1780 - - - - NM_006851 - RefSeq - - - - - - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule1075 - Reactome DB_ID: 2022362 - aliskiren - - - - 400158 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400158 - - - - ENSG00000069667 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature428 - - - - EQUAL - 824 - http://www.reactome.org/biopax/46/48887#SequenceSite21430 - - - - - - MOD_RES 1029 1029 Phosphoserine. - - - - InChI=1S/C18H32O3/c1-2-3-4-5-6-8-11-14-17(19)15-12-9-7-10-13-16-18(20)21/h6,8,11,14,17,19H,2-5,7,9-10,12-13,15-16H2,1H3,(H,20,21)/b8-6-,14-11+/t17-/m1/s1 - InChI - - - - - - - - - - - - - - - - - - - UBIQ_HUMAN - - - - Reactome DB_ID: 68524 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein2471 - ubiquitin - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21451 - - - - EQUAL - 82 - http://www.reactome.org/biopax/46/48887#SequenceSite3901 - - - - REACT_7103 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7103.4 - - - - 159739 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159739 - - - - 549424 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549424 - - - - G8JLM5 - UniProt - - - - - - MOD_RES 1111 1111 Phosphoserine. - - - - EQUAL - 741 - - - - - - MOD_RES 977 977 Phosphoserine (By similarity). - - - - - - pro-protein Z, uncarboxylated - - - - - Reactome DB_ID: 163816 - http://www.reactome.org/biopax/46/48887#Protein11641 - PROZ(24-400) - - - - EQUAL - 402 - - - - 23389 - NCBI Gene - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction147 - Reviewed: Kersten, S, 2009-06-08 - The CPT2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of CPT2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10015 - - - - VKORC1 - HGNC - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5795 - - - - REACT_25978 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25978.2 - - - - GO:0000139 - Gene Ontology - - - - 1368082 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368082 - - - - 421304 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=421304 - - - - 1511 - NCBI Gene - - - - 7926749 - Tini, M - Ong, E - Giguère, V - Otulakowski, G - Flock, G - Evans, RM - Pubmed - Isoform-specific amino-terminal domains dictate DNA-binding properties of ROR alpha, a novel family of orphan hormone nuclear receptors - Genes Dev 8:538-53 - 1994 - - - - REACT_120324 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120324.1 - - - - Q8TAR1 - UniProt - - - - ENST00000322142 - Ensembl - - - - ENST00000456144 - Ensembl - - - - - Angiotensin-converting Enzyme Hydrolyzes Angiotensin I to Yield Angiotensin II - - - - - - - - - - - - - - - - ACE Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-8) - Authored: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4040 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - Angiotensin-converting enzyme (ACE) hydrolyzes angiotensin-(1-10) (angiotensin I) to yield angiotensin-(1-8) (angiotensin II) (Ehlers and Kirsch 1988). ACE is found at the plasma membrane of endothelial cells. This reaction is inhibited by drugs used to treat hypertension (angiotensin converting enzyme inhibitors, ACEI) including captopril (Gronhagen-Riska and Fyhrquist 1980, Stewart et al. 1981, Ehlers et al. 1986, Hayakari et al. 1989, Wei et al. 1991, Baudin and Beneteau-Burnat 1999), enalaprilat (metablized from the prodrug enalapril, Wei et al. 1991, Baudin and Beneteau-Burnat 1999), lisinopril ( Ehlers et al. 1991, Natesh et al. 2003), and ramiprilat (metabolized from the prodrug ramipril, Baudin and Beneteau-Burnat 1999). - - - - - 159773 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159773 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10116 - - - - FBXL3 - HGNC - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite9717 - - - - NM_001248003 - RefSeq - - - - 1368163 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368163 - - - - - - Mediator of RNA polymerase II transcription subunit 13-like - MD13L_HUMAN - - - - - Reactome DB_ID: 556797 - http://www.reactome.org/biopax/46/48887#Protein6494 - MED13L - - - - ENSP00000359878 - Ensembl - - - - 12151789 - Ptok U - Heun R - Shearman MS - Papassotiropoulos A - Jessen F - Bagli M - Schulte A - Lewis HD - PubMed - Cerebrospinal fluid levels of beta-amyloid(42) in patients with Alzheimer's disease are related to the exon 2 polymorphism of the cathepsin D gene. - Neuroreport 13(10);1291-4 - 2002 - - - - NM_000537 - RefSeq - - - - - HMGCR - HMG-CoA reductase - 1.1.1.34 - - - - - - - - - - - - - - - - - - - - - - HMDH_HUMAN - 3-hydroxy-3-methylglutaryl-coenzyme A reductase - FUNCTION: Transmembrane glycoprotein that is the rate-limiting enzyme in cholesterol biosynthesis as well as in the biosynthesis of nonsterol isoprenoids that are essential for normal cell function including ubiquinone and geranylgeranyl proteins.CATALYTIC ACTIVITY: (R)-mevalonate + CoA + 2 NADP(+) = (S)-3- hydroxy-3-methylglutaryl-CoA + 2 NADPH.ENZYME REGULATION: Regulated by a negative feedback mechanism through sterols and non-sterol metabolites derived from mevalonate. Inhibited by statins, a class of hypolipidemic agents used as pharmaceuticals to lower cholesterol levels in individuals at risk from cardiovascular disease due to hypercholesterolemia. Inhibition of HMGCR in the liver stimulates the LDL-receptors, which results in an increased clearance of LDL from the bloodstream and a decrease in blood cholesterol levels. The first results can be seen after one week of statin use and the effect is maximal after four to six weeks.PATHWAY: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step 3/3.SUBUNIT: Homodimer. Interacts (via its SSD) with INSIG1; the interaction, accelerated by sterols, leads to the recruitment of HMGCR to AMFR/gp78 for its ubiquitination by the sterol-mediated ERAD pathway. Interacts with UBIAD1.SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P04035-1; Sequence=Displayed; Name=2; IsoId=P04035-2; Sequence=VSP_002207; Note=No experimental confirmation available; Name=3; Synonyms=HMGCR-1b; IsoId=P04035-3; Sequence=VSP_046492; Note=Most highly expressed transcript in skin, esophagus, and uterine cervix;PTM: N-glycosylated. Deglycosylated by NGLY1 on release from the endoplasmic reticulum (ER) in a sterol-mediated manner.PTM: Undergoes sterol-mediated ubiquitination and ER-association degradation (ERAD). Accumulation of sterols in the endoplasmic reticulum (ER) membrane, triggers binding of the reductase to the ER membrane protein INSIG1. This INSIG1 binding leads to the recruitment of the ubiquitin ligase, AMFR/gp78, initiating ubiquitination of the reductase. The ubiquitinated reductase is then extracted from the ER membrane and delivered to cytosolic 26S proteosomes by a mechanism probably mediated by the ATPase Valosin-containing protein VCP/p97. Lys-248 is the main site of ubiquitination. Ubiquitination is enhanced by the presence of a geranylgeranylated protein.SIMILARITY: Belongs to the HMG-CoA reductase family.SIMILARITY: Contains 1 SSD (sterol-sensing) domain.SEQUENCE CAUTION: Sequence=BAH12375.1; Type=Frameshift; Positions=122; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000405282 - Ensembl - - - - GO:0005782 - Gene Ontology - - - - P23946 - UniProt - - - - 17604218 - Kersten, S - Muller, M - Duval, C - Pubmed - PPARalpha and dyslipidemia - Biochim Biophys Acta 1771:961-71 - 2007 - - - - ENST00000595158 - Ensembl - - - - P48730 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite23024 - - - - 1368140 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368140 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval832 - - - - - - NM_001256659 - RefSeq - - - - - - growth-arrest-specific protein 6 - 11xCbxE-GAS6(39-691) - - - - - - - - - - - - - - - - Reactome DB_ID: 163844 - http://www.reactome.org/biopax/46/48887#Protein11669 - GAS6 - - - - Q9HB03 - UniProt - - - - InChI=1S/C18H32O3/c1-2-3-11-14-17(19)15-12-9-7-5-4-6-8-10-13-16-18(20)21/h7,9,12,15,17,19H,2-6,8,10-11,13-14,16H2,1H3,(H,20,21)/b9-7-,15-12+/t17-/m0/s1 - InChI - - - - REACT_25475 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25475.2 - - - - 2990849 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2990849 - - - - O00147 - UniProt - - - - ENSP00000353528 - Ensembl - - - - Q15832 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10759 - - - - - - - - - - - Carnitine O-palmitoyltransferase I, liver isoform - CPTI-L - CPT1 - 2.3.1.21 - CPT I - Carnitine palmitoyltransferase 1A - CPT1A - CPT1-L - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CPT1A_HUMAN - Carnitine O-palmitoyltransferase 1, liver isoform - FUNCTION: Catalyzes the transfer of the acyl group of long-chain fatty acid-CoA conjugates onto carnitine, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion. Plays an important role in triglyceride metabolism.CATALYTIC ACTIVITY: Palmitoyl-CoA + L-carnitine = CoA + L- palmitoylcarnitine.ENZYME REGULATION: Inhibited by malonyl-CoA.PATHWAY: Lipid metabolism; fatty acid beta-oxidation.SUBUNIT: Homohexamer and homotrimer. Identified in a complex that contains at least CPT1A, ACSL1 and VDAC1. Also identified in complexes with ACSL1 and VDAC2 and VDAC3 (By similarity).SUBCELLULAR LOCATION: Mitochondrion outer membrane; Multi-pass membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P50416-1; Sequence=Displayed; Name=2; IsoId=P50416-2; Sequence=VSP_012167;TISSUE SPECIFICITY: Strong expression in kidney and heart, and lower in liver and skeletal muscle.INDUCTION: Up-regulated by fatty acids.DOMAIN: A conformation change in the N-terminal region spanning the first 42 residues plays an important role in the regulation of enzyme activity by malonyl-CoA.DISEASE: Carnitine palmitoyltransferase 1A deficiency (CPT1AD) [MIM:255120]: Rare autosomal recessive metabolic disorder of long- chain fatty acid oxidation characterized by severe episodes of hypoketotic hypoglycemia usually occurring after fasting or illness. Onset is in infancy or early childhood. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the carnitine/choline acetyltransferase family.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CPT1A"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CYP1A1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation202 - - - - EQUAL - 651 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10064 - - - - - - NP_001246 - RefSeq - - - - EQUAL - 30 - http://www.reactome.org/biopax/46/48887#SequenceSite23012 - - - - HGNC:3373 - HGNC - - - - Q9UCA5 - UniProt - - - - - - ubiquitin (UBA52) - - - - - http://www.reactome.org/biopax/46/48887#Protein2473 - Reactome DB_ID: 939844 - UBA52(1-76) - - - - - - MOD_RES 337 337 Phosphoserine; by SIK1 (By similarity). - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite21698 - - - - ENSP00000413424 - Ensembl - - - - - - MOD_RES 2057 2057 Phosphoserine. - - - - ENST00000389707 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10753 - - - - 54600 - NCBI Gene - - - - - - MCAD - ACADM - 1.3.8.7 - - - - - - - - - - - - - - - - - - - ACADM_HUMAN - Medium-chain specific acyl-CoA dehydrogenase, mitochondrial - FUNCTION: This enzyme is specific for acyl chain lengths of 4 to 16.CATALYTIC ACTIVITY: A medium-chain acyl-CoA + electron-transfer flavoprotein = a medium-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein.COFACTOR: FAD.PATHWAY: Lipid metabolism; mitochondrial fatty acid beta- oxidation.SUBUNIT: Homotetramer. Interacts with the heterodimeric electron transfer flavoprotein ETF.SUBCELLULAR LOCATION: Mitochondrion matrix.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P11310-1; Sequence=Displayed; Name=2; IsoId=P11310-2; Sequence=VSP_038420;DISEASE: Acyl-CoA dehydrogenase medium-chain deficiency (ACADMD) [MIM:201450]: An inborn error of mitochondrial fatty acid beta- oxidation which causes fasting hypoglycemia, hepatic dysfunction and encephalopathy, often resulting in death in infancy. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: A number of straight-chain acyl-CoA dehydrogenases of different substrate specificities are present in mammalian tissues.MISCELLANEOUS: Utilizes the electron transfer flavoprotein (ETF) as electron acceptor that transfers the electrons to the main mitochondrial respiratory chain via ETF-ubiquinone oxidoreductase (ETF dehydrogenase).SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ACADM"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of RGL1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation216 - - - - NP_004822 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12819 - - - - MEF2D - HGNC - - - - REACT_25106 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25106.1 - - - - ENSG00000108590 - Ensembl - - - - ENST00000371997 - Ensembl - - - - 1C3T - PROTEIN DATA BANK - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4769 - - - - - REACT_26499 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26499.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4697 - - - - - ENSG00000117984 - Ensembl - - - - EQUAL - 577 - http://www.reactome.org/biopax/46/48887#SequenceSite6151 - - - - 381325 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381325 - - - - PROS1 - HGNC - - - - EQUAL - 55 - - - - NP_002121 - RefSeq - - - - ENSP00000264110 - Ensembl - - - - PDGF subunit A - PDGF1 - Platelet-derived growth factor alpha polypeptide - PDGFA - Platelet-derived growth factor A chain - PDGF-1 - - - - - - - - - - - - - - - - - - - - PDGFA_HUMAN - Platelet-derived growth factor subunit A - FUNCTION: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal lung alveolar septum formation during embryogenesis, normal development of the gastrointestinal tract, normal development of Leydig cells and spermatogenesis. Required for normal oligodendrocyte development and normal myelination in the spinal cord and cerebellum. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFB (By similarity).SUBUNIT: Homodimer; antiparallel disulfide-linked dimer. Heterodimer with PDGFB; antiparallel disulfide-linked dimer. The PDGFA homodimer interacts with PDGFRA homodimers, and with heterodimers formed by PDGFRA and PDGFRB. The heterodimer composed of PDGFA and PDGFB interacts with PDGFRA homodimers, and with heterodimers formed by PDGFRA and PDGFRB. Interacts with CSPG4.SUBCELLULAR LOCATION: Secreted. Note=Released by platelets upon wounding.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Long; IsoId=P04085-1; Sequence=Displayed; Name=Short; IsoId=P04085-2; Sequence=VSP_004602, VSP_004603;DOMAIN: The long form contains a basic insert which acts as a cell retention signal.SIMILARITY: Belongs to the PDGF/VEGF growth factor family.WEB RESOURCE: Name=R&D Systems' cytokine mini-reviews: PDGF; URL="http://www.rndsystems.com/molecule_detail.aspx?m=1967"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - A2I2P2 - UniProt - - - - REACT_20426 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20426.2 - - - - NM_001977 - RefSeq - - - - NM_004075 - RefSeq - - - - Q96I39 - UniProt - - - - NM_015472 - RefSeq - - - - 1UL6 - PROTEIN DATA BANK - - - - EQUAL - 341 - http://www.reactome.org/biopax/46/48887#SequenceSite399 - - - - 879830 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=879830 - - - - EQUAL - 48 - - - - 8020987 - Chiang JY - Wang DP - PubMed - Structure and nucleotide sequences of the human cholesterol 7 alpha-hydroxylase gene (CYP7). - Genomics 20(2);320-3 - 1994 - - - - P63208 - UniProt - - - - ENSG00000173153 - Ensembl - - - - 212430 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212430 - - - - 1668266 - Chen, YN - Ehlers, MR - Riordan, JF - Pubmed - Purification and characterization of recombinant human testis angiotensin-converting enzyme expressed in Chinese hamster ovary cells - Protein Expr Purif 2:1-9 - 1991 - - - - ENSG00000130304 - Ensembl - - - - ENSP00000397419 - Ensembl - - - - NP_001986 - RefSeq - - - - - - MOD_RES 396 396 Phosphoserine; by AMPK (By similarity). - - - - REACT_13012 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13012.2 - - - - ENST00000486395 - Ensembl - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of APOA2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation199 - - - - - - - - 2.3.3.10 - HMGCS2 - HMG-CoA synthase - 3-hydroxy-3-methylglutaryl coenzyme A synthase - - - - - - - - - - - - - - - - - - - - - - - - - - - HMCS2_HUMAN - Hydroxymethylglutaryl-CoA synthase, mitochondrial - FUNCTION: This enzyme condenses acetyl-CoA with acetoacetyl-CoA to form HMG-CoA, which is the substrate for HMG-CoA reductase.CATALYTIC ACTIVITY: Acetyl-CoA + H(2)O + acetoacetyl-CoA = (S)-3- hydroxy-3-methylglutaryl-CoA + CoA.PATHWAY: Metabolic intermediate biosynthesis; (R)-mevalonate biosynthesis; (R)-mevalonate from acetyl-CoA: step 2/3.SUBUNIT: Homodimer.SUBCELLULAR LOCATION: Mitochondrion.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P54868-1; Sequence=Displayed; Name=2; IsoId=P54868-2; Sequence=VSP_042892; Note=No experimental confirmation available; Name=3; Synonyms=HMGCS2delta4; IsoId=P54868-3; Sequence=VSP_047445;TISSUE SPECIFICITY: Expression in liver is 200-fold higher than in any other tissue. Low expression in colon, kidney, testis, and pancreas. Very low expression in heart and skeletal muscle. Not detected in brain. The relative expression of isoform 3 (at mRNA level) is highest in heart (70%) and skeletal muscle (60%).DISEASE: HMG-CoA synthase deficiency (HMGCS deficiency) [MIM:605911]: Affected individuals present with severe hypoketotic hypoglycemia, mild hepatomegaly, or fatty liver, and a nondiagnostic pattern of urinary organic acids with increase of medium and short chain dicarboxylic acids. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the HMG-CoA synthase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001871 - RefSeq - - - - 549533 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549533 - - - - 159830 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159830 - - - - - - - - - - - - - - Vitamin K-dependent protein C light chain - Anticoagulant protein C - Autoprothrombin IIA - Activation peptide - 3.4.21.69 - Vitamin K-dependent protein C heavy chain - Blood coagulation factor XIV - PROC - - - - - - - - - - - - - - - - - - - - - PROC_HUMAN - Vitamin K-dependent protein C - FUNCTION: Protein C is a vitamin K-dependent serine protease that regulates blood coagulation by inactivating factors Va and VIIIa in the presence of calcium ions and phospholipids.CATALYTIC ACTIVITY: Degradation of blood coagulation factors Va and VIIIa.SUBUNIT: Synthesized as a single chain precursor, which is cleaved into a light chain and a heavy chain held together by a disulfide bond. The enzyme is then activated by thrombin, which cleaves a tetradecapeptide from the amino end of the heavy chain; this reaction, which occurs at the surface of endothelial cells, is strongly promoted by thrombomodulin.TISSUE SPECIFICITY: Plasma; synthesized in the liver.PTM: The vitamin K-dependent, enzymatic carboxylation of some Glu residues allows the modified protein to bind calcium.PTM: N- and O-glycosylated. Partial (70%) N-glycosylation of Asn- 371 with an atypical N-X-C site produces a higher molecular weight form referred to as alpha. The lower molecular weight form, not N- glycosylated at Asn-371, is beta. O-glycosylated with core 1 or possibly core 8 glycans.PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains.PTM: May be phosphorylated on a Ser or Thr in a region (AA 25-30) of the propeptide.DISEASE: Thrombophilia due to protein C deficiency, autosomal dominant (THPH3) [MIM:176860]: A hemostatic disorder characterized by impaired regulation of blood coagulation and a tendency to recurrent venous thrombosis. Individuals with decreased amounts of protein C are classically referred to as having type I protein C deficiency and those with normal amounts of a functionally defective protein as having type II deficiency. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Thrombophilia due to protein C deficiency, autosomal recessive (THPH4) [MIM:612304]: A hemostatic disorder characterized by impaired regulation of blood coagulation and a tendency to recurrent venous thrombosis. It results in a thrombotic condition that can manifest as a severe neonatal disorder or as a milder disorder with late-onset thrombophilia. The severe form leads to neonatal death through massive neonatal venous thrombosis. Often associated with ecchymotic skin lesions which can turn necrotic called purpura fulminans, this disorder is very rare. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: Calcium also binds, with stronger affinity to another site, beyond the GLA domain. This GLA-independent binding site is necessary for the recognition of the thrombin- thrombomodulin complex.SIMILARITY: Belongs to the peptidase S1 family.SIMILARITY: Contains 2 EGF-like domains.SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain.SIMILARITY: Contains 1 peptidase S1 domain.SEQUENCE CAUTION: Sequence=S76088; Type=Erroneous termination; Positions=151; Note=Translated as Cys;WEB RESOURCE: Name=Wikipedia; Note=Protein C entry; URL="http://en.wikipedia.org/wiki/Protein_C";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PROC";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/proc/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000515030 - Ensembl - - - - ABCA1 - HGNC - - - - - - MOD_RES 716 716 Phosphoserine (By similarity). - - - - B0LPF0 - UniProt - - - - REACT_27443 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27443.1 - - - - NP_004453 - RefSeq - - - - - - Grainyhead-like protein 1 homolog - GRHL1_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein13775 - Reactome DB_ID: 561138 - GRHL1 - - - - HGNC:17923 - HGNC - - - - EQUAL - 42 - http://www.reactome.org/biopax/46/48887#SequenceSite25580 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8362 - - - - 1989817 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989817 - - - - NP_001159579 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10030 - - - - EQUAL - 190 - http://www.reactome.org/biopax/46/48887#SequenceSite3902 - - - - Q4W5M7 - UniProt - - - - REACT_20337 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20337.4 - - - - 17488713 - Jones, TE - Han, DH - Geiger, PC - Holloszy, JO - Wright, DC - Pubmed - Calcium induces increases in peroxisome proliferator-activated receptor gamma coactivator-1alpha and mitochondrial biogenesis by a pathway leading to p38 mitogen-activated protein kinase activation - J Biol Chem 282:18793-9 - 2007 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1050 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2634 - - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21461 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25556 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The FADS1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction152 - Expression of FADS1 - - - - Q6GVI5 - UniProt - - - - EQUAL - 957 - http://www.reactome.org/biopax/46/48887#SequenceSite23029 - - - - Q96LE7 - UniProt - - - - ENSP00000443513 - Ensembl - - - - 159835 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159835 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12839 - - - - - - MOD_RES 70 70 Phosphoserine; by MAPK8 and MAPK9 (By similarity). - - - - 549592 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549592 - - - - EQUAL - 750 - http://www.reactome.org/biopax/46/48887#SequenceSite23025 - - - - ENSG00000198646 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10450 - - - - EQUAL - 285 - http://www.reactome.org/biopax/46/48887#SequenceSite25579 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12063 - - - - - - ENST00000487334 - Ensembl - - - - EQUAL - 87 - http://www.reactome.org/biopax/46/48887#SequenceSite3899 - - - - P21934 - UniProt - - - - 81857 - NCBI Gene - - - - EQUAL - 115 - http://www.reactome.org/biopax/46/48887#SequenceSite23038 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10027 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11974 - - - - 380748 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380748 - - - - 603482 - omim - - - - - - RPS27A(1-76) - ubiquitin (RPS27A) - - - - - http://www.reactome.org/biopax/46/48887#Protein1044 - Reactome DB_ID: 939205 - RPS27A - - - - 2032762 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032762 - - - - NP_002388 - RefSeq - - - - EQUAL - 66 - - - - - - MOD_RES 2079 2079 Phosphoserine. - - - - - C18H24N2O5 - Enalaprilate - enalapril diacid - enalaprilatum - N-[(1S)-1-carboxy-3-phenylpropyl]-L-alanyl-L-proline - enalapril acid - enalaprilate - enalaprilat - enalaprilat anhydrous - - - - - - enalaprilat (anhydrous) - enalaprilat (anhydrous) - Enalapril in which the ethyl ester group has been hydrolysed to the corresponding carboxylic acid. Enalaprilat is an angiotensin-converting enzyme (ACE) inhibitor and is used (often in the form of its prodrug, enalapril) in the treatment of hypertension and heart failure, for reduction of proteinuria and renal disease in patients with nephropathies, and for the prevention of stroke, myocardial infarction, and cardiac death in high-risk patients. Unlike enalapril, enalaprilat is not absorbed by mouth but is given by intravenous injection, usually as the dihydrate. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval830 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10808 - - - - - - REACT_27595 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27595.3 - - - - - - Pioglitazone - - - - Reactome DB_ID: 420932 - http://www.reactome.org/biopax/46/48887#SmallMolecule735 - Actos - - - - ENSP00000343159 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25578 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10013 - - - - EQUAL - 2399 - - - - REACT_117947 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117947.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12979 - - - - RNA polymerase II holoenzyme component SRB7 - hSrb7 - SURB7 - SRB7 - Mediator complex subunit 21 - MED21 - RNAPII complex component SRB7 - - - - - - - - - - - - - - - MED21_HUMAN - Mediator of RNA polymerase II transcription subunit 21 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Interacts with PPARG (By similarity). Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with THRA in a ligand-dependent fashion.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 21 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P36956 - UniProt - - - - TEAD2 - HGNC - - - - REACT_119740 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119740.2 - - - - EQUAL - 586 - http://www.reactome.org/biopax/46/48887#SequenceSite21462 - - - - Q6STE5 - UniProt - - - - ENSP00000250378 - Ensembl - - - - Q9H0L5 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12324 - - - - EQUAL - 24 - http://www.reactome.org/biopax/46/48887#SequenceSite21711 - - - - 381904 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381904 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval829 - - - - - - Q6VBQ0 - UniProt - - - - EQUAL - 612 - - - - EQUAL - 622 - http://www.reactome.org/biopax/46/48887#SequenceSite21728 - - - - - - linoleic acid - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule740 - Reactome DB_ID: 400158 - LINA - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21479 - - - - Q53F72 - UniProt - - - - EQUAL - 65 - http://www.reactome.org/biopax/46/48887#SequenceSite23006 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8361 - - - - 8145523 - pubchem - - - - EQUAL - 785 - http://www.reactome.org/biopax/46/48887#SequenceSite5766 - - - - 400346 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400346 - - - - REACT_19763 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19763.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10191 - - - - - - O15413 - UniProt - - - - - - - - - - - - - - - - - - - - pro-factor VII, uncarboxylated + 10 CO2 + 10 O2 + 10 vitamin K hydroquinone -> pro-factor VII + 10 H2O + 10 vitamin K epoxide - At the beginning of this reaction, 10 molecules of 'Oxygen', 10 molecules of 'vitamin K hydroquinone', 10 molecules of 'CO2', and 1 molecule of 'pro-factor VII, uncarboxylated' are present. At the end of this reaction, 1 molecule of 'pro-factor VII', 10 molecules of 'H2O', and 10 molecules of 'vitamin K epoxide' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3885 - - - - - - - NP_689523 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2245 - - - - - - ENSP00000437928 - Ensembl - - - - ENST00000361905 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5623 - - - - REACT_115542 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115542.1 - - - - ENST00000433932 - Ensembl - - - - - LBP32 - MGR - TFCP2L2 - Mammalian grainyhead - NH32 - Transcription factor LBP-32 - GRHL1 - Transcription factor CP2-like 2 - - - - - - - - - - - - - - - - - - - - - - - - GRHL1_HUMAN - Grainyhead-like protein 1 homolog - FUNCTION: Transcription factor. Isoform 1 may function as an activator and isoform 2 as a repressor in tissues where both forms are expressed. May play a role in development. May be involved in epidermal differentiation (By similarity). Binds and transactivates the EN1 promoter.SUBUNIT: Homodimer, also forms heterodimers with GRHL2 or GRHL3.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=p70 MGR; IsoId=Q9NZI5-1; Sequence=Displayed; Name=2; Synonyms=p49 MGR; IsoId=Q9NZI5-2; Sequence=VSP_017636, VSP_017637; Name=3; IsoId=Q9NZI5-3; Sequence=VSP_017638, VSP_017639; Note=No experimental confirmation available;TISSUE SPECIFICITY: Isoform 1 is highly expressed in brain, pancreas, tonsil, placenta and kidney. Isoform 2 is highly expressed in brain and liver. Highly expressed in placental JEG-3 cells and at very low levels in non-steroidogenic cells. No expression detected in adrenal NCI-H295A cells.DEVELOPMENTAL STAGE: Expressed in fetal liver and brain.SIMILARITY: Belongs to the grh/CP2 family. Grainyhead subfamily. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000343796 - Ensembl - - - - EQUAL - 999 - - - - NP_061337 - RefSeq - - - - REACT_24747 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24747.2 - - - - Q6IBF4 - UniProt - - - - 1528846 - DiDonato S - Uziel G - Gellera C - Taroni F - Fiorucci S - Lamantea E - Cavadini P - Verderio E - Finocchiaro G - PubMed - Molecular characterization of inherited carnitine palmitoyltransferase II deficiency. - Proc Natl Acad Sci U S A 89(18);8429-33 - 1992 - - - - NM_012454 - RefSeq - - - - 177318 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=177318 - - - - O75447 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10056 - - - - - - NM_080651 - RefSeq - - - - O75509 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12334 - - - - - ME1 - 1.1.1.40 - Malic enzyme 1 - NADP-ME - - - - - - - - - - - - - - - - - - - - - - - MAOX_HUMAN - NADP-dependent malic enzyme - CATALYTIC ACTIVITY: (S)-malate + NADP(+) = pyruvate + CO(2) + NADPH.CATALYTIC ACTIVITY: Oxaloacetate = pyruvate + CO(2).COFACTOR: Divalent metal cations. Prefers magnesium or manganese (By similarity).SUBUNIT: Homotetramer.SUBCELLULAR LOCATION: Cytoplasm.TISSUE SPECIFICITY: Expressed in all tissues tested including liver, placenta and white adipose tissue.SIMILARITY: Belongs to the malic enzymes family.WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=ME1"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q92926 - UniProt - - - - 2426129 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2426129 - - - - ENST00000369705 - Ensembl - - - - 87324641 - pubchem - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10754 - - - - REACT_25123 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25123.1 - - - - ENSG00000150991 - Ensembl - - - - HGNC:6996 - HGNC - - - - EQUAL - 433 - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of PERIOD-2' - As inferred from mouse, the phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds a noncanonical E-box in the promoter of the PER2 gene and activates transcription of PER2. NPAS2 is predicted to act redundantly with CLOCK. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation106 - - - - EQUAL - 52 - - - - - - MOD_RES 153 153 Phosphoserine. - - - - HGNC:7672 - HGNC - - - - - - MOD_RES 551 551 Phosphoserine. - - - - B2R4I3 - UniProt - - - - - - Ral guanine nucleotide dissociation stimulator-like 1 - RGL1_HUMAN - - - - - Reactome DB_ID: 561160 - http://www.reactome.org/biopax/46/48887#Protein13780 - RGL1 - - - - 1024 - NCBI Gene - - - - TEAD2 - HGNC Symbol - - - - 212414 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212414 - - - - ENST00000265723 - Ensembl - - - - EQUAL - 1872 - - - - 19805222 - Yamada, RG - Takao, T - Ukai-Tadenuma, M - Kishimoto, W - Nakao, K - Masumoto, KH - Takano, A - Ukai, H - Yoo, SH - Kojima, T - Isojima, Y - Nagai, K - Nakajima, M - Ishida, M - Minami, Y - Kito, R - Fujishima, H - Takahashi, JS - Kiuchi, R - Sakaki, Y - Ueda, HR - Shimomura, K - Pubmed - CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock - Proc Natl Acad Sci U S A 106:15744-9 - 2009 - - - - 1BBS - PROTEIN DATA BANK - - - - NP_001132939 - RefSeq - - - - MED25 - HGNC - - - - - - - - Transcriptional coactivator with PDZ-binding motif - TAZ - WWTR1 - - - - - - - - - - - - - - - - - - - - - - - WWTR1_HUMAN - WW domain-containing transcription regulator protein 1 - FUNCTION: Transcriptional coactivator which acts as a downstream regulatory target in the Hippo signaling pathway that plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. WWTR1 enhances PAX8 and NKX2-1/TTF1-dependent gene activation. Regulates the nuclear accumulation of SMADS and has a key role in coupling them to the transcriptional machinery such as the mediator complex. Regulates embryonic stem-cell self-renewal, promotes cell proliferation and epithelial-mesenchymal transition.SUBUNIT: Binds to SLC9A3R2 via the PDZ motif at the plasma membrane. Binds to YWHAZ in vivo and in vitro through the phosphoserine-binding motif RSHSSP (By similarity). Interacts (via coiled-coil domain) with SMAD2 (via MH1 domain), SMAD3 and SMAD4. Interacts with MED15, PAX8 and NKX2-1. Interacts with TEAD1, TEAD2, TEAD3 and TEAD4.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Concentrates along specific portions of the plasma membrane, and accumulates in punctate nuclear bodies. When phosphorylated, is retained in cytoplasm by YWHAZ. Can be retained in the nucleus by MED15.TISSUE SPECIFICITY: Highly expressed in kidney, heart, placenta and lung. Expressed in the thyroid tissue.DOMAIN: The PDZ-binding motif is essential for stimulated gene transcription. It localizes the protein into both punctate nuclear foci and plasma membrane-associated complexes (By similarity).DOMAIN: Binds to transcription factors via its WW domain.PTM: Phosphorylated by LATS2 and STK3/MST2. Phosphorylation by LATS2 results in creation of 14-3-3 binding sites, retention in the cytoplasm, and functional inactivation. Phosphorylation results in the inhibition of transcriptional coactivation through YWHAZ-mediated nuclear export.SIMILARITY: Contains 1 WW domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 174775 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174775 - - - - ENSG00000110090 - Ensembl - - - - Q16376 - UniProt - - - - ENSG00000105085 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12394 - - - - 2032763 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2032763 - - - - 12563009 - Pilegaard, H - Saltin, B - Neufer, PD - Pubmed - Exercise induces transient transcriptional activation of the PGC-1alpha gene in human skeletal muscle - J Physiol 546:851-8 - 2003 - - - - 556827 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556827 - - - - RORA - HGNC - - - - - RGL - RalGDS-like 1 - KIAA0959 - RGL1 - - - - - - - - - - - - - - - - - - - - - - - RGL1_HUMAN - Ral guanine nucleotide dissociation stimulator-like 1 - FUNCTION: Probable guanine nucleotide exchange factor.SUBUNIT: Interacts with Ras (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=A; IsoId=Q9NZL6-1; Sequence=Displayed; Name=B; IsoId=Q9NZL6-2; Sequence=VSP_001824;TISSUE SPECIFICITY: Expressed in a wide variety of tissues with strong expression being seen in the heart, brain, kidney, spleen and testis.SIMILARITY: Contains 1 N-terminal Ras-GEF domain.SIMILARITY: Contains 1 Ras-associating domain.SIMILARITY: Contains 1 Ras-GEF domain.SEQUENCE CAUTION: Sequence=BAA76803.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2111 - - - - - - P45445 - UniProt - - - - REACT_120001 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120001.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval8663 - - - - - - REACT_24393 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24393.2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12412 - - - - EQUAL - 2068 - - - - PTHR10572:SF0 - PANTHER Family - - - - REACT_115997 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_115997.2 - - - - 8530480 - Morris, DP - Stafford, DW - Wright, DJ - Stevens, RD - Pubmed - Processive post-translational modification. Vitamin K-dependent carboxylation of a peptide substrate. - J Biol Chem 270:30491-8 - 1995 - - - - ENST00000551727 - Ensembl - - - - REACT_25233 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25233.2 - - - - CHEBI:8228 - ChEBI - - - - GRHL1 - HGNC Symbol - - - - - - MOD_RES 923 923 Phosphoserine (By similarity). - - - - 6.2.1.- - SLC27A1 - FATP-1 - FATP1 - ACSVL5 - Solute carrier family 27 member 1 - Fatty acid transport protein 1 - - - - - - - - - - - - - - S27A1_HUMAN - Long-chain fatty acid transport protein 1 - FUNCTION: Involved in translocation of long-chain fatty acids (LFCA) across the plasma membrane. The LFCA import appears to be hormone-regulated in a tissue-specific manner. In adipocytes, but not myocytes, insulin induces a rapid translocation of FATP1 from intracellular compartments to the plasma membrane, paralleled by increased LFCA uptake. May act directly as a bona fide transporter, or alternatively, in a cytoplasmic or membrane- associated multimeric protein complex to trap and draw fatty acids towards accumulation. Plays a pivotal role in regulating available LFCA substrates from exogenous sources in tissues undergoing high levels of beta-oxidation or triglyceride synthesis. May be involved in regulation of cholesterol metabolism. Has acyl-CoA ligase activity for long-chain and very-long-chain fatty acids (By similarity).SUBUNIT: Self-associates. May function as a homodimer (By similarity).SUBCELLULAR LOCATION: Cell membrane; Single-pass membrane protein. Endomembrane system; Single-pass membrane protein. Cytoplasm (By similarity). Note=Plasma membrane and intracellular membranes, at least in adipocytes. Predominantly cytoplasmic in myocytes (By similarity).TISSUE SPECIFICITY: Highest levels of expression are detected in muscle and adipose tissue small, intermediate levels in small intestine, and barely detectable in liver.MISCELLANEOUS: FATP1-mediated fatty acid uptake is associated to paramaters related to insulin resistance, which is associated with disturbed fatty acid metabolism and homeostasis, such as obesity.SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000441788 - Ensembl - - - - ENSP00000425006 - Ensembl - - - - 422412 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=422412 - - - - GPRLSGONYQIRFK-UHFFFAOYSA-N - InChIKey - - - - 12406875 - Haverkate, F - van der Bom, JG - Bots, ML - Kluft, C - Grobbee, DE - Pubmed - The 4G5G polymorphism in the gene for PAI-1 and the circadian oscillation of plasma PAI-1 - Blood 101:1841-4 - 2003 - - - - 8474436 - Tsay YH - Kienzle BK - Smith-Monroy CA - Bishop RW - Robinson GW - PubMed - Conservation between human and fungal squalene synthetases: similarities in structure, function, and regulation. - Mol Cell Biol 13(5);2706-17 - 1993 - - - - ENST00000265641 - Ensembl - - - - - - MOD_RES 28 28 Glycine amide. - - - - ENSP00000276914 - Ensembl - - - - EQUAL - 2440 - http://www.reactome.org/biopax/46/48887#SequenceSite5327 - - - - CSNK1E - HGNC Symbol - - - - REACT_117936 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117936.1 - - - - NP_001132940 - RefSeq - - - - - - Furin - - - - - Reactome DB_ID: 157049 - http://www.reactome.org/biopax/46/48887#Protein2641 - FURIN - - - - - - MOD_RES 696 696 Phosphoserine (By similarity). - - - - P62987 - UniProt - - - - - 3.4.15.1 - CD143 - ACE - DCP - DCP1 - 3.2.1.- - Kininase II - Dipeptidyl carboxypeptidase I - Angiotensin-converting enzyme, soluble form - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACE_HUMAN - Angiotensin-converting enzyme - FUNCTION: Converts angiotensin I to angiotensin II by release of the terminal His-Leu, this results in an increase of the vasoconstrictor activity of angiotensin. Also able to inactivate bradykinin, a potent vasodilator. Has also a glycosidase activity which releases GPI-anchored proteins from the membrane by cleaving the mannose linkage in the GPI moiety.CATALYTIC ACTIVITY: Release of a C-terminal dipeptide, oligopeptide-|-Xaa-Yaa, when Xaa is not Pro, and Yaa is neither Asp nor Glu. Thus, conversion of angiotensin I to angiotensin II, with increase in vasoconstrictor activity, but no action on angiotensin II.COFACTOR: Binds 2 zinc ions per subunit. Isoform Testis-specific only binds 1 zinc ion per subunit.COFACTOR: Binds 3 chloride ions per subunit.ENZYME REGULATION: Strongly activated by chloride. Specifically inhibited by lisinopril, captopril and enalaprilat.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=2.51 mM for Hip-His-Leu;SUBCELLULAR LOCATION: Angiotensin-converting enzyme, soluble form: Secreted.SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Name=Somatic-1; IsoId=P12821-1; Sequence=Displayed; Name=Somatic-2; Synonyms=Soluble; IsoId=P12821-2; Sequence=VSP_029932, VSP_029933; Note=Incomplete sequence; Name=Testis-specific; Synonyms=ACE-T; IsoId=P12821-3, P22966-1; Sequence=VSP_035120, VSP_035121; Note=Variant in position: 32:S->P (in dbSNP:rs4317). Variant in position: 49:S->G (in dbSNP:rs4318); Name=4; IsoId=P12821-4; Sequence=VSP_043522, VSP_043523, VSP_043524; Note=No experimental confirmation available;TISSUE SPECIFICITY: Ubiquitously expressed, with highest levels in lung, kidney, heart, gastrointestinal system and prostate. Isoform Testis-specific is expressed in spermatocytes and adult testis.INDUCTION: Up-regulated in failing heart.PTM: Phosphorylated by CK2 on Ser-1299; which allows membrane retention.DISEASE: Ischemic stroke (ISCHSTR) [MIM:601367]: A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Renal tubular dysgenesis (RTD) [MIM:267430]: Autosomal recessive severe disorder of renal tubular development characterized by persistent fetal anuria and perinatal death, probably due to pulmonary hypoplasia from early-onset oligohydramnios (the Potter phenotype). Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Microvascular complications of diabetes 3 (MVCD3) [MIM:612624]: Pathological conditions that develop in numerous tissues and organs as a consequence of diabetes mellitus. They include diabetic retinopathy, diabetic nephropathy leading to end- stage renal disease, and diabetic neuropathy. Diabetic retinopathy remains the major cause of new-onset blindness among diabetic adults. It is characterized by vascular permeability and increased tissue ischemia and angiogenesis. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Intracerebral hemorrhage (ICH) [MIM:614519]: A pathological condition characterized by bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma. Intracerebral bleeding is a common cause of stroke. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.MISCELLANEOUS: Inhibitors of ACE are commonly used to treat hypertension and some types of renal and cardiac dysfunction.MISCELLANEOUS: The glycosidase activity probably uses different active site residues than the metalloprotease activity.SIMILARITY: Belongs to the peptidase M2 family.SEQUENCE CAUTION: Sequence=BAD92208.1; Type=Erroneous initiation;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ACE";WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=ACE"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - FADS1 - HGNC Symbol - - - - ENST00000504342 - Ensembl - - - - - - gamma-glutamyl carboxylase - vitamin K-dependent gamma-carboxylase - - - - - http://www.reactome.org/biopax/46/48887#Protein11629 - Reactome DB_ID: 159860 - GGCX - - - - REACT_27062 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27062.2 - - - - REACT_22783 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22783.1 - - - - 26697064 - pubchem - - - - - - MOD_RES 121 121 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10805 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5674 - - - - - - 400160 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400160 - - - - NM_004898 - RefSeq - - - - 10159 - NCBI Gene - - - - 124097 - omim - - - - REACT_22851 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_22851.3 - - - - REACT_117341 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117341.2 - - - - 422413 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=422413 - - - - ENSP00000355332 - Ensembl - - - - 21479263 - Crumbley, C - Burris, TP - Pubmed - Direct regulation of CLOCK expression by REV-ERB - PLoS One 6:e17290 - 2011 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10031 - - - - 8393577 - Bhat TN - Gulnik S - Hosur MV - Silva AM - Cachau RE - Sowder RC - Collins J - Baldwin ET - Erickson JW - PubMed - Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design. - Proc Natl Acad Sci U S A 90(14);6796-800 - 1993 - - - - FBXO5 - HGNC Symbol - - - - - - MOD_RES 67 67 4-carboxyglutamate. - - - - 1989814 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989814 - - - - 16428347 - Smith, JK - Young, ME - Egbejimi, O - Hotze, MA - Zaha, VG - Durgan, DJ - Cuthbert, KD - Dyck, JR - Abel, ED - Pubmed - Distinct transcriptional regulation of long-chain acyl-CoA synthetase isoforms and cytosolic thioesterase 1 in the rodent heart by fatty acids and insulin - Am J Physiol Heart Circ Physiol 290:H2480-97 - 2006 - - - - 121009 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10126 - - - - MED24 - HGNC Symbol - - - - EQUAL - 605 - http://www.reactome.org/biopax/46/48887#SequenceSite5367 - - - - ENSP00000380207 - Ensembl - - - - TEAD1 - HGNC Symbol - - - - ENST00000217131 - Ensembl - - - - ENST00000371905 - Ensembl - - - - EQUAL - 1216 - - - - 601729 - omim - - - - NM_000902 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10152 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5772 - - - - ENSP00000457466 - Ensembl - - - - ENSP00000217131 - Ensembl - - - - EQUAL - 453 - - - - - - MOD_RES 79 79 4-carboxyglutamate. - - - - SIN3B - HGNC Symbol - - - - EQUAL - 434 - http://www.reactome.org/biopax/46/48887#SequenceSite20841 - - - - NM_004831 - RefSeq - - - - 15135064 - Kimura, T - Nakajima, Y - Ikeda, M - Honma, K - Ohmiya, Y - Honma, S - Pubmed - Bidirectional role of orphan nuclear receptor RORalpha in clock gene transcriptions demonstrated by a novel reporter assay system - FEBS Lett 565:122-6 - 2004 - - - - HGNC:3629 - HGNC - - - - NM_001127444 - RefSeq - - - - - - MOD_RES 103 103 (3R)-3-hydroxyaspartate. - - - - 123811 - omim - - - - 212445 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212445 - - - - MOD_RES N-acetylalanine - - - - REACT_119495 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119495.3 - - - - ENSP00000456763 - Ensembl - - - - - - MOD_RES 1558 1558 N6-acetyllysine. - - - - REACT_117962 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117962.1 - - - - 176880 - omim - - - - Q59GY4 - UniProt - - - - Q86YN6 - UniProt - - - - 422139 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=422139 - - - - NM_001130996 - RefSeq - - - - 4899 - NCBI Gene - - - - EQUAL - 102 - http://www.reactome.org/biopax/46/48887#SequenceSite9891 - - - - EQUAL - 166 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5802 - - - - - - - - - FACL1 - Acyl-CoA synthetase 1 - FACL2 - LACS - ACS1 - Long-chain acyl-CoA synthetase 2 - LACS1 - Long-chain acyl-CoA synthetase 1 - LACS2 - Palmitoyl-CoA ligase 2 - Palmitoyl-CoA ligase 1 - ACSL1 - Long-chain fatty acid-CoA ligase 2 - 6.2.1.3 - LACS 1 - LACS 2 - - - - - - - - - - - - - - - - - - - ACSL1_HUMAN - Long-chain-fatty-acid--CoA ligase 1 - FUNCTION: Activation of long-chain fatty acids for both synthesis of cellular lipids, and degradation via beta-oxidation. Preferentially uses palmitoleate, oleate and linoleate.CATALYTIC ACTIVITY: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA.COFACTOR: Magnesium.SUBCELLULAR LOCATION: Mitochondrion outer membrane; Single-pass type III membrane protein (By similarity). Peroxisome membrane; Single-pass type III membrane protein (By similarity). Microsome membrane; Single-pass type III membrane protein (By similarity). Endoplasmic reticulum membrane; Single-pass type III membrane protein (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P33121-1; Sequence=Displayed; Name=2; IsoId=P33121-2; Sequence=VSP_009604; Note=May be due to a competing acceptor splice site. No experimental confirmation available;TISSUE SPECIFICITY: Highly expressed in liver, heart, skeletal muscle, kidney and erythroid cells, and to a lesser extent in brain, lung, placenta and pancreas.DEVELOPMENTAL STAGE: Expressed during the early stages of erythroid development while expression is very low in reticulocytes and young erythrocytes.SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.SEQUENCE CAUTION: Sequence=BAC04704.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSG00000138792 - Ensembl - - - - ENST00000254657 - Ensembl - - - - - - MOD_RES 204 204 Phosphoserine. - - - - ENSP00000324464 - Ensembl - - - - Q9UN06 - UniProt - - - - - C18H30O2 - (Z,Z,Z)-9,12,15-octadecatrienoic acid - ALA - cis,cis,cis-9,12,15-octadecatrienoic acid - all-cis-9,12,15-octadecatrienoic acid - (9Z,12Z,15Z)-octadeca-9,12,15-trienoic acid - (9,12,15)-linolenic acid - 9-cis,12-cis,15-cis-octadecatrienoic acid - linolenic acid - cis-Delta(9,12,15)-octadecatrienoic acid - - - - - - - - 278.4296 - alpha-linolenic acid - alpha-linolenic acid - A C<smallsub>18</smallsub>, <locant>omega</locant>-3 essential fatty acid with <stereo>cis</stereo>-double bonds at positions 9, 12 and 15. Shown to have antithrombotic effect. - - - - - - UBB(1-76) - ubiquitin (UBB 1) - - - - - http://www.reactome.org/biopax/46/48887#Protein2474 - Reactome DB_ID: 939847 - UBB - - - - REACT_17868 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17868.2 - - - - REACT_17167 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17167.2 - - - - REACT_5166 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5166.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5776 - - - - - - - Transducin beta-like protein 1X - TBL1 - Transducin-beta-like protein 1, X-linked - SMAP55 - TBL1X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TBL1X_HUMAN - F-box-like/WD repeat-containing protein TBL1X - FUNCTION: F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units. Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of corepressor complexes that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of transcription repressor complexes, thereby allowing cofactor exchange.SUBUNIT: Component of the N-Cor repressor complex, at least composed of NCOR1, NCOR2, HDAC3, TBL1X, TBL1R, CORO2A and GPS2. Component of a E3 ubiquitin ligase complex containing UBE2D1, SIAH1, CACYBP/SIP, SKP1, APC and TBL1X. Probably part of other corepressor complexes, that do not contain NCOR1 and NCOR2. Interacts with histones H2B, H3a and H4.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O60907-1; Sequence=Displayed; Name=2; IsoId=O60907-2; Sequence=VSP_036905;TISSUE SPECIFICITY: Ubiquitous.DOMAIN: The F-box-like domain is related to the F-box domain, and apparently displays the same function as component of ubiquitin E3 ligase complexes (By similarity).SIMILARITY: Belongs to the WD repeat EBI family.SIMILARITY: Contains 1 F-box-like domain.SIMILARITY: Contains 1 LisH domain.SIMILARITY: Contains 8 WD repeats. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000394236 - Ensembl - - - - ACADM - HGNC - - - - 603619 - omim - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21469 - - - - 400228 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400228 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5780 - - - - PAI1 - PAI-1 - Serpin E1 - PAI - SERPINE1 - PLANH1 - Endothelial plasminogen activator inhibitor - - - - - - - - - - - - - - - - - - PAI1_HUMAN - Plasminogen activator inhibitor 1 - FUNCTION: Serine protease inhibitor. This inhibitor acts as 'bait' for tissue plasminogen activator, urokinase, protein C and matriptase-3/TMPRSS7. Its rapid interaction with PLAT may function as a major control point in the regulation of fibrinolysis.SUBUNIT: Forms protease inhibiting heterodimer with TMPRSS7. Interacts with VTN. Binds LRP1B; binding is followed by internalization and degradation.SUBCELLULAR LOCATION: Secreted.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P05121-1; Sequence=Displayed; Name=2; IsoId=P05121-2; Sequence=VSP_045493; Note=No experimental confirmation available;TISSUE SPECIFICITY: Found in plasma and platelets and in endothelial, hepatoma and fibrosarcoma cells.PTM: Inactivated by proteolytic attack of the urokinase-type (u- PA) and the tissue-type (TPA), cleaving the 369-Arg-|-Met-370 bond.DISEASE: Plasminogen activator inhibitor-1 deficiency (PAI-1D) [MIM:613329]: A hematologic disorder characterized by increased bleeding after trauma, injury, or surgery. Affected females have menorrhagia. The bleeding defect is due to increased fibrinolysis of fibrin blood clots due to deficiency of plasminogen activator inhibitor-1, which inhibits tissue and urinary activators of plasminogen. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Note=High concentrations of SERPINE1 seem to contribute to the development of venous but not arterial occlusions.SIMILARITY: Belongs to the serpin family.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SERPINE1";WEB RESOURCE: Name=Wikipedia; Note=Plasminogen activator inhibitor-1 entry; URL="http://en.wikipedia.org/wiki/Plasminogen_activator_inhibitor-1";WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/serpine1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000440226 - Ensembl - - - - EQUAL - 59 - http://www.reactome.org/biopax/46/48887#SequenceSite9998 - - - - ENSP00000376922 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4771 - - - - - 163798 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163798 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8354 - - - - ATP6IP2 - ATP6M8-9 - ATP6AP2 - N14F - Renin/prorenin receptor - Embryonic liver differentiation factor 10 - Vacuolar ATP synthase membrane sector-associated protein M8-9 - CAPER - ATPase H(+)-transporting lysosomal-interacting protein 2 - ATPase H(+)-transporting lysosomal accessory protein 2 - V-ATPase M8.9 subunit - ELDF10 - ER-localized type I transmembrane adaptor - - - - - - - - - - - - - - - - - - - - RENR_HUMAN - Renin receptor - FUNCTION: Functions as a renin and prorenin cellular receptor. May mediate renin-dependent cellular responses by activating ERK1 and ERK2. By increasing the catalytic efficiency of renin in AGT/angiotensinogen conversion to angiotensin I, it may also play a role in the renin-angiotensin system (RAS).SUBUNIT: Interacts with renin and the vacuolar proton-ATPase.SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).TISSUE SPECIFICITY: Expressed in brain, heart, placenta, liver, kidney and pancreas. Barely detectable in lung and skeletal muscles. In the kidney cortex it is restricted to the mesangium of glomeruli. In the coronary and kidney artery it is expressed in the subendothelium, associated to smooth muscles where it colocalizes with REN. Expressed in vascular structures and by syncytiotrophoblast cells in the mature fetal placenta.PTM: Phosphorylated.DISEASE: Mental retardation, X-linked, with epilepsy (MRXE) [MIM:300423]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRXE patients manifest mild to moderate mental retardation associated with epilepsy, delays in motor milestones and speech acquisition in infancy. Note=The disease is caused by mutations affecting the gene represented in this entry.SEQUENCE CAUTION: Sequence=AAH10395.1; Type=Erroneous initiation; Sequence=AAQ13511.1; Type=Frameshift; Positions=155; Sequence=CAA76984.1; Type=Erroneous initiation;WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ATP6AP2"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q15189 - UniProt - - - - REACT_120325 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120325.1 - - - - REACT_120186 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120186.1 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite12350 - - - - 123838 - omim - - - - Q8IUK3 - UniProt - - - - 12443882 - Hirano T - Kizaki M - Kato K - Umezawa K - Masuda N - Abe F - PubMed - Enhancement of sensitivity by bestatin of acute promyelocytic leukemia NB4 cells to all-trans retinoic acid. - Leuk Res 26(12);1097-103 - 2002 - - - - NM_015714 - RefSeq - - - - InChI=1S/C31H46O3/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-31-29(33)27-19-8-7-18-26(27)28(32)30(31,6)34-31/h7-8,18-20,22-24H,9-17,21H2,1-6H3 - InChI - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4958 - - - - REACT_25212 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25212.2 - - - - EQUAL - 1382 - - - - - - MOD_RES 133 133 Phosphoserine; by CaMK1, CaMK2, CaMK4, PKB/AKT1 or PKB/AKT2, RPS6KA3, RPS6KA4, RPS6KA5 and SGK1. - - - - - 1.1.4.1 - - - - - - - - - - vitamin K epoxide -> vitamin K hydroquinone - Authored: D'Eustachio, P, 2005-03-17 16:24:57 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3883 - Edited: D'Eustachio, P, 0000-00-00 00:00:00 - The regeneration of reduced vitamin K (vitamin K hydroquinone) from vitamin K epoxide is catalyzed by vitamin K epoxide reductase (VKORC1) (Sadler 2004). This enzyme is the target of the anticoagulant drug warfarin. Two important features of this reaction remain unclear. First, dithiothreitol functions efficiently as a reductant in vitro (Wallin and Martin 1985), but the in vivo reductant remains unknown. Second, while people homozygous for mutations in VKORC1 protein lack epoxide reductase activity (Rost et al. 2004) and cultured insect cells transfected with the cloned human VKORC1 gene express vitamin K epoxide reductase activity (Li et al. 2004), the possibility that the active form of the enzyme is a complex with other proteins cannot be formally excluded. - - - - - ENSP00000472545 - Ensembl - - - - - - Transcriptional enhancer factor TEF-5 - - - - - Reactome DB_ID: 2032767 - http://www.reactome.org/biopax/46/48887#Protein11194 - TEAD3 - - - - Q9Y429 - UniProt - - - - EQUAL - 862 - - - - 159812 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159812 - - - - - - MOD_RES 79 79 4-carboxyglutamate. - - - - EQUAL - 1286 - http://www.reactome.org/biopax/46/48887#SequenceSite25535 - - - - ENST00000589119 - Ensembl - - - - EQUAL - 2214 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25576 - - - - - - Induction of Angiopoietin-related protein 4 (ANGPTL4) Expression - - - - - - The ANGPTL4 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: D'Eustachio, P, 2009-05-26 22:09:50 - http://www.reactome.org/biopax/46/48887#TemplateReaction43 - Reviewed: Kersten, S, 2009-06-08 - Edited: May, B, 2010-03-23 - Reviewed: Sethi, JK, 2011-02-09 - Authored: May, B, 2010-03-23 - Expression of ANGPTL4 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5282 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1060 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25554 - - - - RXRA - HGNC - - - - ENSG00000099917 - Ensembl - - - - 27063 - NCBI Gene - - - - Q9BTH1 - UniProt - - - - EQUAL - 127 - http://www.reactome.org/biopax/46/48887#SequenceSite25531 - - - - EQUAL - 60 - - - - ENSP00000414299 - Ensembl - - - - EQUAL - 86 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2246 - - - - - - - - - - - - - - MEF2C/D:PPARGC1A - http://www.reactome.org/biopax/46/48887#Complex4988 - Reactome DB_ID: 1605560 - - - - NM_001352 - RefSeq - - - - ENSP00000387699 - Ensembl - - - - PTHR23406:SF2 - PANTHER Family - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5621 - - - - EQUAL - 1555 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8350 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2053 - - - - CHEBI:233028 - ChEBI - - - - - - MOD_RES 550 550 Phosphoserine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry8329 - - - - - Cl - chloride(1-) - Chloride(1-) - Chlorine anion - Cl(-) - - - - - - - - - - 35.4527 - chloride - chloride - A halide anion formed when chlorine picks up an electron to form an an anion. - - - - REACT_24929 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24929.2 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4703 - - - - ENST00000418959 - Ensembl - - - - REACT_26942 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26942.2 - - - - EQUAL - 2142 - - - - 14718417 - pubchem - - - - 2738071 - Furie, B - Rabiet, MJ - Stafford, DW - Kasper, CK - Liebman, HA - Ware, J - Diuguid, DL - Furie, BC - Pubmed - Factor IX San Dimas. Substitution of glutamine for Arg-4 in the propeptide leads to incomplete gamma-carboxylation and altered phospholipid binding properties. - J Biol Chem 264:11401-6 - 1989 - - - - - - ACOX1_HUMAN - Peroxisomal acyl-coenzyme A oxidase 1 - ACOX1 isoform 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein13759 - Reactome DB_ID: 400212 - ACOX1-1 - - - - A8K4S5 - UniProt - - - - NP_001234934 - RefSeq - - - - - - MOD_RES 1121 1121 Phosphoserine (By similarity). - - - - REACT_19175 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19175.2 - - - - - - MOD_RES 500 500 Phosphoserine. - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of HMGCS2' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation212 - - - - ENST00000437473 - Ensembl - - - - - - MOD_RES 326 326 Phosphoserine. - - - - 2065401 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065401 - - - - ENST00000447540 - Ensembl - - - - ENST00000354513 - Ensembl - - - - 10748089 - Kellokumpu S - Myllyla R - Suokas M - PubMed - A single C-terminal peptide segment mediates both membrane association and localization of lysyl hydroxylase in the endoplasmic reticulum. - J Biol Chem 275(23);17863-8 - 2000 - - - - 3229247 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3229247 - - - - 116519 - NCBI Gene - - - - 1989749 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989749 - - - - NP_002948 - RefSeq - - - - NM_181659 - RefSeq - - - - EQUAL - 380 - http://www.reactome.org/biopax/46/48887#SequenceSite1783 - - - - EQUAL - 179 - http://www.reactome.org/biopax/46/48887#SequenceSite21659 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4783 - - - - REACT_148691 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148691.1 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12402 - - - - - - MOD_RES 1103 1103 N6-acetyllysine. - - - - EQUAL - 537 - - - - NP_937825 - RefSeq - - - - 8020937 - Bleskan J - Patterson D - McKenzie TL - Schechter I - Hart I - Conrad DG - Berger RC - PubMed - Localization of the squalene synthase gene (FDFT1) to human chromosome 8p22-p23.1. - Genomics 20(1);116-8 - 1994 - - - - TRIB3 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10132 - - - - EQUAL - 857 - - - - - - MOD_RES 396 396 Phosphoserine; by CDK5. - - - - - - MOD_RES 113 113 (3R)-3-hydroxyaspartate. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12376 - - - - ENSP00000387093 - Ensembl - - - - 118938 - omim - - - - TIAM2 - HGNC Symbol - - - - HGNC:11205 - HGNC - - - - 163805 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163805 - - - - - - MOD_RES 2 2 N-acetylalanine (By similarity). - - - - MOD_RES Citrulline - - - - ENSP00000379178 - Ensembl - - - - CLOCK - HGNC Symbol - - - - PTHR11909:SF18 - PANTHER Family - - - - - REACT_7496 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7496.2 - - - - NP_001035199 - RefSeq - - - - EQUAL - 499 - - - - HGNC:24260 - HGNC - - - - 939205 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939205 - - - - ENST00000378438 - Ensembl - - - - - - ubiquitin (UBC 7) - - - - - Reactome DB_ID: 939184 - http://www.reactome.org/biopax/46/48887#Protein1055 - UBC(457-532) - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5768 - - - - - 556783 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556783 - - - - ENSP00000367849 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10050 - - - - - - - - MOD_RES 278 278 Phosphothreonine; by MAPK8. - - - - 601434 - omim - - - - Q5BJG7 - UniProt - - - - O60427 - UniProt - - - - ENSP00000437465 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2090 - - - - EQUAL - 520 - http://www.reactome.org/biopax/46/48887#SequenceSite25569 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10033 - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of DBP' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation92 - As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) heterodimers bind E-boxes in the promoter of the DBP gene and activate transcription of DBP. - - - - ENST00000526390 - Ensembl - - - - ENSP00000246672 - Ensembl - - - - ENST00000417225 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10173 - - - - - - Q9P294 - UniProt - - - - - - MOD_RES 236 236 N6-acetyllysine. - - - - EQUAL - 70 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4785 - - - - - - - - - - - - NR1D1 (REV-ERBA):heme - http://www.reactome.org/biopax/46/48887#Complex4976 - Reactome DB_ID: 1368127 - - - - Q5T6K9 - UniProt - - - - NRF1 - HGNC Symbol - - - - NP_954635 - RefSeq - - - - Q15190 - UniProt - - - - - - - - - - - - SCF-beta-TrCP:phospho-Emi1 complexes - Reactome DB_ID: 174138 - http://www.reactome.org/biopax/46/48887#Complex2830 - - - - ENSP00000385915 - Ensembl - - - - EQUAL - 601 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12818 - - - - EQUAL - 19 - - - - EQUAL - 29 - http://www.reactome.org/biopax/46/48887#SequenceSite21646 - - - - 12582161 - Duhem, C - Barbier, O - Fruchart, JC - Torra, IP - Staels, B - Villeneuve, L - Kosykh, V - Fontaine, C - Guillemette, C - Bocher, V - Pubmed - The UDP-glucuronosyltransferase 1A9 enzyme is a peroxisome proliferator-activated receptor alpha and gamma target gene - J Biol Chem 278:13975-83 - 2003 - - - - - - ATP-binding cassette sub-family A member 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein13660 - Reactome DB_ID: 194209 - ABCA1 - - - - Q16526 - UniProt - - - - NPDSHTNEKLQQIJ-UINYOVNOSA-N - InChIKey - - - - ENSP00000419098 - Ensembl - - - - NP_001191192 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25552 - - - - - - - - - Phosphorylation and Nuclear Translocation of the BMAL1:CLOCK/NPAS2 Heterodimer - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - Reviewed: Hirota, T, 2010-06-23 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3854 - Authored: May, B, 2009-05-17 22:04:50 - As inferred from mouse, BMAL1 (ARNTL), CLOCK, and NPAS2 are phosphorylated by unknown kinases. The phosphorylation is dependent on the heterodimerization of BMAL1 with CLOCK or NPAS2. Phosphorylated BMAL1:CLOCK/NPAS2 is a much stronger transactivator of gene expression than is unphosphorylated BMAL1:CLOCK/NPAS2. - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - CHD9 - HGNC Symbol - - - - Q07075 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12392 - - - - ENSP00000181383 - Ensembl - - - - 11815627 - Parsons, T - Nichols, A - Tang, J - Patane, M - Godbout, K - Hsieh, F - Hales, P - Acton, S - Tummino, P - Vickers, C - Dick, L - Gavin, J - Baronas, E - Kaushik, V - Pubmed - Hydrolysis of biological peptides by human angiotensin-converting enzyme-related carboxypeptidase - J Biol Chem 277:14838-43 - 2002 - - - - 2065551 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065551 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4647 - - - - - - MOD_RES 68 68 Phosphoserine. - - - - 939849 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939849 - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5663 - - - - - - EQUAL - 572 - http://www.reactome.org/biopax/46/48887#SequenceSite25571 - - - - 556786 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=556786 - - - - NM_001270781 - RefSeq - - - - REACT_118009 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118009.2 - - - - ENSP00000445072 - Ensembl - - - - P00734 - UniProt - - - - YASAKCUCGLMORW-UHFFFAOYSA-N - InChIKey - - - - 10899625 - Raymond, WW - Caughey, GH - Wolters, PJ - Pubmed - Angiotensin II generation by mast cell alpha- and beta-chymases - Biochim Biophys Acta 1480:245-57 - 2000 - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite21438 - - - - ENST00000252595 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature25 - - - - MED22 - HGNC Symbol - - - - EQUAL - 266 - http://www.reactome.org/biopax/46/48887#SequenceSite1040 - - - - O43792 - UniProt - - - - EQUAL - 67 - - - - Q8TB34 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite20838 - - - - HGNC:2547 - HGNC - - - - 159765 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159765 - - - - HGNC:30229 - HGNC - - - - REACT_9581 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9581.2 - - - - NP_000679 - RefSeq - - - - NM_001172699 - RefSeq - - - - ENSP00000310701 - Ensembl - - - - PPARG - HGNC Symbol - - - - ENST00000539846 - Ensembl - - - - NM_025134 - RefSeq - - - - EQUAL - 367 - - - - ENST00000566494 - Ensembl - - - - ENST00000181383 - Ensembl - - - - Q6VB41 - UniProt - - - - NP_001124477 - RefSeq - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of NR1D1 (REV-ERBA)' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation109 - Activation of NR1D1 (REV-ERBA) expression by phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) is inferred from mouse. NPAS2 is predicted to act redundantly with CLOCK. - - - - ENST00000340875 - Ensembl - - - - P01019 - UniProt - - - - EQUAL - 1144 - - - - 12464262 - Gainer JV - Bellamine A - Wang Y - Waterman MR - Capdevila JH - Dawson EP - Brown NJ - PubMed - Characterization of the CYP4A11 gene, a second CYP4A gene in humans. - Arch Biochem Biophys 409(1);221-7 - 2003 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1650 - - - - ENST00000426833 - Ensembl - - - - 12464261 - Johnson EF - Savas U - Hsu MH - PubMed - Differential regulation of human CYP4A genes by peroxisome proliferators and dexamethasone. - Arch Biochem Biophys 409(1);212-20 - 2003 - - - - Q6P4B8 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4031 - - - - GO:0005743 - Gene Ontology - - - - NM_033023 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12007 - - - - 939239 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939239 - - - - ENSP00000454853 - Ensembl - - - - EQUAL - 457 - http://www.reactome.org/biopax/46/48887#SequenceSite1786 - - - - ENSP00000437496 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature831 - - - - 11485325 - Toyoshima, H - Shimano, H - Sakakura, Y - Sone, H - Suzuki, S - Takahashi, A - Yamada, N - Inoue, N - Pubmed - Sterol regulatory element-binding proteins induce an entire pathway of cholesterol synthesis - Biochem Biophys Res Commun 286:176-83 - 2001 - - - - EQUAL - 63 - - - - EQUAL - 643 - - - - ENSP00000348069 - Ensembl - - - - REACT_25278 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25278.2 - - - - - - - - - - - - phospho-Emi1(Ser 145, Ser 149):Cdc20/Cdh1 complexes - http://www.reactome.org/biopax/46/48887#Complex2829 - Reactome DB_ID: 177318 - - - - Q5W141 - UniProt - - - - - - - - - - - - - - - - - - - - pro-protein S, uncarboxylated + 11 CO2 + 11 O2 + 11 vitamin K hydroquinone -> pro-protein S + 11 H2O + 11 vitamin K epoxide - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3889 - At the beginning of this reaction, 11 molecules of 'Oxygen', 11 molecules of 'vitamin K hydroquinone', 11 molecules of 'CO2', and 1 molecule of 'pro-protein S, uncarboxylated' are present. At the end of this reaction, 1 molecule of 'pro-protein S', 11 molecules of 'H2O', and 11 molecules of 'vitamin K epoxide' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - - - - - - - REACT_20340 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20340.1 - - - - - - - - Thyroid hormone receptor-associated protein complex 240 kDa component - Thyroid hormone receptor-associated protein 1 - Activator-recruited cofactor 250 kDa component - TRAP240 - ARC250 - MED13 - DRIP250 - Mediator complex subunit 13 - THRAP1 - Vitamin D3 receptor-interacting protein complex component DRIP250 - KIAA0593 - Trap240 - - - - - - - - - - - - - - MED13_HUMAN - Mediator of RNA polymerase II transcription subunit 13 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Ubiquitous.SIMILARITY: Belongs to the Mediator complex subunit 13 family.SEQUENCE CAUTION: Sequence=AAD22032.1; Type=Frameshift; Positions=Several; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - HGNC:2384 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature12015 - - - - - - MOD_RES 411 411 Phosphoserine. - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ALAS1' - http://www.reactome.org/biopax/46/48887#Control382 - - - - 1368119 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1368119 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2091 - - - - REACT_2534 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2534.3 - - - - Q12863 - UniProt - - - - 604311 - omim - - - - 11162494 - Shingu, S - Noshiro, M - Shen, M - Kato, Yoichi - Matsuda, Y - Honda, K - Suardita, K - Yoshida, E - Fujimoto, K - Matsubara, K - Pubmed - Molecular cloning and characterization of DEC2, a new member of basic helix-loop-helix proteins - Biochem Biophys Res Commun 280:164-71 - 2001 - - - - P01127 - UniProt - - - - HGNC:3574 - HGNC - - - - PTHR10795:SF16 - PANTHER Family - - - - - 14507900 - Rickman, DW - Kelly, U - Thompson, CL - Sancar, A - Ebright, JN - Shaw, SJ - Bowes Rickman, C - Pubmed - Expression of the blue-light receptor cryptochrome in the human retina - Invest Ophthalmol Vis Sci 44:4515-21 - 2003 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4961 - - - - - - Q2I5I4 - UniProt - - - - REACT_25524 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25524.2 - - - - ENSP00000377828 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11999 - - - - 12505311 - Johnson, EF - Savas, U - Hsu, MH - Griffin, KJ - Pubmed - Regulation of P450 4A expression by peroxisome proliferator activated receptors - Toxicology 181:203-6 - 2002 - - - - NM_015889 - RefSeq - - - - 2022371 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022371 - - - - Q16728 - UniProt - - - - A8KAC9 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1847 - - - - 1989768 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1989768 - - - - - - KC1D_HUMAN - Casein kinase I isoform delta - - - - - http://www.reactome.org/biopax/46/48887#Protein11520 - Reactome DB_ID: 400304 - CSNK1D - - - - O43810 - UniProt - - - - 2022352 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022352 - - - - EQUAL - 2210 - http://www.reactome.org/biopax/46/48887#SequenceSite12387 - - - - ENSP00000437188 - Ensembl - - - - ENSP00000426983 - Ensembl - - - - ENSP00000308165 - Ensembl - - - - ENST00000398510 - Ensembl - - - - 2065428 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065428 - - - - REACT_118002 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118002.1 - - - - - - - - - - - Nuclear receptor subfamily 3 group C member 1 - GR - GRL - NR3C1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCR_HUMAN - Glucocorticoid receptor - FUNCTION: Receptor for glucocorticoids (GC). Has a dual mode of action: as a transcription factor that binds to glucocorticoid response elements (GRE), both for nuclear and mitochondrial DNA, and as a modulator of other transcription factors. Affects inflammatory responses, cellular proliferation and differentiation in target tissues. Could act as a coactivator for STAT5-dependent transcription upon growth hormone (GH) stimulation and could reveal an essential role of hepatic GR in the control of body growth. Involved in chromatin remodeling. Plays a significant role in transactivation.SUBUNIT: Heteromultimeric cytoplasmic complex with HSP90, HSP70, and FKBP5 or another immunophilin, or the immunophilin homolog PPP5C. Directly interacts with UNC45A. Upon ligand binding FKBP5 dissociates from the complex and FKBP4 takes its place, thereby linking the complex to dynein and mediating transport to the nucleus, where the complex dissociates (By similarity). Binds to DNA as a homodimer, and as a heterodimer with NR3C2 or the retinoid X receptor. Binds STAT5A and STAT5B homodimers and heterodimers. Interacts with NRIP1, POU2F1, POU2F2 and TRIM28. Interacts with NCOA1, NCOA3, SMARCA4, SMARCC1, SMARCD1, and SMARCE1 (By similarity). Interacts with several coactivator complexes, including the SMARCA4 complex, CREBBP/EP300, TADA2L and p160 coactivators such as NCOA2 and NCOA6. Interaction with BAG1 inhibits transactivation. Interacts with HEXIM1, PELP1 and TGFB1I1.SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion. Nucleus. Note=Cytoplasmic in the absence of ligand, nuclear after ligand- binding.SUBCELLULAR LOCATION: Isoform Beta: Nucleus. Note=Localized largely in the nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing, Alternative initiation; Named isoforms=10; Comment=At least 4 isoforms, Alpha (shown here), Alpha-B, Beta and Beta-B, are produced by alternative initiation at Met-1 and Met-27. The existence of isoform Alpha and isoform Alpha-B has been proved by mutagenesis. As the sequence environment of the 2 potential ATG initiator codons is the same for the other altrnatively spliced isoforms, alternative initiation of translation could also occur on these transcripts. Additional isoforms seem to exist; Name=Alpha; Synonyms=Alpha-A; IsoId=P04150-1; Sequence=Displayed; Note=Predominant physiological form. Isoform Alpha-B is produced by alternative initiation at Met-27 of isoform Alpha. Both isoforms exhibit similar subcellular location and nuclear translocation after ligand activation. Isoform Alpha-B appears to be more susceptible to degradation, at least when expressed in mammalian cells, but more effective in transcriptional activation and not in transrepression; Name=Beta; Synonyms=Beta-A; IsoId=P04150-2; Sequence=VSP_003703; Note=No hormone-binding activity. Widely expressed at low level; Name=Alpha-2; Synonyms=Gamma; IsoId=P04150-3; Sequence=VSP_007363; Note=Due to a partial intron retention. Lower transcriptional activity. Expressed at low level; Name=Beta-2; IsoId=P04150-6; Sequence=VSP_007363, VSP_003703; Note=Due to a partial intron retention; Name=GR-A alpha; IsoId=P04150-5; Sequence=VSP_013340; Note=Lacks exons 5, 6 and 7. Found in glucocorticoid-resistant myeloma patients; Name=GR-A beta; IsoId=P04150-7; Sequence=VSP_013340, VSP_003703; Note=Lacks exons 5, 6 and 7; Name=GR-P; IsoId=P04150-4; Sequence=Not described; Note=Encoded by exons 2-7 plus several basepairs from the subsequent intron region. Lacks the ligand binding domain. Accounts for up to 10-20% of mRNAs; Name=Alpha-B; Synonyms=Beta-B; IsoId=P04150-8; Sequence=VSP_018773; Note=Produced by alternative initiation at Met-27 of isoform Alpha. Both isoforms exhibit similar subcellular location and nuclear translocation after ligand activation. Isoform Alpha-B appears to be more susceptible to degradation, at least when expressed in mammalian cells, but more effective in transcriptional activation and not in transrepression; Name=Beta-B; IsoId=P04150-9; Sequence=VSP_018773, VSP_003703; Note=Produced by alternative initiation at Met-27 of isoform Beta; Name=10; Synonyms=hGRDelta313-338; IsoId=P04150-10; Sequence=VSP_043908;TISSUE SPECIFICITY: Widely expressed. In the heart, detected in left and right atria, left and right ventricles, aorta, apex, intraventricular septum, and atrioventricular node as well as whole adult and fetal heart.DOMAIN: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.PTM: Increased proteasome-mediated degradation in response to glucocorticoids.PTM: Phosphorylated in the absence of hormone; becomes hyperphosphorylated in the presence of glucocorticoid. The Ser- 203-phosphorylated form is mainly cytoplasmic, and the Ser-211- phosphorylated form is nuclear. Transcriptional activity correlates with the amount of phosphorylation at Ser-211.PTM: Sumoylated; this reduces transcription transactivation.PTM: Ubiquitinated; restricts glucocorticoid-mediated transcriptional signaling (By similarity).POLYMORPHISM: Carriers of the 22-Glu-Lys-23 allele are relatively more resistant to the effects of GCs with respect to the sensitivity of the adrenal feedback mechanism than non-carriers, resulting in a better metabolic health profile. Carriers have a better survival than non-carriers, as well as lower serum CRP levels. The 22-Glu-Lys-23 polymorphism is associated with a sex- specific, beneficial body composition at young-adult age, as well as greater muscle strength in males.DISEASE: Glucocorticoid resistance (GCRES) [MIM:138040]: Hypertensive, hyperandrogenic disorder characterized by increased serum cortisol concentrations. Inheritance is autosomal dominant. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: High constitutive expression of isoform beta by neutrophils may provide a mechanism by which these cells escape glucocorticoid-induced cell death. Up-regulation by proinflammatory cytokines such as IL8 further enhances their survival in the presence of glucocorticoids during inflammation.MISCELLANEOUS: Can up- or down-modulate aggregation and nuclear localization of expanded polyglutamine polypeptides derived from AR and HD through specific regulation of gene expression. Aggregation and nuclear localization of expanded polyglutamine proteins are regulated cellular processes that can be modulated by this receptor, a well-characterized transcriptional regulator.SIMILARITY: Belongs to the nuclear hormone receptor family. NR3 subfamily.SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/NR3C1";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/nr3c1/";WEB RESOURCE: Name=Wikipedia; Note=Glucocorticoid receptor entry; URL="http://en.wikipedia.org/wiki/Glucocorticoid_receptor"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_001195044 - RefSeq - - - - MOD_RES N6,N6,N6-trimethyllysine (By similarity) - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry5024 - - - - - - 11xCbxE-3D-F10(41-179) - - - - - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11660 - Reactome DB_ID: 159718 - factor X light chain - - - - NM_005746 - RefSeq - - - - ENSG00000141026 - Ensembl - - - - 11533283 - pubchem - - - - ENSG00000117399 - Ensembl - - - - ENSP00000400714 - Ensembl - - - - - - Transcriptional coactivator with PDZ-binding motif - WW domain-containing transcription regulator protein 1 - WWTR1 - - - - - Reactome DB_ID: 1629775 - http://www.reactome.org/biopax/46/48887#Protein3052 - TAZ - - - - REACT_116163 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116163.2 - - - - 159776 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159776 - - - - - - MOD_RES 131 131 Phosphothreonine. - - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CD36 (platelet glycoprotein IV, FAT)' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation70 - - - - ENSP00000354278 - Ensembl - - - - REACT_19760 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19760.2 - - - - ENST00000251871 - Ensembl - - - - - - MOD_RES 412 412 Phosphothreonine; by MAPK8 and MAPK9. - - - - REACT_20313 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20313.1 - - - - NM_005466 - RefSeq - - - - EQUAL - 1112 - - - - ENSG00000117054 - Ensembl - - - - NP_000780 - RefSeq - - - - ENSP00000422518 - Ensembl - - - - 7851882 - Mitchell GA - Duncan A - Robert MF - Boukaftane Y - Schappert K - Sarrazin J - Wang S - Labuda D - PubMed - Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning, chromosome mapping to 1p12-p13, and possible role in vertebrate evolution. - Genomics 23(3);552-9 - 1994 - - - - 10643692 - Langin, D - Larrouy, D - Andreelli, F - Laville, M - Vidal, H - Pubmed - Cloning and mRNA tissue distribution of human PPARgamma coactivator-1 - Int J Obes Relat Metab Disord 23:1327-32 - 1999 - - - - NP_001229468 - RefSeq - - - - REACT_27130 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27130.2 - - - - ENST00000293217 - Ensembl - - - - NM_001127443 - RefSeq - - - - 939192 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939192 - - - - Q96CT0 - UniProt - - - - Q9BZM8 - UniProt - - - - - - pro-factor X light chain, uncarboxylated - - - - - - Reactome DB_ID: 159810 - http://www.reactome.org/biopax/46/48887#Protein11632 - 3D-F10(32-179) - - - - EQUAL - 1162 - http://www.reactome.org/biopax/46/48887#SequenceSite25529 - - - - ENST00000368060 - Ensembl - - - - 400343 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400343 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite21419 - - - - NM_001870 - RefSeq - - - - FDFT1 - HGNC Symbol - - - - - - Peroxisomal membrane protein 11A - PX11A_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein13778 - Reactome DB_ID: 400198 - PEX11A - - - - ENST00000539097 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10156 - - - - - - REACT_1103 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1103.2 - - - - - - MOD_RES 367 367 Phosphoserine; by MAPK8 and MAPK9. - - - - REACT_25132 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25132.1 - - - - 23179 - NCBI Gene - - - - ENST00000394947 - Ensembl - - - - Q92486 - UniProt - - - - EQUAL - 311 - - - - NM_004830 - RefSeq - - - - - - protein C heavy chain - - - - - Reactome DB_ID: 159780 - http://www.reactome.org/biopax/46/48887#Protein11637 - PROC(200-461) - - - - - - MOD_RES 620 620 N6-acetyllysine; by CREBBP. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12978 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11984 - - - - - - factor X heavy chain - - - - - Reactome DB_ID: 159846 - http://www.reactome.org/biopax/46/48887#Protein11647 - F10(183-488) - - - - ENST00000596304 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4766 - - - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - The CYP7A1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Reviewed: Kersten, S, 2009-06-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction150 - Expression of CYP7A1 - - - - EQUAL - 464 - http://www.reactome.org/biopax/46/48887#SequenceSite1303 - - - - - - MOD_RES 885 885 Phosphothreonine. - - - - CYM - Alpha-chymase - CYH - CMA1 - Mast cell protease I - 3.4.21.39 - - - - - - - - - - - - - - - - - CMA1_HUMAN - Chymase - FUNCTION: Major secreted protease of mast cells with suspected roles in vasoactive peptide generation, extracellular matrix degradation, and regulation of gland secretion.CATALYTIC ACTIVITY: Preferential cleavage: Phe-|-Xaa > Tyr-|-Xaa > Trp-|-Xaa > Leu-|-Xaa.SUBCELLULAR LOCATION: Secreted. Cytoplasmic granule. Note=Mast cell granules.TISSUE SPECIFICITY: Mast cells in lung, heart, skin and placenta. Expressed in both normal skin and in urticaria pigmentosa lesions.SIMILARITY: Belongs to the peptidase S1 family. Granzyme subfamily.SIMILARITY: Contains 1 peptidase S1 domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - TIAM2_HUMAN - T-lymphoma invasion and metastasis-inducing protein 2 - - - - - http://www.reactome.org/biopax/46/48887#Protein2436 - Reactome DB_ID: 561165 - TIAM2 - - - - ENSP00000428982 - Ensembl - - - - 158797 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=158797 - - - - - - - - - - - - - - - - NR1D1 (REV-ERBA) Binds Heme and Corepressors - Edited: May, B, 2011-06-22 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3855 - NR1D1 (REV-ERBA) binds heme. The REV-ERBA:heme complex is then able to recruit the corepressors NCoR and HDAC3. Corepressors do not bind REV-ERBA in the absence of heme. - Reviewed: Delaunay, F, 2012-01-28 - Authored: May, B, 2011-06-22 - - - - - CRY2 - HGNC - - - - EQUAL - 75 - http://www.reactome.org/biopax/46/48887#SequenceSite21687 - - - - NFYC - HGNC Symbol - - - - 602984 - omim - - - - ENST00000300056 - Ensembl - - - - 2022361 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022361 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10138 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12062 - - - - - - EQUAL - 419 - - - - EQUAL - 135 - http://www.reactome.org/biopax/46/48887#SequenceSite12367 - - - - - - MOD_RES 795 795 Phosphoserine. - - - - Q9H1W3 - UniProt - - - - 8145820 - pubchem - - - - HGNC:1779 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10079 - - - - - - HGNC:19970 - HGNC - - - - Q9UF23 - UniProt - - - - REACT_20439 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20439.1 - - - - REACT_26188 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26188.2 - - - - EQUAL - 71 - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - Reviewed: Kersten, S, 2009-06-08 - The FATP1 (SLC27A1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - http://www.reactome.org/biopax/46/48887#TemplateReaction153 - Expression of FATP1 (SLC27A1) - - - - 603170 - omim - - - - REACT_20365 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20365.3 - - - - 8144345 - pubchem - - - - - - MOD_RES 397 397 Phosphoserine; by LATS1 and LATS2. - - - - EQUAL - 691 - http://www.reactome.org/biopax/46/48887#SequenceSite21744 - - - - EQUAL - 1232 - http://www.reactome.org/biopax/46/48887#SequenceSite23013 - - - - - - - - - - - p-ARNTL:p-CLOCK/NPAS2:DNA - - - - p-BMAL1:p-CLOCK/NPAS2:DNA - Reactome DB_ID: 421315 - http://www.reactome.org/biopax/46/48887#Complex4978 - - - - REACT_12836 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12836.1 - - - - 1605556 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1605556 - - - - HGNC:119 - HGNC - - - - ENSP00000418525 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12382 - - - - 159722 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159722 - - - - ENST00000427411 - Ensembl - - - - 3D66 - PROTEIN DATA BANK - - - - Q96RS0 - UniProt - - - - REACT_147767 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147767.2 - - - - - Chymase Hydrolyzes Angiotensin-(1-10) to Yields Angiotensin-(1-8) - - - - - - - - - - Chymase Hydrolyzes Angiotensin I to Yield Angiotensin II - Authored: May, B, 2011-11-19 - Chymase hydrolyzes angiotensin-(1-10) (angiotensin) to yield angiotensin-(1-8) (angiotensin II) at a higher rate than does angiotensin-converting enzyme (Reilly et al. 1982, Urata et al. 1990, Caughey et al. 2000, Richard et al. 2001). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4042 - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - - - - - - - PER1_HUMAN - Period circadian protein homolog 1 - - - - - - http://www.reactome.org/biopax/46/48887#Protein11528 - Reactome DB_ID: 3325590 - p-S-PER1 - - - - EQUAL - 105 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14047 - - - - 380742 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=380742 - - - - MOD:00036 - Protein Modification Ontology - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1837 - - - - Q9NX70 - UniProt - - - - - - MOD_RES 539 539 Phosphoserine; by AMPK (By similarity). - - - - Q9H2M4 - UniProt - - - - CHEBI:44819 - ChEBI - - - - - - Ub-p-S-PER2 - PER2_HUMAN - Ubiquitinated Phosphorylated Period circadian protein homolog 2 - - - - - - - Reactome DB_ID: 517835 - http://www.reactome.org/biopax/46/48887#Protein11542 - ub-p-PER2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2616 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1813 - - - - - - - 2.7.11 - - - - - - - - - - - - Phosphorylation of CRY and PER Proteins - Reviewed: Kay, SA, 2010-06-23 - Edited: May, B, 2009-06-02 00:51:49 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3858 - Reviewed: Hirota, T, 2010-06-23 - In the cytosol the kinases CSNK1D (casein kinase I delta) and CSNK1E (casein kinase I epsilon) phosphorylate PER1, PER2, CRY1, and CRY2 at multiple sites. Evidence indicates that PER:CRY complexes form a stable ternary complex with either CSNK1E or CSNK1D. Both kinases are able to bind and phosphorylate PER proteins. CSNK1E has been shown to phosphorylate CRY proteins only when they are complexed with PER proteins.<br>PER proteins contain a nuclear localization sequence and a nuclear export sequence allowing their movement into and out of the nucleus. Phosphorylation is required for transit of PER:CRY:kinase complexes into the nucleus and for interaction of PER proteins with the ubiquitin-mediated degradation process in the cytoplasm.<br>A mutation at Serine662 of PER2 is responsible for familial advanced phase sleep syndrome, however the particular kinase responsible for phosphorylating Serine662 is unknown. - Authored: May, B, 2009-05-17 22:04:50 - Reviewed: Delaunay, F, 2010-06-23 - Reviewed: Albrecht, U, 2010-06-23 - Reviewed: D'Eustachio, P, 2009-05-26 22:13:22 - - - - - REACT_24129 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24129.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature832 - - - - - - - - - http://www.reactome.org/biopax/46/48887#Dna32 - Reactome DB_ID: 2466373 - ALAS1 gene - - - - REACT_3089 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3089.2 - - - - PTHR22846:SF7 - PANTHER Family - - - - - EQUAL - 270 - http://www.reactome.org/biopax/46/48887#SequenceSite21458 - - - - UGT1A9 - HGNC - - - - - - MOD_RES 504 504 N6-acetyllysine. - - - - ENST00000394090 - Ensembl - - - - ENSG00000119915 - Ensembl - - - - SFE - NEP - Common acute lymphocytic leukemia antigen - MME - 3.4.24.11 - CALLA - Neutral endopeptidase - Atriopeptidase - EPN - CD10 - Enkephalinase - Skin fibroblast elastase - Neutral endopeptidase 24.11 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NEP_HUMAN - Neprilysin - FUNCTION: Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids. Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond. Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9. Involved in the degradation of atrial natriuretic factor (ANF). Displays UV- inducible elastase activity toward skin preelastic and elastic fibers.CATALYTIC ACTIVITY: Preferential cleavage of polypeptides between hydrophobic residues, particularly with Phe or Tyr at P1'.COFACTOR: Binds 1 zinc ion per subunit.ENZYME REGULATION: Inhibited in a dose dependent manner by opiorphin.BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=55.1 uM for angiotensin-1; KM=179 uM for angiotensin-2; KM=111.4 uM for angiotensin 1-9;SUBCELLULAR LOCATION: Cell membrane; Single-pass type II membrane protein.PTM: Myristoylation is a determinant of membrane targeting.PTM: Glycosylation at Asn-628 is necessary both for surface expression and neutral endopeptidase activity.MISCELLANEOUS: Important cell surface marker in the diagnostic of human acute lymphocytic leukemia.SIMILARITY: Belongs to the peptidase M13 family.SEQUENCE CAUTION: Sequence=CAA30157.1; Type=Erroneous initiation;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/MMEID41386ch3q25.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q9NYQ5 - UniProt - - - - REACT_26318 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26318.2 - - - - - - MOD_RES 953 953 Phosphoserine (By similarity). - - - - Q8NG15 - UniProt - - - - MED14 - HGNC Symbol - - - - 106180 - omim - - - - B2RAI0 - UniProt - - - - 1376 - NCBI Gene - - - - InChI=1S/C20H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22/h6-7,9-10,12-13,15-16H,2-5,8,11,14,17-19H2,1H3,(H,21,22)/b7-6-,10-9-,13-12-,16-15- - InChI - - - - - - MOD_RES 72 72 4-carboxyglutamate. - - - - ENST00000566029 - Ensembl - - - - - - Palmitate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule741 - Reactome DB_ID: 400150 - Palm - - - - 79001 - NCBI Gene - - - - - - ANGT_HUMAN - Angiotensinogen - - - - - http://www.reactome.org/biopax/46/48887#Protein12333 - Reactome DB_ID: 1998759 - AGT - - - - 1M2Z - PROTEIN DATA BANK - - - - O14935 - UniProt - - - - NM_001018075 - RefSeq - - - - HGNC:894 - HGNC - - - - Protein RTVP-1 - RTVP1 - GLIPR1 - GLIPR - GliPR 1 - - - - - - - - - - - - - - - GLIP1_HUMAN - Glioma pathogenesis-related protein 1 - SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P48060-1; Sequence=Displayed; Name=2; Synonyms=RTVP-1b; IsoId=P48060-2; Sequence=VSP_043902; Note=Highly expressed in glioblastomas;TISSUE SPECIFICITY: According to PubMed:8973356, it is ubiquitously expressed with high levels in lung and kidney and low levels in heart and liver. Highly expressed in cell lines derived from nervous system tumors arising from glia, low or absent in non-glial-derived nervous system tumor cell lines. Also found in fetal kidney. According to PubMed:7607567 it is expressed only in brain tumor glioblastoma multiforme/astrocytoma and not in other nervous system tumors or normal fetal or adult tissues.SIMILARITY: Belongs to the CRISP family.SIMILARITY: Contains 1 SCP domain.SEQUENCE CAUTION: Sequence=AAA82731.3; Type=Frameshift; Positions=3; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - CycC - - - - - Reactome DB_ID: 212418 - http://www.reactome.org/biopax/46/48887#Protein3049 - CCNC - - - - - - protein Z propeptide - - - - - Reactome DB_ID: 163834 - http://www.reactome.org/biopax/46/48887#Protein11668 - PROZ(24-40) - - - - 1CFH - PROTEIN DATA BANK - - - - NM_001150 - RefSeq - - - - - - MOD_RES 161 161 Phosphoserine. - - - - - CO2 - CO(2) - dioxidocarbon - carbonic anhydride - CO2 - [CO2] - - - - - - - - - - - - 44.0095 - carbon dioxide - carbon dioxide - - - - EQUAL - 29 - http://www.reactome.org/biopax/46/48887#SequenceSite21695 - - - - - - ANGL4_HUMAN - Angiopoietin-related protein 4 precursor - - - - - Reactome DB_ID: 381271 - http://www.reactome.org/biopax/46/48887#Protein6506 - ANGPTL4 - - - - Q8WYA1 - UniProt - - - - CHEBI:13357 - ChEBI - - - - Q3SY36 - UniProt - - - - NM_001018076 - RefSeq - - - - ENSP00000266659 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12054 - - - - - - Q68GC2 - UniProt - - - - EQUAL - 89 - http://www.reactome.org/biopax/46/48887#SequenceSite9867 - - - - - - - - - - - - - - - - - - - - - pro-factor IX, uncarboxylated + 12 CO2 + 12 O2 + 12 vitamin K hydroquinone -> pro-factor IX + 12 H2O + 12 vitamin K epoxide - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3884 - At the beginning of this reaction, 12 molecules of 'Oxygen', 12 molecules of 'vitamin K hydroquinone', 12 molecules of 'CO2', and 1 molecule of 'pro-factor IX, uncarboxylated' are present. At the end of this reaction, 12 molecules of 'H2O', 12 molecules of 'vitamin K epoxide', and 1 molecule of 'pro-factor IX' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - - - - - - - - - - - - - - - PPARG:Fatty Acid Ligand - http://www.reactome.org/biopax/46/48887#Complex3138 - Reactome DB_ID: 2026077 - - - - ENSP00000360541 - Ensembl - - - - REACT_117979 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117979.1 - - - - - - MOD_RES 1269 1269 Phosphoserine. - - - - 2065395 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2065395 - - - - ENSP00000308741 - Ensembl - - - - Q9BZN3 - UniProt - - - - REACT_20374 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20374.2 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of CYP7A1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation204 - - - - Q8WYA2 - UniProt - - - - TRG-20 - TRG-17 - Transformation-related gene 17 protein - Mediator complex subunit 10 - Transformation-related gene 20 protein - MED10 - - - - - - - - - - - - - MED10_HUMAN - Mediator of RNA polymerase II transcription subunit 10 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 10 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12372 - - - - NM_003592 - RefSeq - - - - PROC - HGNC - - - - 2022342 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022342 - - - - ENST00000392334 - Ensembl - - - - 1407 - NCBI Gene - - - - Q15180 - UniProt - - - - 11988089 - Rehse PH - Lin SX - Zhou M - PubMed - Crystal structure of human dehydroepiandrosterone sulphotransferase in complex with substrate. - Biochem J 364(Pt 1);165-71 - 2002 - - - - EQUAL - 131 - - - - - - MOD_RES 1786 1786 Phosphoserine. - - - - REACT_148055 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148055.2 - - - - - - - - - - - - - - - - - - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein6507 - Reactome DB_ID: 400216 - Coactivators of PPARalpha - - - - P21439 - UniProt - - - - - - 11xCbxE-PROS1(25-676) - - - - - - - - - - - - - - - Reactome DB_ID: 159770 - http://www.reactome.org/biopax/46/48887#Protein11640 - pro-protein S - - - - 549475 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=549475 - - - - - - - - - ACTIVATION - - 'PPARA:RXRA Coactivator Complex [nucleoplasm]' positively regulates 'Expression of ME1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation213 - - - - ENSG00000124151 - Ensembl - - - - - 13.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12966 - - - - P13196 - UniProt - - - - EQUAL - 196 - http://www.reactome.org/biopax/46/48887#SequenceSite3900 - - - - 1O86 - PROTEIN DATA BANK - - - - 2022390 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2022390 - - - - 107670 - omim - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry14068 - - - - 548785 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=548785 - - - - - - MOD_RES 57 57 Phosphoserine (By similarity). - - - - EQUAL - 278 - - - - REACT_12914 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_12914.2 - - - - ENST00000264110 - Ensembl - - - - 602260 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature11994 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5673 - - - - - - - - ACE2_HUMAN - Angiotensin-converting enzyme 2 - ACE2(18-805) - - - - - Reactome DB_ID: 2022344 - http://www.reactome.org/biopax/46/48887#Protein12349 - ACE2 - - - - 376398 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=376398 - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 3229246 - http://www.reactome.org/biopax/46/48887#Protein12356 - Carboxypeptidase - - - - Q9UCZ8 - UniProt - - - - EQUAL - 1255 - http://www.reactome.org/biopax/46/48887#SequenceSite21472 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12942 - - - - SKP1 - HGNC - - - - EQUAL - 626 - http://www.reactome.org/biopax/46/48887#SequenceSite21418 - - - - PTOV2 - Activator interaction domain-containing protein 1 - Activator-recruited cofactor 92 kDa component - ARC92 - Mediator complex subunit 25 - MED25 - p78 - ACID1 - - - - - - - - - - - - - - - - - - - - - - - MED25_HUMAN - Mediator of RNA polymerase II transcription subunit 25 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Required for RARA/RXRA-mediated transcription.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Interacts with CREBBP. Interacts with ESR1, GR, RARA, RXRA and THRB in a ligand-dependent fashion. Binds the Herpes simplex virus activator VP16.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=6; Name=1; IsoId=Q71SY5-1; Sequence=Displayed; Name=2; IsoId=Q71SY5-2; Sequence=VSP_028144; Name=3; IsoId=Q71SY5-3; Sequence=VSP_028145; Note=No experimental confirmation available; Name=4; IsoId=Q71SY5-4; Sequence=VSP_028146; Note=No experimental confirmation available; Name=5; IsoId=Q71SY5-5; Sequence=VSP_028143; Note=No experimental confirmation available; Name=6; IsoId=Q71SY5-6; Sequence=VSP_047570;TISSUE SPECIFICITY: Ubiquitously expressed. Highest levels in brain, heart, kidney, peripheral leukocytes, placenta, skeletal muscle and spleen.DISEASE: Charcot-Marie-Tooth disease 2B2 (CMT2B2) [MIM:605589]: A recessive axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal regeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. Nerve conduction velocities are normal or slightly reduced. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the Mediator complex subunit 25 family.SEQUENCE CAUTION: Sequence=AAG15589.1; Type=Erroneous initiation; Sequence=CAB66680.1; Type=Frameshift; Positions=567; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1167 - - - - 55090 - NCBI Gene - - - - ANGPTL4 - HGNC Symbol - - - - ENST00000405141 - Ensembl - - - - HGNC:10417 - HGNC - - - - TEAD3 - HGNC - - - - ENST00000353795 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4699 - - - - - - 17994337 - Motzkus, D - Forssmann, WG - Loumi, S - Maronde, E - Vinson, C - Cadenas, C - Pubmed - Activation of human period-1 by PKA or CLOCK/BMAL1 is conferred by separate signal transduction pathways - Chronobiol Int 24:783-92 - 2007 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12847 - - - - 159792 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159792 - - - - - - MOD_RES 437 437 N6-acetyllysine. - - - - REACT_111759 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111759.1 - - - - REACT_2146 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2146.3 - - - - - - MEF2D_HUMAN - Myocyte-specific enhancer factor 2D - - - - - - Reactome DB_ID: 445328 - http://www.reactome.org/biopax/46/48887#Protein6412 - MEF2D - - - - 159824 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159824 - - - - ENST00000305264 - Ensembl - - - - ENSG00000130234 - Ensembl - - - - ENST00000348159 - Ensembl - - - - 180245 - omim - - - - - 3.4.17 - ACE2 Hydrolyzes Angiotensin-(1-8) to Yield Angiotensin-(1-7) - - - - - - - - ACE2 Hydrolyzes Angiotensin II to Yield Angiotensin-(1-7) - Authored: May, B, 2011-11-19 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4051 - Angiotensin-converting enzyme 2 (ACE2) hydrolyzes angiotensin-(1-8) (angiotensin II) to yield angiotensin-(1-7) (Vickers et al. 2002, Rice et al. 2004). The activity of ACE2 on angiotensin-(1-8) is 400-fold higher than on angiotensin-(1-10) (Vickers et al. 2002). - Edited: May, B, 2011-11-19 - Reviewed: Joseph, J, 2012-08-06 - - - - - 17609368 - Spiegelman, BM - St-Pierre, J - Jäger, S - Handschin, C - Pubmed - AMP-activated protein kinase (AMPK) action in skeletal muscle via direct phosphorylation of PGC-1alpha - Proc Natl Acad Sci U S A 104:12017-22 - 2007 - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite9676 - - - - NM_139062 - RefSeq - - - - REACT_4352 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4352.2 - - - - - - Cathepsin G - CATG_HUMAN - - - - - Reactome DB_ID: 538738 - http://www.reactome.org/biopax/46/48887#Protein8390 - CTSG - - - - - - MOD_RES 800 800 S-nitrosocysteine (Probable). - - - - REACT_120353 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120353.1 - - - - A8K044 - UniProt - - - - 184199 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=184199 - - - - - - Cdh1 - - - - - http://www.reactome.org/biopax/46/48887#Protein6078 - Reactome DB_ID: 174249 - FZR1 - - - - - - MOD_RES 635 635 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature5645 - - - - 73531 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=73531 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2395 - - - - EQUAL - 758 - - - - 609878 - omim - - - - 137167 - omim - - - - ENSP00000361065 - Ensembl - - - - E7EU16 - UniProt - - - - EQUAL - 305 - http://www.reactome.org/biopax/46/48887#SequenceSite1782 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite6184 - - - - - - MOD_RES 959 959 N6-acetyllysine. - - - - NM_005518 - RefSeq - - - - ENSG00000134240 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4959 - - - - - REACT_117931 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117931.1 - - - - NM_001020825 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4706 - - - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction52 - Reviewed: Kersten, S, 2009-06-08 - The CTGF gene is transcribed to yield mRNA and the mRNA is translated to yield protein. Transcription of the CTGF gene is increased by both YAP1:TEAD and WWTR1(TAZ):TEAD transcriptional coactivator:transcription factor complexes, so that CTFG is one of the many genes whose expression is downregulated by the action of the hippo cascade (Zhang et al. 2009; Zhao et al. 2008). - Expression of CTGF - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5805 - - - - REACT_9752 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9752.2 - - - - ENST00000503506 - Ensembl - - - - HGNC:25944 - HGNC - - - - - - MOD_RES 872 872 Phosphoserine; by AMPK (By similarity). - - - - - 3.4.17 - Mast Cell Carboxypeptidase Hydrolyzes Angiotensin-(1-10) to Yield Angiotensin-(1-9) - - - - - - - - Mast Cell Carboxypeptidase Hydrolyzes Angiotensin I to Yield Angiotensin-(1-9) - Authored: May, B, 2011-12-23 - Edited: May, B, 2011-12-23 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction4052 - Reviewed: Joseph, J, 2012-08-06 - Mast cell carboxypeptidase (CPA3) hydrolyzes a single amino acid residue from the C-terminus of angiotensin-(1-10) (angiotensin I) to yield angiotensin-(1-9). - - - - - MOD_RES (3R)-3-hydroxyaspartate - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1058 - - - - EQUAL - 851 - - - - NM_001880 - RefSeq - - - - 212429 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=212429 - - - - ENST00000301608 - Ensembl - - - - ENSG00000127511 - Ensembl - - - - PTHR11455:SF0 - PANTHER Family - - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1068 - - - - RPS27A - HGNC Symbol - - - - - - MOD_RES 4 4 Phosphoserine. - - - - - - - - - - - Classical PDGF precursor dimers (AA, AB, BB) - Reactome DB_ID: 186822 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Complex1215 - - - - - 10.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12936 - - - - P27469 - UniProt - - - - NP_573570 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12053 - - - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite1778 - - - - - - MOD_RES 495 495 Phosphoserine. - - - - - - MOD_RES 1977 1977 Phosphoserine. - - - - 56938 - NCBI Gene - - - - REACT_116516 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116516.3 - - - - Q2V504 - UniProt - - - - NP_958851 - RefSeq - - - - 604709 - omim - - - - G3XAG8 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2120 - - - - - - 400123 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400123 - - - - 1XB7 - PROTEIN DATA BANK - - - - - - MOD_RES 273 273 N6-acetyllysine. - - - - ENST00000593998 - Ensembl - - - - - C22H29FO5 - - - - - - - dexamethasone - dexamethasone - - - - EQUAL - 71 - http://www.reactome.org/biopax/46/48887#SequenceSite18496 - - - - NP_001234932 - RefSeq - - - - ENSP00000248054 - Ensembl - - - - EQUAL - 1701 - http://www.reactome.org/biopax/46/48887#SequenceSite4572 - - - - - - MOD_RES 773 773 Phosphoserine; by CK2. - - - - 8499929 - DiDonato S - Taroni F - Cavadini P - Pandolfo M - Verderio E - PubMed - Two novel sequence polymorphisms of the human carnitine palmitoyltransferase II (CPT1) gene. - Hum Mol Genet 2(3);334 - 1993 - - - - CTSG - HGNC - - - - REACT_17827 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17827.2 - - - - Q9UFQ1 - UniProt - - - - NP_001191189 - RefSeq - - - - - SIF and TIAM1-like exchange factor - TIAM2 - TIAM-2 - STEF - KIAA2016 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TIAM2_HUMAN - T-lymphoma invasion and metastasis-inducing protein 2 - FUNCTION: Modulates the activity of RHO-like proteins and connects extracellular signals to cytoskeletal activities. Acts as a GDP- dissociation stimulator protein that stimulates the GDP-GTP exchange activity of RHO-like GTPases and activates them. Mediates extracellular laminin signals to activate Rac1, contributing to neurite growth. Involved in lamellipodial formation and advancement of the growth cone of embryonic hippocampal neurons. Promotes migration of neurons in the cerebral cortex. When overexpressed, induces membrane ruffling accompanied by the accumulation of actin filaments along the altered plasma membrane (By similarity). Activates specifically RAC1, but not CDC42 and RHOA.SUBUNIT: Interacts with MAP1A, MAP1B, PARP1 and YWHAE (By similarity).SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cell projection, lamellipodium (By similarity). Cell projection, filopodium (By similarity). Cell projection, growth cone. Note=Localizes to the plasma membrane in neurites (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=5; Name=1; IsoId=Q8IVF5-1; Sequence=Displayed; Name=2; IsoId=Q8IVF5-2; Sequence=VSP_030975; Name=3; Synonyms=Short; IsoId=Q8IVF5-3; Sequence=VSP_030971; Name=4; IsoId=Q8IVF5-4; Sequence=VSP_030972; Name=5; Synonyms=Long; IsoId=Q8IVF5-5; Sequence=VSP_030974;TISSUE SPECIFICITY: Expressed in the occipital, frontal and temporal lobes, cerebellum, putamen and testis.DOMAIN: The PH 1 domain and amino acids 621-782 (a region called TSS; otherwise known as CC-Ex) are necessary for membrane localization. The PH 1 and TSS domains are necessary for Rac1 activity. The PH 2 domain is engaged in the enhancement of the catalytic activity of the adjacent DH domain. The PH 1, TSS and DH domains are necessary to induce neurite-like structure (By similarity).PTM: Phosphorylated on serine and threonine residues. Phosphorylated on Thr-1648 by Rho-kinase. Its phosphorylation by Rho-kinase inhibits its guanine nucleotide exchange activity, its interaction with MAP1A, MAP1B, PARP1 and YWHAE and reduces its ability to promote neurite growth (By similarity).SIMILARITY: Belongs to the TIAM family.SIMILARITY: Contains 1 DH (DBL-homology) domain.SIMILARITY: Contains 1 PDZ (DHR) domain.SIMILARITY: Contains 2 PH domains.SIMILARITY: Contains 1 RBD (Ras-binding) domain.SEQUENCE CAUTION: Sequence=AAF05900.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC23112.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAC86170.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 67 - http://www.reactome.org/biopax/46/48887#SequenceSite9912 - - - - 15800623 - Saigoh, N - Ptácek, LJ - Saigoh, K - Xu, Y - Fu, YH - Padiath, QS - Shapiro, RE - Wu, SC - Jones, CR - Pubmed - Functional consequences of a CKIdelta mutation causing familial advanced sleep phase syndrome - Nature 434:640-4 - 2005 - - - - O95910 - UniProt - - - - MOD_RES Phosphoserine - - - - HGNC:15819 - HGNC - - - - PPARGC1B - HGNC - - - - P37268 - UniProt - - - - 3588310 - Westley BR - May FE - PubMed - Oestrogen regulates cathepsin D mRNA levels in oestrogen responsive human breast cancer cells. - Nucleic Acids Res 15(9);3773-86 - 1987 - - - - REACT_148686 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148686.1 - - - - - - p-S266,T263,T299-PPARGC1A - p-T263-S266-T299-PPARGC1A - p-T263,S266,T299-PPARGC1A - PRGC1_HUMAN - Peroxisome proliferator-activated receptor gamma coactivator 1-alpha - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein11546 - Reactome DB_ID: 1592224 - PPARGC1A - - - - REACT_120312 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120312.1 - - - - SIN3A - HGNC Symbol - - - - NM_001168280 - RefSeq - - - - Q10586 - UniProt - - - - ENSP00000355996 - Ensembl - - - - EQUAL - 200 - http://www.reactome.org/biopax/46/48887#SequenceSite12393 - - - - G3V2C5 - UniProt - - - - EQUAL - 50 - - - - - - factor X light chain propeptide - - - - - http://www.reactome.org/biopax/46/48887#Protein11659 - Reactome DB_ID: 159824 - F10(32-40) - - - - - - Angiotensin-(1-7) - Ang-(1-7) - ANGT_HUMAN - AGT(34-40) - - - - - Reactome DB_ID: 2022351 - http://www.reactome.org/biopax/46/48887#Protein12350 - AGT - - - - 8202 - NCBI Gene - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12844 - - - - - - ubiquitin (UBC 4) - - - - - Reactome DB_ID: 939192 - http://www.reactome.org/biopax/46/48887#Protein1052 - UBC(229-304) - - - - P08709 - UniProt - - - - PTHR23043:SF7 - PANTHER Family - - - - - REACT_14568 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_14568.2 - - - - P01185 - UniProt - - - - REACT_118060 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118060.1 - - - - Q1WF12 - UniProt - - - - - - MOD_RES 180 180 Phosphoserine; by MAPK7. - - - - EQUAL - 41 - - - - 9575211 - Shechter, I - Dai, P - Guan, G - Pubmed - Differential transcriptional regulation of the human squalene synthase gene by sterol regulatory element-binding proteins (SREBP) 1a and 2 and involvement of 5' DNA sequence elements in the regulation - J Biol Chem 273:12526-35 - 1998 - - - - ENSP00000348551 - Ensembl - - - - 19088433 - Vock, C - Nitz, I - Döring, F - Pubmed - Transcriptional regulation of HMG-CoA synthase and HMG-CoA reductase genes by human ACBP - Cell Physiol Biochem 22:515-24 - 2008 - - - - - - MOD_RES 1981 1981 Phosphoserine. - - - - EQUAL - 133 - http://www.reactome.org/biopax/46/48887#SequenceSite397 - - - - - - Cryptochrome-2 - CRY2_HUMAN - - - - - Reactome DB_ID: 400255 - http://www.reactome.org/biopax/46/48887#Protein11512 - CRY2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10019 - - - - NM_033016 - RefSeq - - - - 99313641 - pubchem-substance - - - - ENSP00000254657 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep4775 - - - - - 3156 - NCBI Gene - - - - EQUAL - 246 - http://www.reactome.org/biopax/46/48887#SequenceSite23015 - - - - - - - - - - Reactome DB_ID: 400344 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein11518 - PER1/2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12330 - - - - Mediator complex subunit 18 - MED18 - p28b - - - - - - - - - - - - - - - - - - MED18_HUMAN - Mediator of RNA polymerase II transcription subunit 18 - FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.SUBUNIT: Component of the Mediator complex, which is composed of MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The MED12, MED13, CCNC and CDK8 subunits form a distinct module termed the CDK8 module. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.SUBCELLULAR LOCATION: Nucleus (Probable).SIMILARITY: Belongs to the Mediator complex subunit 18 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4647 - - - - NM_001001548 - RefSeq - - - - 25937 - NCBI Gene - - - - ENSP00000409612 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1857 - - - - - - MOD_RES 141 141 Phosphoserine (By similarity). - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10160 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval12056 - - - - - - ENST00000314028 - Ensembl - - - - EQUAL - 26 - - - - - - MOD_RES 146 146 Phosphoserine. - - - - 2466384 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2466384 - - - - EQUAL - 1581 - http://www.reactome.org/biopax/46/48887#SequenceSite12375 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10798 - - - - - - Q6DTK9 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10146 - - - - EQUAL - 117 - http://www.reactome.org/biopax/46/48887#SequenceSite12347 - - - - NP_001136061 - RefSeq - - - - 1522 - NCBI Gene - - - - Q6PJT2 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature10039 - - - - EQUAL - 959 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5773 - - - - Q9BSC3 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep5782 - - - - 939847 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939847 - - - - REACT_27936 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27936.4 - - - - REACT_147855 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147855.2 - - - - - - MOD_RES 1128 1128 Phosphoserine. - - - - - - NCOA1_HUMAN - Nuclear receptor coactivator 1 - - - - - Reactome DB_ID: 442496 - http://www.reactome.org/biopax/46/48887#Protein6502 - NCOA1 - - - - REACT_119596 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119596.1 - - - - 381204 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=381204 - - - - - - 13xCbxE-PROZ - - - - - - - - - - - - - - - - - - Reactome DB_ID: 163813 - http://www.reactome.org/biopax/46/48887#Protein11667 - protein Z - - - - Q96G25 - UniProt - - - - NP_003589 - RefSeq - - - - Q9UM67 - UniProt - - - - ENST00000262188 - Ensembl - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of DEC2 (BHLHE41, BHLHB3)' - As inferred from mouse, the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds E-box elements in the promoter of the DEC2 (BHLHE41, BHLHB3) gene and activates transcription of DEC2. - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation95 - - - - Q9P1T3 - UniProt - - - - - - MOD_RES 817 817 Phosphoserine. - - - - Q14686 - UniProt - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite1771 - - - - EQUAL - 499 - - - - 10769175 - Chuang, LT - Bobik, EG - Mukerji, P - Thurmond, JM - Parker-Barnes, JM - Kelder, B - Kopchick, JJ - Leonard, AE - Kroeger, PE - Huang, YS - Pubmed - cDNA cloning and characterization of human Delta5-desaturase involved in the biosynthesis of arachidonic acid - Biochem J 347:719-24 - 2000 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite12338 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1274 - - - - 1L3E - PROTEIN DATA BANK - - - - ENST00000397122 - Ensembl - - - - NM_001168278 - RefSeq - - - - NP_001120929 - RefSeq - - - - REACT_3122 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3122.2 - - - - EQUAL - 50 - http://www.reactome.org/biopax/46/48887#SequenceSite10000 - - - - REACT_116145 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116145.1 - - - - ENST00000542388 - Ensembl - - - - - - ubiquitin (UBC 6) - - - - - http://www.reactome.org/biopax/46/48887#Protein2482 - Reactome DB_ID: 939856 - UBC(381-456) - - - - ENSP00000304697 - Ensembl - - - - 238985 - Lane MD - Miziorko HM - Reed WD - Clinkenbeard KD - PubMed - 3-Hydroxy-3-methylglutaryl coenzyme A synthase. Evidence for an acetyl-S-enzyme intermediate and identification of a cysteinyl sulfhydryl as the site of acetylation. - J Biol Chem 250(15);5768-73 - 1975 - - - - F2RM36 - UniProt - - - - YZXBAPSDXZZRGB-DOFZRALJSA-N - InChIKey - - - - NM_004774 - RefSeq - - - - 10051425 - Hegardt FG - PubMed - Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase: a control enzyme in ketogenesis. - Biochem J 338 ( Pt 3);569-82 - 1999 - - - - Q8IV71 - UniProt - - - - A8K095 - UniProt - - - - O75182 - UniProt - - - - HGNC:17903 - HGNC - - - - NP_001248374 - RefSeq - - - - ENST00000540367 - Ensembl - - - - REACT_26759 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26759.3 - - - - MI:0359 - Molecular Interactions Ontology - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - EP300 - E1A-associated protein p300 - P300 - p300 HAT - 2.3.1.48 - - - - - - - - - - - - - - - EP300_HUMAN - Histone acetyltransferase p300 - FUNCTION: Functions as histone acetyltransferase and regulates transcription via chromatin remodeling. Acetylates all four core histones in nucleosomes. Histone acetylation gives an epigenetic tag for transcriptional activation. Mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. Also functions as acetyltransferase for nonhistone targets. Acetylates 'Lys-131' of ALX1 and acts as its coactivator in the presence of CREBBP. Acetylates SIRT2 and is proposed to indirectly increase the transcriptional activity of TP53 through acetylation and subsequent attenuation of SIRT2 deacetylase function. Acetylates HDAC1 leading to its inactivation and modulation of transcription. Acts as a TFAP2A-mediated transcriptional coactivator in presence of CITED2. Plays a role as a coactivator of NEUROD1-dependent transcription of the secretin and p21 genes and controls terminal differentiation of cells in the intestinal epithelium. Promotes cardiac myocyte enlargement. Can also mediate transcriptional repression. Binds to and may be involved in the transforming capacity of the adenovirus E1A protein. In case of HIV-1 infection, it is recruited by the viral protein Tat. Regulates Tat's transactivating activity and may help inducing chromatin remodeling of proviral genes. Acetylates FOXO1 and enhances its transcriptional activity.CATALYTIC ACTIVITY: Acetyl-CoA + [histone] = CoA + acetyl- [histone].SUBUNIT: Interacts with phosphorylated CREB1 (By similarity). Interacts with HIF1A; the interaction is stimulated in response to hypoxia and inhibited by CITED2. Interacts (via N-terminus) with TFAP2A (via N-terminus); the interaction requires CITED2. Interacts (via CH1 domain) with CITED2 (via C-terminus). Interacts with CITED1 (unphosphorylated form preferentially and via C- terminus). Interacts with ESR1; the interaction is estrogen- dependent and enhanced by CITED1. Interacts with DTX1, EID1, ELF3, FEN1, LEF1, NCOA1, NCOA6, NR3C1, PCAF, PELP1, PRDM6, SP1, SP3, SPIB, SRY, TCF7L2, TP53, DDX5, DDX17, SATB1, SRCAP, TTC5, JMY and TRERF1. The TAZ-type 1 domain interacts with HIF1A. Probably part of a complex with HIF1A and CREBBP. Part of a complex containing CARM1 and NCOA2/GRIP1. Interacts with ING4 and this interaction may be indirect. Interacts with ING5. Interacts with the C- terminal region of CITED4. Interacts with HTLV-1 Tax and p30II. Interacts with and acetylates HIV-1 Tat. Non-sumoylated EP300 preferentially interacts with SENP3. Interacts with SS18L1/CREST. Interacts with ALX1 (via homeobox domain). Interacts with NEUROD1; the interaction is inhibited by NR0B2. Interacts with TCF3. Interacts (via CREB-binding domain) with MYOCD (via C-terminus) (By similarity). Binds to HIPK2 (By similarity). Interacts with ROCK2 and PPARG. Forms a complex made of CDK9, CCNT1/cyclin-T1, EP300 and GATA4 that stimulates hypertrophy in cardiomyocytes. Interacts with IRF1 and this interaction enhances acetylation of p53/TP53 and stimulation of its activity. Interacts with FOXO1; the interaction acetylates FOXO1 and enhances its transcriptional activity. Interacts with ALKBH4 and DDIT3/CHOP.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=In the presence of ALX1 relocalizes from the cytoplasm to the nucleus. Co-localizes with ROCK2 in the nucleus.DOMAIN: The CRD1 domain (cell cycle regulatory domain 1) mediates transcriptional repression of a subset of p300 responsive genes; it can be de-repressed by CDKN1A/p21WAF1 at least at some promoters. It conatins sumoylation and acetylation sites and the same lysine residues may be targeted for the respective modifications. It is proposed that deacetylation by SIRT1 allows sumoylation leading to suppressed activity.PTM: Acetylated on Lys at up to 17 positions by intermolecular autocatalysis. Deacetylated in the transcriptional repression domain (CRD1) by SIRT1, preferentially at Lys-1020.PTM: Citrullinated at Arg-2142 by PADI4, which impairs methylation by CARM1 and promotes interaction with NCOA2/GRIP1.PTM: Methylated at Arg-580 and Arg-604 in the KIX domain by CARM1, which blocks association with CREB, inhibits CREB signaling and activates apoptotic response. Also methylated at Arg-2142 by CARM1, which impairs interaction with NCOA2/GRIP1.PTM: Sumoylated; sumoylation in the transcriptional repression domain (CRD1) mediates transcriptional repression. Desumoylated by SENP3 through the removal of SUMO2 and SUMO3.PTM: Probable target of ubiquitination by FBXO3, leading to rapid proteasome-dependent degradation.PTM: Phosphorylated by HIPK2 in a RUNX1-dependent manner. This phosphorylation that activates EP300 happens when RUNX1 is associated with DNA and CBFB. Phosphorylated by ROCK2 and this enhances its activity. Phosphorylation at Ser-89 by AMPK reduces interaction with nuclear receptors, such as PPARG.DISEASE: Note=Defects in EP300 may play a role in epithelial cancer.DISEASE: Note=Chromosomal aberrations involving EP300 may be a cause of acute myeloid leukemias. Translocation t(8;22)(p11;q13) with KAT6A.DISEASE: Rubinstein-Taybi syndrome 2 (RSTS2) [MIM:613684]: A disorder characterized by craniofacial abnormalities, postnatal growth deficiency, broad thumbs, broad big toes, mental retardation and a propensity for development of malignancies. Some individuals with RSTS2 have less severe mental impairment, more severe microcephaly, and a greater degree of changes in facial bone structure than RSTS1 patients. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Contains 1 bromo domain.SIMILARITY: Contains 1 KIX domain.SIMILARITY: Contains 2 TAZ-type zinc fingers.SIMILARITY: Contains 1 ZZ-type zinc finger.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/P300ID97.html";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/EP300";WEB RESOURCE: Name=Wikipedia; Note=P300/CBP entry; URL="http://en.wikipedia.org/wiki/P300/CBP"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - Nuclear receptor corepressor 2 - NCOR2_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein3071 - Reactome DB_ID: 442469 - NCOR2 - - - - SREBF2 - HGNC - - - - Q9UH74 - UniProt - - - - 1579 - NCBI Gene - - - - - - Cathepsin Z - CATZ_HUMAN - Cathepsin X - - - - - Reactome DB_ID: 2022345 - http://www.reactome.org/biopax/46/48887#Protein12347 - CTSZ - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry12826 - - - - - - - - - - - Authored: May, B, 2011-11-08 - Edited: May, B, 2011-11-08 - http://www.reactome.org/biopax/46/48887#TemplateReaction157 - Reviewed: Kersten, S, 2009-06-08 - The GRHL1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein. - Expression of GRHL1 - - - - ENST00000368068 - Ensembl - - - - - - - - - - - - - - - - - - - - pro-factor X, uncarboxylated + 11 CO2 + 11 O2 + 11 vitamin K hydroquinone -> pro-factor X + 11 H2O + 11 vitamin K epoxide - At the beginning of this reaction, 11 molecules of 'Oxygen', 1 molecule of 'pro-factor X, uncarboxylated', 11 molecules of 'vitamin K hydroquinone', and 11 molecules of 'CO2' are present. At the end of this reaction, 1 molecule of 'pro-factor X', 11 molecules of 'H2O', and 11 molecules of 'vitamin K epoxide' are present.<br><br> This reaction takes place in the 'endoplasmic reticulum membrane' and is mediated by the 'gamma-glutamyl carboxylase activity' of 'vitamin K-dependent gamma-carboxylase'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction3886 - - - - - - - Q53GM5 - UniProt - - - - 19710929 - Kersten, S - Muller, M - Hooiveld, G - Rakhshandehroo, M - Pubmed - Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human - PLoS One 4:e6796 - 2009 - - - - ENST00000403482 - Ensembl - - - - P23511 - UniProt - - - - 3.4.23.5 - CPSD - CTSD - Cathepsin D heavy chain - Cathepsin D light chain - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATD_HUMAN - Cathepsin D - FUNCTION: Acid protease active in intracellular protein breakdown. Involved in the pathogenesis of several diseases such as breast cancer and possibly Alzheimer disease.CATALYTIC ACTIVITY: Specificity similar to, but narrower than, that of pepsin A. Does not cleave the 4-Gln-|-His-5 bond in B chain of insulin.SUBUNIT: Consists of a light chain and a heavy chain.SUBCELLULAR LOCATION: Lysosome. Melanosome. Secreted, extracellular space. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV. In aortic samples, detected as an extracellular protein loosely bound to the matrix (PubMed:20551380).TISSUE SPECIFICITY: Expressed in the aorta extrcellular space (at protein level).PTM: N- and O-glycosylated.POLYMORPHISM: The Val-58 allele is significantly overrepresented in demented patients (11.8%) compared with non-demented controls (4.9%). Carriers of the Val-58 allele have a 3.1-fold increased risk for developing AD than non-carriers.DISEASE: Neuronal ceroid lipofuscinosis 10 (CLN10) [MIM:610127]: A form of neuronal ceroid lipofuscinosis with onset at birth or early childhood. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the peptidase A1 family.WEB RESOURCE: Name=NCL CTSD; Note=Neural Ceroid Lipofuscinoses mutation db; URL="http://www.ucl.ac.uk/ncl/catD.shtml"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_24666 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24666.2 - - - - ENST00000382974 - Ensembl - - - - 6269175 - Fyhrquist, F - Grönhagen-Riska, C - Pubmed - Purification of human lung angiotensin-converting enzyme - Scand J Clin Lab Invest 40:711-9 - 1980 - - - - - - NCOA6_HUMAN - - - - - Reactome DB_ID: 376414 - http://www.reactome.org/biopax/46/48887#Protein6509 - NCOA6 - - - - ENST00000008527 - Ensembl - - - - ENST00000504572 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5659 - - - - - - EQUAL - 826 - - - - ENSG00000125686 - Ensembl - - - - - - Cul1 - - - - - Reactome DB_ID: 174230 - http://www.reactome.org/biopax/46/48887#Protein2847 - CUL1 - - - - - - Mediator of RNA polymerase II transcription subunit 9 - MED9_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein6475 - Reactome DB_ID: 556804 - MED9 - - - - D3DPE9 - UniProt - - - - 8145136 - pubchem - - - - - - - - - ACTIVATION - - 'p-BMAL1:p-CLOCK/NPAS2:DNA [nucleoplasm]' positively regulates 'Expression of CRYPTOCHROME-1' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation103 - The phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) heterodimer binds an E-box in the promoter of the CRY1 gene and activates transcription of CRY1. NPAS2 is predicted to act redundantly with CLOCK. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10162 - - - - - - NM_001031847 - RefSeq - - - - Q96IY8 - UniProt - - - - NM_016060 - RefSeq - - - - 10777541 - Cheema, SK - Agellon, LB - Pubmed - The murine and human cholesterol 7alpha-hydroxylase gene promoters are differentially responsive to regulation by fatty acids mediated via peroxisome proliferator-activated receptor alpha - J Biol Chem 275:12530-6 - 2000 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis1268 - - - - 1BF9 - PROTEIN DATA BANK - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5646 - - - - - - ENSG00000161533 - Ensembl - - - - Q96GT0 - UniProt - - - - REACT_148688 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148688.1 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite23032 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite25542 - - - - EQUAL - 27 - http://www.reactome.org/biopax/46/48887#SequenceSite20846 - - - - REACT_4295 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4295.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval10078 - - - - - - REACT_148235 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148235.2 - - - - 601998 - omim - - - - - C18H32O3 - (13S)-Hydroxyoctadecadienoic acid - (9Z, 11E)-(13S)-13-Hydroxyoctadeca-9,11-dienoic acid - (9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid - - - - - 296.4449 - 13(S)-HODE - 13(S)-HODE - - - - - - MOD_RES 65 65 Phosphoserine (By similarity). - - - - EQUAL - 67 - - - - 163843 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163843 - - - - ENST00000367241 - Ensembl - - - - REACT_19747 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19747.2 - - - - NP_036309 - RefSeq - - - - REACT_25402 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25402.3 - - - - EQUAL - 73 - http://www.reactome.org/biopax/46/48887#SequenceSite9910 - - - - P08047 - UniProt - - - - F8VWM3 - UniProt - - - - REACT_24882 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24882.2 - - - - NP_008861 - RefSeq - - - - UBA52 - HGNC Symbol - - - - - - MOD_RES 1472 1472 Phosphoserine. - - - - - - MOD_RES 239 239 N6-acetyllysine. - - - - 159847 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159847 - - - - Q9UK39 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature824 - - \ No newline at end of file diff --git a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/dna_replication.owl b/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/dna_replication.owl deleted file mode 100755 index 4814e2f32..000000000 --- a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/dna_replication.owl +++ /dev/null @@ -1,37107 +0,0 @@ - - - - - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - 68804 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68804 - - - - EQUAL - 345 - - - - 176846 - omim - - - - GO:0017108 - GENE ONTOLOGY - - - - - EQUAL - 77 - - - - PGAVKCOVUIYSFO-XVFCMESISA-N - InChIKey - - - - - - hPI31 - Proteasome inhibitor PI31 subunit - - - - - Reactome DB_ID: 68818 - http://www.reactome.org/biopax/46/48887#Protein1074 - PSMF1 - - - - NM_001190881 - RefSeq - - - - ENST00000580864 - Ensembl - - - - Q1XBG4 - UniProt - - - - REACT_2583 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2583.2 - - - - NM_178578 - RefSeq - - - - 68549 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68549 - - - - 68961 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68961 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1820 - - - - 68427 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68427 - - - - 113503 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113503 - - - - NP_009042 - RefSeq - - - - NP_057179 - RefSeq - - - - ENSP00000377952 - Ensembl - - - - ENST00000399179 - Ensembl - - - - EQUAL - 310 - http://www.reactome.org/biopax/46/48887#SequenceSite1861 - - - - - - MOD_RES 153 153 Phosphotyrosine; by ABL1 and ABL2. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6434 - - - - ENST00000254719 - Ensembl - - - - ENSP00000408295 - Ensembl - - - - MOD_RES N-acetylmethionine (By similarity) - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2471 - - - - ENST00000370858 - Ensembl - - - - - - PRIM1 - DNA primase small subunit - DNA primase 49 kDa subunit - - - - - http://www.reactome.org/biopax/46/48887#Protein5709 - Reactome DB_ID: 68497 - p49 - - - - HGNC:9370 - HGNC - - - - REACT_3844 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3844.2 - - - - CHEBI:9850 - ChEBI - - - - REACT_26030 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26030.2 - - - - - - MOD_RES 77 77 N6-acetyllysine. - - - - - - MOD_RES 252 252 Phosphothreonine; by CDK1. - - - - Q13533 - UniProt - - - - - - Proteasome gamma chain - PSMB1 - Macropain subunit C5 - 3.4.25.1 - Multicatalytic endopeptidase complex subunit C5 - Proteasome component C5 - PSC5 - - - - - - - - - - - - - - - PSB1_HUMAN - Proteasome subunit beta type-1 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with SERPINB2. Interacts with HIV-1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - - - - - - - Orc1 removal from chromatin - http://www.reactome.org/biopax/46/48887#Pathway506 - - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite4655 - - - - 68463 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68463 - - - - EQUAL - 49 - - - - NP_872590 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval865 - - - - - - 8143371 - pubchem-substance - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4916 - - - - - - 10677495 - Xu, RM - Chong, JP - Hayashi, MK - Stillman, B - Simon, MN - Pubmed - A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase. - Proc Natl Acad Sci U S A 97:1530-5 - 2000 - - - - 4174 - NCBI Gene - - - - - - - - - - - - Orc2 associated with MCM8 - Reactome DB_ID: 176970 - http://www.reactome.org/biopax/46/48887#Complex2550 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6683 - - - - 3.6.4.12 - MCM8 - C20orf154 - Minichromosome maintenance 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - MCM8_HUMAN - DNA helicase MCM8 - FUNCTION: Component of the MCM8-MCM9 complex, a complex involved in homologous recombination repair following DNA interstrand cross-links and plays a key role during gametogenesis. The MCM8- MCM9 complex probably acts as a hexameric helicase downstream of the Fanconi anemia proteins BRCA2 and RAD51 and is required to process aberrant forks into homologous recombination substrates and to orchestrate homologous recombination with resection, fork stabilization and fork restart. May also play a non-essential for DNA replication: may be involved in the activation of the prereplicative complex (pre-RC) during G(1) phase by recruiting CDC6 to the origin recognition complex (ORC). Binds chromatin throughout the cell cycle.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM8-MCM9 complex, which forms a hexamer composed of MCM8 and MCM9. Interacts with CDC6 and ORC2.SUBCELLULAR LOCATION: Nucleus. Note=Localizes to nuclear foci and colocalizes with RAD51.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Name=1; IsoId=Q9UJA3-1; Sequence=Displayed; Name=2; IsoId=Q9UJA3-2; Sequence=VSP_015785; Note=No experimental confirmation available; Name=3; IsoId=Q9UJA3-3; Sequence=VSP_041308; Note=No experimental confirmation available. According to Ref.2, this isoform could be derived from an aberrant mRNA form found in placental choriocarcinoma; Name=4; IsoId=Q9UJA3-4; Sequence=VSP_044179; Note=No experimental confirmation available;TISSUE SPECIFICITY: Highest levels in placenta, lung and pancreas. Low levels in skeletal muscle and kidney. Expressed in various tumors with highest levels in colon and lung cancers.INDUCTION: By E2F1.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain.CAUTION: Was initially thought to play a role in DNA replication (PubMed:15684404). However, it was later shown that it is mainly involved in homologous recombination repair (PubMed:22771115).SEQUENCE CAUTION: Sequence=BAB55260.1; Type=Erroneous initiation; Note=Translation N-terminally extended; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000460590 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval860 - - - - - - 939213 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939213 - - - - EQUAL - 598 - http://www.reactome.org/biopax/46/48887#SequenceSite10873 - - - - 69226 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69226 - - - - - - - - - MCM8 mediated fork unwinding - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2005 - Authored: Tye, BK, 2005-11-29 10:17:56 - Edited: Gopinathrao, G, 2005-11-29 21:05:54 - The MCM2-7 related protein, MCM8, is required to replicate chromosomal DNA in Xenopus egg extracts. MCM8 binds chromatin upon initiation of DNA synthesis. It may function as an helicase in the elongation step. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature826 - - - - 5695 - NCBI Gene - - - - 169510 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=169510 - - - - EQUAL - 422 - http://www.reactome.org/biopax/46/48887#SequenceSite1847 - - - - 607213 - omim - - - - REACT_3542 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3542.2 - - - - EQUAL - 203 - - - - EQUAL - 198 - - - - - - MSS1 - Protein MSS1 - PSMC2 - 26S proteasome AAA-ATPase subunit RPT1 - Proteasome 26S subunit ATPase 2 - - - - - - - - - - - - - - - - - - - PRS7_HUMAN - 26S protease regulatory subunit 7 - FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. In case of HIV-1 infection, positive modulator of Tat-mediated transactivation.SUBUNIT: Interacts with NDC80 and SQSTM1. Interacts with PAAF1. Interacts with HIV-1 Tat. Interacts with TRIM5.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, P-body (By similarity). Note=Co-localizes with TRIM5 in the cytoplasmic bodies (By similarity).SIMILARITY: Belongs to the AAA ATPase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval882 - - - - - - CHEBI:10841 - ChEBI - - - - REACT_24504 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24504.2 - - - - REACT_4235 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4235.2 - - - - EQUAL - 37 - - - - REACT_24232 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24232.2 - - - - 68514 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68514 - - - - REACT_1385 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1385.3 - - - - Q13415 - UniProt - - - - PPP2R3B - HGNC - - - - ENSP00000349667 - Ensembl - - - - 5683 - NCBI Gene - - - - B8ZZH9 - UniProt - - - - Q9P177 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1764 - - - - A6NJG9 - UniProt - - - - REACT_2276 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2276.2 - - - - - - - - - - - - - - - - - - - - Cdc45 associates with the pre-replicative complex at the origin - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1976 - Once the Mcm2-7 complex has been assembled onto the origin of replication, the next step is the assembly of Cdc45, an essential replication protein, in late G1. The assembly of Cdc45 onto origins of replication forms a complex distinct from the pre-replicative complex, sometimes called the pre-initiation complex. The assembly of Cdc45 onto origins correlates with the time of initiation. Like the Mcm2-7 proteins, Cdc45 binds specifically to origins in the G1 phase of the cell cycle and then to non-origin DNA during S phase and is therefore thought to travel with the replication fork. Indeed, S. cerevisiae Cdc45 is required for DNA replication elongation as well as replication initiation. Cdc45 is required for the association of alpha DNA polymerase:primase with chromatin. Based on this observation and the observation that in S. cerevisiae, cCdc45 has been found in large complexes with some components of Mcm2-7 complex, it has been suggested that Cdc45 plays a scaffolding role at the replication fork, coupling Pol-alpha:primase to the replication fork through the helicase. Association of Cdc45 with origin DNA is regulated in the cell cycle and its association is dependent on the activity of cyclin-dependent kinases but not the Cdc7/Dbf4 kinase. In Xenopus egg extracts, association of Cdc45 with chromatin is dependent on Xmus101. TopBP1, the human homolog of Xmus1, is essential for DNA replication and interacts with DNA polymerase epsilon, one of the polymerases involved in replicating the genome. TopBP1 homologs have been found in S. cerevisiae and S. pombe. Sld3, an additional protein required for Cdc45 association with chromatin in S. cerevisiae and S. pombe, has no known human homolog. - - - - - 11948189 - Chafin DR - Veeraraghavan J - Henricksen LA - Bambara RA - PubMed - DNA ligase I competes with FEN1 to expand repetitive DNA sequences in vitro. - J Biol Chem 277(25);22361-9 - 2002 - - - - P47210 - UniProt - - - - 603481 - omim - - - - - - MOD_RES 283 283 Phosphoserine. - - - - ORC5 - ORC5L - - - - - - - - - - - - - - - - - - - ORC5_HUMAN - Origin recognition complex subunit 5 - FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.SUBUNIT: ORC is composed of six subunits. In human, ORC is cell cycle-dependent regulated: it is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O43913-1; Sequence=Displayed; Name=2; Synonyms=ORC5T; IsoId=O43913-2; Sequence=VSP_042037; Note=Does not interact with ORC2;TISSUE SPECIFICITY: Abundant in spleen, ovary, prostate, testis, and colon mucosa.SIMILARITY: Belongs to the ORC5 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P52916 - UniProt - - - - NM_001111046 - RefSeq - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis618 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6631 - - - - EQUAL - 19 - - - - ENSG00000239836 - Ensembl - - - - REACT_4343 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4343.2 - - - - PSMA1 - HGNC - - - - 601681 - omim - - - - EQUAL - 27 - - - - PPP2CA - HGNC Symbol - - - - B4DX18 - UniProt - - - - REACT_9131 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9131.2 - - - - Q16523 - UniProt - - - - EQUAL - 196 - http://www.reactome.org/biopax/46/48887#SequenceSite10902 - - - - 68796 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68796 - - - - InChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 - InChI - - - - 602854 - omim - - - - NP_001029102 - RefSeq - - - - ENSP00000471622 - Ensembl - - - - - - - - - - - - DNA polymerase alpha:primase:DNA polymerase alpha:origin complex - Reactome DB_ID: 68510 - http://www.reactome.org/biopax/46/48887#Complex2608 - - - - 939165 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939165 - - - - NP_006730 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1880 - - - - - - ORC6L - ORC6 - - - - - - - - - - - - - ORC6_HUMAN - Origin recognition complex subunit 6 - FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.SUBUNIT: ORC is composed of six subunits. In human, ORC is cell cycle-dependent regulated: it is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase. Interacts with DBF4 (By similarity).SUBCELLULAR LOCATION: Nucleus.DISEASE: Meier-Gorlin syndrome 3 (MGORS3) [MIM:613803]: A syndrome characterized by bilateral microtia, aplasia/hypoplasia of the patellae, and severe intrauterine and postnatal growth retardation with short stature and poor weight gain. Additional clinical findings include anomalies of cranial sutures, microcephaly, apparently low-set and simple ears, microstomia, full lips, highly arched or cleft palate, micrognathia, genitourinary tract anomalies, and various skeletal anomalies. While almost all cases have primordial dwarfism with substantial prenatal and postnatal growth retardation, not all cases have microcephaly, and microtia and absent/hypoplastic patella are absent in some. Despite the presence of microcephaly, intellect is usually normal. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the ORC6 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 364 - - - - HGNC:16889 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10596 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1856 - - - - - - MOD_RES 174 174 Phosphothreonine. - - - - EQUAL - 2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6433 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6616 - - - - 939844 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939844 - - - - HGNC:9560 - HGNC - - - - 51053 - NCBI Gene - - - - A8MY67 - UniProt - - - - - - MOD_RES 1104 1104 Phosphoserine. - - - - P20248 - UniProt - - - - - - MOD_RES 125 125 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval869 - - - - - - NM_001025097 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6664 - - - - 5425 - NCBI Gene - - - - 5000 - NCBI Gene - - - - NP_002779 - RefSeq - - - - NP_002809 - RefSeq - - - - 69190 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69190 - - - - REACT_4616 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4616.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval880 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4948 - - - - 113566 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113566 - - - - ENSG00000142507 - Ensembl - - - - TFDP1 - HGNC Symbol - - - - REACT_4371 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4371.1 - - - - PTHR32218:SF0 - PANTHER Family - - - - - MOD_RES Leucine methyl ester - - - - ORC4L - ORC4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ORC4_HUMAN - Origin recognition complex subunit 4 - FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.SUBUNIT: ORC is composed of six subunits. In human, ORC is cell cycle-dependent regulated: it is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase. Interacts with DBF4 (By similarity).SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=O43929-1; Sequence=Displayed; Name=2; IsoId=O43929-2; Sequence=VSP_045199; Note=No experimental confirmation available; Name=3; IsoId=O43929-3; Sequence=VSP_046437; Note=No experimental confirmation available;DISEASE: Meier-Gorlin syndrome 2 (MGORS2) [MIM:613800]: A syndrome characterized by bilateral microtia, aplasia/hypoplasia of the patellae, and severe intrauterine and postnatal growth retardation with short stature and poor weight gain. Additional clinical findings include anomalies of cranial sutures, microcephaly, apparently low-set and simple ears, microstomia, full lips, highly arched or cleft palate, micrognathia, genitourinary tract anomalies, and various skeletal anomalies. While almost all cases have primordial dwarfism with substantial prenatal and postnatal growth retardation, not all cases have microcephaly, and microtia and absent/hypoplastic patella are absent in some. Despite the presence of microcephaly, intellect is usually normal. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the ORC4 family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/orc4l/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q8IY91 - UniProt - - - - HGNC:20635 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4996 - - - - - - ENSP00000362815 - Ensembl - - - - ENSG00000133101 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval840 - - - - - - ENSP00000384978 - Ensembl - - - - 11395502 - Dutta, A - Delmolino, L - Dhar, SK - Pubmed - Architecture of the human origin recognition complex. - J Biol Chem 276:29067-71 - 2001 - - - - ENSP00000348902 - Ensembl - - - - EQUAL - 1106 - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite4657 - - - - PPP2R3B - PP2A subunit B isoform PR48 - PPP2R3L - Protein phosphatase 2A 48 kDa regulatory subunit - - - - - - - - - - - - - - - P2R3B_HUMAN - Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - FUNCTION: The B regulatory subunit might modulate substrate selectivity and catalytic activity, and also might direct the localization of the catalytic enzyme to a particular subcellular compartment.SUBUNIT: PP2A consists of a common heterodimeric core enzyme, composed of a 36 kDa catalytic subunit (subunit C) and a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Interacts with N-terminal region of CDC6.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9Y5P8-1; Sequence=Displayed; Name=2; IsoId=Q9Y5P8-2; Sequence=VSP_037310;MISCELLANEOUS: The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.SIMILARITY: Contains 1 EF-hand domain.SEQUENCE CAUTION: Sequence=AAD38515.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSG00000170315 - Ensembl - - - - ENST00000229854 - Ensembl - - - - B5BU76 - UniProt - - - - - - ubiquitin (UBC 7) - - - - - http://www.reactome.org/biopax/46/48887#Protein2483 - Reactome DB_ID: 939862 - UBC(457-532) - - - - - C9H13N2O9P - pU - 5'-UMP - 5'-uridylic acid - uridine 5'-(dihydrogen phosphate) - uridine 5'-phosphate - uridine 5'-phosphoric acid - - - - - - - - - - - - - 324.18137 - UMP - UMP - A pyrimidine ribonucleoside 5'-monophosphate having uracil as the nucleobase. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5799 - - - - Q9UI96 - UniProt - - - - - - - - - - - - Rb1:RNA primer-DNA primer:origin duplex with DNA damage - Reactome DB_ID: 113646 - http://www.reactome.org/biopax/46/48887#Complex2612 - - - - EQUAL - 807 - - - - EQUAL - 73 - - - - REACT_4259 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4259.1 - - - - 68728 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68728 - - - - NP_001184260 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6717 - - - - - - MOD_RES 27 27 N6-acetyllysine. - - - - Q86T01 - UniProt - - - - - CDC7 - huCdc7 - HsCdc7 - CDC7L1 - 2.7.11.1 - CDC7-related kinase - - - - - - - - - - - - - - - - - - - - CDC7_HUMAN - Cell division cycle 7-related protein kinase - FUNCTION: Seems to phosphorylate critical substrates that regulate the G1/S phase transition and/or DNA replication. Can phosphorylates MCM2 and MCM3.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.COFACTOR: Magnesium.SUBUNIT: Forms a complex with either DBF4/DBF4A or DBF4B, leading to the activation of the kinase activity.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=1; Comment=A number of isoforms may be produced; Name=1; IsoId=O00311-1; Sequence=Displayed;SIMILARITY: Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. CDC7 subfamily.SIMILARITY: Contains 1 protein kinase domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc7/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000372723 - Ensembl - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4646 - - - - Q14578 - UniProt - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite1770 - - - - EQUAL - 125 - - - - HGNC:9570 - HGNC - - - - EQUAL - 117 - - - - 5718 - NCBI Gene - - - - GO:0003887 - GENE ONTOLOGY - - - - - EQUAL - 209 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2619 - - - - - - - - GINS4 - GINS complex subunit 4 - DNA replication complex GINS protein SLD5, N-terminally processed - SLD5 - - - - - - - - - - - - - - - - - - - - SLD5_HUMAN - DNA replication complex GINS protein SLD5 - FUNCTION: The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks. GINS4 is important for GINS complex assembly. GINS complex seems to bind preferentially to single-stranded DNA.SUBUNIT: Component of the GINS complex which is a heterotetramer of GINS1, GINS2, GINS3 and GINS4. Forms a stable subcomplex with GINS1. GINS complex interacts with DNA primase in vitro.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9BRT9-1; Sequence=Displayed; Name=2; IsoId=Q9BRT9-2; Sequence=VSP_032738, VSP_032739;INDUCTION: Significantly up-regulated in agressive melanomas.MASS SPECTROMETRY: Mass=98373; Mass_error=13; Method=Electrospray; Range=1-223; Note=This is the measured mass for the GINS complex; Source=PubMed:17557111;SIMILARITY: Belongs to the GINS4/SLD5 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000450033 - Ensembl - - - - EQUAL - 89 - - - - REACT_3540 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3540.1 - - - - O75620 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2467 - - - - - EQUAL - 821 - - - - EQUAL - 2 - - - - HGNC:1722 - HGNC - - - - B7ZKZ8 - UniProt - - - - NM_153001 - RefSeq - - - - NP_001171481 - RefSeq - - - - EQUAL - 190 - - - - REACT_210 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_210.3 - - - - Q6ICQ3 - UniProt - - - - 6117 - NCBI Gene - - - - HGNC:9884 - HGNC - - - - 113646 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113646 - - - - ENSP00000376586 - Ensembl - - - - REACT_1626 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1626.3 - - - - Q9NQI7 - UniProt - - - - HGNC:8488 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10885 - - - - ENSP00000359895 - Ensembl - - - - NP_001171034 - RefSeq - - - - B4DDB4 - UniProt - - - - 600405 - omim - - - - ENSG00000091651 - Ensembl - - - - 939203 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939203 - - - - ENSG00000242711 - Ensembl - - - - ENSG00000100479 - Ensembl - - - - NP_055629 - RefSeq - - - - EQUAL - 356 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2466 - - - - ENST00000431206 - Ensembl - - - - REACT_1572 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1572.3 - - - - 68603 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68603 - - - - ENST00000392481 - Ensembl - - - - EQUAL - 826 - - - - NP_002800 - RefSeq - - - - 602176 - omim - - - - EQUAL - 174 - - - - REACT_3631 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3631.2 - - - - ENSG00000206298 - Ensembl - - - - A8K7B6 - UniProt - - - - 7311 - NCBI Gene - - - - REACT_24765 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24765.2 - - - - HGNC:9300 - HGNC - - - - EQUAL - 164 - http://www.reactome.org/biopax/46/48887#SequenceSite10754 - - - - HGNC:28980 - HGNC - - - - ENSP00000386105 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4931 - - - - EQUAL - 418 - http://www.reactome.org/biopax/46/48887#SequenceSite1871 - - - - - - Guanosine monophosphate - Guanosine 5'-phosphate - Guanylic acid - Guanosine 5'-monophosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule595 - Reactome DB_ID: 29626 - GMP - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4827 - - - - - - MOD_RES 6 6 N6-acetyllysine; alternate (By similarity). - - - - ORC4 - HGNC - - - - ENSP00000371321 - Ensembl - - - - ENSP00000372595 - Ensembl - - - - EQUAL - 321 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2460 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1370 - - - - EQUAL - 304 - http://www.reactome.org/biopax/46/48887#SequenceSite4660 - - - - 1HD0 - PROTEIN DATA BANK - - - - ENSG00000100519 - Ensembl - - - - - - MOD_RES 375 375 Phosphoserine. - - - - REACT_4386 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4386.1 - - - - - - - - - - - - - - - - DNA Polymerase delta tetramer - Reactome DB_ID: 68450 - http://www.reactome.org/biopax/46/48887#Complex2637 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1842 - - - - - - - - - - - - Orc5 associates with Orc3:Orc2:origin complexes - At the beginning of this reaction, 1 molecule of 'Orc3:Orc2:origin', and 1 molecule of 'Orc5' are present. At the end of this reaction, 1 molecule of 'Orc5:Orc3:Orc2:origin' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2142 - - - - - 187857 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187857 - - - - Q6FHX7 - UniProt - - - - - - Adenosine 5'-diphosphate - - - - Reactome DB_ID: 113582 - http://www.reactome.org/biopax/46/48887#SmallMolecule89 - ADP - - - - EQUAL - 104 - - - - REACT_2818 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2818.1 - - - - 113562 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113562 - - - - - - MOD_RES 195 195 Phosphothreonine. - - - - Q6IBI4 - UniProt - - - - ENST00000421445 - Ensembl - - - - EQUAL - 20 - - - - ENST00000434471 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4971 - - - - - - - - ubiquitin (RPS27A) - - - - - Reactome DB_ID: 939849 - http://www.reactome.org/biopax/46/48887#Protein2472 - RPS27A(1-76) - - - - - - - - - RFC dissociates after sliding clamp formation - Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2010 - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6792 - - - - EQUAL - 130 - - - - NM_181578 - RefSeq - - - - Q06323 - UniProt - - - - - - - CDC6 - HsCdc18 - p62(cdc6) - CDC18L - CDC6-related protein - Cdc18-related protein - HsCDC6 - - - - - - - - - - - - - - CDC6_HUMAN - Cell division control protein 6 homolog - FUNCTION: Involved in the initiation of DNA replication. Also participates in checkpoint controls that ensure DNA replication is completed before mitosis is initiated.SUBUNIT: Interacts with PCNA, ORC1L, cyclin-CDK and HUWE1.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=The protein is nuclear in G1 and cytoplasmic in S-phase cells.DISEASE: Meier-Gorlin syndrome 5 (MGORS5) [MIM:613805]: A syndrome characterized by bilateral microtia, aplasia/hypoplasia of the patellae, and severe intrauterine and postnatal growth retardation with short stature and poor weight gain. Additional clinical findings include anomalies of cranial sutures, microcephaly, apparently low-set and simple ears, microstomia, full lips, highly arched or cleft palate, micrognathia, genitourinary tract anomalies, and various skeletal anomalies. While almost all cases have primordial dwarfism with substantial prenatal and postnatal growth retardation, not all cases have microcephaly, and microtia and absent/hypoplastic patella are absent in some. Despite the presence of microcephaly, intellect is usually normal. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the CDC6/cdc18 family.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CDC6ID40014ch17q21.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc6/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1157 - - - - Q53FJ8 - UniProt - - - - - - MOD_RES 380 380 N6-acetyllysine. - - - - EQUAL - 380 - - - - REACT_5687 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5687.2 - - - - - - - - 2.7.7.7 - DNA polymerase alpha catalytic subunit p180 - POLA1 - POLA - - - - - - - - - - - - - - - - - DPOLA_HUMAN - DNA polymerase alpha catalytic subunit - FUNCTION: Plays an essential role in the initiation of DNA replication. During the S phase of the cell cycle, the DNA polymerase alpha complex (composed of a catalytic subunit POLA1/p180, a regulatory subunit POLA2/p70 and two primase subunits PRIM1/p49 and PRIM2/p58) is recruited to DNA at the replicative forks via direct interactions with MCM10 and WDHD1. The primase subunit of the polymerase alpha complex initiates DNA synthesis by oligomerising short RNA primers on both leading and lagging strands. These primers are initially extended by the polymerase alpha catalytic subunit and subsequently transferred to polymerase delta and polymerase epsilon for processive synthesis on the lagging and leading strand, respectively. The reason this transfer occurs is because the polymerase alpha has limited processivity and lacks intrinsic 3' exonuclease activity for proofreading error, and therefore is not well suited for replicating long complexes.CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).COFACTOR: Binds 1 4Fe-4S cluster (By similarity).SUBUNIT: The DNA polymerase alpha complex is composed of four subunits: the catalytic subunit POLA1, the regulatory subunit POLA2, and the small and the large primase subunits PRIM1 and PRIM2 respectively. Interacts with PARP1; this interaction functions as part of the control of replication fork progression. Interacts with MCM10 and WDHD1; these interactions recruit the polymerase alpha complex to the pre-replicative complex bound to DNA. Interacts with RPA1; this interaction stabilizes the replicative complex and reduces the misincorporation rate of DNA polymerase alpha by acting as a fidelity clamp. Interacts with SV40 Large T antigen; this interaction allows viral DNA replication. Interacts with herpes simplex virus 1 (HHV-1) replication origin-binding protein UL9.SUBCELLULAR LOCATION: Nucleus.DOMAIN: The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (By similarity).PTM: A 165 kDa form is probably produced by proteolytic cleavage at Lys-124.MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.SIMILARITY: Belongs to the DNA polymerase type-B family.SIMILARITY: Contains 1 CysA-type zinc finger.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pola/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000216455 - Ensembl - - - - - - - - - - - - - - - - - - - - - - - - - - pre-replicative complex (Orc1-minus) - Reactome DB_ID: 157563 - http://www.reactome.org/biopax/46/48887#Complex2625 - - - - ENSP00000472264 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6785 - - - - NM_014321 - RefSeq - - - - ENSP00000275627 - Ensembl - - - - REACT_1792 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1792.3 - - - - 5516 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4995 - - - - - - Q9NUE7 - UniProt - - - - REACT_3354 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3354.2 - - - - DPE2 - POLE2 - 2.7.7.7 - DNA polymerase II subunit 2 - DNA polymerase epsilon subunit B - - - - - - - - - - - - - - - - - - - - - - - - - - - - - DPOE2_HUMAN - DNA polymerase epsilon subunit 2 - FUNCTION: Participates in DNA repair and in chromosomal DNA replication.CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).SUBUNIT: Component of the epsilon DNA polymerase complex consisting of four subunits: POLE, POLE2, POLE3 and POLE4.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P56282-1; Sequence=Displayed; Name=2; IsoId=P56282-2; Sequence=VSP_042551; Note=No experimental confirmation available; Name=3; IsoId=P56282-3; Sequence=VSP_043796;MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.SIMILARITY: Belongs to the DNA polymerase epsilon subunit B family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pole2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature864 - - - - - - MOD_RES 147 147 Phosphoserine. - - - - EQUAL - 239 - http://www.reactome.org/biopax/46/48887#SequenceSite1875 - - - - ENST00000259457 - Ensembl - - - - ENSG00000204086 - Ensembl - - - - Q9BZ44 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1067 - - - - 165997 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=165997 - - - - ENSG00000085840 - Ensembl - - - - REACT_2874 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2874.2 - - - - NP_001020267 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6436 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2472 - - - - - - O15252 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval826 - - - - - - Q6IUY7 - UniProt - - - - ENST00000438442 - Ensembl - - - - 68435 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68435 - - - - - - MOD_RES 153 153 Phosphoserine (By similarity). - - - - Q9H4I1 - UniProt - - - - ENSG00000198056 - Ensembl - - - - REACT_4881 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4881.1 - - - - 113638 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113638 - - - - 602693 - omim - - - - ENSG00000243958 - Ensembl - - - - ENSP00000400666 - Ensembl - - - - PSMB4 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10911 - - - - B2R975 - UniProt - - - - NP_002795 - RefSeq - - - - 176955 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176955 - - - - B2R897 - UniProt - - - - - - MOD_RES 1106 1106 Phosphoserine. - - - - HGNC:24576 - HGNC - - - - 68962 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68962 - - - - nucleoplasm - - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10646 - - - - 10806216 - Xu, Y - Grindley, ND - Joyce, CM - Pubmed - Coordination between the polymerase and 5'-nuclease components of DNA polymerase I of Escherichia coli. - J Biol Chem 275:20949-55 - 2000 - - - - NP_003324 - RefSeq - - - - ENSP00000305480 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10717 - - - - - - MOD_RES 159 159 Phosphotyrosine (By similarity). - - - - B4DDU3 - UniProt - - - - - - - - - - - - CDK and DDK associate with the Mcm10:pre-replicative complex - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1974 - At the beginning of this reaction, 1 molecule of 'Mcm10:active pre-replicative complex', 1 molecule of 'DDK', and 1 molecule of 'CDK' are present. At the end of this reaction, 1 molecule of 'CDK:DDK:Mcm10:pre-replicative complex' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6432 - - - - ENST00000265728 - Ensembl - - - - Q3LIA5 - UniProt - - - - 9335335 - Bell, SP - Aparicio, OM - Weinstein, DM - Pubmed - Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. - Cell 91:59-69 - 1997 - - - - ENST00000368884 - Ensembl - - - - 187952 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187952 - - - - B2R7J9 - UniProt - - - - NM_007111 - RefSeq - - - - ENSP00000293362 - Ensembl - - - - D3DUM5 - UniProt - - - - - - ubiquitin (UBC 5) - - - - - Reactome DB_ID: 939232 - http://www.reactome.org/biopax/46/48887#Protein1053 - UBC(305-380) - - - - ENSP00000259457 - Ensembl - - - - CHEBI:13235 - ChEBI - - - - Q96DH3 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4955 - - - - ENSP00000253462 - Ensembl - - - - ENSG00000100804 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature830 - - - - - - - - - - - - Lagging Strand Synthesis - Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase. - http://www.reactome.org/biopax/46/48887#Pathway512 - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1084 - - - - NP_002801 - RefSeq - - - - - - - - Replication Fork - Reactome DB_ID: 169515 - http://www.reactome.org/biopax/46/48887#PhysicalEntity253 - - - - HGNC:1579 - HGNC - - - - PTHR10177:SF64 - PANTHER Family - - - - - - - DNA replication licensing factor MCM6 - P105MCM - Mcm6 - - - - - http://www.reactome.org/biopax/46/48887#Protein5588 - Reactome DB_ID: 68553 - MCM6 - - - - REACT_351 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_351.3 - - - - REACT_7812 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7812.1 - - - - - - MOD_RES 381 381 Phosphoserine. - - - - ENST00000266970 - Ensembl - - - - - - MOD_RES 214 214 N6-acetyllysine. - - - - ENSP00000436186 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6429 - - - - 68816 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68816 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2455 - - - - - - - - - ENSP00000396813 - Ensembl - - - - EQUAL - 873 - - - - REACT_2773 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2773.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature837 - - - - EQUAL - 192 - - - - 10970868 - Bell, SP - Klemm, RD - Lee, DG - Makhov, AM - Pubmed - Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding. - EMBO J 19:4774-82 - 2000 - - - - 10430907 - Bell, SP - Aparicio, OM - Stout, AM - Pubmed - Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication. - Proc Natl Acad Sci U S A 96:9130-5 - 1999 - - - - PSMA7 - HGNC Symbol - - - - 68466 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68466 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1812 - - - - HGNC:9563 - HGNC - - - - 1869 - NCBI Gene - - - - - - hPI31 - PSMF1 - - - - - - - - - - - - - - - - - - - - PSMF1_HUMAN - Proteasome inhibitor PI31 subunit - FUNCTION: Plays an important role in control of proteasome function. Inhibits the hydrolysis of protein and peptide substrates by the 20S proteasome. Also inhibits the activation of the proteasome by the proteasome regulatory proteins PA700 and PA28.SUBUNIT: Monomer (Probable).SIMILARITY: Belongs to the proteasome inhibitor PI31 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 939857 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939857 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2100 - - - - EQUAL - 249 - - - - - - MOD_RES 14 14 Phosphoserine. - - - - PCNA - HGNC Symbol - - - - 1682322 - Burgers, PM - Pubmed - Saccharomyces cerevisiae replication factor C. II. Formation and activity of complexes with the proliferating cell nuclear antigen and with DNA polymerases delta and epsilon. - J Biol Chem 266:22698-706 - 1991 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4834 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1864 - - - - CHEBI:40826 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4863 - - - - - - - - 26S proteasome regulatory subunit p55 - 26S proteasome non-ATPase regulatory subunit 12 - - - - - Reactome DB_ID: 68792 - http://www.reactome.org/biopax/46/48887#Protein1075 - PSMD12 - - - - 10766248 - Lygerou, Z - Nurse, P - Nishimoto, T - Nishitani, H - Pubmed - The Cdt1 protein is required to license DNA for replication in fission yeast. - Nature 404:625-8 - 2000 - - - - 10766247 - Méchali, M - Moreau, J - Maiorano, D - Pubmed - XCDT1 is required for the assembly of pre-replicative complexes in Xenopus laevis. - Nature 404:622-5 - 2000 - - - - D3DW02 - UniProt - - - - NM_002692 - RefSeq - - - - EQUAL - 337 - - - - RFC5 - Activator 1 36 kDa subunit - A1 36 kDa subunit - Activator 1 subunit 5 - RF-C 36 kDa subunit - RFC36 - Replication factor C 36 kDa subunit - - - - - - - - - - - - - - - - - - - - - RFC5_HUMAN - Replication factor C subunit 5 - FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.SUBUNIT: Heterotetramer of subunits RFC2, RFC3, RFC4 and RFC5 that can form a complex either with RFC1 or with RAD17. The former interacts with PCNA in the presence of ATP, while the latter has ATPase activity but is not stimulated by PCNA.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P40937-1; Sequence=Displayed; Name=2; IsoId=P40937-2; Sequence=VSP_043067; Note=No experimental confirmation available;SIMILARITY: Belongs to the activator 1 small subunits family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rfc5/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - RF-C 38 kDa subunit - RFC3 - Replication factor C 38 kDa subunit - A1 38 kDa subunit - RFC38 - Activator 1 subunit 3 - Activator 1 38 kDa subunit - - - - - - - - - - - - - - - - - - - RFC3_HUMAN - Replication factor C subunit 3 - FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.SUBUNIT: Heterotetramer of subunits RFC2, RFC3, RFC4 and RFC5 that can form a complex either with RFC1 or with RAD17. The former interacts with PCNA in the presence of ATP, while the latter has ATPase activity but is not stimulated by PCNA.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P40938-1; Sequence=Displayed; Name=2; IsoId=P40938-2; Sequence=VSP_044920; Note=No experimental confirmation available;SIMILARITY: Belongs to the activator 1 small subunits family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rfc3/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - RPA3 - HGNC - - - - EQUAL - 121 - http://www.reactome.org/biopax/46/48887#SequenceSite2928 - - - - CHEBI:27233 - ChEBI - - - - 68759 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68759 - - - - CHEBI:47362 - ChEBI - - - - 9927482 - Koonin, EV - Spouge, JL - Aravind, L - Neuwald, AF - Pubmed - AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. - Genome Res 9:27-43 - 1999 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2654 - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1796 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval851 - - - - - - EQUAL - 195 - - - - - - MOD_RES 821 821 Phosphothreonine; by CDK6. - - - - ENSP00000290541 - Ensembl - - - - 8145531 - pubchem-substance - - - - CHEBI:46382 - ChEBI - - - - NM_001251990 - RefSeq - - - - - - MOD_RES 368 368 Phosphoserine. - - - - - - - - - - - - - - - - - - - - - CDC6 association with the ORC:origin complex - Authored: Davey, MJ, O'Donnell, M, Tye, BK, 2006-03-17 16:01:39 - http://www.reactome.org/biopax/46/48887#Pathway558 - Cdc6 is a regulator of DNA replication initiation in both yeasts and human cells, but its mechanism of action differs between the two systems. Genetic studies in budding yeast (S. cerevisiae) and fission yeast (S. pombe) indicate that the normal function of Cdc6 protein is required to restrict DNA replication to once per cell cycle. Specifically, Cdc6 may function as an ATPase switch linked to Mcm2-7 association with the Cdt1:Cdc6:ORC:origin complex. In S. cerevisiae, Cdc6 protein is expressed late in the M phase of the cell cycle and, in cells with a prolonged G1 phase, late in G1. This protein has a short half-life, and is destroyed by ubiquitin-mediated proteolysis, mediated by the SCF complex. Human Cdc6 protein levels are reduced early in G1 but otherwise are constant throughout the cell cycle. Some reports have suggested that after cells enter S phase, Cdc6 is phosphorylated, excluded from the nucleus and subject to ubiquitination and degradation. Replenishing Cdc6 protein levels during G1 appears to be regulated by E2F transcription factors. - - - - - HGNC:3113 - HGNC - - - - Q8IZL4 - UniProt - - - - ENSP00000393744 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1049 - - - - 8144860 - pubchem-substance - - - - 68616 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68616 - - - - 1027 - NCBI Gene - - - - 2IAE - PROTEIN DATA BANK - - - - PSMA7 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature875 - - - - EQUAL - 87 - http://www.reactome.org/biopax/46/48887#SequenceSite1755 - - - - CHEBI:3285 - ChEBI - - - - O60764 - UniProt - - - - - - - - RNA primer:origin duplex with DNA damage - http://www.reactome.org/biopax/46/48887#PhysicalEntity251 - Reactome DB_ID: 113499 - - - - 10834843 - Tercero, JA - Labib, K - Diffley, JF - Pubmed - Uninterrupted MCM2-7 function required for DNA replication fork progression. - Science 288:1643-7 - 2000 - - - - 9154825 - Lei, M - Chen, Y - Merchant, AM - Kawasaki, Y - Tye, BK - Pubmed - A lesion in the DNA replication initiation factor Mcm10 induces pausing of elongation forks through chromosomal replication origins in Saccharomyces cerevisiae - Mol Cell Biol 17:3261-71 - 1997 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1643 - - - - ENST00000535373 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2210 - - - - Q03527 - UniProt - - - - - - MOD_RES 226 226 Phosphothreonine. - - - - ENST00000408907 - Ensembl - - - - 602670 - omim - - - - NM_005789 - RefSeq - - - - EQUAL - 88 - - - - REACT_533 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_533.3 - - - - NM_002809 - RefSeq - - - - - - DNA Replication factor A protein 3 (14kD) - RP-A - Replication factor-A protein 3 - RPA14 - RF-A - Replication protein A 14 kDa subunit - - - - - Reactome DB_ID: 68459 - http://www.reactome.org/biopax/46/48887#Protein1647 - RPA3 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6711 - - - - O60590 - UniProt - - - - - - MOD_RES 668 668 Phosphoserine. - - - - Q01094 - UniProt - - - - ENSP00000396479 - Ensembl - - - - REACT_1611 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1611.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval839 - - - - - - - - MOD_RES 71 71 Phosphoserine. - - - - 68798 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68798 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1056 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7553 - - - - - - MOD_RES 31 31 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2096 - - - - 11739726 - Li, CJ - DePamphilis, ML - Pubmed - Mammalian Orc1 protein is selectively released from chromatin and ubiquitinated during the S-to-M transition in the cell division cycle. - Mol Cell Biol 22:105-16 - 2001 - - - - - - - - - - - - - - - - - - RFC Heteropentamer - Reactome DB_ID: 68436 - http://www.reactome.org/biopax/46/48887#Complex2632 - - - - P35251 - UniProt - - - - O43913 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4836 - - - - 68380 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68380 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1072 - - - - - - Proteasome chain 7 - Macropain chain 7 - Multicatalytic endopeptidase complex chain 7 - RING12 protein - Proteasome subunit beta type 9 - Low molecular mass protein 2 - Proteasome subunit beta type 9 precursor - - - - - Reactome DB_ID: 68765 - http://www.reactome.org/biopax/46/48887#Protein1076 - PSMB9 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2453 - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2435 - - - - - CHEBI:16027 - ChEBI - - - - REACT_4583 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4583.2 - - - - 69098 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69098 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2118 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4930 - - - - CHEBI:40726 - ChEBI - - - - HGNC:3115 - HGNC - - - - ENST00000230056 - Ensembl - - - - Q9BWA7 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1798 - - - - ENSP00000386541 - Ensembl - - - - REACT_5636 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5636.2 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10978 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature829 - - - - REACT_2645 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2645.3 - - - - CHEBI:17677 - ChEBI - - - - EQUAL - 861 - http://www.reactome.org/biopax/46/48887#SequenceSite10890 - - - - EQUAL - 211 - - - - 890 - NCBI Gene - - - - CHEBI:41675 - ChEBI - - - - 604450 - omim - - - - HGNC:12458 - HGNC - - - - EQUAL - 109 - - - - - - - - - - - Orc6 associates with Orc1:Orc4:Orc5:Orc3:Orc2:origin complexes, forming ORC:origin complexes - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2144 - At the beginning of this reaction, 1 molecule of 'Orc1:Orc4:Orc5:Orc3:Orc2:origin', and 1 molecule of 'Orc6' are present. At the end of this reaction, 1 molecule of 'ORC complex bound to origin' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - - - - - ENSG00000100902 - Ensembl - - - - PSMD5 - HGNC - - - - 187948 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187948 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6416 - - - - - - MOD_RES 874 874 N6-acetyllysine; by PCAF. - - - - - 4.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1039 - - - - CHEBI:45024 - ChEBI - - - - 611525 - omim - - - - 15257295 - Gorospe, M - Lal, A - Martindale, JL - Yang, X - Kawai, T - Mazan-Mamczarz, K - Pubmed - Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs - EMBO J 23:3092-102 - 2004 - - - - ENSP00000379676 - Ensembl - - - - Q8IZL5 - UniProt - - - - NP_859531 - RefSeq - - - - GINS2 - HGNC Symbol - - - - NM_012381 - RefSeq - - - - ENSP00000296273 - Ensembl - - - - Same Catalyst Activity - http://www.reactome.org/biopax/46/48887#RelationshipTypeVocabulary2 - - - - Q15321 - UniProt - - - - 1670772 - Hurwitz, J - Kwong, AD - Lee, SH - Pan, ZQ - Pubmed - Studies on the activator 1 protein complex, an accessory factor for proliferating cell nuclear antigen-dependent DNA polymerase delta. - J Biol Chem 266:594-602 - 1991 - - - - - - MOD_RES 762 762 Phosphoserine. - - - - EQUAL - 2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval849 - - - - - - EQUAL - 305 - http://www.reactome.org/biopax/46/48887#SequenceSite4661 - - - - MCM2 - HGNC Symbol - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1045 - - - - - - MCM10 - HsMCM10 - - - - - - - - - - - - - - - - - - - - - - - - - - - MCM10_HUMAN - Protein MCM10 homolog - FUNCTION: Acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication. Additionally, plays a role in preventing DNA damage during replication.SUBUNIT: Self-associates (By similarity). Interacts with ORC2. May interact with MCM2 and MCM6. Interacts with the DNA polymerase alpha subunit POLA1. Interacts with RECQL4; this interaction regulates RECQL4 unwinding activity. Interacts with WDHD1.SUBCELLULAR LOCATION: Nucleus. Note=Colocalizes with ORC2 in nuclei foci. Associated with chromatin in S phase. From early to mid-S phase located in discrete nuclear foci. In early S phase, several hundred foci appeared throughout the nucleus. In mid-S phase, the foci appeared at the nuclear periphery and nucleolar regions. In the late S and G phases localized to nucleoli.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q7L590-1; Sequence=Displayed; Name=2; IsoId=Q7L590-2; Sequence=VSP_029951;DEVELOPMENTAL STAGE: Expression is cell cycle regulated. Expression increases at the G1/S-boundary. Expression decreases in late M phase, remains low during G(1) phase, and starts to accumulate at the onset of S phase.DOMAIN: Each zinc finger-like domain binds a zinc ion and is involved in both ssDNA and dsDNA binding, as is the OB-fold domain (By similarity).DOMAIN: The N-terminal domain mediates homodimerization (By similarity).SIMILARITY: Belongs to the MCM10 family.SEQUENCE CAUTION: Sequence=AAF69623.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 198 198 Phosphothreonine; by PKB/AKT1, RPS6KA1, RPS6KA3 and PIM1. - - - - ENSP00000391211 - Ensembl - - - - - - MOD_RES 725 725 Phosphothreonine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2232 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature838 - - - - 68483 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68483 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1848 - - - - NP_001129064 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10905 - - - - NP_002707 - RefSeq - - - - 68569 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68569 - - - - ENSP00000327704 - Ensembl - - - - CHEBI:42979 - ChEBI - - - - 11741962 - Linn S - Fuss J - PubMed - Human DNA polymerase epsilon colocalizes with proliferating cell nuclear antigen and DNA replication late, but not early, in S phase. - J Biol Chem 277(10);8658-66 - 2002 - - - - GINS1 - HGNC - - - - REACT_4079 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4079.2 - - - - EQUAL - 4 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6628 - - - - B7ZAI6 - UniProt - - - - REACT_91 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_91.3 - - - - Q75N01 - UniProt - - - - EQUAL - 364 - - - - - - - - - - - DBF4A - DBF4 - Activator of S phase kinase - DBF4-type zinc finger-containing protein 1 - ZDBF1 - Chiffon homolog A - ASK - - - - - - - - - - - - - - - - - - - - DBF4A_HUMAN - Protein DBF4 homolog A - FUNCTION: Regulatory subunit for CDC7 which activates its kinase activity thereby playing a central role in DNA replication and cell proliferation. Required for progression of S phase. The complex CDC7-DBF4A selectively phosphorylates MCM2 subunit at 'Ser-40' and 'Ser-53' and then is involved in regulating the initiation of DNA replication during cell cycle.SUBUNIT: Forms a complex with CDC7. Note that CDC7 forms distinct complex either with DBF4A or DBF4B. Such complexes are stable upon replication stress. Interacts with MEN1, MCM2, ORC2, ORC4 and ORC6.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9UBU7-1; Sequence=Displayed; Name=2; IsoId=Q9UBU7-2; Sequence=VSP_018203, VSP_018204;TISSUE SPECIFICITY: Highly expressed in testis and thymus. Expressed also in most cancer cells lines.INDUCTION: Induced in G1 phase at low level, increased during G1-S phase and remain high during S and G2-M phase.SIMILARITY: Contains 2 BRCT domains.SIMILARITY: Contains 1 DBF4-type zinc finger. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 23 23 Phosphoserine. - - - - 69142 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69142 - - - - 11473323 - Seo, YS - Bae, KH - Bae, SH - Kim, JA - Pubmed - RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes. - Nature 412:456-61 - 2001 - - - - 939232 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939232 - - - - EQUAL - 1060 - http://www.reactome.org/biopax/46/48887#SequenceSite10914 - - - - Q9H211 - UniProt - - - - ENSP00000311121 - Ensembl - - - - 602842 - omim - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - ENSP00000409873 - Ensembl - - - - EQUAL - 248 - - - - NM_002954 - RefSeq - - - - - - P26s4 - 26S protease regulatory subunit 4 - - - - - Reactome DB_ID: 68768 - http://www.reactome.org/biopax/46/48887#Protein1083 - PSMC1 - - - - B3KSX8 - UniProt - - - - Q9BUS6 - UniProt - - - - ENSP00000378529 - Ensembl - - - - REACT_24675 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24675.2 - - - - EQUAL - 15 - - - - E2F3 - HGNC Symbol - - - - ENST00000262193 - Ensembl - - - - 939214 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939214 - - - - NM_004064 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10628 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6682 - - - - RQFCJASXJCIDSX-UUOKFMHZSA-N - InChIKey - - - - REACT_4546 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4546.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6691 - - - - Q99460 - UniProt - - - - EQUAL - 160 - - - - Q5U0G2 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6685 - - - - NP_037479 - RefSeq - - - - CHEBI:40119 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2489 - - - - PSMB2 - HGNC Symbol - - - - - - ubiquitin (UBC 3) - - - - - Reactome DB_ID: 939258 - http://www.reactome.org/biopax/46/48887#Protein1051 - UBC(153-228) - - - - - - MOD_RES 439 439 Phosphotyrosine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2110 - - - - - - P27694 - UniProt - - - - PSMD7 - HGNC Symbol - - - - - - MOD_RES 121 121 Phosphoserine. - - - - Q96D34 - UniProt - - - - EQUAL - 23 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval858 - - - - - - NP_006181 - RefSeq - - - - ENSG00000111276 - Ensembl - - - - 174099 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174099 - - - - REACT_2026 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2026.3 - - - - ENSG00000104738 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4871 - - - - REACT_24537 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24537.2 - - - - ENST00000276533 - Ensembl - - - - 68747 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68747 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval825 - - - - - - Q8WVL2 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4854 - - - - ENST00000216455 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4906 - - - - - - EQUAL - 439 - http://www.reactome.org/biopax/46/48887#SequenceSite1809 - - - - - - MOD_RES 53 53 N6-acetyllysine. - - - - ENSP00000440618 - Ensembl - - - - 187947 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187947 - - - - - - MOD_RES 83 83 Phosphoserine. - - - - REACT_5476 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5476.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature874 - - - - NP_002790 - RefSeq - - - - - - Orc5 - Origin recognition complex subunit 5 - - - - - Reactome DB_ID: 68516 - http://www.reactome.org/biopax/46/48887#Protein5580 - ORC5 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1152 - - - - EQUAL - 377 - http://www.reactome.org/biopax/46/48887#SequenceSite1797 - - - - EQUAL - 500 - - - - EQUAL - 315 - - - - REACT_4388 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4388.1 - - - - NP_004144 - RefSeq - - - - EQUAL - 381 - - - - ENSG00000175166 - Ensembl - - - - Q6PJM7 - UniProt - - - - P24941 - UniProt - - - - - - MOD_RES 141 141 Phosphoserine. - - - - Q14101 - UniProt - - - - 600592 - omim - - - - B2RAI8 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2666 - - - - - - - MOD_RES 56 56 Phosphoserine. - - - - B4DK91 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2116 - - - - - - 9861 - NCBI Gene - - - - EQUAL - 252 - - - - CDC45 - HGNC Symbol - - - - NP_001127891 - RefSeq - - - - - - MOD_RES 6 6 N6-acetyllysine. - - - - NP_001177808 - RefSeq - - - - HGNC:9543 - HGNC - - - - HGNC:1785 - HGNC - - - - CHEBI:2359 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature152 - - - - REACT_2387 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2387.2 - - - - ENST00000427870 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2659 - - - - - - EQUAL - 546 - http://www.reactome.org/biopax/46/48887#SequenceSite10977 - - - - ENSG00000007968 - Ensembl - - - - - - Nuclear protein BM28 - DNA replication licensing factor MCM2 - Mcm2 - - - - - http://www.reactome.org/biopax/46/48887#Protein5585 - Reactome DB_ID: 68557 - MCM2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval841 - - - - - - Q8IV79 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature870 - - - - 5689 - NCBI Gene - - - - 16483939 - Pacek, M - Kubota, Y - Takisawa, H - Tutter, AV - Walter, JC - Pubmed - Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication - Mol Cell 21:581-7 - 2006 - - - - 68615 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68615 - - - - - - DNA polymerase II subunit B - DNA polymerase epsilon subunit B - - - - - Reactome DB_ID: 68482 - http://www.reactome.org/biopax/46/48887#Protein5706 - POLE2 - - - - - - Ub-HNRNPD-4 - Heterogeneous nuclear ribonucleoprotein D0 - Ubiquinated AUF1 isoform p37 - HNRPD_HUMAN - - - - - - http://www.reactome.org/biopax/46/48887#Protein1059 - Reactome DB_ID: 451232 - HNRNPD - - - - CHEBI:24451 - ChEBI - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10750 - - - - NM_005915 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2485 - - - - ENSP00000440485 - Ensembl - - - - MOD_RES Phosphothreonine (By similarity) - - - - CHEBI:22244 - ChEBI - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10594 - - - - ENSP00000448520 - Ensembl - - - - InChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 - InChI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4990 - - - - - - ENSG00000104695 - Ensembl - - - - ENST00000540442 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1371 - - - - ENSP00000382132 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2436 - - - - Q9BQD9 - UniProt - - - - - - HC2 - PROS30 - NU - Multicatalytic endopeptidase complex subunit C2 - PSC2 - 3.4.25.1 - 30 kDa prosomal protein - PSMA1 - PROS-30 - Proteasome nu chain - Proteasome component C2 - Macropain subunit C2 - - - - - - - - - - - - - - - - - - - - - - PSA1_HUMAN - Proteasome subunit alpha type-1 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. Mediates the lipopolysaccharide-induced signal transduction in the macrophage proteasome (By similarity). Might be involved in the anti-inflammatory response of macrophages during the interaction with C.albicans heat-inactivated cells (By similarity).CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with bacterial lipopolysaccharide (LPS) (By similarity). Interacts with NOTCH3.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=Short; IsoId=P25786-1; Sequence=Displayed; Name=Long; IsoId=P25786-2; Sequence=VSP_005279;INDUCTION: Induced in breast cancer tissue (at protein level). Up- regulated in liver tumor tissues.SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 123836 - omim - - - - - - - - - - PSC8 - Multicatalytic endopeptidase complex subunit C8 - PSMA3 - HC8 - Macropain subunit C8 - Proteasome component C8 - 3.4.25.1 - - - - - - - - - - - - - - - - - - - - - PSA3_HUMAN - Proteasome subunit alpha type-3 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. Binds to the C-terminus of CDKN1A and thereby mediates its degradation. Negatively regulates the membrane trafficking of the cell-surface thromboxane A2 receptor (TBXA2R) isoform 2.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with AURKB. Interacts with CDKN1A. Interacts with HIV-1 TAT protein. Interacts with hepatitis C virus (HCV) F protein. Interacts with Epstein-Barr virus EBNA3 proteins. Interacts with MDM2 and RB1. Interacts with the C-terminus of TBXA2R isoform 2.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P25788-1; Sequence=Displayed; Name=2; IsoId=P25788-2; Sequence=VSP_005280;INDUCTION: Down-regulated by antioxidants BO-653 and probucol. Up- regulated by bacterial lipopolysaccharides (LPS) and TNF.SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - PSMA2 - PSC3 - 3.4.25.1 - HC3 - Multicatalytic endopeptidase complex subunit C3 - Proteasome component C3 - Macropain subunit C3 - - - - - - - - - - - - - - - PSA2_HUMAN - Proteasome subunit alpha type-2 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. PSMA2 may have a potential regulatory effect on another component(s) of the proteasome complex through tyrosine phosphorylation.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, P-body (By similarity). Note=Co-localizes with TRIM5 in the cytoplasmic bodies (By similarity).INDUCTION: Down-regulated by antioxidants BO-653 and probucol. Down-regulated in response to enterovirus 71 (EV71) infection (at protein level).PTM: Phosphorylated on tyrosine residues; which may be important for nuclear import (By similarity).SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001177966 - RefSeq - - - - - - - - Multicatalytic endopeptidase complex subunit C9 - PSC9 - Proteasome subunit L - Macropain subunit C9 - PSMA4 - Proteasome component C9 - HC9 - 3.4.25.1 - - - - - - - - - - - - - - - - - - - - - - - - - PSA4_HUMAN - Proteasome subunit alpha type-4 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interaction with HTLV-1 TAX protein favors NFKB1 activation.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, P-body (By similarity). Note=Co-localizes with TRIM5 in the cytoplasmic bodies (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P25789-1; Sequence=Displayed; Name=2; IsoId=P25789-2; Sequence=VSP_043102; Note=No experimental confirmation available;INDUCTION: Down-regulated by antioxidants BO-653 and probucol.SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 120 - - - - HGNC:9548 - HGNC - - - - 602706 - omim - - - - MI:2163 - Molecular Interactions Ontology - - - - REACT_9007 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9007.1 - - - - EQUAL - 57 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6634 - - - - REACT_2243 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2243.4 - - - - Q9NQE2 - UniProt - - - - ENST00000217958 - Ensembl - - - - - - MOD_RES 309 309 Leucine methyl ester. - - - - 10884341 - Yabuta, N - Gotow, T - Nojima, H - Sato, M - Uchiyama, Y - You, Z - Ishimi, Y - Komamura-Kohno, Y - Pubmed - Electron microscopic observation and single-stranded DNA binding activity of the Mcm4,6,7 complex. - J Mol Biol 300:421-31 - 2000 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature845 - - - - NP_001230005 - RefSeq - - - - 30185 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=30185 - - - - NP_203698 - RefSeq - - - - NP_001093250 - RefSeq - - - - 10215605 - Kesti T - Syvaoja JE - Huang D - Pospiech H - PubMed - Structural organization and splice variants of the POLE1 gene encoding the catalytic subunit of human DNA polymerase epsilon. - Biochem J 339 ( Pt 3);657-65 - 1999 - - - - - - MOD_RES 401 401 N6-acetyllysine. - - - - - - - - - - - - - - RPA heterotrimer - Reactome DB_ID: 68462 - http://www.reactome.org/biopax/46/48887#Complex601 - - - - 69052 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69052 - - - - O35051 - UniProt - - - - NM_002810 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4653 - - - - ENST00000413382 - Ensembl - - - - EQUAL - 2 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1158 - - - - REACT_5241 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5241.1 - - - - 9554851 - Zou, L - Stillman, B - Pubmed - Formation of a preinitiation complex by S-phase cyclin CDK-dependent loading of Cdc45p onto chromatin. - Science 280:593-6 - 1998 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10636 - - - - - - - - - Cyclin A:phospho-Cdk2(Thr160) complex - - - - CCNA:p-T160-CDK2 - Reactome DB_ID: 187952 - http://www.reactome.org/biopax/46/48887#Complex2620 - - - - ENST00000256442 - Ensembl - - - - ENSP00000354906 - Ensembl - - - - - - - - - - Removal of RNA primer and dissociation of RPA and Dna2 - The Dna2 endonuclease removes the initiator RNA along with several downstream deoxyribonucleotides. The cleavage of the single-stranded RNA substrate results in the disassembly of RPA and Dna2. The current data for the role of the Dna2 endonuclease has been derived from studies with yeast and Xenopus Dna2. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2017 - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1390 - - - - ENST00000394431 - Ensembl - - - - B0V0T1 - UniProt - - - - EQUAL - 21 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2089 - - - - 600427 - omim - - - - CHEBI:14069 - ChEBI - - - - EQUAL - 874 - - - - O60856 - UniProt - - - - ENSP00000271308 - Ensembl - - - - - - - - - - Ubiquitinated AUF1 Tetramer - Reactome DB_ID: 450417 - http://www.reactome.org/biopax/46/48887#Complex410 - - - - - C10H15N5O10P2 - 5'-adenylphosphoric acid - H3adp - adenosine 5'-(trihydrogen diphosphate) - - - - - - - - - 427.2011 - ADP - ADP - A purine ribonucleoside 5'-diphosphate having adenine as the nucleobase. - - - - Q9Y2M6 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2475 - - - - - A4D0Q1 - UniProt - - - - EQUAL - 413 - - - - HGNC:8491 - HGNC - - - - ENST00000455878 - Ensembl - - - - ENSP00000372155 - Ensembl - - - - NM_001111047 - RefSeq - - - - - - MOD_RES 19 19 Symmetric dimethylarginine; by PRMT5. - - - - ENSG00000101843 - Ensembl - - - - NP_001003810 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6440 - - - - MOD_RES N-acetylmethionine - - - - 68508 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68508 - - - - HGNC:9177 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6791 - - - - ENST00000209728 - Ensembl - - - - - - MOD_RES 163 163 N6-acetyllysine. - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - Q86VH9 - UniProt - - - - REACT_3956 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3956.2 - - - - Q53GY6 - UniProt - - - - REACT_3316 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3316.3 - - - - 5702 - NCBI Gene - - - - 68730 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68730 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6645 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6698 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2623 - - - - - - NP_002682 - RefSeq - - - - UBC - HGNC Symbol - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature819 - - - - 68800 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68800 - - - - 11S regulator complex subunit alpha - PA28alpha - Activator of multicatalytic protease subunit 1 - PA28a - PSME1 - Proteasome activator 28 subunit alpha - IGUP I-5111 - Interferon gamma up-regulated I-5111 protein - REG-alpha - IFI5111 - - - - - - - - - - - - - - - - - - - - PSME1_HUMAN - Proteasome activator complex subunit 1 - FUNCTION: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome.SUBUNIT: Heterodimer of PSME1 and PSME2, which forms a hexameric ring. PSME1 can form homoheptamers.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q06323-1; Sequence=Displayed; Name=2; IsoId=Q06323-2; Sequence=VSP_046880; Note=Gene prediction based on EST data;INDUCTION: By IFNG/IFN-gamma.SIMILARITY: Belongs to the PA28 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_114172 - RefSeq - - - - ENSP00000216122 - Ensembl - - - - ENSG00000068878 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6609 - - - - EQUAL - 16 - - - - 8144764 - pubchem - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2657 - - - - - EQUAL - 608 - http://www.reactome.org/biopax/46/48887#SequenceSite4668 - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - NP_852136 - RefSeq - - - - - 2.7.7.6 - - - - - - The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin - At the beginning of this reaction, 1 molecule of 'DNA polymerase alpha:primase:DNA polymerase alpha:origin complex', and 1 molecule of 'NTP' are present. At the end of this reaction, 1 molecule of 'DNA polymerase epsilon', and 1 molecule of 'RNA primer:origin duplex:DNA polymerase alpha:primase complex' are present.<br><br> This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed RNA polymerase activity' of 'DNA polymerase alpha:primase'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1993 - - - - - - NP_001096138 - RefSeq - - - - 68520 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68520 - - - - - - MOD_RES 413 413 Phosphoserine. - - - - 5709 - NCBI Gene - - - - - - MOD_RES 75 75 Phosphoserine. - - - - REACT_5183 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5183.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature842 - - - - - - - - - - - - DNA polymerase epsilon:origin complex - Reactome DB_ID: 68485 - http://www.reactome.org/biopax/46/48887#Complex2605 - - - - EQUAL - 261 - http://www.reactome.org/biopax/46/48887#SequenceSite10676 - - - - EQUAL - 298 - - - - EQUAL - 55 - - - - NM_002916 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6422 - - - - NM_001251989 - RefSeq - - - - 418076 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=418076 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4816 - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1154 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6795 - - - - ENST00000430157 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6442 - - - - REACT_2484 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2484.2 - - - - EQUAL - 264 - http://www.reactome.org/biopax/46/48887#SequenceSite1873 - - - - 939862 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939862 - - - - RFC1 - HGNC - - - - Q13565 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4987 - - - - - - PSMD4 - HGNC - - - - UBA52 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval855 - - - - - - DJJCXFVJDGTHFX-XVFCMESISA-N - InChIKey - - - - 9539976 - Mackey ZB - Tomkinson AE - PubMed - Structure and function of mammalian DNA ligases. - Mutat Res 407(1);1-9 - 1998 - - - - NP_439892 - RefSeq - - - - NP_006582 - RefSeq - - - - 68462 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68462 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4837 - - - - ENSP00000395206 - Ensembl - - - - HGNC:11749 - HGNC - - - - REACT_18996 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18996.1 - - - - ENST00000261479 - Ensembl - - - - HGNC:9969 - HGNC - - - - - - deoxycytidine 5'-triphosphate - Deoxycytidine triphosphate - 2'-Deoxycytidine 5'-triphosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule588 - Reactome DB_ID: 30185 - dCTP - - - - - - MOD_RES 209 209 Phosphoserine. - - - - EQUAL - 2 - - - - - - MOD_RES 163 163 N6-acetyllysine. - - - - ENST00000581882 - Ensembl - - - - - - Replication factor-A protein 2 - RP-A - Replication protein A 32 kDa subunit - RPA32 - DNA Replication factor A protein 2 (32kD) - RF-A - - - - - Reactome DB_ID: 68457 - http://www.reactome.org/biopax/46/48887#Protein1646 - RPA2 - - - - NP_004055 - RefSeq - - - - NM_002805 - RefSeq - - - - InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 - InChI - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1054 - - - - Q96NW8 - UniProt - - - - Proteasome epsilon chain - 3.4.25.1 - LMPX - MB1 - PSMB5 - Proteasome chain 6 - Macropain epsilon chain - Multicatalytic endopeptidase complex epsilon chain - Proteasome subunit X - Proteasome subunit MB1 - X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PSB5_HUMAN - Proteasome subunit beta type-5 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This unit is responsible of the chymotrypsin-like activity of the proteasome and is one of the principal target of the proteasome inhibitor bortezomib. May catalyze basal processing of intracellular antigens. Plays a role in the protection against oxidative damage through the Nrf2-ARE pathway (By similarity).CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. This subunit can be displaced by the equivalent immune-specific subunit PSMB8. Directly interacts with POMP. Interacts with HIV-1 TAT protein. Interacts with ABCB1 and TAP1.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P28074-1; Sequence=Displayed; Name=2; IsoId=P28074-2; Sequence=VSP_041263; Name=3; IsoId=P28074-3; Sequence=VSP_045686; Note=No experimental confirmation available;INDUCTION: Down-regulated by IFNG/IFN-gamma (at protein level). Induced in breast cancer tissue. Up-regulated by sulforaphane in breast cancer cells.SIMILARITY: Belongs to the peptidase T1B family.SEQUENCE CAUTION: Sequence=AAP35423.1; Type=Erroneous initiation; Sequence=BAA06097.1; Type=Erroneous initiation; Sequence=CAD97956.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - Mcm10:pre-replicative complex - Reactome DB_ID: 68560 - http://www.reactome.org/biopax/46/48887#Complex2601 - - - - - - G2/mitotic-specific cyclin B1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5555 - Reactome DB_ID: 68901 - CCNB1 - - - - ENSG00000145386 - Ensembl - - - - NM_018955 - RefSeq - - - - EQUAL - 29 - - - - CHEBI:10530 - ChEBI - - - - NM_001178011 - RefSeq - - - - - - - - - - Association of MCM8 with ORC:origin complex - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2145 - Authored: Tye, BK, 2006-03-17 14:46:24 - The MCM2-7 complex, an essential component of the pre-replication complex, recruits CDC6 and CDT1 proteins to the origin. MCM8, another member of the MCM family has been found to bind to chromatin during early G1 phase. MCM8 interacts specifically with the ORC2 protein. - Edited: Gopinathrao, G, 2006-03-17 14:47:28 - - - - - Q5JNW6 - UniProt - - - - REACT_9292 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9292.2 - - - - - - Tumor necrosis factor type 1 receptor associated protein 2 - 26S proteasome subunit p97 - 26S proteasome regulatory subunit S2 - 55.11 protein - 26S proteasome non-ATPase regulatory subunit 2 - - - - - Reactome DB_ID: 68796 - http://www.reactome.org/biopax/46/48887#Protein1065 - PSMD2 - - - - MCM8 - HGNC Symbol - - - - NM_052827 - RefSeq - - - - - Multicatalytic endopeptidase complex beta chain - Macropain beta chain - HsBPROS26 - PROS26 - 3.4.25.1 - PSMB4 - Proteasome chain 3 - Proteasome beta chain - HsN3 - 26 kDa prosomal protein - PROS-26 - - - - - - - - - - - - - - - - - PSB4_HUMAN - Proteasome subunit beta type-4 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. Mediates the lipopolysaccharide-induced signal macrophage proteasome (By similarity). SMAD1/OAZ1/PSMB4 complex mediates the degradation of the CREBBP/EP300 repressor SNIP1.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with HIV-1 TAT and HIV-1 NEF proteins. Interaction with HTLV-1 TAX protein favors NFKB1 activation. Interacts with bacterial lipopolysaccharide (LPS) (By similarity). Forms a ternary complex with SMAD1 and OAZ1 before PSMB4 is incorporated into the 20S proteasome. Interacts with PRPF19.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).INDUCTION: Up-regulated in fibrolamellar carcinomas.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 85 - - - - - Proteasome delta chain - Proteasome subunit Y - Multicatalytic endopeptidase complex delta chain - PSMB6 - 3.4.25.1 - Macropain delta chain - Y - LMPY - - - - - - - - - - - - - PSB6_HUMAN - Proteasome subunit beta type-6 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This unit is responsible of the peptidyl glutamyl-like activity. May catalyze basal processing of intracellular antigens.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. This subunit can be displaced by the equivalent immune-specific subunit PSMB9. Interacts with HIV-1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.INDUCTION: Down-regulated by IFNG/IFN-gamma (at protein level). Up-regulated in anaplastic thyroid cancer cell lines.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 1 - - - - EQUAL - 223 - http://www.reactome.org/biopax/46/48887#SequenceSite10900 - - - - EQUAL - 713 - - - - NP_001171482 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6684 - - - - NP_510867 - RefSeq - - - - ENSG00000108344 - Ensembl - - - - - - 26S proteasome-associated pad1 homolog - - - - - Reactome DB_ID: 68722 - http://www.reactome.org/biopax/46/48887#Protein1093 - PSMD14 - - - - REACT_7610 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7610.1 - - - - ENSP00000397057 - Ensembl - - - - REACT_2752 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2752.2 - - - - - - UBC(1-76) - ubiquitin (UBC 1) - - - - - Reactome DB_ID: 939871 - http://www.reactome.org/biopax/46/48887#Protein2477 - UBC - - - - 69151 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69151 - - - - EQUAL - 297 - http://www.reactome.org/biopax/46/48887#SequenceSite10686 - - - - - - P1-CDC21 - DNA replication licensing factor MCM4 - Mcm4 - CDC21 homolog - - - - - Reactome DB_ID: 68549 - http://www.reactome.org/biopax/46/48887#Protein5590 - MCM4 - - - - Q9BWZ9 - UniProt - - - - EQUAL - 281 - - - - ENSP00000402118 - Ensembl - - - - REACT_146 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_146.3 - - - - PSMF1 - HGNC - - - - EQUAL - 241 - http://www.reactome.org/biopax/46/48887#SequenceSite1853 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10907 - - - - 10790374 - Tercero, JA - Labib, K - Diffley, JF - Pubmed - DNA synthesis at individual replication forks requires the essential initiation factor Cdc45p. - EMBO J 19:2082-93 - 2000 - - - - EQUAL - 193 - - - - Q96C42 - UniProt - - - - ENST00000493471 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4927 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4859 - - - - - - 186852 - omim - - - - REACT_4707 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4707.2 - - - - - - MOD_RES 74 74 Phosphotyrosine; by SRC. - - - - - - - - - - - - - - - Removal of remaining Flap - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2018 - The remaining flap, which is too short to support RPA binding, is then processed by FEN-1. There is evidence that binding of RPA to the displaced end of the RNA-containing Okazaki fragment prevents FEN-1 from accessing the substrate. FEN-1 is a structure-specific endonuclease that cleaves near the base of the flap at a position one nucleotide into the annealed region. Biochemical studies have shown that the preferred substrate for FEN-1 consists of a one-nucleotide 3'-tail on the upstream primer in addition to the 5'-flap of the downstream primer. - - - - - ENST00000575443 - Ensembl - - - - HGNC:9556 - HGNC - - - - REACT_1707 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1707.4 - - - - PSMA8 - HGNC Symbol - - - - ENST00000302182 - Ensembl - - - - - - MOD_RES 157 157 Phosphothreonine; by PKB/AKT1 and PIM1. - - - - 5714 - NCBI Gene - - - - NM_001136198 - RefSeq - - - - 600778 - omim - - - - EQUAL - 153 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4941 - - - - ENSG00000137713 - Ensembl - - - - 113788 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113788 - - - - REACT_2696 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2696.1 - - - - 68436 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68436 - - - - EQUAL - 684 - http://www.reactome.org/biopax/46/48887#SequenceSite1791 - - - - 68429 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68429 - - - - - - Replication factor C 40 kDa subunit - RFC40 - A1 40 kDa subunit - RF-C 40 kDa subunit - Activator 1 40 kDa subunit - - - - - Reactome DB_ID: 68433 - http://www.reactome.org/biopax/46/48887#Protein5565 - RFC2 - - - - ENST00000265187 - Ensembl - - - - - - MOD_RES 10 10 Phosphoserine. - - - - REACT_4373 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4373.2 - - - - 2E9X - PROTEIN DATA BANK - - - - ENSG00000112118 - Ensembl - - - - ENSP00000414359 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature820 - - - - - - - - - - - - Processive complex:Okazaki fragment:Flap:RPA heterotrimer:dna2 - http://www.reactome.org/biopax/46/48887#Complex2642 - Reactome DB_ID: 68466 - - - - 68652 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68652 - - - - Q8TAA2 - UniProt - - - - Q5XKF5 - UniProt - - - - REACT_2148 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2148.2 - - - - - - PPP2CB - PP2A-beta - 3.1.3.16 - - - - - - - - - - - - - - - - - - PP2AB_HUMAN - Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform - FUNCTION: PP2A can modulate the activity of phosphorylase B kinase casein kinase 2, mitogen-stimulated S6 kinase, and MAP-2 kinase.CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.COFACTOR: Binds 1 iron ion per subunit (By similarity).COFACTOR: Binds 1 manganese ion per subunit (By similarity).SUBUNIT: Found in a complex with at least ARL2, PPP2CB, PPP2R1A, PPP2R2A, PPP2R5E and TBCD. Interacts with TBCD (By similarity). PP2A consists of a common heterodimeric core enzyme (composed of a 36 kDa catalytic subunit (subunit C) and a 65 kDa constant regulatory subunit (PR65) (subunit A)) that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Binds PPME1. May indirectly interact with SGOL1, most probably through regulatory B56 subunits. Interacts with CTTNBP2NL.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Chromosome, centromere. Cytoplasm, cytoskeleton, spindle pole. Note=In prometaphase cells, but not in anaphase cells, localizes at centromeres. During mitosis, also found at spindle poles.PTM: Reversibly methyl esterified on Leu-309. Carboxyl methylation may play a role in holoenzyme assembly. It varies during the cell cycle. Demethylated by PME1 (in vitro).PTM: Phosphorylation of either threonine (by autophosphorylation- activated protein kinase) or tyrosine results in inactivation of the phosphatase. Auto-dephosphorylation has been suggested as a mechanism for reactivation.SIMILARITY: Belongs to the PPP phosphatase family. PP-1 subfamily. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001940 - RefSeq - - - - CHEBI:13274 - ChEBI - - - - B3KNW2 - UniProt - - - - 182585 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=182585 - - - - O43208 - UniProt - - - - 3359994 - Arai K - Arai N - Wong SW - Yuan PM - Wang TS - Pearson BE - Korn D - Wahl AF - Hunkapiller MW - PubMed - Human DNA polymerase alpha gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. - EMBO J 7(1);37-47 - 1988 - - - - ENSP00000234626 - Ensembl - - - - HGNC:17151 - HGNC - - - - - - MOD_RES 823 823 Phosphothreonine. - - - - EQUAL - 146 - - - - EQUAL - 13 - - - - PRIM2 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4822 - - - - 11282021 - Lei, M - Tye, BK - Pubmed - Initiating DNA synthesis: from recruiting to activating the MCM complex. - J Cell Sci 114:1447-54 - 2001 - - - - NM_001197330 - RefSeq - - - - ENSG00000099341 - Ensembl - - - - ENSP00000221138 - Ensembl - - - - REACT_3087 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3087.1 - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite1777 - - - - A8K2E0 - UniProt - - - - 68750 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68750 - - - - ENST00000253462 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature841 - - - - ENST00000157812 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4974 - - - - - - ENSP00000410369 - Ensembl - - - - REACT_5119 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5119.2 - - - - 603465 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4973 - - - - - - NP_002379 - RefSeq - - - - NM_175932 - RefSeq - - - - EQUAL - 860 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature827 - - - - - - - - - - - - - - - - - - Removal of the Flap Intermediate - Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap. - http://www.reactome.org/biopax/46/48887#Pathway514 - - - - - 10518787 - Kanda, T - Igaki, H - Kukimoto, I - Pubmed - Human CDC45 protein binds to minichromosome maintenance 7 protein and the p70 subunit of DNA polymerase alpha. - Eur J Biochem 265:936-43 - 1999 - - - - - - - - - - - - - Leading Strand Synthesis - The processive complex is responsible for synthesizing at least 5-10 kb of DNA in a continuous manner during leading strand synthesis. The incorporation of nucleotides by pol delta is quite accurate. However, incorporation of an incorrect nucleotide does occur occasionally. Misincorporated nucleotides are removed by the 3' to 5' exonucleolytic proofreading capability of pol delta. - http://www.reactome.org/biopax/46/48887#Pathway510 - - - - - NP_002937 - RefSeq - - - - ENSP00000461254 - Ensembl - - - - ENST00000298852 - Ensembl - - - - EQUAL - 375 - - - - HGNC:3650 - HGNC - - - - - - ORC3L - LATHEO - Origin recognition complex subunit Latheo - ORC3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ORC3_HUMAN - Origin recognition complex subunit 3 - FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.SUBUNIT: ORC is composed of six subunits. In human, ORC is cell cycle-dependent regulated: it is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q9UBD5-1; Sequence=Displayed; Name=2; IsoId=Q9UBD5-2; Sequence=VSP_017129; Note=No experimental confirmation available; Name=3; IsoId=Q9UBD5-3; Sequence=VSP_044893; Note=No experimental confirmation available;SIMILARITY: Belongs to the ORC3 family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/orc3l/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 7502077 - Hidaka, M - Stillman, B - Gavin, KA - Pubmed - Conserved initiator proteins in eukaryotes. - Science 270:1667-71 - 1996 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval863 - - - - - - 11278932 - Nevins, JR - Burke, TW - Cook, JG - Asano, M - Pubmed - Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1. - J Biol Chem 276:15397-408 - 2001 - - - - MI:0355 - Molecular Interactions Ontology - - - - - - MOD_RES 708 708 Phosphotyrosine. - - - - EQUAL - 41 - - - - 68457 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68457 - - - - A2A2T5 - UniProt - - - - HGNC:20932 - HGNC - - - - ENSP00000270586 - Ensembl - - - - - - MOD_RES 67 67 Phosphotyrosine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6782 - - - - O43929 - UniProt - - - - REACT_8893 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_8893.2 - - - - NM_001003810 - RefSeq - - - - ENSG00000226201 - Ensembl - - - - - - 26S protease subunit S5 basic - 26S proteasome subunit S5B - 26S proteasome non-ATPase regulatory subunit 5 - - - - - Reactome DB_ID: 68802 - http://www.reactome.org/biopax/46/48887#Protein1101 - PSMD5 - - - - PSMB11 - HGNC - - - - - - - - Okazaki fragment - Reactome DB_ID: 68452 - http://www.reactome.org/biopax/46/48887#PhysicalEntity256 - - - - Q6PEW2 - UniProt - - - - 69144 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69144 - - - - ENSP00000345584 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4954 - - - - 68642 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68642 - - - - - - DNA polymerase II subunit A - DNA polymerase epsilon, catalytic subunit A - - - - - Reactome DB_ID: 68473 - http://www.reactome.org/biopax/46/48887#Protein5707 - POLE - - - - P18858 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6431 - - - - ENSG00000222028 - Ensembl - - - - NP_001186703 - RefSeq - - - - - - MOD_RES 224 224 Phosphoserine. - - - - ENST00000371568 - Ensembl - - - - EQUAL - 811 - - - - - - - - - - - - - - Processive complex:Okazaki fragments:Remaining Flap - http://www.reactome.org/biopax/46/48887#Complex2643 - Reactome DB_ID: 68468 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4919 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2429 - - - - - Q6P053 - UniProt - - - - HGNC:24575 - HGNC - - - - InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1 - InChI - - - - 68777 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68777 - - - - 10748138 - Choe, W - Budd, ME - Campbell, JL - Pubmed - The nuclease activity of the yeast DNA2 protein, which is related to the RecB-like nucleases, is essential in vivo. - J Biol Chem 275:16518-29 - 2000 - - - - Q8N1D8 - UniProt - - - - CHEBI:13222 - ChEBI - - - - 154365 - omim - - - - CDK1 - HGNC Symbol - - - - REACT_282 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_282.3 - - - - REACT_4222 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4222.2 - - - - NM_001199773 - RefSeq - - - - Q1XBG5 - UniProt - - - - - - PSF1p - - - - - Reactome DB_ID: 176955 - http://www.reactome.org/biopax/46/48887#Protein5729 - GINS1 - - - - Q86UQ7 - UniProt - - - - EQUAL - 456 - http://www.reactome.org/biopax/46/48887#SequenceSite1825 - - - - NP_006494 - RefSeq - - - - 179836 - omim - - - - O43242 - UniProt - - - - - - Cdc45 - CDC45-related protein - PORC-PI-1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5573 - Reactome DB_ID: 68563 - CDC45 - - - - B4DZM8 - UniProt - - - - Q75MS6 - UniProt - - - - - - ubiquitin (UBC 3) - - - - - Reactome DB_ID: 939853 - http://www.reactome.org/biopax/46/48887#Protein2479 - UBC(153-228) - - - - 17991896 - Romani, S - Fasanaro, P - Capogrossi, MC - Magenta, A - Martelli, F - Di Stefano, V - Pubmed - Protein phosphatase 2A subunit PR70 interacts with pRb and mediates its dephosphorylation - Mol Cell Biol 28:873-82 - 2008 - - - - REACT_7878 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7878.1 - - - - 69091 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69091 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6789 - - - - - - - - - - - - RNA primer-DNA primer:origin duplex - http://www.reactome.org/biopax/46/48887#Complex2609 - Reactome DB_ID: 68425 - - - - A6NP15 - UniProt - - - - ENSP00000446313 - Ensembl - - - - NP_877423 - RefSeq - - - - A8K7C4 - UniProt - - - - ENSP00000444695 - Ensembl - - - - ENST00000356509 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval824 - - - - - - EQUAL - 436 - http://www.reactome.org/biopax/46/48887#SequenceSite10623 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature821 - - - - - - - - cyclin - http://www.reactome.org/biopax/46/48887#PhysicalEntity245 - Reactome DB_ID: 68379 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4823 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10602 - - - - NM_002716 - RefSeq - - - - - - 11S regulator complex beta subunit - PA28b - Proteasome activator 28-beta subunit - REG-beta - Proteasome activator complex subunit 2 - PA28beta - Activator of multicatalytic protease subunit 2 - - - - - Reactome DB_ID: 68814 - http://www.reactome.org/biopax/46/48887#Protein1085 - PSME2 - - - - ENSP00000261712 - Ensembl - - - - 189971 - omim - - - - 451208 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=451208 - - - - EQUAL - 496 - http://www.reactome.org/biopax/46/48887#SequenceSite10884 - - - - 9889196 - Sørensen, CS - Lukas, J - Petersen, BO - Helin, K - Pubmed - Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization. - EMBO J 18:396-410 - 1999 - - - - ENSG00000111445 - Ensembl - - - - 10882098 - Walter, J - Newport, J - Pubmed - Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha. - Mol Cell 5:617-27 - 2000 - - - - ENST00000396394 - Ensembl - - - - - - MOD_RES 326 326 N6-acetyllysine. - - - - NM_002797 - RefSeq - - - - POLE2 - HGNC Symbol - - - - - - ubiquitin (UBC 5) - - - - - http://www.reactome.org/biopax/46/48887#Protein2481 - Reactome DB_ID: 939863 - UBC(305-380) - - - - 68762 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68762 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10579 - - - - ENST00000448257 - Ensembl - - - - EQUAL - 160 - - - - 5698 - NCBI Gene - - - - - - MOD_RES 227 227 N6-acetyllysine. - - - - P28062 - UniProt - - - - NM_001127218 - RefSeq - - - - 68756 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68756 - - - - CCNA1 - HGNC - - - - NP_002791 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4963 - - - - - - 75031 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=75031 - - - - - - MOD_RES 23 23 Phosphoserine. - - - - ENSP00000395747 - Ensembl - - - - ENST00000305885 - Ensembl - - - - ENST00000354056 - Ensembl - - - - EQUAL - 230 - - - - P78499 - UniProt - - - - ENSP00000438326 - Ensembl - - - - - - Single-stranded DNA-binding protein - RPA70 - RP-A - Replication factor-A protein 1 - RF-A - DNA Replication factor A protein A1 (70kD) - Replication protein A 70 kDa DNA-binding subunit - - - - - Reactome DB_ID: 68461 - http://www.reactome.org/biopax/46/48887#Protein1648 - RPA1 - - - - ENST00000484800 - Ensembl - - - - EQUAL - 6 - - - - - - PSMD14 - 3.4.19.- - 26S proteasome-associated PAD1 homolog 1 - 26S proteasome regulatory subunit RPN11 - POH1 - - - - - - - - - - - - - - - PSDE_HUMAN - 26S proteasome non-ATPase regulatory subunit 14 - FUNCTION: Metalloprotease component of the 26S proteasome that specifically cleaves 'Lys-63'-linked polyubiquitin chains. The 26S proteasome is involved in the ATP-dependent degradation of ubiquitinated proteins. Plays a role in response to double-strand breaks (DSBs): acts as a regulator of non-homologous end joining (NHEJ) by cleaving 'Lys-63'-linked polyubiquitin, thereby promoting retention of JMJD2A/KDM4A on chromatin and restricting TP53BP1 accumulation. Also involved in homologous recombination repair by promoting RAD51 loading.SUBUNIT: Component of the lid subcomplex of the 19S proteasome regulatory particle complex (also named PA700 complex). The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. Interacts with TXNL1.TISSUE SPECIFICITY: Widely expressed. Highest levels in heart and skeletal muscle.SIMILARITY: Belongs to the peptidase M67A family. PSMD14 subfamily.SIMILARITY: Contains 1 MPN (JAB/Mov34) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_1279 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1279.3 - - - - ENSG00000115233 - Ensembl - - - - 113574 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113574 - - - - PSMD2 - HGNC Symbol - - - - 8144912 - pubchem-substance - - - - CHEBI:13510 - ChEBI - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6623 - - - - RPA1 - HGNC Symbol - - - - CHEBI:47222 - ChEBI - - - - - - MOD_RES 59 59 Phosphothreonine. - - - - NBIIXXVUZAFLBC-UHFFFAOYSA-K - InChIKey - - - - ENSP00000392693 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6671 - - - - E2F2 - E2F-2 - - - - - - - - - - - - - - - E2F2_HUMAN - Transcription factor E2F2 - FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from g1 to s phase. E2F2 binds specifically to RB1 in a cell-cycle dependent manner.SUBUNIT: Component of the DRTF1/E2F transcription factor complex. Forms heterodimers with DP family members. The E2F2 complex binds specifically hypophosphorylated retinoblastoma protein RB1. During the cell cycle, RB1 becomes phosphorylated in mid-to-late G1 phase, detaches from the DRTF1/E2F complex, rendering E2F transcriptionally active. Viral oncoproteins, notably E1A, T- antigen and HPV E7, are capable of sequestering RB1, thus releasing the active complex. Binds EAPP.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Highest level of expression is found in placenta, low levels are found in lung. Found as well in many immortalized cell lines derived from tumor samples.PTM: Phosphorylated by CDK2 and cyclin A-CDK2 in the S-phase (By similarity).SIMILARITY: Belongs to the E2F/DP family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/e2f2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_002794 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10856 - - - - HGNC:9173 - HGNC - - - - ENST00000392844 - Ensembl - - - - NP_787128 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1075 - - - - CHEBI:7793 - ChEBI - - - - - - - - - - - - Loading of PCNA - Sliding Clamp Formation - The binding of the primer recognition complex involves the loading of proliferating cell nuclear antigen (PCNA). Replication Factor C transiently opens the PCNA toroid in an ATP-dependent reaction, and then allows PCNA to re-close around the double helix adjacent to the primer terminus. This leads to the formation of the "sliding clamp". - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2009 - - - - - - - - ubiquitin (UBC 9) - - - - - http://www.reactome.org/biopax/46/48887#Protein2485 - Reactome DB_ID: 939868 - UBC(609-684) - - - - RPA4 - HGNC - - - - 187525 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187525 - - - - ENST00000536769 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval861 - - - - - - 10748114 - You, Z - Kitagawa, M - Komamura-Kohno, Y - Ishimi, Y - Omori, A - Pubmed - Inhibition of Mcm4,6,7 helicase activity by phosphorylation with cyclin A/Cdk2. - J Biol Chem 275:16235-41 - 2000 - - - - NP_000312 - RefSeq - - - - - - - - - - - - phosphorylated Mcm2-7 complex - http://www.reactome.org/biopax/46/48887#Complex2602 - Reactome DB_ID: 68569 - - - - - - geminin - - - - - Reactome DB_ID: 113554 - http://www.reactome.org/biopax/46/48887#Protein5771 - GMNN - - - - - - phospho-Cdh1 - - - - - - Reactome DB_ID: 174257 - http://www.reactome.org/biopax/46/48887#Protein5721 - p-FZR1 - - - - - - MOD_RES 80 80 Phosphoserine. - - - - - - MOD_RES 397 397 N6-acetyllysine. - - - - EQUAL - 560 - http://www.reactome.org/biopax/46/48887#SequenceSite10896 - - - - - - MOD_RES 413 413 Phosphoserine. - - - - - - - - - - - - Destruction of AUF1 and mRNA - Edited: May, B, 2009-12-29 - Ubiquitin-dependent proteolysis of AUF1 and nuclease-dependent destruction of AUF1-bound mRNA are coupled in an unknown way. It is possible that ubiquitinated AUF1 targets other members of the AUF1 and signal transduction regulated complex (ASTRC), such as polyA-binding protein, for degradation and this renders the mRNA susceptible to nucleases. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction203 - Authored: May, B, 2009-12-29 - Reviewed: Wilusz, J, 2010-06-29 - - - - EQUAL - 309 - http://www.reactome.org/biopax/46/48887#SequenceSite4922 - - - - NP_002905 - RefSeq - - - - Q5U0B2 - UniProt - - - - NP_003494 - RefSeq - - - - - - MOD_RES 248 248 N6-acetyllysine. - - - - GO:0003899 - GENE ONTOLOGY - - - - - REACT_4137 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4137.3 - - - - REACT_26155 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26155.2 - - - - REACT_2402 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2402.2 - - - - - - PA28b - REG-beta - Proteasome activator 28 subunit beta - PA28beta - PSME2 - 11S regulator complex subunit beta - Activator of multicatalytic protease subunit 2 - - - - - - - - - - - - - PSME2_HUMAN - Proteasome activator complex subunit 2 - FUNCTION: Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome.SUBUNIT: Heterodimer of PSME1 and PSME2, which forms a hexameric ring.INDUCTION: By IFNG/IFN-gamma.SIMILARITY: Belongs to the PA28 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 248 - - - - ENSP00000264169 - Ensembl - - - - 68455 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68455 - - - - Q9UBD5 - UniProt - - - - CHEBI:46175 - ChEBI - - - - NP_002782 - RefSeq - - - - POLA2 - HGNC Symbol - - - - ENST00000335877 - Ensembl - - - - ENST00000576908 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1766 - - - - - - - - Unwound fork - Reactome DB_ID: 169509 - http://www.reactome.org/biopax/46/48887#PhysicalEntity254 - - - - 68553 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68553 - - - - NP_001120690 - RefSeq - - - - EQUAL - 300 - http://www.reactome.org/biopax/46/48887#SequenceSite1883 - - - - 9288745 - Knapp, D - Tanaka, T - Nasmyth, K - Pubmed - Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. - Cell 90:649-60 - 1997 - - - - NP_055040 - RefSeq - - - - UBC - HGNC - - - - Q6IPR2 - UniProt - - - - EQUAL - 12 - - - - ENST00000383236 - Ensembl - - - - REACT_24153 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24153.2 - - - - EQUAL - 13 - - - - NM_032485 - RefSeq - - - - REACT_4436 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4436.2 - - - - EQUAL - 25 - - - - GO:0003909 - GENE ONTOLOGY - - - - - 3978 - NCBI Gene - - - - EQUAL - 2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval853 - - - - - - 939188 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939188 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1066 - - - - NM_176863 - RefSeq - - - - ENSP00000418447 - Ensembl - - - - - - MOD_RES 206 206 N6-acetyllysine. - - - - NM_001102667 - RefSeq - - - - ENST00000257789 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6719 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1073 - - - - EQUAL - 250 - - - - Q6PKU0 - UniProt - - - - ENST00000244741 - Ensembl - - - - EQUAL - 45 - - - - 11825897 - Kao, HI - Bambara, RA - Henricksen, LA - Liu, Y - Pubmed - Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate. - J Biol Chem 277:14379-89 - 2002 - - - - 109965 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109965 - - - - ENST00000539074 - Ensembl - - - - ENST00000313433 - Ensembl - - - - REACT_4364 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4364.2 - - - - ENSG00000173692 - Ensembl - - - - - - - - - - - - CDT1:CDC6:ORC:origin complex - Reactome DB_ID: 68544 - http://www.reactome.org/biopax/46/48887#Complex2600 - - - - PSMB9 - HGNC Symbol - - - - 68741 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68741 - - - - - - - - - - - - Multiple proteins are localized at replication fork - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2007 - Authored: Tye, BK, 2006-03-17 14:46:24 - By applying the chromatin immunoprecipitation technique to paused forks, certain proteins like DNA pol alpha, DNA pol delta, DNA pol epsilon, MCM2-7, CDC45, GINS and MCM10 were identified. By uncoupling a helicase at the site using a polymerase inhibitor, MCM2-7, GINS complex and CDC45 alone were found to be enriched at the paused fork suggesting these proteins may form a part of an "unwindosome" at the replicating fork. - Edited: Gopinathrao, G, 2006-03-17 14:47:28 - - - - - 5427 - NCBI Gene - - - - - - - - - - - - - - - - - - - ubiquitin - - - - http://www.reactome.org/biopax/46/48887#Protein1043 - Converted from EntitySet in Reactome - Reactome DB_ID: 113595 - Ub - - - - 600404 - omim - - - - PSMA1 - HGNC Symbol - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6712 - - - - HGNC:8487 - HGNC - - - - - - Origin recognition complex subunit Latheo - Origin recognition complex subunit 3 - Orc3 - - - - - Reactome DB_ID: 68513 - http://www.reactome.org/biopax/46/48887#Protein5579 - ORC3 - - - - GINS2 - HGNC - - - - 5696 - NCBI Gene - - - - CHEBI:27231 - ChEBI - - - - Q14102 - UniProt - - - - NM_015895 - RefSeq - - - - Q5VWC5 - UniProt - - - - 10436018 - Herbig, U - Marlar, CA - Pubmed - The Cdc6 nucleotide-binding site regulates its activity in DNA replication in human cells. - Mol Biol Cell 10:2631-45 - 1999 - - - - ENSG00000159377 - Ensembl - - - - - - MOD_RES 13 13 Phosphoserine. - - - - HNRNPD - HGNC Symbol - - - - - - MOD_RES 182 182 Phosphoserine. - - - - EQUAL - 229 - - - - Q0P6J7 - UniProt - - - - O-phospho-L-serine - - - - - ENST00000312419 - Ensembl - - - - O-phospho-L-threonine - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6784 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10901 - - - - PSME4 - HGNC - - - - EQUAL - 437 - http://www.reactome.org/biopax/46/48887#SequenceSite5798 - - - - EQUAL - 129 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature861 - - - - CHEBI:24449 - ChEBI - - - - PSMB2 - HGNC - - - - ENSP00000376272 - Ensembl - - - - REACT_3720 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3720.2 - - - - ENST00000392542 - Ensembl - - - - ENST00000379160 - Ensembl - - - - REACT_5498 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5498.3 - - - - - - DNA replication helicase-like homolog - DNA2-like homolog - dna2 endonuclease - - - - - Reactome DB_ID: 68465 - http://www.reactome.org/biopax/46/48887#Protein5735 - DNA2 - - - - - - MOD_RES 309 309 Leucine methyl ester. - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - ENSP00000413869 - Ensembl - - - - - - MOD_RES 1 1 N-acetylmethionine (By similarity). - - - - 75032 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=75032 - - - - EQUAL - 26 - - - - PSMD8 - HGNC - - - - P40938 - UniProt - - - - PRIM1 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4829 - - - - - - MOD_RES 197 197 Phosphoserine. - - - - Q495R7 - UniProt - - - - EQUAL - 2 - - - - ENSG00000115942 - Ensembl - - - - - - Origin recognition complex subunit 2 - Orc2 - - - - - http://www.reactome.org/biopax/46/48887#Protein5583 - Reactome DB_ID: 68405 - ORC2 - - - - - - MOD_RES 16 16 Phosphoserine. - - - - REACT_4370 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4370.2 - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule198 - Converted from EntitySet in Reactome - Reactome DB_ID: 30595 - NTP - - - - HGNC:1744 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4645 - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite1776 - - - - ENSP00000368164 - Ensembl - - - - ORC1 - HGNC - - - - - - MOD_RES 108 108 Phosphoserine. - - - - - - MOD_RES 259 259 N6-acetyllysine. - - - - REACT_24496 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24496.2 - - - - - - - - - - - - - - - DNA Replication Factor A (RPA) associates with the pre-replicative complex at the origin - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1977 - After pre-RC assembly and Cdc45 association with the origin of replication, Replication Protein A (RPA) also associates with chromatin. RPA is a heterotrimeric complex containing p70, p34, and p11 subunits, and also is required for DNA recombination and DNA repair. The p70 subunit of RPA binds to the primase subunits of Pol alpha:primase. The p70 and p34 subunits of RPA are phosphorylated in a cell cycle-dependent manner. RPA is a single-strand DNA (ssDNA) binding protein and its association with chromatin at this stage suggests that DNA is partially unwound. This suggestion has been confirmed by detection of ssDNA in budding yeast origins of replication using chemical methods. - - - - - 1110244 - Stolwijk, JA - Roberts, MF - Wenger, CB - Nadel, ER - Pubmed - Forearm blood flow during body temperature transients produced by leg exercise. - J Appl Physiol 38:58-63 - 1975 - - - - ENST00000373904 - Ensembl - - - - A4D2A2 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4858 - - - - - - HGNC:9299 - HGNC - - - - 68452 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68452 - - - - O75831 - UniProt - - - - REACT_4813 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4813.1 - - - - CHEBI:13740 - ChEBI - - - - ENST00000425762 - Ensembl - - - - Q96HD3 - UniProt - - - - - - MOD_RES 6 6 N6-acetyllysine. - - - - CHEBI:47721 - ChEBI - - - - - - MOD_RES 12 12 Phosphoserine. - - - - 51781 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=51781 - - - - 68812 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68812 - - - - Low molecular mass protein 7 - Y2 - LMP7 - Really interesting new gene 10 protein - PSMB5i - 3.4.25.1 - RING10 - PSMB8 - Proteasome component C13 - Multicatalytic endopeptidase complex subunit C13 - Macropain subunit C13 - Proteasome subunit beta-5i - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PSB8_HUMAN - Proteasome subunit beta type-8 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides. Replacement of PSMB5 by PSMB8 increases the capacity of the immunoproteasome to cleave model peptides after hydrophobic and basic residues. Acts as a major component of interferon gamma-induced sensitivity. Plays a key role in apoptosis via the degradation of the apoptotic inhibitor MCL1. May be involved in the inflammatory response pathway. In cancer cells, substitution of isoform 1 (E2) by isoform 2 (E1) results in immunoproteasome deficiency. Required for the differentiation of preadipocytes into adipocytes.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. This subunit is part of the immunoproteasome where it displaces the equivalent housekeeping subunit PSMB5. Component of the spermatoproteasome, a form of the proteasome specifically found in testis. Directly interacts with POMP. Interacts with HIV-1 TAT protein. Interacts with TAP1.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Comment=Additional isoforms seem to exist; Name=1; Synonyms=LMP7B, LMP7-E2; IsoId=P28062-1; Sequence=Displayed; Name=2; Synonyms=LMP7A, LMP7-E1; IsoId=P28062-2; Sequence=VSP_005287; Note=Contains a phosphothreonine at position 5;DEVELOPMENTAL STAGE: Highly expressed in immature dendritic cells (at protein level).INDUCTION: Up-regulated by IFNG/IFN-gamma and IRF1 (at protein level). Up-regulated by TNF (at protein level). Up-regulated by tetrodotoxin (TTX) in glial cells. Up-regulated in Crohn's bowel disease (CD). Down-regulated by the selective inhibitor PR-957. Down-regulated in mature dendritic cells by HSV-1 infection. Up- regulated by heat shock treatment.PTM: Autocleaved. The resulting N-terminal Thr residue of the mature subunit is responsible for the nucleophile proteolytic activity (By similarity).DISEASE: Nakajo syndrome (NKJO) [MIM:256040]: An autosomal recessive autoinflammatory disorder characterized by early childhood onset of recurrent fever, joint stiffness and severe contractures of the hands and feet, and erythematous skin lesions with subsequent development of lipodystrophy and laboratory evidence of immune dysregulation. Accompanying features may include muscle weakness and atrophy, hepatosplenomegaly, and microcytic anemia. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Note=Mutation Met-75 has been found in chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature syndrome (CANDLE syndrome). CANDLE patients have some overlapping features with NKJO patients, including a cutaneous eruption and lipodystrophy. They show a characteristic neutrophilic dermatosis with a mononuclear interstitial infiltrate in the dermis that seems pathognomonic for CANDLE syndrome (PubMed:21953331).SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - LMP2 - Really interesting new gene 12 protein - 3.4.25.1 - PSMB6i - Low molecular mass protein 2 - PSMB9 - Proteasome chain 7 - RING12 - Macropain chain 7 - Multicatalytic endopeptidase complex chain 7 - Proteasome subunit beta-1i - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PSB9_HUMAN - Proteasome subunit beta type-9 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides. Replacement of PSMB6 by PSMB9 increases the capacity of the immunoproteasome to cleave model peptides after hydrophobic and basic residues.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. This subunit is part of the immunoproteasome where it displaces the equivalent houskeeping subunit PSMB6. Component of the spermatoproteasome, a form of the proteasome specifically found in testis. Interacts with HIV-1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=LMP2.L; IsoId=P28065-1; Sequence=Displayed; Name=LMP2.S; IsoId=P28065-2; Sequence=VSP_005288;DEVELOPMENTAL STAGE: Highly expressed in immature dendritic cells (at protein level).INDUCTION: Up-regulated by interferon gamma (at protein level). Up-regulated by IRF1. Up-regulated by tumor necrosis factor-alpha (at protein level). Up-regulated by tetrodotoxin (TTX) in glial cells. Up-regulated in Crohn's bowel disease (CD). Up-regulated by heat shock treatment. Up-regulated by CD40L via the NFKB1 pathway in cancer cells.PTM: Autocleaved. The resulting N-terminal Thr residue of the mature subunit is responsible for the nucleophile proteolytic activity.MISCELLANEOUS: Encoded in the MHC class II region.MISCELLANEOUS: A model for self-activation in which residue Thr-21 serves as nucleophile and Lys-53 as proton donor/acceptor has been proposed. Subunit processing of mammalian beta-subunits proceeds via a novel ordered two-step mechanism involving autocatalysis.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2097 - - - - - - - - Proteasome zeta chain - Multicatalytic endopeptidase complex zeta chain - Macropain zeta chain - PSMA5 - 3.4.25.1 - - - - - - - - - - - - - - - - - - - - - - - - - PSA5_HUMAN - Proteasome subunit alpha type-5 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. PSMA5 interacts directly with the PSMG1-PSMG2 heterodimer which promotes 20S proteasome assembly.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P28066-1; Sequence=Displayed; Name=2; IsoId=P28066-2; Sequence=VSP_046241; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in fetal brain (at protein level).INDUCTION: Up-regulated in colon cancer cell lines. Up-regulated in fetal Down syndrome (DS) brain (at protein level). May be the target of the transcriptional activator NFE2L2.SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 469 - http://www.reactome.org/biopax/46/48887#SequenceSite10906 - - - - EQUAL - 2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4995 - - - - EQUAL - 34 - - - - ENSP00000376775 - Ensembl - - - - - - MOD_RES 252 252 Phosphoserine. - - - - REACT_24312 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24312.2 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1844 - - - - 29358 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29358 - - - - ENSG00000168496 - Ensembl - - - - EQUAL - 23 - - - - 68913 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68913 - - - - - - Adenosine 5'-triphosphate - - - - Reactome DB_ID: 113592 - http://www.reactome.org/biopax/46/48887#SmallMolecule5 - ATP - - - - - - MOD_RES 64 64 Phosphoserine. - - - - Q96GL1 - UniProt - - - - ENSG00000240118 - Ensembl - - - - 69068 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69068 - - - - CHEBI:17345 - ChEBI - - - - ENST00000426998 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6677 - - - - 6233 - NCBI Gene - - - - PSMD13 - HGNC - - - - ENSG00000133119 - Ensembl - - - - NP_037371 - RefSeq - - - - 9733749 - Ritzi, M - Knippers, R - Musahl, C - Baack, M - Romanowski, P - Laskey, RA - Pubmed - Human minichromosome maintenance proteins and human origin recognition complex 2 protein on chromatin. - J Biol Chem 273:24543-9 - 1998 - - - - HGNC:9541 - HGNC - - - - EQUAL - 190 - - - - 4172 - NCBI Gene - - - - - - - - - - - - - - - - - Unwinding of DNA - http://www.reactome.org/biopax/46/48887#Pathway509 - DNA Replication is regulated accurately and precisely by various protein complexes. Many members of the MCM protein family are assembled into the pre-Replication Complexes (pre-RC) at the end of M phase of the cell cycle. DNA helicase activity of some of the MCM family proteins are important for the unwinding of DNA and initiation of replication processes. This section contains four events which have been proved in different eukaryotic experimental systems to involve various proteins for this essential step during DNA Replication. - Authored: Tye, BK, 2006-03-17 14:46:24 - Edited: Gopinathrao, G, 2006-03-17 14:47:28 - - - - - - - MOD_RES 180 180 Phosphothreonine. - - - - - - DNA ligase I - Polydeoxyribonucleotide synthase (ATP) - - - - - Reactome DB_ID: 53787 - http://www.reactome.org/biopax/46/48887#Protein5737 - LIG1 - - - - PSMB11 - HGNC Symbol - - - - EQUAL - 326 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6797 - - - - EQUAL - 259 - - - - 169461 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=169461 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature865 - - - - ENSP00000265465 - Ensembl - - - - POLE - HGNC - - - - ENST00000571902 - Ensembl - - - - ENSG00000221983 - Ensembl - - - - EQUAL - 533 - http://www.reactome.org/biopax/46/48887#SequenceSite4667 - - - - O60785 - UniProt - - - - ENSG00000165916 - Ensembl - - - - EQUAL - 861 - http://www.reactome.org/biopax/46/48887#SequenceSite10631 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6612 - - - - P35244 - UniProt - - - - EQUAL - 80 - - - - NP_002792 - RefSeq - - - - PTHR10539:SF0 - PANTHER Family - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1808 - - - - - - MOD_RES 229 229 Phosphothreonine. - - - - EQUAL - 928 - http://www.reactome.org/biopax/46/48887#SequenceSite10847 - - - - ENSP00000453887 - Ensembl - - - - EQUAL - 2 - - - - 176843 - omim - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2465 - - - - REACT_3707 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3707.2 - - - - EQUAL - 120 - - - - Q5JNW4 - UniProt - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis619 - - - - REACT_2436 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2436.2 - - - - HGNC:9534 - HGNC - - - - ENSP00000408825 - Ensembl - - - - - - - - - - - - DDK - Reactome DB_ID: 68388 - http://www.reactome.org/biopax/46/48887#Complex2544 - - - - ENST00000392857 - Ensembl - - - - ENSG00000159352 - Ensembl - - - - - - MOD_RES 27 27 Phosphoserine. - - - - ENSP00000254719 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6614 - - - - 11175741 - Blow, JJ - Li, A - Tada, S - Méchali, M - Maiorano, D - Pubmed - Repression of origin assembly in metaphase depends on inhibition of RLF-B/Cdt1 by geminin. - Nat Cell Biol 3:107-13 - 2001 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5026 - - - - - - 4171 - NCBI Gene - - - - F8W8G1 - UniProt - - - - ENSP00000274026 - Ensembl - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1876 - - - - Q7Z3B5 - UniProt - - - - - - - - - - RPA binds to the Flap - The first step in the removal of the flap intermediate is the binding of Replication Protein A (RPA) to the long flap structure. RPA is a eukaryotic single-stranded DNA binding protein. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2015 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2439 - - - - Q6GPG8 - UniProt - - - - SUYVUBYJARFZHO-RRKCRQDMSA-N - InChIKey - - - - Q96AE1 - UniProt - - - - - - MOD_RES 222 222 Phosphothreonine. - - - - ENSG00000138346 - Ensembl - - - - 68940 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68940 - - - - 1X9N - PROTEIN DATA BANK - - - - HGNC:9567 - HGNC - - - - Q9UNM6 - UniProt - - - - NM_007370 - RefSeq - - - - 11801723 - Dimitrova, DS - Blow, JJ - Todorov, IT - Gilbert, DM - Prokhorova, TA - Pubmed - Mammalian nuclei become licensed for DNA replication during late telophase. - J Cell Sci 115:51-9 - 2002 - - - - 68419 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68419 - - - - 68425 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68425 - - - - 68519 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68519 - - - - ENST00000380071 - Ensembl - - - - NM_002811 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4838 - - - - ENSG00000139687 - Ensembl - - - - ENSP00000244741 - Ensembl - - - - 69007 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69007 - - - - EQUAL - 159 - - - - - - uridine 5'-monophosphate - Uridine monophosphate - uridylic acid - 5'Uridylic acid - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule592 - Reactome DB_ID: 418075 - UMP - - - - ENSG00000113575 - Ensembl - - - - NM_002945 - RefSeq - - - - 2175912 - Eki, T - Hurwitz, J - Matsumoto, T - Pubmed - Studies on the initiation and elongation reactions in the simian virus 40 DNA replication system. - Proc Natl Acad Sci U S A 87:9712-6 - 1991 - - - - 68827 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68827 - - - - ENSP00000470419 - Ensembl - - - - - - MOD_RES 13 13 N6-acetyllysine. - - - - 68950 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68950 - - - - NP_112737 - RefSeq - - - - ENSP00000363017 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6443 - - - - EQUAL - 9 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6786 - - - - NP_066996 - RefSeq - - - - 451223 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=451223 - - - - Q1XBG6 - UniProt - - - - ENST00000393055 - Ensembl - - - - HGNC:9561 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature862 - - - - ENST00000308268 - Ensembl - - - - PSMA3 - HGNC - - - - Q96GK5 - UniProt - - - - CHEBI:40553 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4884 - - - - - - B7Z5F1 - UniProt - - - - ENSP00000223321 - Ensembl - - - - 2KRK - PROTEIN DATA BANK - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6626 - - - - 8145706 - pubchem-substance - - - - NP_061828 - RefSeq - - - - EQUAL - 1 - - - - 604449 - omim - - - - 4173 - NCBI Gene - - - - 68744 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68744 - - - - - - MOD_RES 76 76 Phosphoserine. - - - - Q3B865 - UniProt - - - - REACT_5801 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5801.1 - - - - EQUAL - 71 - - - - 69002 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69002 - - - - E2F3 - HGNC - - - - - - - - - - - Mcm4,6,7 complex - replicative helicase - - - - Mcm4:Mcm6:Mcm7 - Reactome DB_ID: 69018 - http://www.reactome.org/biopax/46/48887#Complex2629 - - - - REACT_9246 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9246.1 - - - - ENSG00000103035 - Ensembl - - - - PTHR10678:SF2 - PANTHER Family - - - - NP_002784 - RefSeq - - - - EQUAL - 157 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4949 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1063 - - - - P0CG48 - UniProt - - - - REACT_160569 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160569.2 - - - - 11986310 - Carastro LM - Lu X - Downey KM - Tan CK - Zhou JQ - You M - So AG - PubMed - Direct interaction of proliferating cell nuclear antigen with the small subunit of DNA polymerase delta. - J Biol Chem 277(27);24340-5 - 2002 - - - - - - MOD_RES 15 15 Phosphotyrosine; by PKMYT1, WEE1, WEE2 and PKC/PRKCD. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Activation of the pre-replicative complex - In S. cerevisiae, two ORC subunits, Orc1 and Orc5, both bind ATP, and Orc1 in addition has ATPase activity. Both ATP binding and ATP hydrolysis appear to be essential functions in vivo. ATP binding by Orc1 is unaffected by the association of ORC with origin DNA (ARS) sequences, but ATP hydrolysis is ARS-dependent, being suppressed by associated double-stranded DNA and stimulated by associated single-stranded DNA. These data are consistent with the hypothesis that ORC functions as an ATPase switch, hydrolyzing bound ATP and changing state as DNA unwinds at the origin immediately before replication. It is attractive to speculate that ORC likewise functions as a switch as human pre-replicative complexes are activated, but human Orc proteins are not well enough characterized to allow the model to be critically tested. mRNAs encoding human orthologs of all six Orc proteins have been cloned, and ATP-binding amino acid sequence motifs have been identified in Orc1, Orc4, and Orc5. Interactions among proteins expressed from the cloned genes have been characterized, but the ATP-binding and hydrolyzing properties of these proteins and complexes of them have not been determined. - http://www.reactome.org/biopax/46/48887#Pathway497 - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2209 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6676 - - - - - - Proteasome gamma chain - Proteasome subunit beta type 1 - Macropain subunit C5 - Multicatalytic endopeptidase complex subunit C5 - Proteasome component C5 - - - - - http://www.reactome.org/biopax/46/48887#Protein1089 - Reactome DB_ID: 68738 - PSMB1 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2464 - - - - - - - - - - Ubiquitinated geminin is degraded by the proteasome - At the beginning of this reaction, 1 molecule of 'geminin:ubiquitin complex' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present.<br><br> This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2147 - - - - - - C10H17N2O14P3 - 5'-TTP - pppdT - 2'-deoxythymidine triphosphate - dThd5'PPP - deoxy-TTP - thymidine 5'-(tetrahydrogen triphosphate) - thymidine 5'-triphosphate - - - - - - - - - 482.16833 - dTTP - dTTP - - - - 113571 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113571 - - - - Q9ULH8 - UniProt - - - - - - - - - - - - - - - - - - - - - - - - Assembly of the pre-replicative complex - Authored: Davey, MJ, O'Donnell, M, Tye, BK, 2006-03-17 16:01:39 - DNA replication pre-initiation in eukaryotic cells begins with the formation of the pre-replicative complex (pre-RC) during the late M phase and continues in the G1 phase of the mitotic cell cycle, a process also called DNA replication origin licensing. The association of initiation proteins (ORC, Cdc6, Cdt1, Mcm2-7) with the origin of replication in both <i>S. cerevisiae</i> and humans has been demonstrated by chromatin immunoprecipitation experiments. In <i>S. cerevisiae</i>, pre-replicative complexes are assembled from late M to G1. In mammalian cells as well, pre-replicative complexes are assembled from late M to G1, as shown by biochemical fractionation and immunostaining. There are significant sequence similarities among some of the proteins in the pre-replicative complex. The ORC subunits Orc1, Orc4 and Orc5 are homologous to one another and to Cdc6. The six subunits of the Mcm2-7 complex are homologous to one another. In addition, Orc1, Orc4, Orc5, Cdc6, and the Mcm2-7 subunits, are members of the AAA+ superfamily of ATPases. Since the initial identification of these pre-RC components other factors that participate in this complex have been found, including Cdt1 in human, <i>Xenopus</i>, <i>S. pombe</i>, and <i>S. cerevisiae</i> cells. - http://www.reactome.org/biopax/46/48887#Pathway556 - - - - - PSMD6 - HGNC - - - - 68610 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68610 - - - - - - MOD_RES 307 307 Phosphotyrosine. - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2456 - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6716 - - - - ORC2 - HGNC Symbol - - - - PSMB4 - HGNC - - - - REACT_3633 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3633.2 - - - - 5684 - NCBI Gene - - - - 10712901 - Perkins, G - Diffley, JF - Drury, LS - Pubmed - The cyclin-dependent kinase Cdc28p regulates distinct modes of Cdc6p proteolysis during the budding yeast cell cycle. - Curr Biol 10:231-40 - 2000 - - - - PSMA6 - HGNC Symbol - - - - ENSP00000405726 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6661 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6714 - - - - EQUAL - 116 - - - - - - MOD_RES 417 417 Phosphoserine. - - - - ENSP00000262904 - Ensembl - - - - REACT_6747 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6747.2 - - - - EQUAL - 139 - - - - NP_002583 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4846 - - - - - - 68732 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68732 - - - - EQUAL - 160 - http://www.reactome.org/biopax/46/48887#SequenceSite10843 - - - - EQUAL - 36 - - - - 8530069 - Zhang J - McMullen B - Downey KM - Tan CK - So AG - PubMed - Cloning of the cDNAs for the small subunits of bovine and human DNA polymerase delta and chromosomal location of the human gene (POLD2). - Genomics 29(1);179-86 - 1995 - - - - PSMD7 - HGNC - - - - UBC - Ubiquitin - - - - - - - - - - UBC_HUMAN - Polyubiquitin-C - FUNCTION: Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: For the sake of clarity sequence features are annotated only for the first chain, and are not repeated for each of the following chains.SIMILARITY: Belongs to the ubiquitin family.SIMILARITY: Contains 9 ubiquitin-like domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 41 41 Phosphoserine. - - - - UBB - Ubiquitin - - - - - - - - - - - - - - - UBB_HUMAN - Polyubiquitin-B - FUNCTION: Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: The mRNA encoding variant UBB(+1) is produced by an unknown mechanism involving the deletion of a GT dinucleotide in the close proximity of a GAGAG motif (PubMed:9422699). This variant mRNA is found in normal brain, but the encoded protein accumulates only in brain neurofibrillary tangles and neuritic plaques in Alzheimer disease and other tauopathies, as well as polyglutaminopathies (PubMed:14597671). UBB(+1) variant cannot be used for polyubiquitination, is not effectively degraded by the proteasome when ubiquitinated and ubiquitinated UBB(+1) is refractory to disassembly by deubiquitinating enzymes (DUBs). In healthy brain, UBB(+1) C-terminus can be cleaved by UCHL3 (PubMed:21762696).MISCELLANEOUS: For a better understanding, features related to ubiquitin are only indicated for the first chain.SIMILARITY: Belongs to the ubiquitin family.SIMILARITY: Contains 3 ubiquitin-like domains. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 68566 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68566 - - - - ENSG00000105568 - Ensembl - - - - PSMC3 - HGNC - - - - - - MOD_RES 6 6 N6-acetyllysine. - - - - 5422 - NCBI Gene - - - - ENSP00000325970 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4805 - - - - gene ontology term for cellular function - - - - - - - MOD_RES 810 810 N6-methyllysine; by SMYD2. - - - - P28072 - UniProt - - - - 5700 - NCBI Gene - - - - gene ontology term for cellular process - - - - - REACT_3388 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3388.1 - - - - - - MOD_RES 69 69 Phosphoserine. - - - - 179835 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval862 - - - - - - 113499 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113499 - - - - P52915 - UniProt - - - - PSMB5 - HGNC - - - - 5111 - NCBI Gene - - - - NP_004517 - RefSeq - - - - 5519 - NCBI Gene - - - - 4998 - NCBI Gene - - - - 69183 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69183 - - - - B2RBG7 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4884 - - - - EQUAL - 276 - http://www.reactome.org/biopax/46/48887#SequenceSite1833 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6641 - - - - 29470 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29470 - - - - REACT_8806 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_8806.2 - - - - Proteasome subunit p58 - 26S proteasome regulatory subunit RPN3 - PSMD3 - 26S proteasome regulatory subunit S3 - - - - - - - - - - - - - - - - PSMD3_HUMAN - 26S proteasome non-ATPase regulatory subunit 3 - FUNCTION: Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.SUBUNIT: The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively.SIMILARITY: Belongs to the proteasome subunit S3 family.SIMILARITY: Contains 1 PCI domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 560 - http://www.reactome.org/biopax/46/48887#SequenceSite10621 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6653 - - - - - - MOD_RES 176 176 N6-acetyllysine. - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1830 - - - - - - UBC(1-76) - ubiquitin (UBC 1) - - - - - Reactome DB_ID: 939188 - http://www.reactome.org/biopax/46/48887#Protein1049 - UBC - - - - 10409700 - Ma, W - Kaiser, MW - Miller, C - Fors, L - Lyamicheva, N - Lyamichev, VI - Neri, B - Pubmed - A comparison of eubacterial and archaeal structure-specific 5'-exonucleases. - J Biol Chem 274:21387-94 - 1999 - - - - PTHR10758:SF2 - PANTHER Family - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10722 - - - - NP_057347 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature843 - - - - 1AQ1 - PROTEIN DATA BANK - - - - Q96H98 - UniProt - - - - 68544 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68544 - - - - NM_181747 - RefSeq - - - - EQUAL - 138 - - - - P14635 - UniProt - - - - REACT_3451 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3451.2 - - - - ENST00000404735 - Ensembl - - - - NP_004150 - RefSeq - - - - - - MOD_RES 151 151 Phosphoserine. - - - - ENST00000395095 - Ensembl - - - - ENSP00000402406 - Ensembl - - - - PSMC1 - HGNC - - - - - - ubiquitin (UBC 8) - - - - - Reactome DB_ID: 939239 - http://www.reactome.org/biopax/46/48887#Protein1056 - UBC(533-608) - - - - B3KN89 - UniProt - - - - EQUAL - 392 - - - - EQUAL - 450 - - - - Q9H3P9 - UniProt - - - - EQUAL - 64 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4861 - - - - - - - - Cyclin A - Cyclin A2 - - - - - Reactome DB_ID: 68905 - http://www.reactome.org/biopax/46/48887#Protein5608 - CCNA2 - - - - - - Proteasome subunit p58 - 26S proteasome non-ATPase regulatory subunit 3 - 26S proteasome regulatory subunit S3 - - - - - http://www.reactome.org/biopax/46/48887#Protein1069 - Reactome DB_ID: 68798 - PSMD3 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6787 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2663 - - - - NP_001191676 - RefSeq - - - - CHEBI:42290 - ChEBI - - - - EQUAL - 913 - - - - 11931757 - Kim, SY - Zou-Yang, XH - Hidaka, M - Tansey, WP - Mendez, J - Stillman, B - Pubmed - Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replication. - Mol Cell 9:481-91 - 2002 - - - - Q4VXG8 - UniProt - - - - REACT_3929 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3929.2 - - - - PSMC1 - HGNC Symbol - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite5751 - - - - REACT_1181 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1181.3 - - - - REACT_951 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_951.3 - - - - NP_002799 - RefSeq - - - - ENSP00000338039 - Ensembl - - - - PCNA - HGNC - - - - ENSP00000414083 - Ensembl - - - - PSME2 - HGNC Symbol - - - - EQUAL - 161 - - - - REACT_3813 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3813.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1041 - - - - ENST00000392858 - Ensembl - - - - 5720 - NCBI Gene - - - - 51343 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval874 - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6611 - - - - EQUAL - 171 - - - - - - - - - - - - RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer - Reactome DB_ID: 68471 - http://www.reactome.org/biopax/46/48887#Complex2635 - - - - 5704 - NCBI Gene - - - - NP_002798 - RefSeq - - - - 11836525 - Tanaka, S - Diffley, JF - Pubmed - Interdependent nuclear accumulation of budding yeast Cdt1 and Mcm2-7 during G1 phase. - Nat Cell Biol 4:198-207 - 2002 - - - - RPA2 - HGNC - - - - EQUAL - 205 - - - - ENST00000599595 - Ensembl - - - - MOD_RES Phosphotyrosine - - - - NM_001251991 - RefSeq - - - - 68780 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68780 - - - - REACT_4363 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4363.2 - - - - ENSP00000364016 - Ensembl - - - - 8143180 - pubchem - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - Q14566 - UniProt - - - - - - - - - - - - - Phosphorylation of proteins involved in the G1/S transition by Cyclin A:Cdk2 - Reviewed: Coqueret, O, 2006-10-06 08:59:06 - Active Cyclin A:Cdk2 complexes phosphorylate and inactivate proteins required for maintaining the G1/S phase including: Cdh1, RB1, p21 and p27. All this creates auto-amplification loops that render Cdk2 increasingly more active. In G2, Cdk2, in association with cyclin A, phosphorylates E2F1 and E2F3 resulting in the inactivation and possibly degradation of these two transcription factors (Dynlacht et al., 1994; Krek et al., 1994). - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1992 - Edited: Matthews, L, 2006-09-28 04:25:14 - Authored: Pagano, M, 2006-09-19 08:23:10 - - - - - - NP_777360 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4951 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature822 - - - - NM_005805 - RefSeq - - - - Q9BS70 - UniProt - - - - EQUAL - 47 - - - - HGNC:9554 - HGNC - - - - ENSP00000264639 - Ensembl - - - - MCM10 - HGNC - - - - PSMD9 - HGNC - - - - ENSP00000360621 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10862 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval871 - - - - - - - - DRTF1 - E2F dimerization partner 1 - Transcription factor Dp-1 - DRTF1- polypeptide-1 - Transcription factor DP-1 (E2F dimerization partner 1)(DRTF1-polypeptide-1) (DRTF1) - TFDP1 - - - - - http://www.reactome.org/biopax/46/48887#Protein3059 - Reactome DB_ID: 68652 - DP-1 - - - - EQUAL - 725 - - - - 68467 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68467 - - - - HGNC:6944 - HGNC - - - - NP_862820 - RefSeq - - - - 1K0P - PROTEIN DATA BANK - - - - P0CG47 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2463 - - - - - HGNC:9176 - HGNC - - - - REACT_567 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_567.4 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2433 - - - - - - Q53XP2 - UniProt - - - - ENST00000272317 - Ensembl - - - - 4175 - NCBI Gene - - - - REACT_3288 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3288.1 - - - - NP_001186701 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6663 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4986 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4862 - - - - - - ENSP00000367986 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6701 - - - - 68819 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68819 - - - - MOD_RES N-acetylthreonine - - - - EQUAL - 130 - - - - ENSP00000368349 - Ensembl - - - - - - Phospho-Rb - phospho-Retinoblastoma protein - - - - - - Reactome DB_ID: 69226 - http://www.reactome.org/biopax/46/48887#Protein5635 - p-S795-RB1 - - - - DBF4 - HGNC Symbol - - - - PSMB6 - HGNC Symbol - - - - 9745018 - Foster, AJ - Aves, SJ - Tongue, N - Hart, EA - Pubmed - The essential schizosaccharomyces pombe cdc23 DNA replication gene shares structural and functional homology with the Saccharomyces cerevisiae DNA43 (MCM10) gene - Curr Genet 34:164-71 - 1998 - - - - ENSG00000166508 - Ensembl - - - - ENST00000206451 - Ensembl - - - - - - PSMB4 - Multicatalytic endopeptidase complex beta chain - Proteasome chain 3 - Macropain beta chain - HsBPROS26 - Proteasome beta chain - Proteasome subunit beta type 4 precursor - Proteasome subunit beta type 4 - - - - - http://www.reactome.org/biopax/46/48887#Protein1099 - Reactome DB_ID: 68750 - HSN3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4983 - - - - - - - - MOD_RES 250 250 Phosphothreonine (By similarity). - - - - NM_002814 - RefSeq - - - - - - MOD_RES 26 26 Phosphoserine. - - - - NM_005047 - RefSeq - - - - - - - - - - - - Joining of adjacent Okazaki fragments - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2019 - Removal of the flap by FEN-1 leads to the generation of a nick between the 3'-end of the upstream Okazaki fragment and the 5'-end of the downstream Okazaki fragment. DNA ligase I then seals the nicks between adjacent processed Okazaki fragments to generate intact double-stranded DNA. - - - - - PTHR11599:SF11 - PANTHER Family - - - - - NM_000234 - RefSeq - - - - 2237 - NCBI Gene - - - - ENSG00000008018 - Ensembl - - - - EQUAL - 187 - http://www.reactome.org/biopax/46/48887#SequenceSite10749 - - - - ENSP00000369411 - Ensembl - - - - B2R8V1 - UniProt - - - - HGNC:6949 - HGNC - - - - HGNC:6945 - HGNC - - - - - - MOD_RES 2 2 N-acetylvaline. - - - - ENSP00000359910 - Ensembl - - - - - - - - - - - - - DNA Replication Factor A - RPA - - - - RFA - Reactome DB_ID: 68567 - http://www.reactome.org/biopax/46/48887#Complex2603 - - - - ENSG00000126067 - Ensembl - - - - E1P663 - UniProt - - - - - - MOD_RES 377 377 N6-acetyllysine. - - - - - - Proteasome chain 6 - Macropain epsilon chain - Multicatalytic endopeptidase complex epsilon chain - Proteasome subunit X - Proteasome epsilon chain - Proteasome subunit MB1 - Proteasome subunit beta type 5 precursor - Proteasome subunit beta type 5 - - - - - Reactome DB_ID: 68753 - http://www.reactome.org/biopax/46/48887#Protein1102 - PSMB5 - - - - 68947 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68947 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10616 - - - - Q99741 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10719 - - - - ENSG00000131467 - Ensembl - - - - RFC1 - HGNC Symbol - - - - - - MOD_RES 315 315 Phosphoserine. - - - - GO:0005654 - Gene Ontology - - - - 1871 - NCBI Gene - - - - HGNC:9544 - HGNC - - - - 9660172 - Mossi, R - Hubscher, U - Pubmed - Clamping down on clamps and clamp loaders--the eukaryotic replication factor C. - Eur J Biochem 254:209-16 - 1998 - - - - - - Cell division protein kinase 2 - p33 protein kinase - Cell division protein kinase 2 (EC 2.7.1.-)(p33 protein kinase)(CDK2) - Cdk2 - - - - - http://www.reactome.org/biopax/46/48887#Protein1666 - Reactome DB_ID: 68365 - CDK2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4854 - - - - - - 11842200 - Schneider, RJ - Laroia, G - Sarkar, B - Pubmed - Ubiquitin-dependent mechanism regulates rapid turnover of AU-rich cytokine mRNAs - Proc Natl Acad Sci U S A 99:1842-6 - 2002 - - - - 176842 - omim - - - - NM_001190819 - RefSeq - - - - NP_056979 - RefSeq - - - - NM_181837 - RefSeq - - - - 68461 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68461 - - - - RPA1 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature876 - - - - NM_013347 - RefSeq - - - - - - MOD_RES 243 243 Phosphoserine. - - - - REACT_1889 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1889.3 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2478 - - - - REACT_3782 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3782.1 - - - - NM_002818 - RefSeq - - - - REACT_3672 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3672.3 - - - - EQUAL - 248 - http://www.reactome.org/biopax/46/48887#SequenceSite1881 - - - - - - - - Activating E2F transcription factors - Cell cycle promoting E2Fs - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 68640 - http://www.reactome.org/biopax/46/48887#Protein5632 - E2F1/2/3 - - - - - - CDC46 homolog - P1-CDC46 - DNA replication licensing factor MCM5 - Mcm5 - - - - - Reactome DB_ID: 68551 - http://www.reactome.org/biopax/46/48887#Protein5586 - MCM5 - - - - ENSP00000261479 - Ensembl - - - - O75419 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2469 - - - - EQUAL - 795 - - - - - - Cdc6 - - - - - - http://www.reactome.org/biopax/46/48887#Protein5726 - Reactome DB_ID: 113566 - CDC6 - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite4652 - - - - HGNC:6948 - HGNC - - - - - - DNA polymerase delta subunit 3 - DNA pol delta subunit 3 - DNA polymerase delta subunit p66 - - - - - Reactome DB_ID: 68445 - http://www.reactome.org/biopax/46/48887#Protein5733 - POLD3 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2094 - - - - 126391 - omim - - - - 68825 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68825 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6689 - - - - REACT_5625 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5625.3 - - - - NP_002807 - RefSeq - - - - EQUAL - 1843 - http://www.reactome.org/biopax/46/48887#SequenceSite1849 - - - - 1722322 - Downey KM - Tan CK - So AG - Davie EW - Zhang JA - Chung DW - PubMed - Primary structure of the catalytic subunit of human DNA polymerase delta and chromosomal location of the gene. - Proc Natl Acad Sci U S A 88(24);11197-201 - 1991 - - - - PTHR10416:SF0 - PANTHER Family - - - - 28227 - NCBI Gene - - - - REACT_2443 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2443.2 - - - - ENST00000412908 - Ensembl - - - - EQUAL - 13 - - - - 604972 - omim - - - - ENSP00000219097 - Ensembl - - - - - - MOD_RES 66 66 Phosphoserine. - - - - EQUAL - 616 - http://www.reactome.org/biopax/46/48887#SequenceSite2930 - - - - PSMA4 - HGNC - - - - EQUAL - 516 - - - - - 3.1.3.16 - - - - - - - PP2A mediated localization of RB1 protein in chromatin - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1981 - At the beginning of this reaction, 1 molecule of 'phospho-Retinoblastoma protein', and 1 molecule of 'RNA primer-DNA primer:origin duplex with DNA damage' are present. At the end of this reaction, 1 molecule of 'Rb1:RNA primer-DNA primer:origin duplex with DNA damage' is present.<br><br> This reaction takes place in the 'nucleus' and is mediated by the 'phosphoprotein phosphatase activity' of 'PP2A'.<br> - - - - - NP_002706 - RefSeq - - - - REACT_1673 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1673.2 - - - - - - MOD_RES 63 63 Phosphoserine. - - - - MOD_RES Nitrated tyrosine - - - - NM_001144932 - RefSeq - - - - Q92768 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1794 - - - - ENST00000447452 - Ensembl - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10846 - - - - ENST00000262460 - Ensembl - - - - - - MOD_RES 364 364 Phosphothreonine. - - - - NM_182649 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2119 - - - - - - C9JU95 - UniProt - - - - - - PSMB3 - Proteasome theta chain - 3.4.25.1 - Proteasome component C10-II - Proteasome chain 13 - - - - - - - - - - - - - - - - PSB3_HUMAN - Proteasome subunit beta type-3 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with HIV-1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.INDUCTION: Up-regulated in asthenozoospermic sperm.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - Macropain subunit C7-I - Multicatalytic endopeptidase complex subunit C7-I - PSMB2 - Proteasome component C7-I - 3.4.25.1 - - - - - - - - - - - - - - - PSB2_HUMAN - Proteasome subunit beta type-2 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit has a trypsin-like activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with HIV-1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.INDUCTION: Up-regulated in ovarian cancer cell lines.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 143471 - NCBI Gene - - - - ENSP00000379675 - Ensembl - - - - EQUAL - 163 - - - - ENSP00000357879 - Ensembl - - - - - - - - - - Recruitment of Dna2 endonuclease - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2016 - After RPA binds the long flap, it recruits the Dna2 endonuclease. Dna2 endonuclease removes most of the flap, but the job of complete removal of the flap is then completed by FEN-1. - - - - - G3V1Q6 - UniProt - - - - REACT_3560 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3560.1 - - - - PTHR10223:SF0 - PANTHER Family - - - - 68469 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68469 - - - - 169468 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=169468 - - - - REACT_70 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_70.3 - - - - CHEBI:14093 - ChEBI - - - - ENSP00000428754 - Ensembl - - - - EQUAL - 373 - - - - Q9BQ42 - UniProt - - - - - - 2.7.7.7 - DNA polymerase II subunit A - POLE - POLE1 - - - - - - - - - - - - - - - - - - DPOE1_HUMAN - DNA polymerase epsilon catalytic subunit A - FUNCTION: Participates in DNA repair and in chromosomal DNA replication.CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).COFACTOR: Binds 1 4Fe-4S cluster (By similarity).SUBUNIT: Catalytic and central component of the epsilon DNA polymerase complex consisting of four subunits: POLE, POLE2, POLE3 and POLE4. Interacts with RAD17 and TOPBP1.SUBCELLULAR LOCATION: Nucleus.DOMAIN: The DNA polymerase activity domain resides in the N- terminal half of the protein, while the C-terminus is necessary for complexing subunits B and C. The C-terminus may also regulate the catalytic activities of the enzyme.DOMAIN: The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (By similarity).DISEASE: Colorectal cancer 12 (CRCS12) [MIM:615083]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. CRCS12 is characterized by a high-penetrance predisposition to the development of colorectal adenomas and carcinomas, with a variable tendency to develop multiple and large tumors. Onset is usually before age 40 years. The histologic features of the tumors are unremarkable. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Facial dysmorphism, immunodeficiency, livedo, and short stature (FILS) [MIM:615139]: A syndrome characterized by mild facial dysmorphism, mainly malar hypoplasia, livedo on the skin since birth, and immunodeficiency resulting in recurrent infections. Growth impairment is observed during early childhood and results in variable short stature in adulthood. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the DNA polymerase type-B family.SIMILARITY: Contains 1 CysA-type zinc finger.SEQUENCE CAUTION: Sequence=AAA15448.1; Type=Frameshift; Positions=443, 448; Sequence=AAA15448.1; Type=Miscellaneous discrepancy;WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pole/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1053 - - - - - - Cytidine-5'-monophosphate - cytidine 5'-monophosphate - cytidylic acid - - - - Reactome DB_ID: 418076 - http://www.reactome.org/biopax/46/48887#SmallMolecule594 - CMP - - - - 8223461 - Méchali, M - Hyrien, O - Pubmed - Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. - EMBO J 12:4511-20 - 1993 - - - - NP_115712 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2101 - - - - ENSP00000055077 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature860 - - - - REACT_5663 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5663.2 - - - - Q68DT0 - UniProt - - - - EQUAL - 384 - - - - 7711022 - Müller, F - Podust, VN - Hubscher, U - Podust, LM - Pubmed - DNA polymerase delta holoenzyme: action on single-stranded DNA and on double-stranded DNA in the presence of replicative DNA helicases. - Biochemistry 34:5003-10 - 1995 - - - - 11125146 - Dutta, A - Dwyer, BT - Cvetic, C - Wohlschlegel, JA - Walter, JC - Dhar, SK - Pubmed - Inhibition of eukaryotic DNA replication by geminin binding to Cdt1. - Science 290:2309-12 - 2000 - - - - 8223465 - Tseng BY - Kelly TJ - Collins KL - Russo AA - PubMed - The role of the 70 kDa subunit of human DNA polymerase alpha in DNA replication. - EMBO J 12(12);4555-66 - 1993 - - - - - - - - - - - - - - - - - - - 3.6.4.12 - KIAA0030 - Nuclear protein BM28 - CDCL1 - Minichromosome maintenance protein 2 homolog - CCNL1 - MCM2 - BM28 - - - - - - - - - - - - - - - - - - MCM2_HUMAN - DNA replication licensing factor MCM2 - FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Required for the entry in S phase and for cell division.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6- MCM4-MCM7-MCM3-MCM5 (By simililarity). Interacts with DBF4 (By similarity). Interacts with KAT7. May interact with MCM10.SUBCELLULAR LOCATION: Nucleus.PTM: Phosphorylated on Ser-108 by ATR in proliferating cells. Ser- 108 proliferation is increased by genotoxic agents. Ser-40 is mediated by the CDC7-DBF4 and CDC7-DBF4B complexes, while Ser-53 phosphorylation is only mediated by the CDC7-DBF4 complex. Phosphorylation by the CDC7-DBF4 complex during G1/S phase is required for the initiation of DNA replication.MISCELLANEOUS: Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain.SEQUENCE CAUTION: Sequence=BAA04642.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA12177.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAA47749.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAA47749.1; Type=Frameshift; Positions=115, 124, 127, 129, 154, 158, 773, 811;WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/mcm2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 2AZE - PROTEIN DATA BANK - - - - Q92524 - UniProt - - - - REACT_4338 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4338.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7552 - - - - - - MOD_RES 1 1 N-acetylmethionine (By similarity). - - - - - - Origin recognition complex subunit 1 - Replication control protein 1 - phosphorylated Orc1 - - - - - - - Reactome DB_ID: 68943 - http://www.reactome.org/biopax/46/48887#Protein5722 - p-S,T-ORC1 - - - - 23595 - NCBI Gene - - - - ENSP00000385659 - Ensembl - - - - NM_181471 - RefSeq - - - - ORC3 - HGNC - - - - EQUAL - 2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval834 - - - - - - ENSP00000396937 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval875 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4875 - - - - - - MOD_RES 93 93 Phosphoserine. - - - - ENST00000370861 - Ensembl - - - - P14798 - UniProt - - - - NM_001191037 - RefSeq - - - - D3DQ34 - UniProt - - - - Q7Z6H1 - UniProt - - - - EQUAL - 14 - - - - 68567 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68567 - - - - 69172 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69172 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4940 - - - - ENST00000454402 - Ensembl - - - - 5705 - NCBI Gene - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature849 - - - - HGNC:1739 - HGNC - - - - - - MOD_RES 113 113 N6-acetyllysine. - - - - NM_002913 - RefSeq - - - - NM_001130725 - RefSeq - - - - ENSG00000062822 - Ensembl - - - - ENST00000361282 - Ensembl - - - - 10402192 - Velinzon, K - Smith, P - Austin, RJ - Quintana, DG - Jones, CJ - Boynton, S - Lane, WS - Hendricks, M - Wohlschlegel, JA - Tully, T - Dutta, A - Mihalek, RM - Hou, ZH - Pinto, S - Pubmed - latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant. - Neuron 23:45-54 - 1999 - - - - EQUAL - 198 - http://www.reactome.org/biopax/46/48887#SequenceSite10543 - - - - NP_000938 - RefSeq - - - - ENSG00000123374 - Ensembl - - - - 69173 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69173 - - - - ENSP00000364015 - Ensembl - - - - EQUAL - 368 - - - - - - - - - - - - - - AUF1 - hnRNP D0 - HNRPD - HNRNPD - AU-rich element RNA-binding protein 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HNRPD_HUMAN - Heterogeneous nuclear ribonucleoprotein D0 - FUNCTION: Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto- oncogenes and cytokine mRNAs. Also binds to double- and single- stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'- TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.SUBUNIT: Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and untranslated mRNAs. Part of a complex associated with the FOS mCRD domain and consisting of PABPC1, PAIP1, CSDE1/UNR and SYNCRIP. Interacts with IGF2BP2. Interacts with GTPBP1.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Component of ribonucleosomes.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Name=1; Synonyms=p45, Dx9; IsoId=Q14103-1; Sequence=Displayed; Name=2; Synonyms=p42, Dx4; IsoId=Q14103-2; Sequence=VSP_005834; Name=3; Synonyms=p40, Dx7; IsoId=Q14103-3; Sequence=VSP_005835; Note=Contains a N6-acetyllysine at position 292; Name=4; Synonyms=p37; IsoId=Q14103-4; Sequence=VSP_005834, VSP_005835; Note=Contains a N6-acetyllysine at position 273;PTM: Arg-345 is dimethylated, probably to asymmetric dimethylarginine.PTM: Methylated by PRMT1, in an insulin-dependent manner. The PRMT1-mediated methylation regulates tyrosine phosphorylation (By similarity).SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.SEQUENCE CAUTION: Sequence=AAA35781.1; Type=Frameshift; Positions=45, 59, 355; Sequence=AAA35781.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part; Sequence=CAA27544.1; Type=Miscellaneous discrepancy; Note=Several sequence conflicts;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/HNRNPDID40840ch4q21.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 15494305 - Bielinsky, AK - Ricke, RM - Pubmed - Mcm10 regulates the stability and chromatin association of DNA polymerase-alpha - Mol Cell 16:173-85 - 2004 - - - - CCNA1 - HGNC Symbol - - - - ENSP00000379914 - Ensembl - - - - 600307 - omim - - - - 5985 - NCBI Gene - - - - HGNC:9533 - HGNC - - - - - - MOD_RES 273 273 Phosphothreonine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4984 - - - - - - NM_001256879 - RefSeq - - - - Q6UW54 - UniProt - - - - - - Proteasome subunit p42 - PSMC6 - SUG2 - 26S proteasome AAA-ATPase subunit RPT4 - Proteasome 26S subunit ATPase 6 - - - - - - - - - - - - - - - - PRS10_HUMAN - 26S protease regulatory subunit 10B - FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.SUBUNIT: Found in the multi-protein complexes: the 26S proteasome (formed from the 20S proteasome and PA700), and the modulator. PA700 consists of 28 subunits arranged to form a cylinder-shaped complex by four stacked rings, each containing seven subunits. Interacts with PAAF1.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).SIMILARITY: Belongs to the AAA ATPase family.CAUTION: Alternative initiation from an upstream conserved methionine cannot be fully excluded but is not experimentally supported while initiation from the displayed methionine is supported by PubMed:17323924. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - 26S proteasome non-ATPase regulatory subunit 13 - 26S proteasome regulatory subunit p40.5 - 26S proteasome regulatory subunit S11 - - - - - Reactome DB_ID: 68794 - http://www.reactome.org/biopax/46/48887#Protein1073 - PSMD13 - - - - Q9BQ77 - UniProt - - - - ENSP00000262105 - Ensembl - - - - - - MOD_RES 85 85 Phosphothreonine. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10868 - - - - 3008955 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3008955 - - - - EQUAL - 420 - http://www.reactome.org/biopax/46/48887#SequenceSite10871 - - - - Q14691 - UniProt - - - - - - - - - FYR - FZR1 - FZR - CDC20-like protein 1 - KIAA1242 - Fzr - CDH1 - hCDH1 - Cdh1/Hct1 homolog - - - - - - - - - - - - - - - - - - - - - - - - - - - - FZR_HUMAN - Fizzy-related protein homolog - FUNCTION: Key regulator of ligase activity of the anaphase promoting complex/cyclosome (APC/C), which confers substrate specificity upon the complex. Associates with the APC/C in late mitosis, in replacement of CDC20, and activates the APC/C during anaphase and telophase. The APC/C remains active in degrading substrates to ensure that positive regulators of the cell cycle do not accumulate prematurely. At the G1/S transition FZR1 is phosphorylated, leading to its dissociation from the APC/C. Following DNA damage, it is required for the G2 DNA damage checkpoint: its dephosphorylation and reassociation with the APC/C leads to the ubiquitination of PLK1, preventing entry into mitosis.PATHWAY: Protein modification; protein ubiquitination.SUBUNIT: The unphosphorylated form interacts with APC/C during mitosis. Interacts with NINL. Interacts (in complex with the anaphase promoting complex APC) with MAD2L2; inhibits FZR1- mediated APC/C activation. Interacts with USP37. Interacts (via WD repeats) with MAK.SUBCELLULAR LOCATION: Isoform 2: Nucleus.SUBCELLULAR LOCATION: Isoform 3: Cytoplasm.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q9UM11-1; Sequence=Displayed; Name=2; Synonyms=CDH1alpha, Fzr1; IsoId=Q9UM11-2; Sequence=VSP_008504; Note=Major; Name=3; Synonyms=CDH1beta, Fzr2; IsoId=Q9UM11-3; Sequence=VSP_008503, VSP_008504; Note=Minor;TISSUE SPECIFICITY: Isoform 2 is expressed at high levels in heart, liver, spleen and some cancer cell lines whereas isoform 3 is expressed only at low levels in these tissues.PTM: Phosphorylated during mitosis, probably by maturation promoting factor (MPF), leading to its dissociation of the APC/C. Following DNA damage, it is dephosphorylated by CDC14B in G2 phase, leading to its reassociation with the APC/C, and allowing an efficient G2 DNA damage checkpoint. Phosphorylated by MAK.SIMILARITY: Belongs to the WD repeat CDC20/Fizzy family.SIMILARITY: Contains 7 WD repeats.SEQUENCE CAUTION: Sequence=AAD26623.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part; Sequence=AAD26624.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part; Sequence=BAA86556.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 57804 - NCBI Gene - - - - - - phosphorylated Cdc6 - - - - - - http://www.reactome.org/biopax/46/48887#Protein5725 - Reactome DB_ID: 68583 - p-CDC6 - - - - 68495 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68495 - - - - - - Proteasome zeta chain - Multicatalytic endopeptidase complex zeta chain - Macropain zeta chain - Proteasome subunit alpha type 5 - - - - - http://www.reactome.org/biopax/46/48887#Protein1071 - Reactome DB_ID: 68732 - PSMA5 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1810 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1060 - - - - - - MOD_RES 411 411 Phosphothreonine. - - - - MOD_RES Phosphoserine (By similarity) - - - - NM_002817 - RefSeq - - - - EQUAL - 270 - http://www.reactome.org/biopax/46/48887#SequenceSite2926 - - - - EQUAL - 63 - - - - EQUAL - 65 - - - - NM_002802 - RefSeq - - - - ENSP00000393139 - Ensembl - - - - EQUAL - 762 - - - - HAAZLUGHYHWQIW-KVQBGUIXSA-N - InChIKey - - - - PTHR10648:SF2 - PANTHER Family - - - - - PSME1 - HGNC Symbol - - - - EQUAL - 478 - - - - EQUAL - 16 - - - - - - - - - DP-1:E2F1 complex - - - - E2F1:TFDP1 - Reactome DB_ID: 68653 - http://www.reactome.org/biopax/46/48887#Complex2598 - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite4658 - - - - PSMC5 - HGNC - - - - Q9BWM0 - UniProt - - - - O14818 - UniProt - - - - Q20WK8 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6666 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6646 - - - - - - Proteasome component C13 - Multicatalytic endopeptidase complex subunit C13 - Macropain subunit C13 - Proteasome subunit beta type 8 - Proteasome subunit beta type 8 precursor - - - - - http://www.reactome.org/biopax/46/48887#Protein1079 - Reactome DB_ID: 68762 - PSMB8 - - - - EQUAL - 130 - - - - HGNC:9973 - HGNC - - - - ENSG00000132646 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4964 - - - - EQUAL - 191 - - - - PTHR10536:SF0 - PANTHER Family - - - - - REACT_5149 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5149.1 - - - - EQUAL - 560 - http://www.reactome.org/biopax/46/48887#SequenceSite10892 - - - - 8318 - NCBI Gene - - - - NM_182751 - RefSeq - - - - - - MOD_RES 567 567 Phosphoserine; by CDK2. - - - - HGNC:9530 - HGNC - - - - REACT_5709 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5709.1 - - - - 68768 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68768 - - - - - - MOD_RES 13 13 Phosphoserine. - - - - ENST00000221138 - Ensembl - - - - EQUAL - 433 - http://www.reactome.org/biopax/46/48887#SequenceSite1831 - - - - CDC6 - HGNC Symbol - - - - - - MOD_RES 298 298 N6-acetyllysine. - - - - REACT_5120 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5120.1 - - - - EQUAL - 340 - http://www.reactome.org/biopax/46/48887#SequenceSite10597 - - - - ENST00000371566 - Ensembl - - - - 69298 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69298 - - - - InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 - InChI - - - - ENSG00000231631 - Ensembl - - - - A5LHX3 - UniProt - - - - ENSP00000368438 - Ensembl - - - - 947607 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=947607 - - - - NM_031369 - RefSeq - - - - CDT1 - HGNC Symbol - - - - NM_181573 - RefSeq - - - - PCDQPRRSZKQHHS-XVFCMESISA-N - InChIKey - - - - EQUAL - 151 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4904 - - - - - - REACT_3361 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3361.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1044 - - - - 12136087 - Schneider, RJ - Laroia, G - Pubmed - Alternate exon insertion controls selective ubiquitination and degradation of different AUF1 protein isoforms - Nucleic Acids Res 30:3052-8 - 2002 - - - - ENSP00000384211 - Ensembl - - - - Q6IBF7 - UniProt - - - - EQUAL - 1148 - http://www.reactome.org/biopax/46/48887#SequenceSite10904 - - - - - - MOD_RES 160 160 Phosphoserine; by PKC; in vitro. - - - - - - MOD_RES 29 29 Phosphoserine. - - - - REACT_3010 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3010.1 - - - - 8131753 - Lieber, MR - Harrington, JJ - Pubmed - The characterization of a mammalian DNA structure-specific endonuclease. - EMBO J 13:1235-46 - 1994 - - - - ENSG00000101003 - Ensembl - - - - O00558 - UniProt - - - - EQUAL - 127 - - - - ENSP00000459838 - Ensembl - - - - REACT_9368 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9368.1 - - - - EQUAL - 566 - http://www.reactome.org/biopax/46/48887#SequenceSite10613 - - - - PTHR11352:SF0 - PANTHER Family - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1868 - - - - B2RD35 - UniProt - - - - EQUAL - 280 - - - - - - MOD_RES 54 54 Phosphoserine. - - - - - - Orc4 - Origin recognition complex subunit 4 - - - - - http://www.reactome.org/biopax/46/48887#Protein5578 - Reactome DB_ID: 68519 - ORC4 - - - - - - MOD_RES 164 164 Phosphoserine. - - - - 5981 - NCBI Gene - - - - NP_001129669 - RefSeq - - - - - - MOD_RES 345 345 Phosphothreonine. - - - - - - MOD_RES 178 178 Phosphoserine. - - - - 604281 - omim - - - - ENSP00000410671 - Ensembl - - - - ENSP00000363015 - Ensembl - - - - PPP2R1B - HGNC Symbol - - - - 182563 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=182563 - - - - 68891 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68891 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1376 - - - - - - 68513 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68513 - - - - 605129 - omim - - - - ENSP00000262460 - Ensembl - - - - - - - - - - - - - - - - GINS complex - http://www.reactome.org/biopax/46/48887#Complex2630 - Reactome DB_ID: 176952 - - - - 68439 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68439 - - - - B2RCK6 - UniProt - - - - ENSP00000261303 - Ensembl - - - - EQUAL - 197 - - - - REACT_3167 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3167.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval838 - - - - - - NP_001245 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval876 - - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10980 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1055 - - - - - - - - - - - - - - Mcm2-7 associates with the Cdt1:CDC6:ORC:origin complex, forming the pre-replicative complex (preRC) - Genetic studies in S. cerevisiae indicate that wild-type Cdc6 function is required for correctly timed loading of Mcm2-7 onto ORC. Biochemical studies indicate that the human and Xenopus Cdc6 proteins likewise are required for Mcm2-7 loading, and that they are ATPase switches. Specifically, Cdc6 may function as a clamp loader, assembling Mcm2-7 onto DNA in an ATP-dependent reaction. All known Cdc6 proteins have the Walker A and Walker B sequence motifs characteristic of the AAA+ superfamily of ATPases. As expected for an AAA+ protein, human Cdc6 binds and slowly hydrolyzes ATP in vitro. ATP hydrolysis was disrupted by mutations of the Walker B motif, while both binding and hydrolysis were disrupted by Walker A mutations. Microinjection of either mutant protein into HeLa cells blocked their progression through S phase. Both wild-type and mutant proteins can dimerize in vitro, and studies with Xenopus egg extracts suggest that Cdc6 functions in vivo as a dimer or larger multimer. In Xenopus extracts depleted of Cdc6 and reconstituted with either mutant protein, recruitment of Mcm2-7 to chromatin failed. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2149 - - - - - - - MOD_RES 27 27 Phosphoserine. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10624 - - - - - - - - - - - - - Association of licensing factors with the pre-replicative complex - http://www.reactome.org/biopax/46/48887#Pathway519 - The eukaryotic six-subunit origin recognition complex (ORC) governs the initiation site of DNA replication and formation of the prereplication complex. - - - - - - - ubiquitin (UBC 4) - - - - - http://www.reactome.org/biopax/46/48887#Protein2480 - Reactome DB_ID: 939857 - UBC(229-304) - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10917 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6619 - - - - EQUAL - 457 - http://www.reactome.org/biopax/46/48887#SequenceSite4665 - - - - - - MOD_RES 160 160 Phosphothreonine; by CAK and CCRK. - - - - REACT_5274 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5274.2 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2655 - - - - - - - MOD_RES 422 422 N6-acetyllysine. - - - - DNA polymerase subunit delta p125 - 2.7.7.7 - POLD1 - POLD - - - - - - - - - - - - - - - - - - - - - - - - - DPOD1_HUMAN - DNA polymerase delta catalytic subunit - FUNCTION: Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex.CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).COFACTOR: Binds 1 4Fe-4S cluster (By similarity).SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. The 125 kDa subunit contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity. Interacts with WRNIP1. Interacts with POLD4 and PCNA.SUBCELLULAR LOCATION: Nucleus.DOMAIN: The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (By similarity).DISEASE: Colorectal cancer 10 (CRCS10) [MIM:612591]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.MISCELLANEOUS: In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.SIMILARITY: Belongs to the DNA polymerase type-B family.SIMILARITY: Contains 1 CysA-type zinc finger.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pold1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4644 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4812 - - - - ENST00000535432 - Ensembl - - - - ENSG00000006634 - Ensembl - - - - REACT_541 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_541.3 - - - - ORC5 - HGNC - - - - EQUAL - 46 - http://www.reactome.org/biopax/46/48887#SequenceSite1872 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature863 - - - - ENST00000378896 - Ensembl - - - - P60900 - UniProt - - - - POLA1 - HGNC Symbol - - - - 601902 - omim - - - - REACT_24369 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24369.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4856 - - - - NP_001009552 - RefSeq - - - - ENSG00000087191 - Ensembl - - - - - - 26S proteasome non-ATPase regulatory subunit 9 - 26S proteasome regulatory subunit p27 - - - - - http://www.reactome.org/biopax/46/48887#Protein1081 - Reactome DB_ID: 68810 - PSMD9 - - - - P43686 - UniProt - - - - - - DNA pol delta catalytic subunit - DNA polymerase delta catalytic subunit - DNA polymerase delta subunit p125 - - - - - Reactome DB_ID: 68449 - http://www.reactome.org/biopax/46/48887#Protein5734 - POLD1 - - - - Q9UEX3 - UniProt - - - - Q9UCE9 - UniProt - - - - PSMA5 - HGNC - - - - ENSP00000305860 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4856 - - - - - - - - Cdk1 - Cdc2 - - - - - http://www.reactome.org/biopax/46/48887#Protein5609 - Reactome DB_ID: 68889 - CDK1 - - - - EQUAL - 380 - http://www.reactome.org/biopax/46/48887#SequenceSite4662 - - - - 187965 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187965 - - - - Q5W0E8 - UniProt - - - - ENSP00000470507 - Ensembl - - - - - - - - - - DNA polymerase alpha 70 kDa subunit - POLA2 - - - - - - - - - - - - - - DPOA2_HUMAN - DNA polymerase alpha subunit B - FUNCTION: May play an essential role at the early stage of chromosomal DNA replication by coupling the polymerase alpha/primase complex to the cellular replication machinery (By similarity).SUBUNIT: DNA polymerase alpha:primase is a four subunit enzyme complex, which is assembled throughout the cell cycle, and consists of the two DNA polymerase subunits A and B, and the DNA primase large and small subunits. Subunit B binds to subunit A.SUBCELLULAR LOCATION: Nucleus.DOMAIN: The N-terminal 240 amino acids are sufficient to mediate complex formation.PTM: Phosphorylated in a cell cycle-dependent manner, in G2/M phase.SIMILARITY: Belongs to the DNA polymerase alpha subunit B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 5706 - NCBI Gene - - - - RFC2 - HGNC Symbol - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2425 - - - - - - ENSP00000409284 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite2966 - - - - 602161 - omim - - - - - - MOD_RES 195 195 Phosphothreonine. - - - - CHEBI:13286 - ChEBI - - - - PTHR11599:SF14 - PANTHER Family - - - - - 68405 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68405 - - - - HGNC:9972 - HGNC - - - - ENST00000270586 - Ensembl - - - - PPP2R1B - PP2A subunit A isoform PR65-beta - PP2A subunit A isoform R1-beta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2AAB_HUMAN - Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform - FUNCTION: The PR65 subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit.SUBUNIT: PP2A consists of a common heterodimeric core enzyme, composed of a 36 kDa catalytic subunit (subunit C) and a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Interacts with IPO9. Interacts with SGOL1. Interacts with RAF1.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=5; Name=1; IsoId=P30154-1; Sequence=Displayed; Name=2; IsoId=P30154-2; Sequence=VSP_036460; Name=3; IsoId=P30154-3; Sequence=VSP_043379, VSP_036460; Note=No experimental confirmation available; Name=4; IsoId=P30154-4; Sequence=VSP_045275; Note=No experimental confirmation available; Name=5; IsoId=P30154-5; Sequence=VSP_046684;DOMAIN: Each HEAT repeat appears to consist of two alpha helices joined by a hydrophilic region, the intrarepeat loop. The repeat units may be arranged laterally to form a rod-like structure.SIMILARITY: Belongs to the phosphatase 2A regulatory subunit A family.SIMILARITY: Contains 15 HEAT repeats.SEQUENCE CAUTION: Sequence=AAA59983.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part; Sequence=BAG59103.1; Type=Frameshift; Positions=540; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P49736 - UniProt - - - - - - - - - - ASF - Multiubiquitin chain-binding protein - AF - 26S proteasome regulatory subunit RPN10 - 26S proteasome regulatory subunit S5A - Antisecretory factor 1 - PSMD4 - MCB1 - - - - - - - - - - - - - - - - - PSMD4_HUMAN - 26S proteasome non-ATPase regulatory subunit 4 - FUNCTION: Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion.SUBUNIT: The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively. Directly interacts with NUB1. Interacts with SQSTM1. Interacts with UBQLN4. Interacts with UBE3A.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Comment=Additional isoforms seem to exist; Name=Rpn10A; IsoId=P55036-1; Sequence=Displayed; Name=Rpn10E; IsoId=P55036-2; Sequence=VSP_005291, VSP_005292; Note=May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay;DOMAIN: The 2 UIM motifs are involved in the binding to a multi- ubiquitin chain in a cooperative way.SIMILARITY: Belongs to the proteasome subunit S5A family.SIMILARITY: Contains 2 UIM (ubiquitin-interacting motif) repeats.SIMILARITY: Contains 1 VWFA domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - DRTF1-polypeptide 1 - DRTF1 - DP1 - E2F dimerization partner 1 - TFDP1 - - - - - - - - - - - - - - - TFDP1_HUMAN - Transcription factor Dp-1 - FUNCTION: Can stimulate E2F-dependent transcription. Binds DNA cooperatively with E2F family members through the E2 recognition site, 5'-TTTC[CG]CGC-3', found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DP2/E2F complex functions in the control of cell-cycle progression from G1 to S phase. The E2F1/DP complex appears to mediate both cell proliferation and apoptosis.SUBUNIT: Component of the E2F/DP transcription factor complex. Forms heterodimers with E2F family members. The complex can interact with hypophosphorylated retinoblastoma protein RB1 and related proteins (RBL1 and RBL2) that inhibit the E2F transactivation domain. This repression involves recruitment of histone deacetylase (HDAC). During the cell cycle, from mid-to- late G1 phase, RB family members become phosphorylated, detach from the DRTF1/E2F complex to render E2F transcriptionally active. Viral oncoproteins, notably E1A, T-antigen and HPV E7, are capable of sequestering RB protein, thus releasing the active complex. Part of the E2F6.com-1 complex in G0 phase is composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 YAF2. Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Highest levels in muscle. Also expressed in brain, placenta, liver and kidney. Lower levels in lung and pancreas. Not detected in heart.INDUCTION: Down-regulated during differentiation.PTM: Phosphorylation by E2F1-bound cyclin A-CDK2, in the S phase, inhibits E2F-mediated DNA binding and transactivation.MISCELLANEOUS: E2F/DP transactivation can be mediated by several cofactors including TBP, TFIIH, MDM2 and CBP.SIMILARITY: Belongs to the E2F/DP family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/tfdp1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P06400 - UniProt - - - - 10898791 - Whittaker, AJ - Orr-Weaver, TL - Royzman, I - Pubmed - Drosophila double parked: a conserved, essential replication protein that colocalizes with the origin recognition complex and links DNA replication with mitosis and the down-regulation of S phase transcripts. - Genes Dev 14:1765-76 - 2000 - - - - EQUAL - 1 - - - - - - PPP2R1A - PP2A subunit A isoform PR65-alpha - PP2A subunit A isoform R1-alpha - Medium tumor antigen-associated 61 kDa protein - - - - - - - - - - - - - - - - - 2AAA_HUMAN - Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform - FUNCTION: The PR65 subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. Required for proper chromosome segregation and for centromeric localization of SGOL1 in mitosis.SUBUNIT: Found in a complex with at least ARL2, PPP2CB, PPP2R1A, PPP2R2A, PPP2R5E and TBCD. Interacts with FOXO1; the interaction dephosphorylates FOXO1 on AKT-mediated phosphoylation sites (By similarity). PP2A consists of a common heterodimeric core enzyme, composed of PPP2CA a 36 kDa catalytic subunit (subunit C) and PPP2R1A a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Interacts with IPO9. Interacts with TP53 and SGOL1. Interacts with PLA2G16; this interaction might decrease PP2A activity. Interacts with CTTNBP2NL.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Chromosome, centromere. Note=Centromeric localization requires the presence of BUB1.DOMAIN: Each HEAT repeat appears to consist of two alpha helices joined by a hydrophilic region, the intrarepeat loop. The repeat units may be arranged laterally to form a rod-like structure.SIMILARITY: Belongs to the phosphatase 2A regulatory subunit A family.SIMILARITY: Contains 15 HEAT repeats. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 861 - http://www.reactome.org/biopax/46/48887#SequenceSite10888 - - - - REACT_2601 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2601.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6636 - - - - 5711 - NCBI Gene - - - - 113643 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113643 - - - - EQUAL - 83 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6438 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6679 - - - - 22395957 - pubchem-substance - - - - 12169736 - Stillman, B - Prasanth, SG - Prasanth, KV - Pubmed - Orc6 involved in DNA replication, chromosome segregation, and cytokinesis. - Science 297:1026-31 - 2002 - - - - CHEBI:13509 - ChEBI - - - - 8143371 - pubchem - - - - HGNC:9369 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10632 - - - - 23198 - NCBI Gene - - - - ENST00000274026 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval835 - - - - - - NP_736606 - RefSeq - - - - ENSP00000210313 - Ensembl - - - - NM_006231 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2596 - - - - P62714 - UniProt - - - - - - MOD_RES 826 826 Phosphothreonine; by CDK4. - - - - REACT_7859 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7859.1 - - - - EQUAL - 1 - - - - 601182 - omim - - - - - - MOD_RES 3 3 N6-acetyllysine. - - - - - - MOD_RES 73 73 N6-acetyllysine. - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2486 - - - - - - - - - - - Cell division protein kinase 2 - p33 protein kinase - 2.7.11.22 - CDKN2 - CDK2 - - - - - - - - - - - - - - - - - - - - CDK2_HUMAN - Cyclin-dependent kinase 2 - FUNCTION: Serine/threonine-protein kinase involved in the control of the cell cycle; essential for meiosis, but dispensable for mitosis. Phosphorylates CTNNB1, USP37, p53/TP53, NPM1, CDK7, RB1, BRCA2, MYC, NPAT, EZH2. Interacts with cyclins A, B1, B3, D, or E. Triggers duplication of centrosomes and DNA. Acts at the G1-S transition to promote the E2F transcriptional program and the initiation of DNA synthesis, and modulates G2 progression; controls the timing of entry into mitosis/meiosis by controlling the subsequent activation of cyclin B/CDK1 by phosphorylation, and coordinates the activation of cyclin B/CDK1 at the centrosome and in the nucleus. Crucial role in orchestrating a fine balance between cellular proliferation, cell death, and DNA repair in human embryonic stem cells (hESCs). Activity of CDK2 is maximal during S phase and G2; activated by interaction with cyclin E during the early stages of DNA synthesis to permit G1-S transition, and subsequently activated by cyclin A2 (cyclin A1 in germ cells) during the late stages of DNA replication to drive the transition from S phase to mitosis, the G2 phase. EZH2 phosphorylation promotes H3K27me3 maintenance and epigenetic gene silencing. Phosphorylates CABLES1 (By similarity). Cyclin E/CDK2 prevents oxidative stress-mediated Ras-induced senescence by phosphorylating MYC. Involved in G1-S phase DNA damage checkpoint that prevents cells with damaged DNA from initiating mitosis; regulates homologous recombination-dependent repair by phosphorylating BRCA2, this phosphorylation is low in S phase when recombination is active, but increases as cells progress towards mitosis. In response to DNA damage, double-strand break repair by homologous recombination a reduction of CDK2-mediated BRCA2 phosphorylation. Phosphorylation of RB1 disturbs its interaction with E2F1. NPM1 phosphorylation by cyclin E/CDK2 promotes its dissociates from unduplicated centrosomes, thus initiating centrosome duplication. Cyclin E/CDK2-mediated phosphorylation of NPAT at G1-S transition and until prophase stimulates the NPAT- mediated activation of histone gene transcription during S phase. Required for vitamin D-mediated growth inhibition by being itself inactivated. Involved in the nitric oxide- (NO) mediated signaling in a nitrosylation/activation-dependent manner. USP37 is activated by phosphorylation and thus triggers G1-S transition. CTNNB1 phosphorylation regulates insulin internalization.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.ENZYME REGULATION: Phosphorylation at Thr-14 or Tyr-15 inactivates the enzyme, while phosphorylation at Thr-160 activates it. Inhibited by 1,25-dihydroxyvitamin D(3) (1,25-(OH)(2)D(3)), AG- 024322, N-(4-Piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H- pyrazole-3-carboxamide (AT7519), R547 (Ro-4584820), purine, pyrimidine and pyridine derivatives, 2-aminopyrimidines, paullones, thiazo derivatives, macrocyclic quinoxalin-2-one, pyrazolo[1,5-a]-1,3,5-triazine, pyrazolo[1,5-a]pyrimidine, 2-(1- ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropylpurine (roscovitine, seliciclib and CYC202), SNS-032 (BMS-387032), triazolo[1,5-a]pyrimidines, staurosporine and olomoucine. Stimulated by MYC. Inactivated by CDKN1A (p21).SUBUNIT: Found in a complex with CABLES1, CCNA1 and CCNE1. Interacts with CABLES1 (By similarity). Interacts with UHRF2. Part of a complex consisting of UHRF2, CDK2 and CCNE1. Interacts with the Speedy/Ringo proteins SPDYA and SPDYC. Found in a complex with both SPDYA and CDKN1B/KIP1. Binds to RB1 and CDK7. Binding to CDKN1A (p21) leads to CDK2/cyclin E inactivation at the G1-S phase DNA damage checkpoint, thereby arresting cells at the G1-S transition during DNA repair. Associated with PTPN6 and beta- catenin/CTNNB1. Interacts with CACUL1. May interact with CEP63.SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Nucleus, Cajal body. Cytoplasm. Endosome. Note=Localized at the centrosomes in late G2 phase after separation of the centrosomes but before the start of prophase. Nuclear-cytoplasmic trafficking is mediated during the inhibition by 1,25-(OH)(2)D(3).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P24941-1; Sequence=Displayed; Name=2; Synonyms=CDK2deltaT; IsoId=P24941-2; Sequence=VSP_041998;INDUCTION: Induced transiently by TGFB1 at an early phase of TGFB1-mediated apoptosis.PTM: Phosphorylated at Thr-160 by CDK7 in a CAK complex. Phosphorylation at Thr-160 promotes kinase activity, whereas phosphorylation at Tyr-15 by WEE1 reduces slightly kinase activity. Phosphorylated on Thr-14 and Tyr-15 during S and G2 phases before being dephosphorylated by CDC25A.PTM: Nitrosylated after treatment with nitric oxide (DETA-NO).SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.SIMILARITY: Contains 1 protein kinase domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdk2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis624 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis623 - - - - EQUAL - 76 - - - - GINS1 - HGNC Symbol - - - - EQUAL - 14 - - - - EQUAL - 133 - - - - A8MZ62 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval857 - - - - - - ENSP00000310129 - Ensembl - - - - - - MOD_RES 133 133 Phosphoserine; by PLK1. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4953 - - - - 8900 - NCBI Gene - - - - ENSP00000230056 - Ensembl - - - - PPP2R1B - HGNC - - - - 68788 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68788 - - - - P15927 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2088 - - - - PSMB8 - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval823 - - - - - - 8144170 - pubchem-substance - - - - 600426 - omim - - - - Q969I5 - UniProt - - - - NM_001786 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7550 - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite1773 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1767 - - - - Q5VW46 - UniProt - - - - 8392066 - Turchi, JJ - Bambara, RA - Pubmed - Completion of mammalian lagging strand DNA replication using purified proteins. - J Biol Chem 268:15136-41 - 1993 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1077 - - - - P46527 - UniProt - - - - EQUAL - 178 - - - - NM_001270472 - RefSeq - - - - ENST00000546794 - Ensembl - - - - B2R9W1 - UniProt - - - - CHEBI:42647 - ChEBI - - - - REACT_3488 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3488.3 - - - - ENST00000262105 - Ensembl - - - - EQUAL - 250 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6607 - - - - NM_001220778 - RefSeq - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - 8143900 - pubchem-substance - - - - - Proteasome activator PA200 - PSME4 - KIAA0077 - - - - - - - - - - - - - - - - - PSME4_HUMAN - Proteasome activator complex subunit 4 - FUNCTION: Associated component of the proteasome that specifically recognizes acetylated histones and promotes ATP- and ubiquitin- independent degradation of core histones during spermatogenesis and DNA damage response. Recognizes and binds acetylated histones via its bromodomain-like (BRDL) region and activates the proteasome by opening the gated channel for substrate entry. Binds to the core proteasome via its C-terminus, which occupies the same binding sites as the proteasomal ATPases, opening the closed structure of the proteasome via an active gating mechanism. Component of the spermatoproteasome, a form of the proteasome specifically found in testis: binds to acetylated histones and promotes degradation of histones, thereby participating actively to the exchange of histones during spermatogenesis. Also involved in DNA damage response in somatic cells, by promoting degradation of histones following DNA double-strand breaks.SUBUNIT: Homodimer. Interacts with the 20S and 26S proteasomes. Component of the spermatoproteasome, a form of the proteasome specifically found in testis.SUBCELLULAR LOCATION: Cytoplasm, cytosol (By similarity). Nucleus. Nucleus speckle (By similarity). Note=Found in nuclear foci following treatment with ionizing radiation, but not with ultraviolet irradiation or H(2)O(2).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Name=1; IsoId=Q14997-1; Sequence=Displayed; Name=2; IsoId=Q14997-2; Sequence=VSP_023878; Name=3; IsoId=Q14997-3; Sequence=VSP_023877, VSP_023879; Name=4; IsoId=Q14997-4; Sequence=VSP_023876; Note=No experimental confirmation available;DOMAIN: The bromodomain-like (BRDL) region specifically recognizes and binds acetylated histones (PubMed:23706739).SIMILARITY: Belongs to the BLM10 family.SIMILARITY: Contains 6 HEAT repeats.SEQUENCE CAUTION: Sequence=AAI12170.1; Type=Erroneous initiation; Sequence=AAI13669.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000298852 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6624 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4976 - - - - - - ENSP00000209728 - Ensembl - - - - ENST00000597451 - Ensembl - - - - Q9BU93 - UniProt - - - - EQUAL - 60 - http://www.reactome.org/biopax/46/48887#SequenceSite1878 - - - - Q9BR53 - UniProt - - - - CHEBI:27000 - ChEBI - - - - D3DNV2 - UniProt - - - - HGNC:9539 - HGNC - - - - HGNC:9537 - HGNC - - - - Q96NB6 - UniProt - - - - HGNC:8489 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4864 - - - - - - 3006646 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3006646 - - - - 55388 - NCBI Gene - - - - ENSG00000132383 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10870 - - - - - - MOD_RES 108 108 Phosphoserine; by ATR. - - - - 5982 - NCBI Gene - - - - - - Proteasome subunit Z - Multicatalytic endopeptidase complex chain Z - Proteasome subunit beta type 7 - Proteasome subunit beta type 7 precursor - Macropain chain Z - - - - - Reactome DB_ID: 68759 - http://www.reactome.org/biopax/46/48887#Protein1090 - PSMB7 - - - - 68867 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68867 - - - - - 26S protease subunit S5 basic - 26S proteasome subunit S5B - PSMD5 - KIAA0072 - - - - - - - - - - - - - - - - - - - PSMD5_HUMAN - 26S proteasome non-ATPase regulatory subunit 5 - FUNCTION: Acts as a chaperone during the assembly of the 26S proteasome, specifically of the base subcomplex of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD5:PSMC2:PSMC1:PSMD2 module which probably assembles with a PSMD10:PSMC4:PSMC5:PAAF1 module followed by dissociation of PSMD5.SUBUNIT: Interacts with PSMC1, PSMC2, PSMD1 and PSMD6. Part of transient complex containing PSMD5, PSMC2, PSMC1 and PSMD2 formed during the assembly of the 26S proteasome.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q16401-1; Sequence=Displayed; Name=2; IsoId=Q16401-2; Sequence=VSP_045176;DOMAIN: Rich in dileucine repeats, which have been implicated in trafficking of a variety of transmembrane proteins.SIMILARITY: Belongs to the proteasome subunit S5B/HSM3 family.CAUTION: Was initially identified as a genuine component of the 26S proteasome. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q13416 - UniProt - - - - ENSP00000307288 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2113 - - - - - - EQUAL - 534 - http://www.reactome.org/biopax/46/48887#SequenceSite1813 - - - - - - MOD_RES 211 211 Phosphotyrosine; by EGFR. - - - - - - MOD_RES 1 1 N-acetylmethionine (By similarity). - - - - NP_002796 - RefSeq - - - - REACT_3596 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3596.2 - - - - - - - - - - - - Orc3:Orc2:origin - Reactome DB_ID: 68514 - http://www.reactome.org/biopax/46/48887#Complex2666 - - - - REACT_2683 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2683.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6693 - - - - F5H069 - UniProt - - - - 68561 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68561 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval872 - - - - - - REACT_1277 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1277.2 - - - - POLD1 - HGNC - - - - ENST00000452573 - Ensembl - - - - 5693 - NCBI Gene - - - - InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 - InChI - - - - Q3T1C1 - UniProt - - - - - - MOD_RES 205 205 Phosphothreonine (By similarity). - - - - 68559 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68559 - - - - A8K954 - UniProt - - - - - - omim - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6700 - - - - - - MOD_RES 24 24 Phosphothreonine. - - - - EQUAL - 389 - http://www.reactome.org/biopax/46/48887#SequenceSite1867 - - - - - - MOD_RES 193 193 Phosphothreonine. - - - - CHEBI:17361 - ChEBI - - - - A8K3Z3 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6790 - - - - E2F2 - HGNC - - - - REACT_4572 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4572.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature828 - - - - 606607 - omim - - - - EQUAL - 71 - - - - 6693436 - Hu, SZ - Wang, TS - Korn, D - Pubmed - DNA primase from KB cells. Characterization of a primase activity tightly associated with immunoaffinity-purified DNA polymerase-alpha. - J Biol Chem 259:1854-65 - 1984 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2477 - - - - - - EQUAL - 908 - http://www.reactome.org/biopax/46/48887#SequenceSite1805 - - - - PSMB6 - HGNC - - - - REACT_26985 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26985.2 - - - - E9PDH7 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1151 - - - - InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1 - InChI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2117 - - - - - - - - - - - - Reactome DB_ID: 68536 - http://www.reactome.org/biopax/46/48887#Protein5698 - CDT1 - - - - PSMB9 - HGNC - - - - B2R9L3 - UniProt - - - - - - MOD_RES 516 516 Phosphoserine. - - - - GO:0006271 - GENE ONTOLOGY - - - - - P55036 - UniProt - - - - NM_001271781 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6674 - - - - - - MOD_RES 266 266 Phosphoserine. - - - - PPP2CB - HGNC Symbol - - - - 9407030 - Stillman, B - Liang, C - Pubmed - Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants. - Genes Dev 11:3375-86 - 1998 - - - - EQUAL - 74 - - - - REACT_3850 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3850.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6718 - - - - 113757 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113757 - - - - EQUAL - 56 - - - - 9443964 - Syvaoja JE - Lehtonen S - Makiniemi M - Hellman U - Jokela M - Szpirer C - PubMed - The small subunits of human and mouse DNA polymerase epsilon are homologous to the second largest subunit of the yeast Saccharomyces cerevisiae DNA polymerase epsilon. - Nucleic Acids Res 26(3);730-4 - 1998 - - - - 9765232 - Ligon, AH - Dutta, A - Morton, CC - Hou, ZH - Quintana, DG - Thome, KC - Pubmed - ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases. - J Biol Chem 273:27137-45 - 1998 - - - - - - MOD_RES 49 49 Phosphoserine. - - - - NM_000947 - RefSeq - - - - 23649 - NCBI Gene - - - - REACT_664 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_664.4 - - - - ENSP00000257789 - Ensembl - - - - - - MOD_RES 5 5 Phosphoserine. - - - - EQUAL - 380 - http://www.reactome.org/biopax/46/48887#SequenceSite10916 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6613 - - - - A8K9I6 - UniProt - - - - EQUAL - 146 - - - - 5682 - NCBI Gene - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1836 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 26S proteasome - Reactome DB_ID: 68819 - http://www.reactome.org/biopax/46/48887#Complex411 - - - - - - MOD_RES 791 791 Phosphothreonine. - - - - NP_653263 - RefSeq - - - - EQUAL - 2 - - - - NM_013239 - RefSeq - - - - ENST00000310144 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1071 - - - - 23594 - NCBI Gene - - - - - - - DUP - Double parked homolog - CDT1 - - - - - - - - - - - - - - - - - - - CDT1_HUMAN - DNA replication factor Cdt1 - FUNCTION: Cooperates with CDC6 to promote the loading of the mini- chromosome maintenance complex onto chromatin to form the pre- replication complex necessary to initiate DNA replication. Binds DNA in a sequence-, strand-, and conformation-independent manner. Potential oncogene.SUBUNIT: Interacts with GMNN; inhibits both binding of the MCM complex to origins of replication and DNA-binding activity. Interacts with PCNA.SUBCELLULAR LOCATION: Nucleus.DEVELOPMENTAL STAGE: Present during G1 and early S phase of the cell cycle. Degraded during the late S, G2, and M phases.DOMAIN: The PIP-box K+4 motif mediates both the interaction with PCNA and the recuitment of the DCX(DTL) complex: while the PIP-box interacts with PCNA, the presence of the K+4 submotif, recruits the DCX(DTL) complex, leading to its ubiquitination (By similarity).PTM: Ubiquitinated by the DCX(DTL) complex, also named CRL4(CDT2) complex, in response to DNA damage, leading to its degradation. Ubiquitination by the DCX(DTL) complex is necessary to ensure proper cell cycle regulation and is PCNA-dependent: interacts with PCNA via its PIP-box, while the presence of the containing the 'K+4' motif in the PIP box, recruit the DCX(DTL) complex, leading to its degradation. The interaction with GMNN protects it against ubiquitination.PTM: Phosphorylated by cyclin A-dependent kinases which results in the binding of CDT1 to the F-box protein SKP2 and subsequent degradation. Phosphorylated at Thr-29 by MAPK8/JNK1, which blocks replication licensing in response to stress. Binding to GMNN is not affected by phosphorylation.DISEASE: Meier-Gorlin syndrome 4 (MGORS4) [MIM:613804]: A syndrome characterized by bilateral microtia, aplasia/hypoplasia of the patellae, and severe intrauterine and postnatal growth retardation with short stature and poor weight gain. Additional clinical findings include anomalies of cranial sutures, microcephaly, apparently low-set and simple ears, microstomia, full lips, highly arched or cleft palate, micrognathia, genitourinary tract anomalies, and various skeletal anomalies. While almost all cases have primordial dwarfism with substantial prenatal and postnatal growth retardation, not all cases have microcephaly, and microtia and absent/hypoplastic patella are absent in some. Despite the presence of microcephaly, intellect is usually normal. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the Cdt1 family.SEQUENCE CAUTION: Sequence=AF070552; Type=Frameshift; Positions=278, 312;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CDT1ID44175ch16q24.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 10846177 - Tamai, K - Arai, K - Matsui, E - You, Z - Masai, H - Ishimi, Y - Pubmed - Human Cdc7-related kinase complex. In vitro phosphorylation of MCM by concerted actions of Cdks and Cdc7 and that of a critical threonine residue of Cdc7 by Cdks. - J Biol Chem 275:29042-52 - 2000 - - - - - - - - - - Switching of origins to a post-replicative state - http://www.reactome.org/biopax/46/48887#Pathway505 - - - - - EQUAL - 116 - - - - ENSG00000115947 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4832 - - - - EQUAL - 504 - http://www.reactome.org/biopax/46/48887#SequenceSite1877 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6603 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval852 - - - - - - REACT_3335 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3335.2 - - - - ENSG00000100911 - Ensembl - - - - ENST00000263681 - Ensembl - - - - Q99859 - UniProt - - - - ENSP00000384849 - Ensembl - - - - ENSP00000414731 - Ensembl - - - - Q8TBD1 - UniProt - - - - GINS4 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4788 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6423 - - - - - - TBP1 - TBP-1 - PSMC3 - 26S proteasome AAA-ATPase subunit RPT5 - Proteasome subunit P50 - Proteasome 26S subunit ATPase 3 - Tat-binding protein 1 - - - - - - - - - - - - - - - - - - - PRS6A_HUMAN - 26S protease regulatory subunit 6A - FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex (By similarity). In case of HIV-1 infection, suppresses Tat-mediated transactivation.SUBUNIT: May form a heterodimer with a related family member. Interacts with PAAF1. Interacts with HIV-1 Tat.SUBCELLULAR LOCATION: Cytoplasm (Potential). Nucleus (Potential). Cytoplasm, P-body (By similarity). Note=Co-localizes with TRIM5 in the cytoplasmic bodies (By similarity).PTM: Sumoylated by UBE2I in response to MEKK1-mediated stimuli.SIMILARITY: Belongs to the AAA ATPase family.SEQUENCE CAUTION: Sequence=AAI07805.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001257356 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature855 - - - - CDK1 - HGNC - - - - ENSP00000407233 - Ensembl - - - - ENST00000370873 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4860 - - - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1846 - - - - PSMA2 - HGNC Symbol - - - - 608187 - omim - - - - REACT_5364 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5364.2 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis631 - - - - MCM6 - HGNC Symbol - - - - EQUAL - 433 - http://www.reactome.org/biopax/46/48887#SequenceSite10580 - - - - - - - - - - - - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein5720 - Reactome DB_ID: 187920 - phosphorylated Cyclin A:Cdk2 substrate proteins - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature851 - - - - 5925 - NCBI Gene - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1143 - - - - ENSG00000175482 - Ensembl - - - - - - MOD_RES 89 89 Phosphotyrosine. - - - - GMNN - HGNC Symbol - - - - NP_006707 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4938 - - - - - - - - ACTIVATION - - 'RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex' positively regulates 'DNA polymerase alpha:primase binds at the origin' - http://www.reactome.org/biopax/46/48887#Control184 - - - - ENSP00000344006 - Ensembl - - - - 5688 - NCBI Gene - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1862 - - - - 68468 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68468 - - - - REACT_4670 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4670.1 - - - - O75869 - UniProt - - - - 10783164 - Lei, M - Kawasaki, Y - Christensen, T - Homesley, L - Sawyer, S - Tye, BK - Pubmed - Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins. - Genes Dev 14:913-26 - 2000 - - - - - - PSME4_HUMAN - Proteasome activator complex subunit 4 - - - - - http://www.reactome.org/biopax/46/48887#Protein1087 - Reactome DB_ID: 947606 - PSME4 - - - - - - MOD_RES 141 141 Phosphoserine. - - - - EQUAL - 672 - - - - P49643 - UniProt - - - - Q86XX9 - UniProt - - - - NM_144662 - RefSeq - - - - HGNC:9549 - HGNC - - - - REACT_2883 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2883.1 - - - - NP_002794 - RefSeq - - - - ENSP00000414770 - Ensembl - - - - - - MOD_RES 1121 1121 Phosphoserine. - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - 1H24 - PROTEIN DATA BANK - - - - ENSP00000372721 - Ensembl - - - - - - - - - - - At the end of this reaction, 1 molecule of 'Cdc6' is present. <br><br><br> - http://www.reactome.org/biopax/46/48887#TemplateReaction10 - CDC6 protein is synthesized under the control of E2F transcription factors - - - - EQUAL - 156 - - - - 9442876 - Dutta, A - Bell, SP - Pubmed - Initiation of DNA replication in eukaryotic cells. - Annu Rev Cell Dev Biol 13:293-332 - 1998 - - - - EQUAL - 221 - - - - 601648 - omim - - - - REACT_2365 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2365.2 - - - - ENSP00000351314 - Ensembl - - - - 29935 - NCBI Gene - - - - ENST00000311129 - Ensembl - - - - 116899 - omim - - - - - - MOD_RES 201 201 Phosphoserine. - - - - CDKN1A - HGNC - - - - EQUAL - 204 - - - - - - MOD_RES 458 458 Phosphoserine. - - - - NM_001199772 - RefSeq - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10753 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10540 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2508 - - - - EQUAL - 1 - - - - ENSP00000376598 - Ensembl - - - - REACT_480 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_480.3 - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite4656 - - - - ENSP00000362738 - Ensembl - - - - MOD_RES N,N-dimethylproline (By similarity) - - - - REACT_3768 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3768.2 - - - - ENST00000406655 - Ensembl - - - - 68592 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68592 - - - - - C10H16N5O13P3 - Adenosine triphosphate - H4atp - adenosine 5'-(tetrahydrogen triphosphate) - - - - - - - - - - - 507.181 - ATP - ATP - - - - EQUAL - 239 - http://www.reactome.org/biopax/46/48887#SequenceSite1845 - - - - Q6ICS6 - UniProt - - - - EQUAL - 810 - - - - UBB - HGNC - - - - MCM8 - HGNC - - - - Q16401 - UniProt - - - - - - MOD_RES 1184 1184 Phosphoserine. - - - - - - MOD_RES 29 29 Phosphothreonine; by MAPK8. - - - - 602638 - omim - - - - CHEBI:23522 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4997 - - - - - - - - UBB(1-76) - ubiquitin (UBB 1) - - - - - http://www.reactome.org/biopax/46/48887#Protein1046 - Reactome DB_ID: 939214 - UBB - - - - 5719 - NCBI Gene - - - - - - - - - - CCNB1 - CCNB - - - - - - - - - - - - - - CCNB1_HUMAN - G2/mitotic-specific cyclin-B1 - FUNCTION: Essential for the control of the cell cycle at the G2/M (mitosis) transition.SUBUNIT: Interacts with the CDC2 protein kinase to form a serine/threonine kinase holoenzyme complex also known as maturation promoting factor (MPF). The cyclin subunit imparts substrate specificity to the complex. Binds HEI10. Interacts with catalytically active RALBP1 and CDC2 during mitosis to form an endocytotic complex during interphase. Interacts with CCNF; interaction is required for nuclear localization.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.DEVELOPMENTAL STAGE: Accumulates steadily during G2 and is abruptly destroyed at mitosis.PTM: Ubiquitinated by the SCF(NIPA) complex during interphase, leading to its destruction. Not ubiquitinated during G2/M phases.PTM: Phosphorylated by PLK1 at Ser-133 on centrosomes during prophase: phosphorylation by PLK1 does not cause nuclear import. Phosphorylation at Ser-147 was also reported to be mediated by PLK1 but Ser-133 seems to be the primary phosphorylation site.SIMILARITY: Belongs to the cyclin family. Cyclin AB subfamily.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CCNB1ID951ch5q13.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ccnb1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 10375532 - Sun, H - Zhang, H - Tsvetkov, LM - Yeh, KH - Lee, SJ - Pubmed - p27(Kip1) ubiquitination and degradation is regulated by the SCF(Skp2) complex through phosphorylated Thr187 in p27 - Curr Biol 9:661-4 - 1999 - - - - ENST00000559082 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2434 - - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10909 - - - - EQUAL - 226 - - - - - - - - - - - Single-stranded DNA-binding protein - RPA1 - RPA70 - REPA1 - RF-A protein 1 - RP-A p70 - Replication factor A protein 1 - Replication protein A 70 kDa DNA-binding subunit, N-terminally processed - - - - - - - - - - - - - - - RFA1_HUMAN - Replication protein A 70 kDa DNA-binding subunit - FUNCTION: Plays an essential role in several cellular processes in DNA metabolism including replication, recombination and DNA repair. Binds and subsequently stabilizes single-stranded DNA intermediates and thus prevents complementary DNA from reannealing.FUNCTION: Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S- phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.SUBUNIT: Heterotrimer composed of RPA1, RPA2 and RPA3 (canonical replication protein A complex). Component of the alternative replication protein A complex (aRPA) composed of RPA1, RPA3 and RPA4. The DNA-binding activity may reside exclusively on the RPA1 subunit. Interacts with RIPK1 and XPA. Interacts with RPA4. Interacts with the polymerase alpha subunit POLA1/p180; this interaction stabilizes the replicative complex and reduces the misincorporation rate of DNA polymerase alpha by acting as a fidelity clamp. Interacts with RAD51 and SENP6 to regulate DNA repair. Interacts with HELB; this interaction promotes HELB recruitment to chromatin following DNA damage.SUBCELLULAR LOCATION: Nucleus.PTM: Sumoylated on lysine residues Lys-449 and Lys-577, with Lys- 449 being the major site. Sumoylation promotes recruitment of RAD51 to the DNA damage foci to initiate DNA repair through homologous recombination. Desumoylated by SENP6.SIMILARITY: Belongs to the replication factor A protein 1 family.SEQUENCE CAUTION: Sequence=BAD92969.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rpa1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P33992 - UniProt - - - - Q8IVP4 - UniProt - - - - EQUAL - 185 - http://www.reactome.org/biopax/46/48887#SequenceSite10898 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4813 - - - - ENST00000219097 - Ensembl - - - - 113550 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113550 - - - - NP_001243799 - RefSeq - - - - EQUAL - 1462 - http://www.reactome.org/biopax/46/48887#SequenceSite10857 - - - - - - - - DNA primer - Reactome DB_ID: 68424 - http://www.reactome.org/biopax/46/48887#PhysicalEntity249 - - - - 3.6.4.12 - DNA2 - 3.1.-.- - KIAA0083 - DNA replication nuclease DNA2 - DNA2L - DNA replication ATP-dependent helicase-like homolog - DNA replication ATP-dependent helicase DNA2 - hDNA2 - - - - - - - - - - - - - - - - - - - - - - DNA2_HUMAN - DNA replication ATP-dependent helicase/nuclease DNA2 - FUNCTION: Key enzyme involved in DNA replication and DNA repair in nucleus and mitochondrion. Involved in Okazaki fragments processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. Also involved in 5'-end resection of DNA during double- strand break (DSB) repair: recruited by BLM and mediates the cleavage of 5'-ssDNA, while the 3'-ssDNA cleavage is prevented by the presence of RPA. Also involved in DNA replication checkpoint independently of Okazaki fragments processing. Possesses different enzymatic activities, such as single-stranded DNA (ssDNA)- dependent ATPase, 5'-3' helicase and endonuclease activities. While the ATPase and endonuclease activities are well-defined and play a key role in Okazaki fragments processing and DSB repair, the 5'-3' DNA helicase activity is subject to debate. According to various reports, the helicase activity is weak and its function remains largely unclear. Helicase activity may promote the motion of DNA2 on the flap, helping the nuclease function.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.COFACTOR: Binds 1 4Fe-4S cluster (By similarity).SUBUNIT: Interacts with BLM and WDHD1.SUBCELLULAR LOCATION: Nucleus. Mitochondrion. Note=Was initially reported to be exclusively mitochondrial (PubMed:18995831). However, it was later shown to localize both in mitochondrion and nucleus (PubMed:19487465).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=4; Name=1; IsoId=P51530-1; Sequence=Displayed; Name=2; IsoId=P51530-2; Sequence=VSP_021870, VSP_021871; Note=No experimental confirmation available; Name=3; IsoId=P51530-3; Sequence=VSP_021869; Note=No experimental confirmation available; Name=4; IsoId=P51530-4; Sequence=VSP_044185; Note=No experimental confirmation available;PTM: Acetylated by EP300, leading to stimulate the 5'-3' endonuclease, the 5'-3' helicase and DNA-dependent ATPase activities, possibly by increasing DNA substrate affinity.SIMILARITY: Belongs to the DNA2/NAM7 helicase family.SEQUENCE CAUTION: Sequence=AAH28188.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH63664.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA07647.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAI17237.1; Type=Erroneous gene model prediction; Sequence=CAI17238.1; Type=Erroneous gene model prediction; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_4035 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4035.2 - - - - 176942 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176942 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10622 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2664 - - - - - ENST00000422729 - Ensembl - - - - 8104944 - Brown, WC - Campbell, JL - Pubmed - Interaction of proliferating cell nuclear antigen with yeast DNA polymerase delta. - J Biol Chem 268:21706-10 - 1993 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4975 - - - - - - REACT_4173 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4173.2 - - - - ENSG00000205220 - Ensembl - - - - - - - - - Tat-binding protein 7 - MB67-interacting protein - PSMC4 - Proteasome 26S subunit ATPase 4 - TBP-7 - 26S proteasome AAA-ATPase subunit RPT3 - TBP7 - MIP224 - - - - - - - - - - - - - - - - - - - - PRS6B_HUMAN - 26S protease regulatory subunit 6B - FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.SUBUNIT: Interacts with NR1I3. Interacts with PAAF1. Interacts with TRIM5.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P43686-1; Sequence=Displayed; Name=2; IsoId=P43686-2; Sequence=VSP_000022; Note=No experimental confirmation available;SIMILARITY: Belongs to the AAA ATPase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - CDC7 - HGNC Symbol - - - - 69127 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69127 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6678 - - - - Q6LER8 - UniProt - - - - A4D2A1 - UniProt - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - HGNC:16147 - HGNC - - - - D3DWS9 - UniProt - - - - HGNC:6947 - HGNC - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite1772 - - - - ENSP00000324804 - Ensembl - - - - - - - Cyclin A - - - - Reactome DB_ID: 75202 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein5606 - CCNA - - - - - - MOD_RES 222 222 N6-acetyllysine. - - - - EQUAL - 224 - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - EQUAL - 119 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval856 - - - - - - EQUAL - 229 - http://www.reactome.org/biopax/46/48887#SequenceSite4659 - - - - CHEBI:41691 - ChEBI - - - - NM_006814 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2479 - - - - PRIM1 - p49 - 2.7.7.- - DNA primase 49 kDa subunit - - - - - - - - - - - - - PRI1_HUMAN - DNA primase small subunit - FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.SUBUNIT: Heterodimer of a small subunit and a large subunit.MISCELLANEOUS: The bound zinc ion is not a cofactor. It is bound to a zinc knuckle motif that may be involved in sequence recognition and the binding of ssDNA (By similarity).SIMILARITY: Belongs to the eukaryotic-type primase small subunit family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - Regulation of DNA replication - http://www.reactome.org/biopax/46/48887#Pathway518 - DNA replication is regulated at various levels via ORC proteins. This pathway includes annotation of individual events that lead to the regulation of replication. - Reviewed: Manfredi, J, 0000-00-00 00:00:00 - - - - - DNA primase 58 kDa subunit - PRIM2A - PRIM2 - 2.7.7.- - p58 - - - - - - - - - - - - - PRI2_HUMAN - DNA primase large subunit - FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.COFACTOR: Binds 1 4Fe-4S cluster.SUBUNIT: Heterodimer of a small subunit and a large subunit.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P49643-1; Sequence=Displayed; Name=2; IsoId=P49643-2; Sequence=VSP_015111, VSP_015112; Note=No experimental confirmation available;SIMILARITY: Belongs to the eukaryotic-type primase large subunit family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval836 - - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10630 - - - - Q5JXJ2 - UniProt - - - - - - MOD_RES 280 280 Phosphoserine. - - - - ENST00000538610 - Ensembl - - - - NM_001009552 - RefSeq - - - - PSMD11 - HGNC - - - - EQUAL - 180 - - - - ENST00000264639 - Ensembl - - - - 176916 - omim - - - - MOD:00046 - Protein Modification Ontology - - - - REACT_5903 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5903.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2092 - - - - EQUAL - 39 - - - - 68423 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68423 - - - - Q9UEU8 - UniProt - - - - EQUAL - 674 - http://www.reactome.org/biopax/46/48887#SequenceSite10617 - - - - 69152 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69152 - - - - NM_002946 - RefSeq - - - - NM_002793 - RefSeq - - - - Q5QNR8 - UniProt - - - - EQUAL - 609 - http://www.reactome.org/biopax/46/48887#SequenceSite4669 - - - - 1311258 - Erdile, LF - von Winkler, D - Dornreiter, I - Kelly, TJ - Gilbert, IU - Pubmed - Interaction of DNA polymerase alpha-primase with cellular replication protein A and SV40 T antigen. - EMBO J 11:769-76 - 1992 - - - - 68889 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68889 - - - - ENST00000374881 - Ensembl - - - - 1536007 - Marahrens, Y - Stillman, B - Pubmed - A yeast chromosomal origin of DNA replication defined by multiple functional elements. - Science 255:817-23 - 1992 - - - - NM_002816 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10844 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature871 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10598 - - - - EQUAL - 410 - http://www.reactome.org/biopax/46/48887#SequenceSite5752 - - - - 1AXC - PROTEIN DATA BANK - - - - - - MOD_RES 15 15 Phosphoserine. - - - - REACT_3425 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3425.3 - - - - EQUAL - 14 - - - - 10438470 - Iizuka, M - Stillman, B - Pubmed - Histone acetyltransferase HBO1 interacts with the ORC1 subunit of the human initiator protein. - J Biol Chem 274:23027-34 - 1999 - - - - CHEBI:13341 - ChEBI - - - - EQUAL - 222 - - - - - - - - - - DNA Replication Pre-Initiation - Authored: Davey, MJ, O'Donnell, M, Tye, BK, 2006-03-17 16:01:39 - http://www.reactome.org/biopax/46/48887#Pathway555 - Edited: Joshi-Tope, G, 0000-00-00 00:00:00 - Although, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during G1 phase. - - - - - 69063 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69063 - - - - EQUAL - 108 - - - - CHEBI:42887 - ChEBI - - - - 113592 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113592 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1046 - - - - ENSP00000388107 - Ensembl - - - - NP_001257401 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval866 - - - - - - - - Deoxythymidine 5'-triphosphate - dTTP - Deoxythymidine triphosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule590 - Reactome DB_ID: 30187 - TTP - - - - ENST00000418988 - Ensembl - - - - 603056 - omim - - - - ENSP00000354945 - Ensembl - - - - O43560 - UniProt - - - - REACT_24758 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24758.2 - - - - ENSP00000452424 - Ensembl - - - - - - MOD_RES 14 14 Phosphothreonine; by PKMYT1. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6796 - - - - HGNC:9546 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1079 - - - - NP_001104515 - RefSeq - - - - - - MOD_RES 104 104 Symmetric dimethylarginine; by PRMT5. - - - - 68583 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68583 - - - - Q96AZ3 - UniProt - - - - - - MOD_RES 478 478 Phosphoserine. - - - - Q14577 - UniProt - - - - - - MOD_RES 811 811 Phosphoserine; by CDK1 and CDK3. - - - - - C10H14N5O7P - ADENOSINE MONOPHOSPHATE - adenosine 5'-(dihydrogen phosphate) - PAdo - Adenosine-5'-monophosphoric acid - 5'-adenylic acid - 5'-O-phosphonoadenosine - Ado5'P - adenosine phosphate - adenosine-5'P - - - - - - - - - - - - - - - - - - 347.2212 - AMP - AMP - A purine ribonucleoside 5'-monophosphate having adenine as the nucleobase. - - - - 1B3U - PROTEIN DATA BANK - - - - Q9UP68 - UniProt - - - - REACT_2353 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2353.1 - - - - 8144860 - pubchem - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6687 - - - - ENST00000406581 - Ensembl - - - - ENSP00000404585 - Ensembl - - - - CHEBI:23520 - ChEBI - - - - REACT_4070 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4070.2 - - - - NP_002804 - RefSeq - - - - - 2.7.7.7 - - - - - - - - - - Formation of Okazaki fragments - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2013 - After RFC initiates the assembly of the primer recognition complex, the complex of pol delta and PCNA is responsible for incorporating the additional nucleotides prior to the position of the next downstream initiator RNA primer. On the lagging strand, short discontinuous segments of DNA, called Okazaki fragments, are synthesized on RNA primers. The average length of the Okazaki fragments is 100 nucleotides. Polymerase switching is a key event that allows the processive synthesis of DNA by the pol delta and PCNA complex. - - - - - - - MOD_RES 88 88 N6-acetyllysine. - - - - ENSP00000458995 - Ensembl - - - - Q9UNT6 - UniProt - - - - Q9H0D7 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature857 - - - - ENSG00000163636 - Ensembl - - - - CHEBI:14791 - ChEBI - - - - HGNC:1745 - HGNC - - - - A4D0P8 - UniProt - - - - ENSG00000049541 - Ensembl - - - - ENST00000379059 - Ensembl - - - - - - - - - - - - - - - - Unwinding complex at replication fork - http://www.reactome.org/biopax/46/48887#Complex2631 - Reactome DB_ID: 176949 - - - - - - MOD_RES 82 82 Phosphoserine. - - - - Q9HCU8 - UniProt - - - - 6118 - NCBI Gene - - - - Q15076 - UniProt - - - - ENSP00000215071 - Ensembl - - - - P78396 - UniProt - - - - REACT_24411 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24411.2 - - - - P40937 - UniProt - - - - 68449 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68449 - - - - 176952 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176952 - - - - B3KMM8 - UniProt - - - - PTHR10540:SF7 - PANTHER Family - - - - REACT_2568 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2568.1 - - - - Q13172 - UniProt - - - - - - MOD_RES 913 913 Phosphoserine. - - - - P25787 - UniProt - - - - 5716 - NCBI Gene - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1866 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4993 - - - - - - REACT_5315 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5315.3 - - - - - - MOD_RES 130 130 Phosphothreonine. - - - - - - - - - - - - - - - - - - - - - - - - - Assembly of the ORC complex at the origin of replication - In Saccharomyces cerevisiae, the entire ORC complex is constitutively bound to the origin of replication. However, in mammalian cells, Orc1, and possibly other Orc subunits, dissociate from origins of replication, while Orc2 remains stably associated with chromatin across the cell cycle. The first step in formation of the pre-RC is assembly of the hexameric Origin Recognition Complex (ORC) at the origin of replication. Recent work on human (Hs) ORC has suggested that the heterohexamer assembles in an ordered manner. HsOrc2 appears to be constitutively bound to origins of replication. HsOrc2 and HsOrc3 form a complex that interacts with HsOrc4 and HsOrc5. Recruitment of HsOrc5 into the complex is important for the association of HsOrc1. HsOrc6 is also capable of interacting with the core HsOrc2:3:4:5 complex, but not smaller complexes. Interestingly, HsOrc1 and a subunit of the Mcm2-7 complex (HsMcm2) interact with a histone acetyltransferase, HsHBO1 (Bell & Stillman 1992; Diffley et al. 1994; Lee & Bell 1997; Wenger et al. 1975; Li & DePamphili;s 2001; Dhar et al. 2001; Vashee et al, 2001; Iizuka & Stillman 1999 Burke et al. 2001). - http://www.reactome.org/biopax/46/48887#Pathway557 - Authored: Davey, MJ, O'Donnell, M, 2003-06-05 08:03:13 - - - - - NP_004102 - RefSeq - - - - REACT_1095 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1095.3 - - - - 69015 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69015 - - - - 5690 - NCBI Gene - - - - NP_001258710 - RefSeq - - - - EQUAL - 6 - - - - Q14209 - UniProt - - - - 5721 - NCBI Gene - - - - GO:0004721 - GENE ONTOLOGY - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1860 - - - - C9J497 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1068 - - - - Q5TBG6 - UniProt - - - - EQUAL - 28 - - - - Proteasome subunit Z - PSMB7 - Multicatalytic endopeptidase complex chain Z - 3.4.25.1 - Macropain chain Z - Z - - - - - - - - - - - - - - - - PSB7_HUMAN - Proteasome subunit beta type-7 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This unit is responsible of the trypsin-like activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. This subunit can be displaced by the equivalent immune-specific subunit PSMB10. Interacts with HIV- 1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.TISSUE SPECIFICITY: Expressed at a low level in colonic mucosa. Up-regulated in colorectal cancer tissues.SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001170884 - RefSeq - - - - Q6IAG9 - UniProt - - - - - - - - - - - - Processive complex - Reactome DB_ID: 68451 - http://www.reactome.org/biopax/46/48887#Complex2638 - - - - NP_002945 - RefSeq - - - - Q59ES9 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2099 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis622 - - - - 10995389 - Denchi, EL - Peters, JM - Wagener, C - Gieffers, C - Kramer, ER - Petersen, BO - Helin, K - Marinoni, F - Matteucci, C - Melixetian, M - Pubmed - Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1. - Genes Dev 14:2330-43 - 2000 - - - - EQUAL - 33 - - - - 8144912 - pubchem - - - - 68901 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68901 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6675 - - - - D3DT31 - UniProt - - - - Q6PKI2 - UniProt - - - - Q6P455 - UniProt - - - - EQUAL - 1 - - - - - - - - - - - - Cyclin A:Cdk2:substrate complex - Reactome DB_ID: 187947 - http://www.reactome.org/biopax/46/48887#Complex2623 - - - - O00311 - UniProt - - - - ENSP00000401001 - Ensembl - - - - Q6PKG9 - UniProt - - - - ORC5 - HGNC Symbol - - - - Q6UV22 - UniProt - - - - - - MOD_RES 713 713 Phosphothreonine. - - - - EQUAL - 108 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2484 - - - - - ENSP00000272317 - Ensembl - - - - - - - - - - - - - - CDK:DDK:Mcm10:pre-replicative complex - http://www.reactome.org/biopax/46/48887#Complex2543 - Reactome DB_ID: 68561 - - - - 68447 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68447 - - - - NP_000225 - RefSeq - - - - NM_021067 - RefSeq - - - - EQUAL - 256 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4963 - - - - EQUAL - 601 - http://www.reactome.org/biopax/46/48887#SequenceSite4928 - - - - - - MOD_RES 9 9 Phosphoserine. - - - - EQUAL - 304 - - - - ENST00000520710 - Ensembl - - - - FZR1 - HGNC Symbol - - - - 156562 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=156562 - - - - NP_001257411 - RefSeq - - - - REACT_2492 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2492.2 - - - - IERHLVCPSMICTF-XVFCMESISA-N - InChIKey - - - - Q2M3U6 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6706 - - - - ENSP00000444780 - Ensembl - - - - 7378348 - So, AG - Tan, CK - Downey, KM - Lee, MY - Pubmed - Purification of deoxyribonucleic acid polymerase delta from calf thymus: partial characterization of physical properties. - Biochemistry 19:2096-101 - 1980 - - - - - - MOD_RES 32 32 Phosphoserine. - - - - REACT_4878 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4878.3 - - - - REACT_1221 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1221.3 - - - - Q5U098 - UniProt - - - - EQUAL - 198 - http://www.reactome.org/biopax/46/48887#SequenceSite10751 - - - - ENSG00000262764 - Ensembl - - - - NP_001104516 - RefSeq - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2461 - - - - - NM_001099780 - RefSeq - - - - ENSP00000276533 - Ensembl - - - - Q96J55 - UniProt - - - - - - - - - - - - Orc1:Orc4:Orc5:Orc3:Orc2:origin - http://www.reactome.org/biopax/46/48887#Complex2668 - Reactome DB_ID: 68592 - - - - - - - - - - 26S proteasome subunit p112 - 26S proteasome regulatory subunit RPN2 - PSMD1 - 26S proteasome regulatory subunit S1 - - - - - - - - - - - - - - - - - - - - - - - - - - - PSMD1_HUMAN - 26S proteasome non-ATPase regulatory subunit 1 - FUNCTION: Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.SUBUNIT: Interacts with ADRM1.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q99460-1; Sequence=Displayed; Name=2; IsoId=Q99460-2; Sequence=VSP_011475; Note=No experimental confirmation available;SIMILARITY: Belongs to the proteasome subunit S1 family.SIMILARITY: Contains 10 PC repeats.SEQUENCE CAUTION: Sequence=AAH01053.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH14013.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH39845.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH47897.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH64398.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH73833.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 145 145 Phosphoserine. - - - - MCM7 - HGNC Symbol - - - - 68487 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68487 - - - - CDC6 - HGNC - - - - 9081985 - Murante, RS - Bambara, RA - Henricksen, LA - Pubmed - Enzymes and reactions at the eukaryotic DNA replication fork. - J Biol Chem 272:4647-50 - 1997 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6644 - - - - NM_002801 - RefSeq - - - - - - MOD_RES 32 32 Phosphothreonine. - - - - P30153 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval850 - - - - - - CHEBI:15996 - ChEBI - - - - REACT_734 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_734.3 - - - - REACT_9113 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9113.2 - - - - EQUAL - 266 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite2925 - - - - EQUAL - 287 - - - - 10567526 - Komamura, Y - You, Z - Ishimi, Y - Pubmed - Biochemical analysis of the intrinsic Mcm4-Mcm6-mcm7 DNA helicase activity. - Mol Cell Biol 19:8003-15 - 2000 - - - - 68558 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68558 - - - - NM_000321 - RefSeq - - - - NP_055136 - RefSeq - - - - EQUAL - 795 - http://www.reactome.org/biopax/46/48887#SequenceSite10721 - - - - ENST00000339647 - Ensembl - - - - Q86XF8 - UniProt - - - - - - - - - - - Formation of the Flap Intermediate - When the polymerase delta:PCNA complex reaches a downstream Okazaki fragment, strand displacement synthesis occurs. The primer containing 5'-terminus of the downstream Okazaki fragment is folded into a single-stranded flap. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2014 - - - - - EQUAL - 2 - - - - 176974 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176974 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6672 - - - - 10339564 - Hunter, T - Jiang, W - Wells, NJ - Pubmed - Multistep regulation of DNA replication by Cdk phosphorylation of HsCdc6. - Proc Natl Acad Sci U S A 96:6193-8 - 1999 - - - - CHEBI:10789 - ChEBI - - - - Q9BRV9 - UniProt - - - - - - MOD_RES 102 102 Phosphotyrosine. - - - - Q7Z6H9 - UniProt - - - - ENSP00000362334 - Ensembl - - - - 30187 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=30187 - - - - GO:0004175 - GENE ONTOLOGY - - - - - REACT_3977 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3977.2 - - - - - - ubiquitin (UBC 2) - - - - - http://www.reactome.org/biopax/46/48887#Protein2478 - Reactome DB_ID: 939869 - UBC(77-152) - - - - EQUAL - 277 - http://www.reactome.org/biopax/46/48887#SequenceSite1855 - - - - EQUAL - 1104 - - - - NM_003504 - RefSeq - - - - ENSP00000362131 - Ensembl - - - - Q9Y248 - UniProt - - - - - - - - - - - Reactome DB_ID: 68542 - http://www.reactome.org/biopax/46/48887#Protein5577 - CDC6 - - - - ENSP00000216367 - Ensembl - - - - - - Cyclin A1 - - - - - Reactome DB_ID: 68891 - http://www.reactome.org/biopax/46/48887#Protein5607 - CCNA1 - - - - NP_001238919 - RefSeq - - - - REACT_2843 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2843.2 - - - - ENST00000352131 - Ensembl - - - - MOD_RES N-acetylserine - - - - EQUAL - 422 - - - - NP_005216 - RefSeq - - - - - - - - - - - - - - RNA primer:origin duplex:DNA polymerase alpha:primase complex - Reactome DB_ID: 68423 - http://www.reactome.org/biopax/46/48887#Complex2610 - - - - Q15054 - UniProt - - - - - - MOD_RES 860 860 N6-methyllysine; by SMYD2. - - - - 600654 - omim - - - - REACT_7682 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7682.1 - - - - ENSG00000163918 - Ensembl - - - - - C9H16N3O14P3 - cytidine 5'-(tetrahydrogen triphosphate) - 5'-CTP - H4ctp - - - - - - - - - 483.15643 - CTP - CTP - - - - NM_005225 - RefSeq - - - - ENST00000263274 - Ensembl - - - - EQUAL - 532 - http://www.reactome.org/biopax/46/48887#SequenceSite4666 - - - - ENSP00000372725 - Ensembl - - - - CHEBI:10497 - ChEBI - - - - - - - - - - - - DNA polymerase epsilon - Reactome DB_ID: 68483 - http://www.reactome.org/biopax/46/48887#Complex2606 - - - - NP_001020268 - RefSeq - - - - 51659 - NCBI Gene - - - - REACT_4394 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4394.1 - - - - EQUAL - 59 - - - - HGNC:9302 - HGNC - - - - - - Multicatalytic endopeptidase complex subunit C8 - Proteasome subunit alpha type 3 - Macropain subunit C8 - Proteasome component C8 - - - - - Reactome DB_ID: 68728 - http://www.reactome.org/biopax/46/48887#Protein1084 - PSMA3 - - - - - - MOD_RES 2 2 N-acetylserine. - - - - ENSP00000263274 - Ensembl - - - - A4LBB7 - UniProt - - - - A8K6E7 - UniProt - - - - NP_694546 - RefSeq - - - - ENST00000571959 - Ensembl - - - - ENST00000374859 - Ensembl - - - - Q15129 - UniProt - - - - EQUAL - 840 - http://www.reactome.org/biopax/46/48887#SequenceSite10635 - - - - B2R6H2 - UniProt - - - - HGNC:14106 - HGNC - - - - HGNC:1577 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1074 - - - - ENSP00000267163 - Ensembl - - - - NP_060988 - RefSeq - - - - Q13204 - UniProt - - - - - - Probable 26S protease regulatory subunit 8 - - - - - http://www.reactome.org/biopax/46/48887#Protein1094 - Reactome DB_ID: 68780 - PSMC5 - - - - - - MOD_RES 312 312 Phosphoserine. - - - - Q07864 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4868 - - - - - - 68379 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68379 - - - - 68543 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68543 - - - - Q9UBM3 - UniProt - - - - EQUAL - 312 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10730 - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite4650 - - - - A8K9A3 - UniProt - - - - EQUAL - 273 - http://www.reactome.org/biopax/46/48887#SequenceSite1839 - - - - CCNA1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - CCNA1_HUMAN - Cyclin-A1 - FUNCTION: May be involved in the control of the cell cycle at the G1/S (start) and G2/M (mitosis) transitions. May primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells.SUBUNIT: Interacts with the CDK2 and the CDC2 protein kinases to form a serine/threonine kinase holoenzyme complex. The cyclin subunit imparts substrate specificity to the complex. Does not bind CDK4 and CDK5 (in vitro). The cyclin A1-CDK2 complex interacts with transcription factor E2F-1 and RB proteins. Found in a complex with CDK2, CABLES1 and CCNE1 (By similarity). Interacts with INCA1 and KLHDC9.SUBCELLULAR LOCATION: Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P78396-1; Sequence=Displayed; Name=2; IsoId=P78396-2; Sequence=VSP_034392; Name=3; IsoId=P78396-3; Sequence=VSP_044257;TISSUE SPECIFICITY: Very high levels in testis and very low levels in brain. Also found in myeloid leukemia cell lines.DEVELOPMENTAL STAGE: Expression increases in early G1 phase and reaches highest levels during the S and G2/M phases.PTM: Polyubiquitinated via 'Lys-11'-linked ubiquitin by the anaphase-promoting complex (APC/C), leading to its degradation by the proteasome. Deubiquitinated and stabilized by USP37 enables entry into S phase.SIMILARITY: Belongs to the cyclin family. Cyclin AB subfamily.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CCNA1ID949ch13q13.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000373909 - Ensembl - - - - - - - - - - - POLD3 - KIAA0039 - DNA polymerase delta subunit p66 - - - - - - - - - - - - - - DPOD3_HUMAN - DNA polymerase delta subunit 3 - FUNCTION: Required for optimal DNA polymerase delta activity.SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with POLD2. Interacts with PCNA.SUBCELLULAR LOCATION: Nucleus.SEQUENCE CAUTION: Sequence=BAA05039.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - 2'-deoxyadenosine 5'-triphosphate - Deoxyadenosine 5'-triphosphate - Deoxyadenosine triphosphate - - - - Reactome DB_ID: 29604 - http://www.reactome.org/biopax/46/48887#SmallMolecule589 - dATP - - - - A8K7C6 - UniProt - - - - ENSP00000243067 - Ensembl - - - - CHEBI:42934 - ChEBI - - - - NM_001270427 - RefSeq - - - - ENST00000576276 - Ensembl - - - - - - - - - - - - Cyclin A:Cdk2:phosphorylated substrate complex - Reactome DB_ID: 187965 - http://www.reactome.org/biopax/46/48887#Complex2624 - - - - Q53YE8 - UniProt - - - - EQUAL - 152 - - - - - - - - - - - - Processive complex:nicked DNA from adjacent Okazaki fragments - Reactome DB_ID: 68470 - http://www.reactome.org/biopax/46/48887#Complex2644 - - - - NM_001134419 - RefSeq - - - - EQUAL - 195 - - - - Q969L6 - UniProt - - - - 69116 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69116 - - - - PSMD4 - HGNC Symbol - - - - Q53FT5 - UniProt - - - - NP_877954 - RefSeq - - - - NM_001136197 - RefSeq - - - - EQUAL - 10 - - - - Q86V41 - UniProt - - - - Q86U66 - UniProt - - - - 2DVW - PROTEIN DATA BANK - - - - 1671046 - Stillman, B - Tsurimoto, T - Pubmed - Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis. - J Biol Chem 266:1961-8 - 1991 - - - - 939191 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939191 - - - - ENSG00000135336 - Ensembl - - - - NM_152132 - RefSeq - - - - PSMB10 - HGNC - - - - Q5U0H2 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4866 - - - - - - REACT_4313 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4313.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6633 - - - - - - MOD_RES 19 19 Phosphotyrosine. - - - - - - - - - - - - - - - - - - Polymerase switching - After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA. - http://www.reactome.org/biopax/46/48887#Pathway511 - - - - - E9PGN9 - UniProt - - - - HNRNPD - HGNC - - - - ENST00000595683 - Ensembl - - - - CHEBI:14072 - ChEBI - - - - ENSG00000105325 - Ensembl - - - - ENSG00000117748 - Ensembl - - - - NM_001177563 - RefSeq - - - - ENSP00000313199 - Ensembl - - - - 5983 - NCBI Gene - - - - FEN1 - HGNC - - - - NM_016095 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6632 - - - - EQUAL - 2 - - - - CHEBI:48799 - ChEBI - - - - EQUAL - 142 - - - - REACT_3566 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3566.2 - - - - 68433 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68433 - - - - 1974050 - Hurwitz, J - Lee, SH - Pubmed - Mechanism of elongation of primed DNA by DNA polymerase delta, proliferating cell nuclear antigen, and activator 1. - Proc Natl Acad Sci U S A 87:5672-6 - 1990 - - - - EQUAL - 121 - - - - ENST00000210313 - Ensembl - - - - PSMB3 - HGNC Symbol - - - - - - MOD_RES 29 29 Phosphoserine; by CDK1; in vitro. - - - - ENSG00000235715 - Ensembl - - - - REACT_9192 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9192.1 - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein1058 - Converted from EntitySet in Reactome - Reactome DB_ID: 451208 - Ubiquitinated AUF1 (isoform p37 or p40) - - - - - - phosphorylated Cdc6 - - - - - Reactome DB_ID: 113574 - http://www.reactome.org/biopax/46/48887#Protein5724 - CDC6 - - - - ENST00000358514 - Ensembl - - - - CHEBI:22249 - ChEBI - - - - NP_002781 - RefSeq - - - - REACT_6768 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6768.1 - - - - - - MOD_RES 127 127 N6-acetyllysine. - - - - 10801458 - Bell, SP - Lee, DG - Pubmed - ATPase switches controlling DNA replication initiation. - Curr Opin Cell Biol 12:280-5 - 2000 - - - - Phosphonoformate immuno-associated protein 4 - Proteasome regulatory particle subunit p44S10 - 26S proteasome regulatory subunit S10 - Breast cancer-associated protein SGA-113M - PFAAP4 - p42A - 26S proteasome regulatory subunit RPN7 - PSMD6 - KIAA0107 - - - - - - - - - - - - - - - - - - - - - - PSMD6_HUMAN - 26S proteasome non-ATPase regulatory subunit 6 - FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.SUBUNIT: Component of the PA700 complex.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q15008-1; Sequence=Displayed; Name=2; IsoId=Q15008-2; Sequence=VSP_047711;SIMILARITY: Belongs to the proteasome subunit S10 family.SIMILARITY: Contains 1 PCI domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSP00000255465 - Ensembl - - - - Q86V46 - UniProt - - - - ENST00000316629 - Ensembl - - - - ENST00000396393 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10893 - - - - - Homo sapiens - Homo sapiens - - - - ENSP00000360623 - Ensembl - - - - EQUAL - 57 - - - - NP_036513 - RefSeq - - - - - - MOD_RES 361 361 Phosphoserine. - - - - NP_002803 - RefSeq - - - - HGNC:9540 - HGNC - - - - ENST00000415576 - Ensembl - - - - HGNC:9542 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4952 - - - - 68954 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68954 - - - - EQUAL - 863 - http://www.reactome.org/biopax/46/48887#SequenceSite10647 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2108 - - - - - - - - MOD_RES 110 110 Phosphothreonine. - - - - P62333 - UniProt - - - - 9305914 - Ishimi, Y - Pubmed - A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex. - J Biol Chem 272:24508-13 - 1997 - - - - PTHR11668:SF21 - PANTHER Family - - - - - 174257 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=174257 - - - - Q9UG44 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1080 - - - - EQUAL - 456 - http://www.reactome.org/biopax/46/48887#SequenceSite1785 - - - - MCM3 - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval833 - - - - - - ENSG00000100764 - Ensembl - - - - HGNC:9571 - HGNC - - - - Q8N2V1 - UniProt - - - - MOD:00696 - Protein Modification Ontology - - - - ENSP00000343317 - Ensembl - - - - EQUAL - 150 - - - - P40306 - UniProt - - - - Q495R6 - UniProt - - - - NP_788955 - RefSeq - - - - ENSG00000013275 - Ensembl - - - - PSMA3 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1792 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7549 - - - - 187920 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187920 - - - - P56282 - UniProt - - - - 68916 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68916 - - - - NP_005905 - RefSeq - - - - ENST00000590720 - Ensembl - - - - DNA2 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1058 - - - - 68726 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68726 - - - - CHEBI:42892 - ChEBI - - - - EQUAL - 734 - http://www.reactome.org/biopax/46/48887#SequenceSite10639 - - - - PSMC6 - HGNC - - - - HGNC:12463 - HGNC - - - - 5558 - NCBI Gene - - - - P32846 - UniProt - - - - 26S proteasome regulatory subunit S14 - p31 - 26S proteasome regulatory subunit RPN12 - PSMD8 - - - - - - - - - - - - - - PSMD8_HUMAN - 26S proteasome non-ATPase regulatory subunit 8 - FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. Necessary for activation of the CDC28 kinase.SIMILARITY: Belongs to the proteasome subunit S14 family.CAUTION: It is uncertain whether Met-1 or Met-64 is the initiator.SEQUENCE CAUTION: Sequence=AAC62833.1; Type=Erroneous gene model prediction; Sequence=AAH01164.3; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAH65006.2; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA07237.1; Type=Erroneous initiation; Note=Translation N-terminally extended; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval878 - - - - - - EQUAL - 841 - - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#Protein5718 - Converted from EntitySet in Reactome - Reactome DB_ID: 187963 - Cyclin A:Cdk1 substrate proteins - - - - PPP2R1A - HGNC Symbol - - - - 5687 - NCBI Gene - - - - POLE - HGNC Symbol - - - - REACT_2586 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2586.2 - - - - - - MOD_RES 2 2 N-acetylserine. - - - - NP_002777 - RefSeq - - - - NP_687033 - RefSeq - - - - - - - - - - - - Cdt1:geminin - Reactome DB_ID: 156502 - http://www.reactome.org/biopax/46/48887#Complex2671 - - - - 116940 - omim - - - - REACT_5172 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5172.2 - - - - 68388 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68388 - - - - ENSP00000295901 - Ensembl - - - - 68905 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68905 - - - - 69299 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69299 - - - - 7314 - NCBI Gene - - - - EQUAL - 164 - - - - ENSP00000265187 - Ensembl - - - - EQUAL - 57 - - - - - - Orc6 - Origin recognition complex subunit 6 - - - - - Reactome DB_ID: 68539 - http://www.reactome.org/biopax/46/48887#Protein5581 - ORC6 - - - - 191343 - omim - - - - ENSG00000243067 - Ensembl - - - - POLD4 - HGNC - - - - 68952 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68952 - - - - 610609 - omim - - - - REACT_1725 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1725.4 - - - - EQUAL - 271 - - - - - - MOD_RES 53 53 Phosphoserine; by CDC7. - - - - 8696349 - Samuel K - Hole N - Melton DW - Bentley D - Selfridge J - Ansell JD - Millar JK - PubMed - DNA ligase I is required for fetal liver erythropoiesis but is not essential for mammalian cell viability. - Nat Genet 13(4);489-91 - 1996 - - - - Q8N346 - UniProt - - - - MOD:00047 - Protein Modification Ontology - - - - EQUAL - 358 - - - - EQUAL - 113 - - - - 179837 - omim - - - - MCM5 - HGNC Symbol - - - - D3DSV4 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4789 - - - - HGNC:5036 - HGNC - - - - EQUAL - 5 - - - - 68917 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68917 - - - - NP_005907 - RefSeq - - - - CDK2 - HGNC Symbol - - - - 11724925 - Spadari, S - Locatelli, GA - Villani, G - Hubscher, U - Tillement, V - Maga, G - Stucki, M - Pubmed - Okazaki fragment processing: modulation of the strand displacement activity of DNA polymerase delta by the concerted action of replication protein A, proliferating cell nuclear antigen, and flap endonuclease-1. - Proc Natl Acad Sci U S A 98:14298-303 - 2001 - - - - EQUAL - 608 - http://www.reactome.org/biopax/46/48887#SequenceSite1789 - - - - P25786 - UniProt - - - - Q99658 - UniProt - - - - ENSP00000311368 - Ensembl - - - - - - MOD_RES 203 203 Phosphothreonine. - - - - CHEBI:16284 - ChEBI - - - - - - MOD_RES 535 535 Phosphoserine; by ATM. - - - - P62979 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval870 - - - - - - REACT_2227 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2227.4 - - - - PSME3 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature856 - - - - 6119 - NCBI Gene - - - - Q14103 - UniProt - - - - B4DUM9 - UniProt - - - - 11950940 - Tikhmyanova, N - Frolova, NS - Schek, N - Coleman, TR - Pubmed - Xenopus Cdc6 performs separate functions in initiating DNA replication. - Mol Biol Cell 13:1298-312 - 2002 - - - - NM_001271780 - RefSeq - - - - EQUAL - 2 - - - - NP_001124197 - RefSeq - - - - NP_000937 - RefSeq - - - - ENSP00000309474 - Ensembl - - - - - - MOD_RES 229 229 Nitrated tyrosine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6662 - - - - Q32P23 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2458 - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6793 - - - - 68688 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68688 - - - - 601806 - omim - - - - ENST00000373040 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10685 - - - - NM_001178010 - RefSeq - - - - EQUAL - 612 - - - - 176949 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176949 - - - - 1362456 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1362456 - - - - NP_683720 - RefSeq - - - - Q8NHV8 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6426 - - - - REACT_3477 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3477.2 - - - - - - MOD_RES 672 672 Phosphoserine. - - - - EQUAL - 207 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6421 - - - - REACT_4621 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4621.1 - - - - 983 - NCBI Gene - - - - 68736 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68736 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature825 - - - - - - phospho-Cdk2(Thr160) - - - - - - Reactome DB_ID: 187967 - http://www.reactome.org/biopax/46/48887#Protein5695 - p-T160-CDK2 - - - - 8144688 - pubchem - - - - - - Mcm7 - P1.1-MCM3 - DNA replication licensing factor MCM7 - CDC47 homolog - - - - - http://www.reactome.org/biopax/46/48887#Protein5589 - Reactome DB_ID: 68555 - MCM7 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6642 - - - - - - MOD_RES 57 57 N6-acetyllysine. - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - 68960 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68960 - - - - NM_001130112 - RefSeq - - - - B3KT15 - UniProt - - - - PSMD12 - HGNC Symbol - - - - REACT_5173 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5173.1 - - - - - - TRIP1 - SUG1 - PSMC5 - 26S proteasome AAA-ATPase subunit RPT6 - Proteasome 26S subunit ATPase 5 - Proteasome subunit p45 - p45/SUG - Thyroid hormone receptor-interacting protein 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - PRS8_HUMAN - 26S protease regulatory subunit 8 - FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.SUBUNIT: Interacts, in vitro, with the thyroid hormone receptor (in a thyroid hormone T3-dependent manner) and with retinoid X receptor (RXR) (By similarity). Interacts with NDC80. Interacts with PAAF1. Interacts with TRIM5. Component of a complex with USP49 and RUVBL1.SUBCELLULAR LOCATION: Cytoplasm (Potential). Nucleus (Potential).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P62195-1; Sequence=Displayed; Name=2; IsoId=P62195-2; Sequence=VSP_045441;SIMILARITY: Belongs to the AAA ATPase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4857 - - - - D3DW08 - UniProt - - - - NP_002802 - RefSeq - - - - 68640 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68640 - - - - EQUAL - 355 - http://www.reactome.org/biopax/46/48887#SequenceSite1793 - - - - PTHR10322:SF11 - PANTHER Family - - - - - - - P26s4 - PSMC1 - 26S proteasome AAA-ATPase subunit RPT2 - Proteasome 26S subunit ATPase 1 - - - - - - - - - - - - - - - - PRS4_HUMAN - 26S protease regulatory subunit 4 - FUNCTION: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.SUBUNIT: Interacts with SCA7. Interacts with NGLY1. Interacts with PAAF1.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.SIMILARITY: Belongs to the AAA ATPase family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 69306 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69306 - - - - PTHR11599:SF13 - PANTHER Family - - - - - - - MOD_RES 187 187 Phosphothreonine; by PKB/AKT1 and CDK2. - - - - ENSP00000437193 - Ensembl - - - - 68653 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68653 - - - - REACT_2279 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2279.3 - - - - NM_174871 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1828 - - - - 5557 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2231 - - - - - - PTHR11599:SF8 - PANTHER Family - - - - - 176915 - omim - - - - NP_002797 - RefSeq - - - - 165978 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=165978 - - - - EQUAL - 466 - http://www.reactome.org/biopax/46/48887#SequenceSite10910 - - - - 68724 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68724 - - - - REACT_2327 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2327.2 - - - - 604030 - omim - - - - 1EWI - PROTEIN DATA BANK - - - - EQUAL - 413 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature872 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6620 - - - - - - ubiquitin (UBC 8) - - - - - http://www.reactome.org/biopax/46/48887#Protein2484 - Reactome DB_ID: 939866 - UBC(533-608) - - - - - - - - - - - - - DNA Pol alpha:primase - DNA polymerase alpha:primase - - - - primosome - Reactome DB_ID: 68507 - http://www.reactome.org/biopax/46/48887#Complex2607 - - - - PTHR11599:SF1 - PANTHER Family - - - - - REACT_24649 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24649.2 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2462 - - - - - NM_000946 - RefSeq - - - - ENSP00000350491 - Ensembl - - - - - - MOD_RES 361 361 Phosphoserine. - - - - ENST00000293362 - Ensembl - - - - EQUAL - 409 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6427 - - - - CHEBI:40510 - ChEBI - - - - EQUAL - 407 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6445 - - - - - - 26S proteasome regulatory subunit S9 - 26S proteasome non-ATPase regulatory subunit 11 - 26S proteasome regulatory subunit p44.5 - - - - - Reactome DB_ID: 68790 - http://www.reactome.org/biopax/46/48887#Protein1086 - PSMD11 - - - - Q9UDI3 - UniProt - - - - 611415 - omim - - - - ENSP00000441953 - Ensembl - - - - CHEBI:40786 - ChEBI - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10626 - - - - - - MOD_RES 104 104 N6-acetyllysine. - - - - 1DPU - PROTEIN DATA BANK - - - - REACT_5308 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5308.1 - - - - PSMD10 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6627 - - - - - - MOD_RES 104 104 N6-acetyllysine. - - - - EQUAL - 911 - - - - NM_002552 - RefSeq - - - - ENSP00000346171 - Ensembl - - - - EQUAL - 456 - http://www.reactome.org/biopax/46/48887#SequenceSite4664 - - - - 9191022 - Hindges, R - Hubscher, U - Pubmed - DNA polymerase delta, an essential enzyme for DNA transactions. - Biol Chem 378:345-62 - 1997 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2115 - - - - - - REACT_4491 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4491.1 - - - - EQUAL - 280 - - - - ENST00000216802 - Ensembl - - - - EQUAL - 304 - http://www.reactome.org/biopax/46/48887#SequenceSite1781 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature840 - - - - CHEBI:16497 - ChEBI - - - - ENST00000375370 - Ensembl - - - - - PSMD13 - 26S proteasome regulatory subunit S11 - 26S proteasome regulatory subunit p40.5 - 26S proteasome regulatory subunit RPN9 - - - - - - - - - - - - - - - - - - - - - PSD13_HUMAN - 26S proteasome non-ATPase regulatory subunit 13 - FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.SUBUNIT: Component of the PA700 complex.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9UNM6-1; Sequence=Displayed; Name=2; IsoId=Q9UNM6-2; Sequence=VSP_041067;SIMILARITY: Belongs to the proteasome subunit S11 family.SIMILARITY: Contains 1 PCI domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 113840 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113840 - - - - REACT_1295 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1295.3 - - - - HGNC:8729 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1800 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1840 - - - - - - cytidine 5'-triphosphate - Cytidine triphosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule199 - Reactome DB_ID: 29470 - CTP - - - - ENSG00000129084 - Ensembl - - - - - - - - - - PCNA homotrimer - Reactome DB_ID: 68440 - http://www.reactome.org/biopax/46/48887#Complex2634 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis629 - - - - REACT_1303 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1303.1 - - - - - - MOD_RES 122 122 Phosphoserine. - - - - - - MOD_RES 120 120 Phosphoserine. - - - - - - DNA-binding protein PO-GA - Activator 1 140 kDa subunit - RFC140 - RF-C 140 kDa subunit - Activator 1 large subunit - A1 140 kDa subunit - Replication factor C large subunit - - - - - Reactome DB_ID: 68435 - http://www.reactome.org/biopax/46/48887#Protein5730 - RFC1 - - - - 169514 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=169514 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval864 - - - - - - 12604790 - Seo, YS - Hurwitz, J - Lee, JK - Pubmed - The Cdc23 (Mcm10) protein is required for the phosphorylation of minichromosome maintenance complex by the Dfp1-Hsk1 kinase - Proc Natl Acad Sci U S A 100:2334-9 - 2003 - - - - NP_002783 - RefSeq - - - - EQUAL - 195 - - - - - - - - RNA primer - http://www.reactome.org/biopax/46/48887#PhysicalEntity250 - Reactome DB_ID: 68422 - - - - REACT_1024 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1024.3 - - - - - - - - - - - - CDK - http://www.reactome.org/biopax/46/48887#Complex2545 - Reactome DB_ID: 68380 - - - - NP_112738 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4887 - - - - - - - - ubiquitin (UBC 6) - - - - - Reactome DB_ID: 939191 - http://www.reactome.org/biopax/46/48887#Protein1054 - UBC(381-456) - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1065 - - - - ENSG00000147536 - Ensembl - - - - ENSG00000065328 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1802 - - - - ENSP00000321800 - Ensembl - - - - EQUAL - 44 - http://www.reactome.org/biopax/46/48887#SequenceSite1854 - - - - 165991 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=165991 - - - - REACT_24844 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24844.2 - - - - NM_002789 - RefSeq - - - - REACT_4191 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4191.2 - - - - EQUAL - 13 - - - - 8143535 - pubchem - - - - NP_005906 - RefSeq - - - - EQUAL - 458 - - - - 1579162 - Bell, SP - Stillman, B - Pubmed - ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. - Nature 357:128-34 - 1992 - - - - NP_001777 - RefSeq - - - - EQUAL - 131 - - - - B4DGQ6 - UniProt - - - - - - - - - - Mcm2-7 is phosphorylated by DDK - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1975 - At the beginning of this reaction, 1 molecule of 'Mcm2-7 complex', and 1 molecule of 'ATP' are present. At the end of this reaction, 1 molecule of 'phosphorylated Mcm2-7 complex', and 1 molecule of 'ADP' are present.<br><br> This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'DDK'.<br> - - - - - - - - - - - - Cdt1 associates with geminin - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2031 - At the beginning of this reaction, 1 molecule of 'geminin', and 1 molecule of 'CDT1' are present. At the end of this reaction, 1 molecule of 'Cdt1:geminin' is present.<br><br> This reaction takes place in the 'nucleoplasm'.<br> - - - - - ENSP00000359898 - Ensembl - - - - NHVNXKFIZYSCEB-XLPZGREQSA-N - InChIKey - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4831 - - - - Q53TX5 - UniProt - - - - NM_182802 - RefSeq - - - - A6NH58 - UniProt - - - - EQUAL - 153 - - - - 9353276 - Dutta, A - Hou, Zh - Quintana, DG - Saha, P - Hendricks, M - Thome, KC - Pubmed - Identification of HsORC4, a member of the human origin of replication recognition complex. - J Biol Chem 272:28247-51 - 1997 - - - - 30595 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=30595 - - - - EQUAL - 509 - http://www.reactome.org/biopax/46/48887#SequenceSite10869 - - - - MOD:01148 - Protein Modification Ontology - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4957 - - - - REACT_9372 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9372.2 - - - - ENSP00000407539 - Ensembl - - - - REACT_2024 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2024.3 - - - - 5515 - NCBI Gene - - - - PSMD14 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature858 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10913 - - - - 939230 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939230 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4830 - - - - ENST00000395837 - Ensembl - - - - ENSP00000459644 - Ensembl - - - - EQUAL - 361 - - - - REACT_6731 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6731.2 - - - - ENSP00000390491 - Ensembl - - - - - - MOD_RES 138 138 Phosphoserine. - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10620 - - - - REACT_24883 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24883.2 - - - - ENST00000303887 - Ensembl - - - - Q9BRT9 - UniProt - - - - 69053 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69053 - - - - 68365 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68365 - - - - EQUAL - 190 - - - - - - - - - - - CDC6 association with ORC:origin complexes mediated by MCM8 - Authored: Davey, MJ, O'Donnell, M, Tye, BK, 2006-03-17 16:01:39 - At the beginning of this reaction, 1 molecule of 'ORC:origin', and 1 molecule of 'CDC6' are present. At the end of this reaction, 1 molecule of 'CDC6:ORC:origin complex' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2146 - - - - - PSMC4 - HGNC - - - - PTHR11599:SF7 - PANTHER Family - - - - - ENST00000428239 - Ensembl - - - - 68511 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68511 - - - - - - - - - - - - - - - - - - - - - - ORC:origin - Reactome DB_ID: 68540 - http://www.reactome.org/biopax/46/48887#Complex2549 - - - - - - - - - - - - - - - - - - - - Mcm2-7 complex - http://www.reactome.org/biopax/46/48887#Complex2551 - Reactome DB_ID: 68558 - - - - PRIM1 - HGNC Symbol - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1768 - - - - EQUAL - 15 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1042 - - - - REACT_3276 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3276.1 - - - - HGNC:8490 - HGNC - - - - ENST00000215071 - Ensembl - - - - NM_002800 - RefSeq - - - - 8486689 - Kesti T - Syvaoja JE - Frantti H - PubMed - Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase epsilon. - J Biol Chem 268(14);10238-45 - 1993 - - - - REACT_3725 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3725.2 - - - - NM_014814 - RefSeq - - - - PSMC3 - HGNC Symbol - - - - - - MOD_RES 72 72 N6-acetyllysine. - - - - By Homology - - - - - - - DNA helicase MCM8 - MCM8_HUMAN - - - - - http://www.reactome.org/biopax/46/48887#Protein5584 - Reactome DB_ID: 3006646 - MCM8 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4867 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature844 - - - - 891 - NCBI Gene - - - - REACT_5344 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5344.1 - - - - Q5SZS5 - UniProt - - - - - - MOD_RES 16 16 Phosphoserine. - - - - ENSP00000345571 - Ensembl - - - - - - MOD_RES 354 354 Phosphoserine. - - - - Q9Y5N6 - UniProt - - - - NP_006221 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6617 - - - - EQUAL - 164 - http://www.reactome.org/biopax/46/48887#SequenceSite10541 - - - - 68637 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68637 - - - - ENSP00000473048 - Ensembl - - - - HGNC:9555 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6618 - - - - REACT_5537 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5537.1 - - - - - - - - - - - - RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex - Reactome DB_ID: 68568 - http://www.reactome.org/biopax/46/48887#Complex2604 - - - - ENST00000457261 - Ensembl - - - - NM_001256849 - RefSeq - - - - REACT_5651 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5651.2 - - - - P35249 - UniProt - - - - Q9UEF4 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1822 - - - - NM_005916 - RefSeq - - - - 141607 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=141607 - - - - NP_001207706 - RefSeq - - - - - - - Cyclin-A - CCNA - CCNA2 - CCN1 - - - - - - - - - - - - - - - - - CCNA2_HUMAN - Cyclin-A2 - FUNCTION: Essential for the control of the cell cycle at the G1/S (start) and the G2/M (mitosis) transitions.SUBUNIT: Interacts with the CDK1 and CDK2 protein kinases to form a serine/threonine kinase holoenzyme complex. The cyclin subunit imparts substrate specificity to the complex. When associated with CDK2 (but not with CDK1), interacts with SCAPER.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Cytoplasmic when associated with SCAPER.DEVELOPMENTAL STAGE: Accumulates steadily during G2 and is abruptly destroyed at mitosis.PTM: Polyubiquitinated via 'Lys-11'-linked ubiquitin by the anaphase-promoting complex (APC/C), leading to its degradation by the proteasome. Deubiquitinated and stabilized by USP37 enables entry into S phase (By similarity).SIMILARITY: Belongs to the cyclin family. Cyclin AB subfamily.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ccna2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6610 - - - - NM_001199774 - RefSeq - - - - EQUAL - 567 - - - - EQUAL - 309 - http://www.reactome.org/biopax/46/48887#SequenceSite4920 - - - - EQUAL - 389 - http://www.reactome.org/biopax/46/48887#SequenceSite1857 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1052 - - - - 9080773 - Lieber, MR - Pubmed - The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. - Bioessays 19:233-40 - 1997 - - - - - DNA polymerase delta subunit p50 - 2.7.7.7 - POLD2 - - - - - - - - - - - - - - - - - - - - - - DPOD2_HUMAN - DNA polymerase delta subunit 2 - FUNCTION: The function of the small subunit is not yet clear.CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with KCTD10 (By similarity). Interacts with KCTD13/POLDIP1, POLDIP2 and POLDIP3. Interacts with WRNIP1. Interacts with POLD4.SUBCELLULAR LOCATION: Nucleus.SIMILARITY: Belongs to the DNA polymerase delta/II small subunit family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pold2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_058633 - RefSeq - - - - REACT_1156 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1156.2 - - - - ENST00000416134 - Ensembl - - - - ENSP00000394155 - Ensembl - - - - PPP2CB - HGNC - - - - - - - - - - - - ubiquitinated Cdc6 - http://www.reactome.org/biopax/46/48887#Complex2628 - Reactome DB_ID: 68570 - - - - EQUAL - 246 - http://www.reactome.org/biopax/46/48887#SequenceSite1801 - - - - EQUAL - 176 - - - - - - MOD_RES 73 73 Phosphoserine. - - - - Q9TNN9 - UniProt - - - - EQUAL - 2 - - - - P49005 - UniProt - - - - EQUAL - 722 - - - - HGNC:1578 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1834 - - - - ENST00000223129 - Ensembl - - - - REACT_4398 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4398.2 - - - - NP_001238918 - RefSeq - - - - PSMB8 - HGNC - - - - CHEBI:13234 - ChEBI - - - - - - MOD_RES 16 16 Phosphoserine. - - - - REACT_4699 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4699.1 - - - - 939854 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939854 - - - - - - MOD_RES 71 71 Phosphoserine. - - - - - - MOD_RES 233 233 Phosphothreonine. - - - - PSMD3 - HGNC Symbol - - - - EQUAL - 228 - http://www.reactome.org/biopax/46/48887#SequenceSite1779 - - - - - - MOD_RES 249 249 Phosphoserine; by CDK1. - - - - P62191 - UniProt - - - - - - MOD_RES 2 2 N-acetylthreonine; in DNA replication complex GINS protein SLD5, N-terminally processed. - - - - NM_181742 - RefSeq - - - - 418075 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=418075 - - - - EQUAL - 711 - http://www.reactome.org/biopax/46/48887#SequenceSite10625 - - - - - - - - - - - - Orc4:Orc5:Orc3:Orc2:origin - Reactome DB_ID: 68520 - http://www.reactome.org/biopax/46/48887#Complex2664 - - - - REACT_3687 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3687.2 - - - - ENST00000416564 - Ensembl - - - - B2R4N9 - UniProt - - - - Q29824 - UniProt - - - - REACT_3869 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3869.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4989 - - - - - - 11779870 - Tsurumi, T - Fujita, M - Kiyono, T - Nakamura, H - Ishimi, Y - Pubmed - Nuclear organization of DNA replication initiation proteins in mammalian cells. - J Biol Chem 277:10354-61 - 2002 - - - - - - MOD_RES 358 358 Phosphoserine. - - - - ENSP00000362915 - Ensembl - - - - Q92660 - UniProt - - - - 187967 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187967 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature839 - - - - NM_001798 - RefSeq - - - - NP_002680 - RefSeq - - - - B2R515 - UniProt - - - - NP_001191382 - RefSeq - - - - NM_002796 - RefSeq - - - - - - MOD_RES 173 173 Phosphoserine. - - - - - - - - - - - - - Formation of Processive Complex - The loading of proliferating cell nuclear antigen (PCNA) leads to recruitment of pol delta. Human PCNA is a homotrimer of 36 kDa subunits that form a toroidal structure. The loading of PCNA by RFC is a key event in the transition from the priming mode to the extension mode of DNA synthesis. The processive complex is composed of the pol delta holoenzyme and PCNA. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2011 - - - - - Q96I12 - UniProt - - - - ENSG00000230669 - Ensembl - - - - ENSP00000386212 - Ensembl - - - - Q4W5P4 - UniProt - - - - ENSP00000471062 - Ensembl - - - - NP_001138404 - RefSeq - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis626 - - - - NP_001129670 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6673 - - - - HGNC:9568 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval868 - - - - - - EQUAL - 126 - - - - - - MOD_RES 161 161 Phosphothreonine. - - - - EQUAL - 77 - - - - - - MOD_RES 127 127 Phosphoserine. - - - - - - MOD_RES 345 345 Dimethylated arginine. - - - - ENST00000404724 - Ensembl - - - - - - - - - MCM2-7 mediated fork unwinding - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2004 - Authored: Tye, BK, 2005-11-29 10:17:56 - Edited: Gopinathrao, G, 2005-11-29 21:05:54 - In budding yeast, all MCM proteins have been proved to be essential for elongation. The active form of this protein complex may be a heterohexamer. A subcomplex of MCM proteins consisting fo MCM4,6, and -7 has a weak helicase activity that may contribute to DNA unwinding. - - - - - 113637 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113637 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2098 - - - - - - MOD_RES 394 394 Phosphoserine. - - - - - - MOD_RES 2 2 N-acetylserine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6694 - - - - POLD1 - HGNC Symbol - - - - REACT_7157 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7157.3 - - - - - - PP2A-catalytic subunit C beta isoform - - - - - Reactome DB_ID: 165991 - http://www.reactome.org/biopax/46/48887#Protein2612 - PPP2CB - - - - CHEBI:13236 - ChEBI - - - - - - - - - - - - - - DNA replication initiation - DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA (Frick & Richardson 2002; Wang et al 1984). - http://www.reactome.org/biopax/46/48887#Pathway504 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2665 - - - - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis109 - - - - EQUAL - 261 - http://www.reactome.org/biopax/46/48887#SequenceSite10863 - - - - B4DWW5 - UniProt - - - - 602855 - omim - - - - - - MOD_RES 167 167 N6-acetyllysine. - - - - TFDP1 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2114 - - - - - - HGNC:17493 - HGNC - - - - EQUAL - 2 - - - - PSMA7L - 3.4.25.1 - PSMA8 - - - - - - - - - - - - - - - - - - - - - - - - PSA7L_HUMAN - Proteasome subunit alpha type-7-like - FUNCTION: Component of the spermatoproteasome, a form of the proteasome specifically found in testis that promotes degradation of histones, thereby participating actively to the exchange of histones during spermatogenesis. The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH (By similarity).CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel (By similarity). Component of the spermatoproteasome, a form of the proteasome specifically found in testis.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Comment=Experimental confirmation may be lacking for some isoforms; Name=1; IsoId=Q8TAA3-1; Sequence=Displayed; Note=Predicted but not yet described; Name=2; IsoId=Q8TAA3-2; Sequence=VSP_005285; Name=3; IsoId=Q8TAA3-5; Sequence=VSP_018602; Note=No experimental confirmation available;SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6713 - - - - NM_002914 - RefSeq - - - - MOD_RES N6-acetyllysine - - - - ENSG00000105486 - Ensembl - - - - HGNC:9531 - HGNC - - - - EQUAL - 26 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1043 - - - - PSMF1 - HGNC Symbol - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - Q52II0 - UniProt - - - - 8144677 - Waga, S - Bauer, G - Stillman, B - Pubmed - Reconstitution of complete SV40 DNA replication with purified replication factors. - J Biol Chem 269:10923-34 - 1994 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4654 - - - - NM_001080449 - RefSeq - - - - REACT_2014 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2014.3 - - - - Q86U83 - UniProt - - - - 939866 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939866 - - - - E2F3 - E2F-3 - KIAA0075 - - - - - - - - - - - - - - - - - - - E2F3_HUMAN - Transcription factor E2F3 - FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F3 binds specifically to RB1 in a cell-cycle dependent manner.SUBUNIT: Component of the DRTF1/E2F transcription factor complex. Binds cooperatively with TFDP1/Dp-1 to E2F sites. Interacts with retinoblastoma protein RB1 and related proteins (such as RBL1) that inhibit the E2F transactivation domain. Binds EAPP.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O00716-1; Sequence=Displayed; Name=2; IsoId=O00716-2; Sequence=VSP_045066, VSP_045067, VSP_045068; Note=No experimental confirmation available;SIMILARITY: Belongs to the E2F/DP family.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/E2F3ID40384ch6p22.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/e2f3/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_1009 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1009.3 - - - - NM_004153 - RefSeq - - - - NM_014614 - RefSeq - - - - 68808 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68808 - - - - B5BU07 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6441 - - - - - - - - - - - - Orc5:Orc3:Orc2:origin - Reactome DB_ID: 68517 - http://www.reactome.org/biopax/46/48887#Complex2665 - - - - Q3B757 - UniProt - - - - 22395957 - pubchem - - - - - - phospho-p27(Thr 187) - - - - - - http://www.reactome.org/biopax/46/48887#Protein5648 - Reactome DB_ID: 187525 - p-T187-CDKN1B - - - - REACT_25754 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25754.1 - - - - - - Maturation factor 1 - FEN1 - Flap endonuclease-1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5736 - Reactome DB_ID: 54745 - MF1 - - - - - - - - - - DNA polymerase epsilon binds at the origin - At the beginning of this reaction, 1 molecule of 'origin of replication', and 1 molecule of 'DNA polymerase epsilon' are present. At the end of this reaction, 1 molecule of 'DNA polymerase epsilon:origin complex' is present.<br><br> <br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1979 - - - - - 939869 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939869 - - - - - - MOD_RES 508 508 Phosphoserine. - - - - - - - - - - Orc1 is phosphorylated by cyclin A/CDK2 - At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'pre-replicative complex' are present. At the end of this reaction, 1 molecule of 'phosphorylated Orc1', 1 molecule of 'pre-replicative complex (Orc1-minus)', and 1 molecule of 'ADP' are present.<br><br> This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'Cyclin A:Cdk2 complex'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1995 - - - - - - - NP_002787 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2109 - - - - - - 602696 - omim - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10640 - - - - REACT_3283 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3283.1 - - - - 68385 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68385 - - - - CHEBI:19243 - ChEBI - - - - - - MOD_RES 807 807 Phosphoserine; by CDK1 and CDK3. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6659 - - - - EQUAL - 80 - - - - NM_001190818 - RefSeq - - - - Q9UJA3 - UniProt - - - - RFC5 - HGNC - - - - REACT_24888 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24888.2 - - - - - - MOD_RES 55 55 Phosphothreonine. - - - - ENSP00000363021 - Ensembl - - - - 5694 - NCBI Gene - - - - - 3.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6696 - - - - - - - - - - Cdc6 protein is phosphorylated by CDK - At the beginning of this reaction, 1 molecule of 'CDC6', and 1 molecule of 'ATP' are present. At the end of this reaction, 1 molecule of 'ADP', and 1 molecule of 'phosphorylated Cdc6' are present.<br><br> This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'CDK'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1999 - - - - - - REACT_757 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_757.2 - - - - - - - - - - - - - - - DNA ligase I - LIG1 - 6.5.1.1 - Polydeoxyribonucleotide synthase [ATP] 1 - - - - - - - - - - - - - - - - - - - - - - DNLI1_HUMAN - DNA ligase 1 - FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).COFACTOR: Magnesium.SUBCELLULAR LOCATION: Nucleus.SIMILARITY: Belongs to the ATP-dependent DNA ligase family.WEB RESOURCE: Name=LIG1base; Note=LIG1 mutation db; URL="http://bioinf.uta.fi/LIG1base/";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/lig1/";WEB RESOURCE: Name=Wikipedia; Note=DNA ligase entry; URL="http://en.wikipedia.org/wiki/DNA_ligase"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - UDMBCSSLTHHNCD-KQYNXXCUSA-N - InChIKey - - - - ENST00000320574 - Ensembl - - - - EQUAL - 53 - - - - EQUAL - 241 - http://www.reactome.org/biopax/46/48887#SequenceSite1817 - - - - DBF4 - HGNC - - - - REACT_5617 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5617.1 - - - - REACT_2817 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2817.2 - - - - HGNC:31963 - HGNC - - - - - - MOD_RES 373 373 Phosphothreonine; by CDK1. - - - - - - MOD_RES 192 192 Symmetric dimethylarginine; by PRMT5. - - - - 113504 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113504 - - - - - - - - - - - - - - - - - - - - - - - Rb - p105-Rb - pRb - pp110 - RB1 - - - - - - - - - - - - - - - - - RB_HUMAN - Retinoblastoma-associated protein - FUNCTION: Key regulator of entry into cell division that acts as a tumor suppressor. Promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. Acts as a transcription repressor of E2F1 target genes. The underphosphorylated, active form of RB1 interacts with E2F1 and represses its transcription activity, leading to cell cycle arrest. Directly involved in heterochromatin formation by maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin by stabilizing histone methylation. Recruits and targets histone methyltransferases SUV39H1, SUV420H1 and SUV420H2, leading to epigenetic transcriptional repression. Controls histone H4 'Lys-20' trimethylation. Inhibits the intrinsic kinase activity of TAF1. Mediates transcriptional repression by SMARCA4/BRG1 by recruiting a histone deacetylase (HDAC) complex to the c-FOS promoter. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex (By similarity). In case of viral infections, interactions with SV40 large T antigen, HPV E7 protein or adenovirus E1A protein induce the disassembly of RB1-E2F1 complex thereby disrupting RB1's activity.SUBUNIT: Interacts with ATAD5. Interacts with PRMT2, CDK1 and CDK2 (By similarity). The hypophosphorylated form interacts with and sequesters the E2F1 transcription factor. Interacts with heterodimeric E2F/DP transcription factor complexes containing TFDP1 and either E2F1, E2F3, E2F4 or E2F5, or TFDP2 and E2F4. The unphosphorylated form interacts with EID1, ARID3B, KDM5A, SUV39H1, MJD2A/JHDM3A and THOC1. Interacts with the N-terminal domain of TAF1. Interacts with SNW1, AATF, DNMT1, LIN9, LMNA, SUV420H1, SUV420H2, PELP1, UHRF2 and TMPO-alpha. May interact with NDC80. Interacts with GRIP1 and UBR4. Interacts with ARID4A and KDM5B. Interacts with E4F1 and LIMD1. Interacts with SMARCA4/BRG1 AND HDAC1 (By similarity). Interacts with adenovirus E1A protein, HPV E7 protein and SV40 large T antigen. Interacts with PSMA3 and USP4. Interacts (when methylated at Lys-860) with L3MBTL1. Interacts with CHEK2; phosphorylates RB1. Interacts with human cytomegalovirus/HHV-5 protein UL123.SUBCELLULAR LOCATION: Nucleus.TISSUE SPECIFICITY: Expressed in the retina.DOMAIN: The Pocket domain binds to the threonine-phosphorylated domain C, thereby preventing interaction with heterodimeric E2F/DP transcription factor complexes.PTM: Phosphorylated by CDK6 and CDK4, and subsequently by CDK2 at Ser-567 in G1, thereby releasing E2F1 which is then able to activate cell growth. Dephosphorylated at the late M phase. SV40 large T antigen, HPV E7 and adenovirus E1A bind to the underphosphorylated, active form of pRb. Phosphorylation at Thr- 821 and Thr-826 promotes interaction between the C-terminal domain C and the Pocket domain, and thereby inhibits interactions with heterodimeric E2F/DP transcription factor complexes. Dephosphorylated at Ser-795 by calcineruin upon calcium stimulation. CDK3/cyclin-C-mediated phosphorylation at Ser-807 and Ser-811 is required for G0-G1 transition. Phosphorylated by CDK1 and CDK2 upon TGFB1-mediated apoptosis (By similarity).PTM: N-terminus is methylated by METTL11A/NTM1 (By similarity). Monomethylation at Lys-810 by SMYD2 enhances phosphorylation at Ser-807 and Ser-811, and promotes cell cycle progression. Monomethylation at Lys-860 by SMYD2 promotes interaction with L3MBTL1.PTM: Acetylation at Lys-873 and Lys-874 regulates subcellular localization, at least during keratinocytes differentiation.DISEASE: Childhood cancer retinoblastoma (RB) [MIM:180200]: Congenital malignant tumor that arises from the nuclear layers of the retina. It occurs in about 1:20'000 live births and represents about 2% of childhood malignancies. It is bilateral in about 30% of cases. Although most RB appear sporadically, about 20% are transmitted as an autosomal dominant trait with incomplete penetrance. The diagnosis is usually made before the age of 2 years when strabismus or a gray to yellow reflex from pupil ('cat eye') is investigated. Note=The disease is caused by mutations affecting the gene represented in this entry.DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.DISEASE: Osteogenic sarcoma (OSRC) [MIM:259500]: A sarcoma originating in bone-forming cells, affecting the ends of long bones. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the retinoblastoma protein (RB) family.WEB RESOURCE: Name=RB1base; Note=RB1 mutation db; URL="http://rb1-lsdb.d-lohmann.de/";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/RB1ID90.html";WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/RB1";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rb1/";WEB RESOURCE: Name=Wikipedia; Note=Retinoblastoma protein entry; URL="http://en.wikipedia.org/wiki/Retinoblastoma_protein"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSG00000100567 - Ensembl - - - - D3DV16 - UniProt - - - - - - - - - - Phosphorylated Orc1 is ubiquitinated while still associated with chromatin - At the beginning of this reaction, 1 molecule of 'ubiquitin', and 1 molecule of 'phosphorylated Orc1' are present. At the end of this reaction, 1 molecule of 'ubiquitinated Orc1' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1996 - - - - - 600815 - omim - - - - - - MOV34L - 26S proteasome regulatory subunit S12 - 26S proteasome regulatory subunit RPN8 - PSMD7 - Mov34 protein homolog - Proteasome subunit p40 - - - - - - - - - - - - - - - - - PSMD7_HUMAN - 26S proteasome non-ATPase regulatory subunit 7 - FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.SUBUNIT: Homodimer. Interacts with TRIM5.MISCELLANEOUS: Does not bind a metal ion.SIMILARITY: Belongs to the peptidase M67A family.SIMILARITY: Contains 1 MPN (JAB/Mov34) domain.SEQUENCE CAUTION: Sequence=AAH00338.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4873 - - - - - - - - - - - - geminin:ubiquitin complex - Reactome DB_ID: 68585 - http://www.reactome.org/biopax/46/48887#Complex2670 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2207 - - - - B2R8H5 - UniProt - - - - RFC2 - HGNC - - - - - - MOD_RES 126 126 Phosphoserine. - - - - EQUAL - 1 - - - - ENSG00000185627 - Ensembl - - - - EQUAL - 182 - - - - RFC4 - HGNC Symbol - - - - - - - - - - - - - - - - CDK1 - P34CDC2 - Cell division protein kinase 1 - Cell division control protein 2 homolog - CDC2 - p34 protein kinase - 2.7.11.23 - 2.7.11.22 - CDC28A - CDKN1 - - - - - - - - - - - - - - - - - - - - - - - - CDK1_HUMAN - Cyclin-dependent kinase 1 - FUNCTION: Plays a key role in the control of the eukaryotic cell cycle by modulating the centrosome cycle as well as mitotic onset; promotes G2-M transition, and regulates G1 progress and G1-S transition via association with multiple interphase cyclins. Required in higher cells for entry into S-phase and mitosis. Phosphorylates PARVA/actopaxin, APC, AMPH, APC, BARD1, Bcl- xL/BCL2L1, BRCA2, CALD1, CASP8, CDC7, CDC20, CDC25A, CDC25C, CC2D1A, CSNK2 proteins/CKII, FZR1/CDH1, CDK7, CEBPB, CHAMP1, DMD/dystrophin, EEF1 proteins/EF-1, EZH2, KIF11/EG5, EGFR, FANCG, FOS, GFAP, GOLGA2/GM130, GRASP1, UBE2A/hHR6A, HIST1H1 proteins/histone H1, HMGA1, HIVEP3/KRC, LMNA, LMNB, LMNC, LBR, LATS1, MAP1B, MAP4, MARCKS, MCM2, MCM4, MKLP1, MYB, NEFH, NFIC, NPC/nuclear pore complex, PITPNM1/NIR2, NPM1, NCL, NUCKS1, NPM1/numatrin, ORC1, PRKAR2A, EEF1E1/p18, EIF3F/p47, p53/TP53, NONO/p54NRB, PAPOLA, PLEC/plectin, RB1, UL40/R2, RAB4A, RAP1GAP, RCC1, RPS6KB1/S6K1, KHDRBS1/SAM68, ESPL1, SKI, BIRC5/survivin, STIP1, TEX14, beta-tubulins, MAPT/TAU, NEDD1, VIM/vimentin, TK1, FOXO1, RUNX1/AML1 and RUNX2. CDK1/CDC2-cyclin-B controls pronuclear union in interphase fertilized eggs. Essential for early stages of embryonic development. During G2 and early mitosis, CDC25A/B/C-mediated dephosphorylation activates CDK1/cyclin complexes which phosphorylate several substrates that trigger at least centrosome separation, Golgi dynamics, nuclear envelope breakdown and chromosome condensation. Once chromosomes are condensed and aligned at the metaphase plate, CDK1 activity is switched off by WEE1- and PKMYT1-mediated phosphorylation to allow sister chromatid separation, chromosome decondensation, reformation of the nuclear envelope and cytokinesis. Inactivated by PKR/EIF2AK2- and WEE1-mediated phosphorylation upon DNA damage to stop cell cycle and genome replication at the G2 checkpoint thus facilitating DNA repair. Reactivated after successful DNA repair through WIP1-dependent signaling leading to CDC25A/B/C- mediated dephosphorylation and restoring cell cycle progression. In proliferating cells, CDK1-mediated FOXO1 phosphorylation at the G2-M phase represses FOXO1 interaction with 14-3-3 proteins and thereby promotes FOXO1 nuclear accumulation and transcription factor activity, leading to cell death of postmitotic neurons. The phosphorylation of beta-tubulins regulates microtubule dynamics during mitosis. NEDD1 phosphorylation promotes PLK1-mediated NEDD1 phosphorylation and subsequent targeting of the gamma-tubulin ring complex (gTuRC) to the centrosome, an important step for spindle formation. In addition, CC2D1A phosphorylation regulates CC2D1A spindle pole localization and association with SCC1/RAD21 and centriole cohesion during mitosis. The phosphorylation of Bcl- xL/BCL2L1 after prolongated G2 arrest upon DNA damage triggers apoptosis. In contrast, CASP8 phosphorylation during mitosis prevents its activation by proteolysis and subsequent apoptosis. This phosphorylation occurs in cancer cell lines, as well as in primary breast tissues and lymphocytes. EZH2 phosphorylation promotes H3K27me3 maintenance and epigenetic gene silencing. CALD1 phosphorylation promotes Schwann cell migration during peripheral nerve regeneration.CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.CATALYTIC ACTIVITY: ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.ENZYME REGULATION: Phosphorylation at Thr-14 or Tyr-15 inactivates the enzyme, while phosphorylation at Thr-161 activates it. Activated through a multistep process; binding to cyclin-B is required for relocation of cyclin-kinase complexes to the nucleus, activated by CAK/CDK7-mediated phosphorylation on Thr-161, and CDC25-mediated dephosphorylation of inhibitory phosphorylation on Thr-14 and Tyr-15. Inhibited by flavopiridol and derivatives, pyrimidine derivatives, pyridine derivatives, purine derivatives, staurosporine, paullones, oxoindoles, indazole analogs, indolin-2- ones, pyrazolo[3,4-b]pyridines, imidazo[1,2-a]pyridine (AZ703), thiazolinone analogs(RO-3306), thiazol urea, macrocyclic quinoxalin-2-one, pyrrolo[2,3-a]carbazole, pyrazolo[1,5-a]-1,3,5- triazine, pyrazolo[1,5-a]pyrimidine (Dinaciclib, SCH 727965), 2- (1-ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropylpurine (roscovitine), olomoucine, AG-024322, AT-7519, P276-00, R547/Ro- 4584820 and SNS-032/BMS-387032. Repressed by the CDK inhibitors CDKN1A/p21 and CDKN1B/p27 during the G1 phase and by CDKN1A/p21 at the G1-S checkpoint upon DNA damage. Transient activation by rapid and transient dephosphorylation at Tyr-15 triggered by TGFB1.SUBUNIT: Forms a stable but non-covalent complex with a regulatory subunit and with a cyclin. Interacts with cyclins-B (CCNB1, CCNB2 and CCNB3) to form a serine/threonine kinase holoenzyme complex also known as maturation promoting factor (MPF). The cyclin subunit imparts substrate specificity to the complex. Can also form CDK1-cylin-D and CDK1-cyclin-E complexes that phosphorylate RB1 in vitro. Binds to RB1 and other transcription factors such as FOXO1 and RUNX2. Promotes G2-M transition when in complex with a cyclin-B. Interacts with DLGAP5. Binds to the CDK inhibitors CDKN1A/p21 and CDKN1B/p27. Isoform 2 is unable to complex with cyclin-B1 and also fails to bind to CDKN1A/p21. Interacts with catalytically active CCNB1 and RALBP1 during mitosis to form an endocytotic complex during interphase. Associates with cyclins-A and B1 during S-phase in regenerating hepatocytes. Interacts with FANCC. Interacts with CEP63; this interaction recruits CDK1 to centrosomes.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Mitochondrion. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Cytoplasmic during the interphase. Reversibly translocated from cytoplasm to nucleus when phosphorylated before G2-M transition when associated with cyclin- B1. Accumulates in mitochondria in G2-arrested cells upon DNA- damage.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P06493-1; Sequence=Displayed; Name=2; Synonyms=CDC2deltaT; IsoId=P06493-2; Sequence=VSP_021375;TISSUE SPECIFICITY: Isoform 2 is found in breast cancer tissues.INDUCTION: Follows a cyclic expression; during interphase, accumulates gradually following G1, S to reach a critical threshold at the end of G2, which promotes self-activation and triggers onset of mitosis. Induced transiently by TGFB1 at an early phase of TGFB1-mediated apoptosis, but later repressed. Triggered by CKS1B during mitotic entry in breast cancer cells. Down-regulated under genotoxic stresses triggered by PKR/EIF2AK2- mediated phosphorylation.PTM: Phosphorylation at Thr-161 by CAK/CDK7 activates kinase activity. Phosphorylation at Thr-14 and Tyr-15 by PKMYT1 prevents nuclear translocation. Phosphorylation at Tyr-15 by WEE1 and WEE2 inhibits the protein kinase activity and acts as a negative regulator of entry into mitosis (G2 to M transition). Phosphorylation by PKMYT1 and WEE1 takes place during mitosis to keep CDK1-cyclin-B complexes inactive until the end of G2. By the end of G2, PKMYT1 and WEE1 are inactivated, but CDC25A and CDC25B are activated. Dephosphorylation by active CDC25A and CDC25B at Thr-14 and Tyr-15, leads to CDK1 activation at the G2-M transition. Phosphorylation at Tyr-15 by WEE2 during oogenesis is required to maintain meiotic arrest in oocytes during the germinal vesicle (GV) stage, a long period of quiescence at dictyate prophase I, leading to prevent meiotic reentry. Phosphorylation by WEE2 is also required for metaphase II exit during egg activation to ensure exit from meiosis in oocytes and promote pronuclear formation. Phosphorylated at Tyr-4 by PKR/EIF2AK2 upon genotoxic stress. This phosphorylation triggers CDK1 polyubiquitination and subsequent proteolysis, thus leading to G2 arrest. In response to UV irradiation, phosphorylation at Tyr-15 by PRKCD activates the G2/M DNA damage checkpoint.PTM: Polyubiquitinated upon genotoxic stress.MISCELLANEOUS: As a key regulator of the cell cycle, CDK1 is a potent therapeutic target for inhibitors in cancer treatment (PubMed:21517772).SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.SIMILARITY: Contains 1 protein kinase domain.SEQUENCE CAUTION: Sequence=EAW54204.1; Type=Erroneous gene model prediction;WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4959 - - - - GINS4 - HGNC Symbol - - - - HGNC:9551 - HGNC - - - - 81620 - NCBI Gene - - - - CHEBI:13508 - ChEBI - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval828 - - - - - - 69016 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69016 - - - - ENSP00000234296 - Ensembl - - - - ENSP00000379180 - Ensembl - - - - - - SLD5P - - - - - Reactome DB_ID: 176963 - http://www.reactome.org/biopax/46/48887#Protein5728 - GINS4 - - - - 10751307 - Liu, L - Rodriguez-Belmonte, EM - Lee, MY - Mo, J - Pubmed - Identification of a fourth subunit of mammalian DNA polymerase delta. - J Biol Chem 275:18739-44 - 2000 - - - - 68949 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68949 - - - - EQUAL - 574 - http://www.reactome.org/biopax/46/48887#SequenceSite10615 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6783 - - - - NM_002804 - RefSeq - - - - ENST00000457654 - Ensembl - - - - 939164 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939164 - - - - - - Cyclin - Proliferating cell nuclear antigen - - - - - Reactome DB_ID: 68439 - http://www.reactome.org/biopax/46/48887#Protein5603 - PCNA - - - - NM_001243076 - RefSeq - - - - - - MOD_RES 873 873 N6-acetyllysine; by PCAF. - - - - - - - - - - - - ubiquitinated Orc1 - http://www.reactome.org/biopax/46/48887#Complex2627 - Reactome DB_ID: 68586 - - - - 113570 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113570 - - - - Q86US4 - UniProt - - - - 68557 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68557 - - - - EQUAL - 107 - http://www.reactome.org/biopax/46/48887#SequenceSite10908 - - - - 69018 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69018 - - - - ENSG00000035928 - Ensembl - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - - - MOD_RES 98 98 N6,N6,N6-trimethyllysine (By similarity). - - - - ENST00000441960 - Ensembl - - - - ENSP00000412618 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10542 - - - - REACT_24708 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24708.2 - - - - CHEBI:42615 - ChEBI - - - - O00231 - UniProt - - - - 10757793 - Zou, L - Stillman, B - Pubmed - Assembly of a complex containing Cdc45p, replication protein A, and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase. - Mol Cell Biol 20:3086-96 - 2000 - - - - ENSG00000143947 - Ensembl - - - - 12364596 - Knippers, R - Ladenburger, EM - Keller, C - Schaarschmidt, D - Pubmed - Human Mcm proteins at a replication origin during the G1 to S phase transition. - Nucleic Acids Res 30:4176-85 - 2002 - - - - NM_181700 - RefSeq - - - - NP_002788 - RefSeq - - - - HGNC:6598 - HGNC - - - - P39748 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval859 - - - - - - NM_001190879 - RefSeq - - - - CHEBI:22242 - ChEBI - - - - CHEBI:5228 - ChEBI - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6670 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4962 - - - - NP_001186092 - RefSeq - - - - EQUAL - 411 - - - - ENSP00000348442 - Ensembl - - - - EQUAL - 271 - http://www.reactome.org/biopax/46/48887#SequenceSite1823 - - - - - - DNA primase large subunit - DNA primase 58 kDa subunit - PRIM2 - - - - - Reactome DB_ID: 68495 - http://www.reactome.org/biopax/46/48887#Protein5708 - p58 - - - - ENSG00000101182 - Ensembl - - - - - - - - - - - - active pre-replicative complex - Reactome DB_ID: 156562 - http://www.reactome.org/biopax/46/48887#Complex2547 - - - - HGNC:17364 - HGNC - - - - REACT_3295 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3295.2 - - - - ENSP00000363011 - Ensembl - - - - - - MOD_RES 37 37 Phosphoserine. - - - - EQUAL - 114 - - - - 68810 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68810 - - - - P28074 - UniProt - - - - 68792 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68792 - - - - HGNC:9547 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2430 - - - - - - NM_002691 - RefSeq - - - - B2R8F6 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10634 - - - - Q9UM10 - UniProt - - - - ENSP00000471464 - Ensembl - - - - Q9BTJ4 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2656 - - - - - ENST00000374882 - Ensembl - - - - - RPA14 - RF-A protein 3 - RP-A p14 - REPA3 - Replication factor A protein 3 - RPA3 - - - - - - - - - - - - - - - - - RFA3_HUMAN - Replication protein A 14 kDa subunit - FUNCTION: Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions.FUNCTION: Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S- phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.SUBUNIT: Heterotrimer of 70, 32 and 14 kDa chains (canonical replication protein A complex). Component of the alternative replication protein A complex (aRPA) composed of RPA1, RPA3 and RPA4. The DNA-binding activity may reside exclusively on the 70 kDa subunit. Interacts with RPA4.SUBCELLULAR LOCATION: Nucleus.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rpa3/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - - - - Removal of licensing factors from origins - http://www.reactome.org/biopax/46/48887#Pathway520 - Licensing factors are removed from the origin by various means like biochemical modification (phosphorylation) or by physical association with other proteins. This pathway includes the annotations of events in which the fates of different proteins at the origin are outlined. - - - - - phosphorylated residue - - - - - - - - RFC4 - Activator 1 subunit 4 - RF-C 37 kDa subunit - A1 37 kDa subunit - RFC37 - Activator 1 37 kDa subunit - Replication factor C 37 kDa subunit - - - - - - - - - - - - - - - - - - RFC4_HUMAN - Replication factor C subunit 4 - FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit may be involved in the elongation of the multiprimed DNA template.SUBUNIT: Heterotetramer of subunits RFC2, RFC3, RFC4 and RFC5 that can form a complex either with RFC1 or with RAD17. The former interacts with PCNA in the presence of ATP, while the latter has ATPase activity but is not stimulated by PCNA.SUBCELLULAR LOCATION: Nucleus (Probable).MISCELLANEOUS: Despite of the presence of a putative ATP-binding motif, this protein does not bind ATP.SIMILARITY: Belongs to the activator 1 small subunits family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rfc4/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - 26S proteasome regulatory subunit S14 - 26S proteasome non-ATPase regulatory subunit 8 - PSMD8 - - - - - Reactome DB_ID: 68808 - http://www.reactome.org/biopax/46/48887#Protein1064 - p31 - - - - EQUAL - 298 - http://www.reactome.org/biopax/46/48887#SequenceSite2967 - - - - REACT_2542 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2542.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2093 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6788 - - - - REACT_3995 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3995.3 - - - - Q96GX4 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4960 - - - - EQUAL - 205 - http://www.reactome.org/biopax/46/48887#SequenceSite1851 - - - - NM_006190 - RefSeq - - - - EQUAL - 696 - - - - CDT1 - HGNC - - - - D3DVW3 - UniProt - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis625 - - - - EQUAL - 147 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10683 - - - - - - 26S proteasome non-ATPase regulatory subunit 7 - 26S proteasome regulatory subunit S12 - Mov34 protein homolog - Proteasome subunit p40 - - - - - http://www.reactome.org/biopax/46/48887#Protein1068 - Reactome DB_ID: 68806 - PSMD7 - - - - Q9H413 - UniProt - - - - 176973 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176973 - - - - - origin - autonomously replicating sequence - origin of replication - - - - ARS - http://www.reactome.org/biopax/46/48887#PhysicalEntity246 - Reactome DB_ID: 68419 - - - - 68689 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68689 - - - - EQUAL - 252 - http://www.reactome.org/biopax/46/48887#SequenceSite10629 - - - - - - MOD_RES 4 4 Phosphotyrosine; by PKR. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval843 - - - - - - 8143535 - pubchem-substance - - - - NP_002907 - RefSeq - - - - PSMB1 - HGNC Symbol - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1064 - - - - - - Replication factor C 40 kDa subunit - RFC40 - A1 40 kDa subunit - RFC2 - RF-C 40 kDa subunit - Activator 1 subunit 2 - Activator 1 40 kDa subunit - - - - - - - - - - - - - - - - - - - - - - - - - RFC2_HUMAN - Replication factor C subunit 2 - FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1. This subunit binds ATP (By similarity).SUBUNIT: Heterotetramer of subunits RFC2, RFC3, RFC4 and RFC5 that can form a complex either with RFC1 or with RAD17. The former interacts with PCNA in the presence of ATP, while the latter has ATPase activity but is not stimulated by PCNA. RFC2 also interacts with PRKAR1A; the complex may be involved in cell survival.SUBCELLULAR LOCATION: Nucleus (Probable).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P35250-1; Sequence=Displayed; Name=2; IsoId=P35250-2; Sequence=VSP_005660; Note=No experimental confirmation available;DISEASE: Note=RFC2 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.SIMILARITY: Belongs to the activator 1 small subunits family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rfc2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - - - - - - - - - - Activator 1 140 kDa subunit - DNA-binding protein PO-GA - RFC1 - RFC140 - RF-C 140 kDa subunit - A1 140 kDa subunit - Activator 1 large subunit - Replication factor C 140 kDa subunit - Activator 1 subunit 1 - Replication factor C large subunit - - - - - - - - - - - - - - - - - - - - - - RFC1_HUMAN - Replication factor C subunit 1 - FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. This subunit binds to the primer-template junction. Binds the PO-B transcription element as well as other GA rich DNA sequences. Could play a role in DNA transcription regulation as well as DNA replication and/or repair. Can bind single- or double-stranded DNA.FUNCTION: Interacts with C-terminus of PCNA. 5' phosphate residue is required for binding of the N-terminal DNA-binding domain to duplex DNA, suggesting a role in recognition of non-primer template DNA structures during replication and/or repair.SUBUNIT: Heterotetramer of subunits RFC2, RFC3, RFC4 and RFC5 that can form a complex either with RFC1 or with RAD17. The former interacts with PCNA in the presence of ATP, while the latter has ATPase activity but is not stimulated by PCNA.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P35251-1; Sequence=Displayed; Name=2; IsoId=P35251-2; Sequence=VSP_008443; Note=Alternative use of an acceptor site;TISSUE SPECIFICITY: Wide tissue distribution. Undetectable in placental tissue.SIMILARITY: Belongs to the activator 1 large subunit family.SIMILARITY: Contains 1 BRCT domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rfc1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_001104517 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval867 - - - - - - A8K5E3 - UniProt - - - - O75226 - UniProt - - - - Q12920 - UniProt - - - - reactome - Reactome - Source type: BIOPAX, Reactome v46 (using only 'Homo sapiens.owl') 23-SEP-2013 - - - - ENST00000297431 - Ensembl - - - - - - MOD_RES 14 14 N6-acetyllysine. - - - - - - MOD_RES 2 2 N-acetylalanine (By similarity). - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4935 - - - - MCM6 - HGNC - - - - Q9H4K5 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1085 - - - - - - MOD_RES 6 6 N6-acetyllysine. - - - - Q5TEI9 - UniProt - - - - - - MOD_RES 190 190 Phosphoserine. - - - - ENST00000373237 - Ensembl - - - - 7713898 - Zeng, XR - Chuang, RY - Toomey, NL - Zhang, SJ - Chang, LS - Zhang, P - Lee, MY - Pubmed - A conserved region in the amino terminus of DNA polymerase delta is involved in proliferating cell nuclear antigen binding. - J Biol Chem 270:7988-92 - 1995 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2661 - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4821 - - - - - - - - MOD_RES 841 841 Phosphothreonine. - - - - 68712 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68712 - - - - 10523313 - Hunter, T - Jiang, W - McDonald, D - Hope, TJ - Pubmed - Mammalian Cdc7-Dbf4 protein kinase complex is essential for initiation of DNA replication. - EMBO J 18:5703-13 - 1999 - - - - EQUAL - 1 - - - - 10473346 - Borowiec, JA - Daniely, Y - Iftode, C - Pubmed - Replication protein A (RPA): the eukaryotic SSB. - Crit Rev Biochem Mol Biol 34:141-80 - 1999 - - - - MCM7 - HGNC - - - - - - - - - - - - - Orc3 associates with Orc2 constitutively bound at origins of replication - At the beginning of this reaction, 1 molecule of 'Orc2:origin', and 1 molecule of 'Orc3' are present. At the end of this reaction, 1 molecule of 'Orc3:Orc2:origin' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2141 - - - - - Q5T5U5 - UniProt - - - - ENSP00000311344 - Ensembl - - - - ENSP00000262193 - Ensembl - - - - EQUAL - 2 - - - - - - PSF2p - - - - - http://www.reactome.org/biopax/46/48887#Protein5727 - Reactome DB_ID: 176975 - GINS2 - - - - NM_031966 - RefSeq - - - - O00232 - UniProt - - - - 450466 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=450466 - - - - - - MOD_RES 711 711 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature878 - - - - - - - - - pre-replicative complex - - - - preRC - http://www.reactome.org/biopax/46/48887#Complex2599 - Reactome DB_ID: 68559 - - - - 8143900 - pubchem - - - - - - - - - Cdt1 is displaced from the pre-replicative complex. - At the beginning of this reaction, 1 molecule of 'Mcm10:pre-replicative complex' is present. At the end of this reaction, 1 molecule of 'Mcm10:active pre-replicative complex', and 1 molecule of 'CDT1' are present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1973 - - - - - - - O4P - tetraoxidophosphate(3-) - tetraoxophosphate(3-) - tetraoxophosphate(V) - phosphate - PO4(3-) - [PO4](3-) - - - - - - - - 94.97136 - phosphate(3-) - phosphate(3-) - - - - MCM4 - HGNC - - - - PSMB1 - HGNC - - - - P07029 - UniProt - - - - ENST00000383238 - Ensembl - - - - 10611290 - Kelman, Z - Hurwitz, J - Lee, JK - Pubmed - The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity. - Proc Natl Acad Sci U S A 96:14783-8 - 2000 - - - - - - - - - - - - ubiquitinated Orc1 - Reactome DB_ID: 113570 - http://www.reactome.org/biopax/46/48887#Complex2626 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2427 - - - - - - REACT_2422 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2422.1 - - - - ENSG00000108294 - Ensembl - - - - NP_000380 - RefSeq - - - - EQUAL - 681 - - - - ENSG00000131153 - Ensembl - - - - 68794 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68794 - - - - 11296242 - Tak, YS - Araki, H - Sugino, A - Kamimura, Y - Pubmed - Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae. - EMBO J 20:2097-107 - 2001 - - - - NP_001177748 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10891 - - - - NP_002778 - RefSeq - - - - Q96HE6 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6639 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2667 - - - - PRIM2 - HGNC Symbol - - - - ENST00000434425 - Ensembl - - - - NM_182746 - RefSeq - - - - - - MOD_RES 120 120 N6-acetyllysine. - - - - 10373557 - Lees, E - Kumagai, H - Mahony, D - Arai, K - Sato, N - Seghezzi, W - Yamada, M - Masai, H - Pubmed - A novel growth- and cell cycle-regulated protein, ASK, activates human Cdc7-related kinase and is essential for G1/S transition in mammalian cells. - Mol Cell Biol 19:5083-95 - 1999 - - - - CHEBI:2356 - ChEBI - - - - - - P1-MCM3 - DNA polymerase alpha holoenzyme-associated protein P1 - RLF beta subunit - P102 protein - DNA replication licensing factor MCM3 - Mcm3 - - - - - http://www.reactome.org/biopax/46/48887#Protein5587 - Reactome DB_ID: 68546 - MCM3 - - - - EQUAL - 2 - - - - CHEBI:9849 - ChEBI - - - - NM_002807 - RefSeq - - - - - - - - - - - - - - - - 3.6.4.12 - RLF subunit beta - P1-MCM3 - DNA polymerase alpha holoenzyme-associated protein P1 - p102 - MCM3 - - - - - - - - - - - - - - - - - MCM3_HUMAN - DNA replication licensing factor MCM3 - FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Required for DNA replication and cell proliferation.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6- MCM4-MCM7-MCM3-MCM5 (By simililarity). Associated with the replication-specific DNA polymerase alpha. Interacts with MCMBP.SUBCELLULAR LOCATION: Nucleus.PTM: O-glycosylated (O-GlcNAcylated), in a cell cycle-dependent manner.MISCELLANEOUS: Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/mcm3/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - 3184 - NCBI Gene - - - - - - MOD_RES 2 2 N,N-dimethylproline (By similarity). - - - - NM_002915 - RefSeq - - - - A0AVQ9 - UniProt - - - - ENSG00000101412 - Ensembl - - - - EQUAL - 560 - http://www.reactome.org/biopax/46/48887#SequenceSite10894 - - - - ENST00000435765 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2206 - - - - - - - - - - - The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2030 - At the beginning of this reaction, 1 molecule of 'ubiquitin', and 1 molecule of 'Cdt1:geminin' are present. At the end of this reaction, 1 molecule of 'geminin:ubiquitin complex', and 1 molecule of 'Cdt1' are present.<br><br> This reaction takes place in the 'cytosol'.<br> - - - - - - ENST00000228872 - Ensembl - - - - ENSG00000125885 - Ensembl - - - - - - MOD_RES 318 318 Phosphoserine. - - - - DNA2 - HGNC Symbol - - - - REACT_161344 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161344.2 - - - - - - MOD_RES 304 304 N6-acetyllysine. - - - - EQUAL - 214 - - - - - - Guanosine 5'-triphosphate - - - - Reactome DB_ID: 113571 - http://www.reactome.org/biopax/46/48887#SmallMolecule200 - GTP - - - - P25205 - UniProt - - - - PTHR24056:SF123 - PANTHER Family - - - - - Q86TN5 - UniProt - - - - ENST00000358410 - Ensembl - - - - Q9BPV3 - UniProt - - - - - - MOD_RES 47 47 Phosphoserine. - - - - ENSP00000463938 - Ensembl - - - - ENSP00000451621 - Ensembl - - - - EQUAL - 953 - http://www.reactome.org/biopax/46/48887#SequenceSite1835 - - - - 68918 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68918 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1395 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4992 - - - - - - 69304 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69304 - - - - - - - - - - - PA28gamma - 11S regulator complex subunit gamma - PA28g - REG-gamma - Proteasome activator 28 subunit gamma - PSME3 - Ki nuclear autoantigen - Activator of multicatalytic protease subunit 3 - - - - - - - - - - - - - - - - - - - - - - - PSME3_HUMAN - Proteasome activator complex subunit 3 - FUNCTION: Subunit of the 11S REG-gamma (also called PA28-gamma) proteasome regulator, a doughnut-shaped homoheptamer which associates with the proteasome. 11S REG-gamma activates the trypsin-like catalytic subunit of the proteasome but inhibits the chymotrypsin-like and postglutamyl-preferring (PGPH) subunits. Facilitates the MDM2-p53/TP53 interaction which promotes ubiquitination- and MDM2-dependent proteasomal degradation of p53/TP53, limiting its accumulation and resulting in inhibited apoptosis after DNA damage. May also be involved in cell cycle regulation.SUBUNIT: Homoheptamer; the stability of the heptamer is essential for the specific activation of the trypsine-like subunit and inhibition of the chymotrypsin-like and postglutamyl-preferring (PGPH) subunits of the proteasome. Interacts with p53/TP53 and MDM2. Interacts with MAP3K3 (By similarity). Associates with the proteasome.SUBCELLULAR LOCATION: Nucleus. Cytoplasm (By similarity). Note=Localizes to the cytoplasm during mitosis following nuclear envelope breakdown at this distinct stage of the cell cycle which allows its interaction with MAP3K3 kinase (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P61289-1, Q12920-1; Sequence=Displayed; Name=2; IsoId=P61289-2, Q12920-2; Sequence=VSP_004516;INDUCTION: Up-regulated in thyroid carcinoma cells.DOMAIN: The C-terminal sequences affect heptamer stability and proteasome affinity.PTM: Phosphorylated by MAP3K3 (By similarity).PTM: Acetylation at the major site Lys-195 is important for oligomerization and ability to degrade its target substrates. Deacetylated by SIRT1.SIMILARITY: Belongs to the PA28 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 68497 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68497 - - - - Q13504 - UniProt - - - - - - - - - - - - RNA primer-DNA primer:origin duplex with DNA damage - http://www.reactome.org/biopax/46/48887#Complex2611 - Reactome DB_ID: 113656 - - - - 7708676 - Dalton, S - Whitbread, L - Pubmed - Cell cycle-regulated nuclear import and export of Cdc47, a protein essential for initiation of DNA replication in budding yeast. - Proc Natl Acad Sci U S A 92:2514-8 - 1995 - - - - CHEBI:16695 - ChEBI - - - - ENSG00000094804 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2476 - - - - Q8TAA3 - UniProt - - - - REACT_829 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_829.4 - - - - 68595 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68595 - - - - Q53XU2 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2507 - - - - - - ENST00000295901 - Ensembl - - - - POLE2 - HGNC - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4889 - - - - - - LIG1 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6640 - - - - EQUAL - 144 - - - - ENSP00000441502 - Ensembl - - - - GO:0005829 - Gene Ontology - - - - EQUAL - 14 - - - - EQUAL - 311 - - - - CHEBI:19247 - ChEBI - - - - NP_859051 - RefSeq - - - - - - ubiquitin (UBC 9) - - - - - Reactome DB_ID: 939165 - http://www.reactome.org/biopax/46/48887#Protein1057 - UBC(609-684) - - - - EQUAL - 719 - http://www.reactome.org/biopax/46/48887#SequenceSite10645 - - - - 69005 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69005 - - - - REACT_24885 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24885.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature877 - - - - 11046155 - Mendez, J - Stillman, B - Pubmed - Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis. - Mol Cell Biol 20:8602-12 - 2000 - - - - - - DNA polymerase delta subunit 4 - DNA polymerase delta subunit p12 - DNA pol delta subunit 4 - - - - - Reactome DB_ID: 68447 - http://www.reactome.org/biopax/46/48887#Protein5732 - POLD4 - - - - CHEBI:41666 - ChEBI - - - - ENSG00000261911 - Ensembl - - - - Q9UM11 - UniProt - - - - FZR1 - HGNC - - - - ENSP00000322570 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4993 - - - - ENSP00000228872 - Ensembl - - - - 68849 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68849 - - - - ENST00000265465 - Ensembl - - - - EQUAL - 368 - - - - - - MOD_RES 80 80 N6-acetyllysine. - - - - - - MOD_RES 14 14 Phosphothreonine. - - - - 68946 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68946 - - - - ENST00000446762 - Ensembl - - - - REACT_4763 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4763.1 - - - - REACT_24326 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24326.2 - - - - NP_112190 - RefSeq - - - - ENSP00000443418 - Ensembl - - - - EQUAL - 381 - http://www.reactome.org/biopax/46/48887#SequenceSite4663 - - - - B0UZC0 - UniProt - - - - EQUAL - 67 - - - - - - - - - Ubiquitinated Cdc6 is degraded by the proteasome - At the beginning of this reaction, 1 molecule of 'ubiquitinated Cdc6' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present.<br><br> This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2002 - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature846 - - - - - - MOD_RES 290 290 Phosphoserine. - - - - 606223 - omim - - - - HGNC:9303 - HGNC - - - - ENSG00000164815 - Ensembl - - - - ENSG00000106628 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4855 - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6637 - - - - PSMC4 - HGNC Symbol - - - - ENST00000354230 - Ensembl - - - - Q8TA98 - UniProt - - - - NP_005780 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7554 - - - - EQUAL - 6 - - - - Q7RTT1 - UniProt - - - - NM_002790 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6660 - - - - PSME4 - HGNC Symbol - - - - 68611 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68611 - - - - ENST00000216122 - Ensembl - - - - - - MOD_RES 119 119 N6-methyllysine. - - - - ENSP00000407810 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2468 - - - - 1328683 - Zlotkin, T - Nethanel, T - Kaufmann, G - Pubmed - Assembly of simian virus 40 Okazaki pieces from DNA primers is reversibly arrested by ATP depletion. - J Virol 66:6634-40 - 1992 - - - - EQUAL - 465 - http://www.reactome.org/biopax/46/48887#SequenceSite10682 - - - - ENSP00000395231 - Ensembl - - - - ENSG00000077514 - Ensembl - - - - CHEBI:46362 - ChEBI - - - - CCNA2 - HGNC - - - - REACT_5748 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5748.2 - - - - EQUAL - 708 - - - - ENST00000536575 - Ensembl - - - - - - - PSF2 - GINS2 - GINS complex subunit 2 - - - - - - - - - - - - - - - PSF2_HUMAN - DNA replication complex GINS protein PSF2 - FUNCTION: The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks. GINS complex seems to bind preferentially to single- stranded DNA.SUBUNIT: Component of the GINS complex which is a heterotetramer of GINS1, GINS2, GINS3 and GINS4. Forms a stable subcomplex with GINS3. GINS complex interacts with DNA primase in vitro.SUBCELLULAR LOCATION: Nucleus (By similarity).MASS SPECTROMETRY: Mass=98373; Mass_error=13; Method=Electrospray; Range=1-185; Note=This is the measured mass for the GINS complex; Source=PubMed:17557111;SIMILARITY: Belongs to the GINS2/PSF2 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 53787 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=53787 - - - - EQUAL - 32 - - - - 188389 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=188389 - - - - HGNC:9545 - HGNC - - - - - - MOD_RES 911 911 Phosphoserine. - - - - 68451 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68451 - - - - PSMB10 - Proteasome subunit beta-2i - Low molecular mass protein 10 - Multicatalytic endopeptidase complex subunit MECl-1 - Proteasome MECl-1 - LMP10 - Macropain subunit MECl-1 - 3.4.25.1 - MECL1 - - - - - - - - - - - - - - - PSB10_HUMAN - Proteasome subunit beta type-10 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. This subunit is part of the immunoproteasome where it displaces the equivalent houskeeping subunit PSMB7. Component of the spermatoproteasome, a form of the proteasome specifically found in testis. Interacts with HIV-1 TAT protein.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).DEVELOPMENTAL STAGE: Highly expressed in immature dendritic cells (at protein level).INDUCTION: Up-regulated by IFNG/IFN-gamma (at protein level). Up- regulated by IRF1. Up-regulated by TNF (at protein level). Up- regulated by tetrodotoxin (TTX) in glial cells. Up-regulated in Crohn's bowel disease (CD). Up-regulated by CD40L via the NFKB1 pathway in cancer cells.PTM: Autocleaved. The resulting N-terminal Thr residue of the mature subunit is responsible for the nucleophile proteolytic activity (By similarity).SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 138 - - - - ENSP00000364970 - Ensembl - - - - 69006 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69006 - - - - RFC3 - HGNC Symbol - - - - - - MOD_RES 190 190 Phosphoserine. - - - - - - - - - - - - - - - - - - - - CDT1 association with the CDC6:ORC:origin complex - http://www.reactome.org/biopax/46/48887#Pathway559 - Initiation protein Cdt1 was first identified in X. laevis, where it has been shown to be the second component of licensing factor (RLF-B) and in S. pombe. Cdt1 homologs have been identified in D. melanogaster, humans, and S. cerevisiae. Genetic studies in S. pombe have shown that binding of Cdc6 to chromatin requires the prior binding of Cdc18, the S. pombe homolog of Cdc6. In humans, the function of CDT1 is regulated during the cell cycle by its tight association with an inhibitory factor, geminin. - - - - - EQUAL - 21 - http://www.reactome.org/biopax/46/48887#SequenceSite1826 - - - - EQUAL - 14 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10864 - - - - P31145 - UniProt - - - - NM_006716 - RefSeq - - - - ENSP00000386932 - Ensembl - - - - 84296 - NCBI Gene - - - - ENST00000361729 - Ensembl - - - - NP_006254 - RefSeq - - - - 11532947 - Perkins, G - Diffley, JF - Drury, LS - Pubmed - Separate SCF(CDC4) recognition elements target Cdc6 for proteolysis in S phase and mitosis. - EMBO J 20:4836-45 - 2001 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6638 - - - - P11082 - UniProt - - - - 84515 - NCBI Gene - - - - 176963 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176963 - - - - 604036 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval873 - - - - - - PSMD14 - HGNC Symbol - - - - Q6IAW0 - UniProt - - - - REACT_5228 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5228.2 - - - - EQUAL - 29 - - - - NP_853551 - RefSeq - - - - RB1 - HGNC - - - - ENSP00000044462 - Ensembl - - - - - - MOD_RES 253 253 Phosphothreonine (By similarity). - - - - - - - - - - - - - - - - Processive synthesis on the lagging strand - The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a single-stranded flap, which is removed by endonucleases. This is followed by the ligation of adjacent Okazaki fragments. - http://www.reactome.org/biopax/46/48887#Pathway513 - - - - - ENST00000357146 - Ensembl - - - - - - - - - Retinoblastoma-binding protein 3 - E2F1 - RBBP3 - RBBP-3 - PBR3 - Retinoblastoma-associated protein 1 - E2F-1 - RBAP-1 - pRB-binding protein E2F-1 - - - - - - - - - - - - - - - E2F1_HUMAN - Transcription factor E2F1 - FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F1 binds preferentially RB1 in a cell-cycle dependent manner. It can mediate both cell proliferation and TP53/p53-dependent apoptosis.ENZYME REGULATION: BIRC2/c-IAP1 stimulates its transcriptional activity.SUBUNIT: Component of the DRTF1/E2F transcription factor complex. Forms heterodimers with DP family members. The E2F1 complex binds specifically hypophosphorylated retinoblastoma protein RB1. During the cell cycle, RB1 becomes phosphorylated in mid-to-late G1 phase, detaches from the DRTF1/E2F complex, rendering E2F transcriptionally active. Viral oncoproteins, notably E1A, T- antigen and HPV E7, are capable of sequestering RB1, thus releasing the active complex. Interacts with TRRAP, which probably mediates its interaction with histone acetyltransferase complexes, leading to transcription activation. Binds TOPBP1 and EAPP. Interacts with ARID3A. Interacts with TRIM28; the interaction inhibits E2F1 acetylation through recruiting HDAC1 and represses its transcriptional activity. Interaction with KAT2B; the interaction acetylates E2F1 enhancing its DNA-binding and transcriptional activity. Interacts with BIRC2/c-IAP1 (via BIR domains). Interacts with human cytomegalovirus/HHV-5 protein UL123.SUBCELLULAR LOCATION: Nucleus.PTM: Phosphorylated by CDK2 and cyclin A-CDK2 in the S-phase. Phosphorylation at Ser-364 by CHEK2 stabilizes E2F1 upon DNA damage and regulates its effect on transcription and apoptosis.PTM: Acetylation stimulates DNA-binding. Enhanced under stress conditions such as DNA damage and inhibited by retinoblastoma protein RB1. Regulated by KAP1/TRIM28 which recruits HDAC1 to E2F1 resulting in deacetylation. Acetylated by P/CAF/KAT2B.SIMILARITY: Belongs to the E2F/DP family.SEQUENCE CAUTION: Sequence=AAB24289.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/E2F1ID40382ch20q11.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/e2f1/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - - DNA polymerase alpha:primase binds at the origin - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1978 - DNA polymerase alpha:primase is comprised of four subunits, p180, p70, p58, and p49. The two primase subunits, p58 and p49, form a tight complex. The p49 subunit contains the DNA primase activity and one role of p58 appears to be tethering p49 to p180, the DNA polymerase catalytic subunit. The fourth subunit, p70, binds p180 and may tether the DNA polymerase alpha:primase complex to Cdc45. - - - - - PSMD10 - HGNC Symbol - - - - 8432525 - Trask B - Fertitta A - Christensen M - Olsen A - de Jong P - Youngblom J - Copeland A - Carrano A - Bergmann A - Mohrenweiser H - PubMed - Fluorescence in situ hybridization mapping of human chromosome 19: cytogenetic band location of 540 cosmids and 70 genes or DNA markers. - Genomics 15(1);133-45 - 1993 - - - - ENST00000402285 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature852 - - - - - - E2F-3 - Transcription factor E2F3 - - - - - Reactome DB_ID: 68655 - http://www.reactome.org/biopax/46/48887#Protein3088 - E2F3 - - - - - - - - - - TRAP2 - 26S proteasome regulatory subunit RPN1 - 26S proteasome subunit p97 - Protein 55.11 - Tumor necrosis factor type 1 receptor-associated protein 2 - PSMD2 - 26S proteasome regulatory subunit S2 - - - - - - - - - - - - - - - - PSMD2_HUMAN - 26S proteasome non-ATPase regulatory subunit 2 - FUNCTION: Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.FUNCTION: Binds to the intracellular domain of tumor necrosis factor type 1 receptor. The binding domain of TRAP1 and TRAP2 resides outside the death domain of TNFR1.TISSUE SPECIFICITY: Found in skeletal muscle, liver, heart, brain, kidney, pancreas, lung and placenta.SIMILARITY: Belongs to the proteasome subunit S2 family.SIMILARITY: Contains 7 PC repeats.SEQUENCE CAUTION: Sequence=AAA87705.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - MOD_RES 220 220 N6-acetyllysine. - - - - EQUAL - 15 - - - - HGNC:10290 - HGNC - - - - E2F2 - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2112 - - - - - - ENST00000322088 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4833 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6439 - - - - - - MOD_RES 127 127 Phosphothreonine. - - - - EQUAL - 354 - http://www.reactome.org/biopax/46/48887#SequenceSite10599 - - - - EQUAL - 12 - - - - EQUAL - 88 - - - - - - E2F-2 - Transcription factor E2F2 - - - - - http://www.reactome.org/biopax/46/48887#Protein5633 - Reactome DB_ID: 68649 - E2F2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval848 - - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2487 - - - - 9635433 - McGarry, TJ - Kirschner, MW - Pubmed - Geminin, an inhibitor of DNA replication, is degraded during mitosis. - Cell 93:1043-53 - 1998 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4844 - - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4905 - - - - - - - - - - - - - - - Synthesis of DNA - The actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of the primer. The DNA replication preinitiation events begin in late M or early G1 phase. - http://www.reactome.org/biopax/46/48887#Pathway503 - - - - - EQUAL - 29 - http://www.reactome.org/biopax/46/48887#SequenceSite1852 - - - - 9242902 - Wold, MS - Pubmed - Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. - Annu Rev Biochem 66:61-92 - 1997 - - - - P61289 - UniProt - - - - Q53HA2 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6794 - - - - ENSG00000106399 - Ensembl - - - - - - MOD_RES 273 273 Phosphothreonine. - - - - P51530 - UniProt - - - - HGNC:30073 - HGNC - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6643 - - - - REACT_1787 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1787.2 - - - - 11454864 - Komamura-Kohno, Y - Ishimi, Y - Pubmed - Phosphorylation of Mcm4 at specific sites by cyclin-dependent kinase leads to loss of Mcm4,6,7 helicase activity. - J Biol Chem 276:34428-33 - 2001 - - - - NM_001220777 - RefSeq - - - - - - CDKN1B - - - - - http://www.reactome.org/biopax/46/48887#Protein5538 - Reactome DB_ID: 182563 - p27 - - - - - C9H16N3O13P3 - 2'-deoxycytidine 5'-(tetrahydrogen triphosphate) - - - - - - - - 467.1569 - dCTP - dCTP - A 2'-deoxycytidine phosphate having cytosine as the nucleobase. - - - - REACT_25343 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25343.1 - - - - 9829972 - Tugal, T - Kobayashi, R - Zou-Yang, XH - Canas, B - Pappin, D - Stillman, B - Gavin, K - Hunt, T - Pubmed - The Orc4p and Orc5p subunits of the Xenopus and human origin recognition complex are related to Orc1p and Cdc6p. - J Biol Chem 273:32421-9 - 1999 - - - - - - Proteasome regulatory particle subunit p44S10 - 26S proteasome regulatory subunit S10 - 26S proteasome non-ATPase regulatory subunit 6 - PSMD6 - - - - - http://www.reactome.org/biopax/46/48887#Protein1096 - Reactome DB_ID: 68804 - p42A - - - - EQUAL - 19 - - - - Q13200 - UniProt - - - - ENSP00000206451 - Ensembl - - - - 450417 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=450417 - - - - REACT_7015 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7015.2 - - - - - - - - - M/G1 Transition - Finally, progression out of mitosis and division of the cell into two daughters (cytokinesis) requires the inactivation of Cyclin B - Cdc2 by ubiquitin-dependent proteolysis of Cyclin A and B, which is regulated by a large E3 ubiquitin ligase complex known as the Anaphase Promoting Complex (APC).<p>The detailed annotation of the M/G1 transition will be completed in a later version of GK. - http://www.reactome.org/biopax/46/48887#Pathway554 - Reviewed: Manfredi, J, 0000-00-00 00:00:00 - - - - - Q9UL46 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4994 - - - - P05323 - UniProt - - - - - - MOD_RES 15 15 Phosphotyrosine; by WEE1. - - - - ENSP00000223129 - Ensembl - - - - EQUAL - 273 - - - - Q5T3V0 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2454 - - - - - - - - MOD_RES 310 310 N6-acetyllysine. - - - - EQUAL - 75 - - - - - - - - PSF3p - Reactome DB_ID: 176944 - http://www.reactome.org/biopax/46/48887#PhysicalEntity255 - - - - - - - - - - - - Cdc45:CDK:DDK:Mcm10:pre-replicative complex - Reactome DB_ID: 68564 - http://www.reactome.org/biopax/46/48887#Complex2542 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature850 - - - - REACT_448 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_448.3 - - - - 187963 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=187963 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1858 - - - - Q549U6 - UniProt - - - - 5984 - NCBI Gene - - - - - - geminin - - - - - http://www.reactome.org/biopax/46/48887#Protein5770 - Reactome DB_ID: 68534 - GMNN - - - - A8K9J2 - UniProt - - - - EQUAL - 160 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1769 - - - - - - ubiquitin (UBB 2) - - - - - Reactome DB_ID: 939870 - http://www.reactome.org/biopax/46/48887#Protein2475 - UBB(77-152) - - - - CDC7 - HGNC - - - - 7644470 - Budd, ME - Campbell, JL - Pubmed - A yeast gene required for DNA replication encodes a protein with homology to DNA helicases. - Proc Natl Acad Sci U S A 92:7642-6 - 1995 - - - - Q9BU45 - UniProt - - - - 68786 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68786 - - - - 5715 - NCBI Gene - - - - 68540 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68540 - - - - Q8NER3 - UniProt - - - - EQUAL - 381 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6605 - - - - ENSP00000313327 - Ensembl - - - - 15684404 - Volkening, M - Hoffmann, I - Pubmed - Involvement of human MCM8 in prereplication complex assembly by recruiting hcdc6 to chromatin - Mol Cell Biol 25:1560-8 - 2005 - - - - - - MOD_RES 80 80 N6-acetyllysine. - - - - EQUAL - 77 - - - - REACT_24415 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24415.2 - - - - EQUAL - 16 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6430 - - - - 68919 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68919 - - - - 68507 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68507 - - - - - - MOD_RES 364 364 Phosphoserine; by CHEK2 (Probable). - - - - - - MOD_RES 13 13 Phosphoserine. - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - EQUAL - 14 - - - - EQUAL - 904 - http://www.reactome.org/biopax/46/48887#SequenceSite10637 - - - - EQUAL - 251 - - - - 176847 - omim - - - - 11923315 - Podust VN - Dianova II - Budworth H - Dianov GL - PubMed - Repair of clustered DNA lesions. Sequence-specific inhibition of long-patch base excision repair be 8-oxoguanine. - J Biol Chem 277(24);21300-5 - 2002 - - - - ENST00000310118 - Ensembl - - - - - - MOD_RES 612 612 Phosphoserine; by CHEK2 and CHEK1. - - - - NP_001258708 - RefSeq - - - - REACT_26074 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26074.2 - - - - ORC6 - HGNC Symbol - - - - 17487135 - pubchem - - - - 69074 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69074 - - - - 11459976 - Bell, SP - Klemm, RD - Pubmed - ATP bound to the origin recognition complex is important for preRC formation. - Proc Natl Acad Sci U S A 98:8361-7 - 2001 - - - - - - MOD_RES 114 114 Phosphoserine; by GSK3-beta. - - - - 5691 - NCBI Gene - - - - ENST00000599551 - Ensembl - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2506 - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature867 - - - - EQUAL - 6 - - - - EQUAL - 98 - - - - ENSP00000344818 - Ensembl - - - - ENST00000219313 - Ensembl - - - - ENSP00000375080 - Ensembl - - - - 602708 - omim - - - - 102577 - omim - - - - ZKHQWZAMYRWXGA-KQYNXXCUSA-N - InChIKey - - - - EQUAL - 3 - - - - EQUAL - 821 - http://www.reactome.org/biopax/46/48887#SequenceSite10643 - - - - 69019 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69019 - - - - 68560 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68560 - - - - REACT_4462 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4462.1 - - - - 68765 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68765 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4853 - - - - - - NP_001184259 - RefSeq - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis627 - - - - NM_001197259 - RefSeq - - - - Q6GMU5 - UniProt - - - - ENST00000346618 - Ensembl - - - - 2165567 - Melendy, T - Stillman, B - Tsurimoto, T - Pubmed - Sequential initiation of lagging and leading strand synthesis by two different polymerase complexes at the SV40 DNA replication origin. - Nature 346:534-9 - 1990 - - - - Q6IB60 - UniProt - - - - - - - - - - - - Cyclin B:Cdk1 complex - Reactome DB_ID: 75032 - http://www.reactome.org/biopax/46/48887#Complex2615 - - - - - - MOD_RES 368 368 N6-acetyllysine. - - - - 68564 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68564 - - - - - - - Proteasome iota chain - p27K - 27 kDa prosomal protein - PSMA6 - Multicatalytic endopeptidase complex iota chain - PROS27 - PROS-27 - 3.4.25.1 - Macropain iota chain - - - - - - - - - - - - - - - - PSA6_HUMAN - Proteasome subunit alpha type-6 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Interacts with ALKBH4.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasm, P-body (By similarity). Note=Co-localizes with TRIM5 in the cytoplasmic bodies (By similarity).SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - MOD_RES N-acetylvaline - - - - Q24JU0 - UniProt - - - - Q2M1Z0 - UniProt - - - - REACT_5621 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5621.1 - - - - 947606 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=947606 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4929 - - - - O00487 - UniProt - - - - Q7LD55 - UniProt - - - - 5708 - NCBI Gene - - - - NP_001789 - RefSeq - - - - POLD2 - HGNC - - - - - - MOD_RES 795 795 Phosphoserine (By similarity). - - - - NM_001134420 - RefSeq - - - - 10966477 - Brown, GW - Kelly, TJ - Pubmed - Regulation of chromosome replication. - Annu Rev Biochem 69:829-80 - 2000 - - - - 602707 - omim - - - - NM_000389 - RefSeq - - - - ENST00000554396 - Ensembl - - - - Q9Y2T8 - UniProt - - - - REACT_4065 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4065.2 - - - - 69385 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69385 - - - - Q9Y5P8 - UniProt - - - - NP_877428 - RefSeq - - - - - - - CDC45 - CDC45L - PORC-PI-1 - CDC45L2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CDC45_HUMAN - Cell division control protein 45 homolog - FUNCTION: Required for initiation of chromosomal DNA replication.SUBUNIT: Associated with ORC2.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=O75419-1; Sequence=Displayed; Name=2; IsoId=O75419-2; Sequence=VSP_043129; Note=No experimental confirmation available; Name=3; IsoId=O75419-3; Sequence=VSP_045411; Note=No experimental confirmation available;TISSUE SPECIFICITY: Widely expressed, highest levels are found in adult testis and thymus and in fetal liver.DEVELOPMENTAL STAGE: Transcript peaks at G1-S transition, but total protein remains constant throughout the cell cycle. Expressed in multiple tissues during embryogenesis, including neural crest-derived structures.SIMILARITY: Belongs to the CDC45 family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc45l/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - PA28gamma - Proteasome activator complex subunit 3 - Proteasome activator 28-gamma subunit - PA28g - REG-gamma - Ki nuclear autoantigen - Activator of multicatalytic protease subunit 3 - 11S regulator complex gamma subunit - - - - - http://www.reactome.org/biopax/46/48887#Protein1095 - Reactome DB_ID: 68816 - PSME3 - - - - 8145524 - pubchem-substance - - - - - - - - Flap - Reactome DB_ID: 68454 - http://www.reactome.org/biopax/46/48887#PhysicalEntity257 - - - - ENSP00000265056 - Ensembl - - - - P49720 - UniProt - - - - RP-A p30 - RF-A protein 4 - Replication factor A protein 4 - RPA4 - - - - - - - - - - - - - RFA4_HUMAN - Replication protein A 30 kDa subunit - FUNCTION: Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S- phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.SUBUNIT: Component of the alternative replication protein A complex (aRPA) composed of RPA1, RPA3 and RPA4. Interacts with RPA1 and RPA3.SUBCELLULAR LOCATION: Nucleus. Note=Localizes to DNA repair foci after DNA damage.TISSUE SPECIFICITY: Preferentially expressed in placental and colon mucosa. Widely expressed at intermediate or lower levels.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/hsu24186/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NM_002799 - RefSeq - - - - NM_002795 - RefSeq - - - - 602175 - omim - - - - ENST00000598780 - Ensembl - - - - CHEBI:22245 - ChEBI - - - - NM_001177413 - RefSeq - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - 8317 - NCBI Gene - - - - ENSP00000310572 - Ensembl - - - - ENSP00000376597 - Ensembl - - - - 5001 - NCBI Gene - - - - - - MOD_RES 77 77 Phosphotyrosine. - - - - REACT_1949 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1949.4 - - - - - - MOD_RES 191 191 Phosphothreonine. - - - - REACT_5474 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5474.1 - - - - ENST00000361815 - Ensembl - - - - Q96E97 - UniProt - - - - HGNC:9553 - HGNC - - - - MCM10 - HGNC Symbol - - - - HGNC:9532 - HGNC - - - - 15201046 - Cheng, IH - Sawyer, SL - Chai, W - Tye, BK - Pubmed - Mcm10 and Cdc45 cooperate in origin activation in Saccharomyces cerevisiae - J Mol Biol 340:195-202 - 2004 - - - - EQUAL - 21 - - - - REACT_5610 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5610.1 - - - - - - - - - RPA2 - RPA34 - RPA32 - RF-A protein 2 - REPA2 - RP-A p32 - Replication factor A protein 2 - RP-A p34 - Replication protein A 34 kDa subunit - - - - - - - - - - - - - - - - - - - - - RFA2_HUMAN - Replication protein A 32 kDa subunit - FUNCTION: Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required for the efficient recruitment of the DNA double-strand break repair factor RAD51 to chromatin in response to DNA damage.FUNCTION: Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S- phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.SUBUNIT: Heterotrimer of 70, 32 and 14 kDa chains (canonical replication protein A complex). Component of the alternative replication protein A complex (aRPA) composed of RPA1, RPA3 and RPA4. The DNA-binding activity may reside exclusively on the 70 kDa subunit. Binds to SERTAD3/RBT1. Interacts with TIPIN. Directly interacts with PPP4R2, but not with SMEK2; this interaction is DNA damage-dependent and leads RPA2 dephosphorylation by PPP4C recruitment. Interacts with RAD51, preferentially when hyperphosphorylated. Directly interacts with RFWD3.SUBCELLULAR LOCATION: Nucleus. Nucleus, PML body. Note=Also present in PML nuclear bodies. Redistributes to discrete nuclear foci upon DNA damage.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P15927-1; Sequence=Displayed; Name=2; IsoId=P15927-2; Sequence=VSP_017201; Note=No experimental confirmation available; Name=3; IsoId=P15927-3; Sequence=VSP_017202; Note=No experimental confirmation available;PTM: Phosphorylated in a cell-cycle-dependent manner (from the S phase until mitosis). In response to DNA damage, recruited to DNA- repair nuclear foci, as a hypophosphorylated form. The necessary dephosphorylation step is catalyzed by PP4. Subsequent hyperphosphorylation, catalyzed by ATR, is required for RAD51 recruitment to chromatin and efficient DNA repair. Can be phosphorylated in vitro by PRKDC/DNA-PK in the presence of Ku and DNA, and by CDK1. Phosphorylation at Thr-21 depends upon RFWD3 presence.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rpa2/";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/RPA2ID42146ch1p35.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - Aborted replication complex - Reactome DB_ID: 113648 - http://www.reactome.org/biopax/46/48887#Complex2614 - - - - 9660782 - Dutta, A - Weremowicz, S - Hou, Z - Saha, P - Yamaguchi, R - Thome, KC - Pubmed - The human homolog of Saccharomyces cerevisiae CDC45. - J Biol Chem 273:18205-9 - 1998 - - - - ENST00000404125 - Ensembl - - - - EQUAL - 19 - - - - 1LFS - PROTEIN DATA BANK - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1040 - - - - 14527418 - Hofmann, F - Livingston, DM - Ganesan, S - Yang, H - Scully, R - Avni, D - ElShamy, WM - Martelli, F - Pubmed - Active localization of the retinoblastoma protein in chromatin and its response to S phase DNA damage. - Mol Cell 12:735-46 - 2003 - - - - - - MOD_RES 34 34 Phosphoserine. - - - - - - MOD_RES 131 131 Phosphoserine. - - - - 2EBU - PROTEIN DATA BANK - - - - PSMD12 - HGNC - - - - PSMA4 - HGNC Symbol - - - - NM_032336 - RefSeq - - - - NP_001171033 - RefSeq - - - - - - MOD_RES 156 156 Phosphoserine. - - - - EQUAL - 437 - http://www.reactome.org/biopax/46/48887#SequenceSite10718 - - - - - - MOD_RES 340 340 Phosphoserine. - - - - ubiquitinylated lysine - - - - - - - MOD_RES 204 204 N6-acetyllysine. - - - - - - PA28alpha - Proteasome activator complex subunit 1 - Proteasome activator 28-alpha subunit - Activator of multicatalytic protease subunit 1 - PA28a - IGUP I-5111 - 11S regulator complex alpha subunit - Interferon gamma up-regulated I-5111 protein - REG-alpha - - - - - http://www.reactome.org/biopax/46/48887#Protein1097 - Reactome DB_ID: 68812 - PSME1 - - - - NP_001073918 - RefSeq - - - - 68471 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68471 - - - - REACT_6922 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6922.1 - - - - B3KMW9 - UniProt - - - - 174761 - omim - - - - P48556 - UniProt - - - - EQUAL - 148 - - - - ENST00000308696 - Ensembl - - - - 69115 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69115 - - - - 1017 - NCBI Gene - - - - - - Cdc7 - huCdc7 - HsCdc7 - Cell division cycle 7-related protein kinase - CDC7- related kinase - Cell division protein kinase 7 - Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7- related kinase) (HsCdc7) (huCdc7) - - - - - http://www.reactome.org/biopax/46/48887#Protein5574 - Reactome DB_ID: 51781 - CDC7 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2490 - - - - PSMD2 - HGNC - - - - ENSG00000101868 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6420 - - - - 1QYM - PROTEIN DATA BANK - - - - NM_004159 - RefSeq - - - - EQUAL - 823 - - - - P97373 - UniProt - - - - 75202 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=75202 - - - - REACT_7318 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7318.2 - - - - NM_004111 - RefSeq - - - - - - - - - - - PP2A complex (containing PPP2R3B) - Serine/threonine-protein phosphatase 2A complex with regulatory subunit PPP2R3B - - - - PP2A - Reactome DB_ID: 1362456 - http://www.reactome.org/biopax/46/48887#Complex2613 - - - - NM_002798 - RefSeq - - - - ENSG00000177084 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10612 - - - - NM_002787 - RefSeq - - - - ENSG00000073111 - Ensembl - - - - 605983 - omim - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - - - - - ACTIVATION - - 'Transcription factor E2F [nucleoplasm]' positively regulates 'Cdc6 protein is synthesized under the control of E2F transcription factors' - http://www.reactome.org/biopax/46/48887#TemplateReactionRegulation7 - - - - EQUAL - 72 - - - - Q7L590 - UniProt - - - - - C10H16N5O12P3 - 2'-deoxyadenosine 5'-(tetrahydrogen triphosphate) - - - - - - - - - 491.1816 - dATP - dATP - A purine 2'-deoxyribonucleoside 5'-triphosphate having adenine as the nucleobase. - - - - REACT_932 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_932.6 - - - - - C9H14N3O8P - cytidine-5'-monophosphate - 5'-cytidylic acid - - - - - - - - - - - - - - 323.19662 - CMP - CMP - - - - CHEBI:16311 - ChEBI - - - - EQUAL - 201 - - - - EQUAL - 361 - - - - NP_002785 - RefSeq - - - - EQUAL - 24 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1642 - - - - 4176 - NCBI Gene - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6608 - - - - - - DNA polymerase alpha 70 kDa subunit - DNA polymerase subunit B - POLA2 - - - - - http://www.reactome.org/biopax/46/48887#Protein5710 - Reactome DB_ID: 68493 - p70 - - - - 69014 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69014 - - - - 68431 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68431 - - - - P14793 - UniProt - - - - REACT_2531 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2531.1 - - - - - - MOD_RES 207 207 Phosphothreonine (By similarity). - - - - EQUAL - 93 - - - - 451232 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=451232 - - - - ENSG00000097046 - Ensembl - - - - - - MOD_RES 221 221 N6-acetyllysine. - - - - HGNC:22985 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature868 - - - - - - MOD_RES 216 216 N6-acetyllysine. - - - - 1T6F - PROTEIN DATA BANK - - - - - C10H14N5O8P - 5'-GMP - 5'-guanylic acid - [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen phosphate - - - - - - - - - - - - - - - - - - - 363.22083 - GMP - GMP - A purine ribonucleoside 5'-monophosphate having guanine as the nucleobase. - - - - ORC6 - HGNC - - - - - - MOD_RES 409 409 Phosphoserine. - - - - 68517 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68517 - - - - ENST00000382708 - Ensembl - - - - MOD_RES N-acetylalanine (By similarity) - - - - EQUAL - 354 - - - - 11809796 - Knippers, R - Ladenburger, EM - Keller, C - Pubmed - Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication. - Mol Cell Biol 22:1036-48 - 2002 - - - - A8K0Y9 - UniProt - - - - P49719 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4826 - - - - EQUAL - 324 - http://www.reactome.org/biopax/46/48887#SequenceSite1811 - - - - P35998 - UniProt - - - - CHEBI:41319 - ChEBI - - - - EQUAL - 83 - http://www.reactome.org/biopax/46/48887#SequenceSite1754 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4869 - - - - - - 5686 - NCBI Gene - - - - NM_176783 - RefSeq - - - - EQUAL - 532 - http://www.reactome.org/biopax/46/48887#SequenceSite1787 - - - - 176956 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176956 - - - - 69300 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69300 - - - - EQUAL - 6 - - - - - - MOD_RES 4 4 Phosphoserine. - - - - ENST00000481195 - Ensembl - - - - REACT_6981 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6981.2 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4943 - - - - REACT_3796 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3796.2 - - - - ENST00000440264 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4820 - - - - - - Q96CJ5 - UniProt - - - - PSMC5 - HGNC Symbol - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval827 - - - - - - - - MOD_RES 696 696 N6-acetyllysine. - - - - EQUAL - 243 - - - - ENST00000267163 - Ensembl - - - - 122706 - NCBI Gene - - - - - - MOD_RES 28 28 Phosphoserine. - - - - 68522 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68522 - - - - Q86VU1 - UniProt - - - - NP_002808 - RefSeq - - - - HGNC:18043 - HGNC - - - - NP_001258709 - RefSeq - - - - - - - - - - - - Processive complex:Okazaki fragment:Flap:RPA heterotrimer - Reactome DB_ID: 68463 - http://www.reactome.org/biopax/46/48887#Complex2641 - - - - 7876218 - Lieber, MR - Harrington, JJ - Pubmed - DNA structural elements required for FEN-1 binding. - J Biol Chem 270:4503-8 - 1995 - - - - 29604 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29604 - - - - CHEBI:18367 - ChEBI - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6604 - - - - - - MOD_RES 20 20 N6-acetyllysine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6437 - - - - EQUAL - 668 - - - - - - MOD_RES 375 375 N6-acetyllysine. - - - - RFC4 - HGNC - - - - PPP2CA - HGNC - - - - REACT_2838 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2838.1 - - - - GINS1 - KIAA0186 - PSF1 - GINS complex subunit 1 - - - - - - - - - - - - - PSF1_HUMAN - DNA replication complex GINS protein PSF1 - FUNCTION: The GINS complex plays an essential role in the initiation of DNA replication, and progression of DNA replication forks. GINS complex seems to bind preferentially to single- stranded DNA. GINS1 is essential for function.SUBUNIT: Component of the GINS complex which is a heterotetramer of GINS1, GINS2, GINS3 and GINS4. Forms a stable subcomplex with GINS4. GINS complex interacts with DNA primase in vitro.SUBCELLULAR LOCATION: Nucleus (By similarity).INDUCTION: Significantly up-regulated in agressive melanomas.MASS SPECTROMETRY: Mass=98373; Mass_error=13; Method=Electrospray; Range=1-196; Note=This is the measured mass for the GINS complex; Source=PubMed:17557111;SIMILARITY: Belongs to the GINS1/PSF1 family.SEQUENCE CAUTION: Sequence=BAA11503.2; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - PSB11_HUMAN - Proteasome subunit beta type-11 - - - - - Reactome DB_ID: 947607 - http://www.reactome.org/biopax/46/48887#Protein1104 - PSMB11 - - - - EQUAL - 432 - http://www.reactome.org/biopax/46/48887#SequenceSite10684 - - - - NP_002936 - RefSeq - - - - - - MOD_RES 55 55 Phosphoserine. - - - - NP_001096137 - RefSeq - - - - ENSG00000167393 - Ensembl - - - - 1870 - NCBI Gene - - - - 176975 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176975 - - - - Q8N648 - UniProt - - - - NM_004091 - RefSeq - - - - 1LC9 - PROTEIN DATA BANK - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2480 - - - - - - - - - GMNN - - - - - - - - - - - - - - - - - - - - - - - GEMI_HUMAN - Geminin - FUNCTION: Inhibits DNA replication by preventing the incorporation of MCM complex into pre-replication complex (pre-RC). It is degraded during the mitotic phase of the cell cycle. Its destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle.FUNCTION: Inhibits the transcriptional activity of a subset of Hox proteins, enrolling them in cell proliferative control.SUBUNIT: Homotetramer. Interacts with CDT1; inhibits binding of the MCM complex to origins of replication, the complex exists in two forms, a "permissive" heterotrimer and an "inhibitory" heterohexamer. Interacts with IDAS; which targets GMNN to the nucleus, prevents GMNN interaction with CDT1 and competes with IDAS homodimerization. Interacts with a subset of Hox proteins, affinity increasing from anterior to posterior types, the strongest interaction being with HOXB1, HOXC9 and HOXD10.SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Mainly cytoplasmic but can be relocalized to the nucleus.DEVELOPMENTAL STAGE: Absent during G1 phase, accumulates during S, G2, and M phases, and disappears at the time of the metaphase- anaphase transition.PTM: Phosphorylation at Ser-184 by CK2 results in enhanced binding to Hox proteins and more potent inhibitory effect on Hox transcriptional activity.SIMILARITY: Belongs to the geminin family.SEQUENCE CAUTION: Sequence=CAC21511.1; Type=Erroneous initiation; Note=Translation N-terminally extended; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_5467 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5467.2 - - - - 68534 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68534 - - - - ENST00000405375 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4965 - - - - ENSP00000429581 - Ensembl - - - - - - MOD_RES 145 145 Phosphothreonine; by PKA; PKB/AKT1, PIM1 and PIM2. - - - - 990 - NCBI Gene - - - - REACT_5979 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5979.1 - - - - NP_001186702 - RefSeq - - - - 68453 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68453 - - - - Q3MIR3 - UniProt - - - - 68470 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68470 - - - - REACT_2812 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2812.1 - - - - ENSP00000351185 - Ensembl - - - - - - MOD_RES 171 171 N6-acetyllysine. - - - - - - MOD_RES 116 116 Phosphothreonine. - - - - P17980 - UniProt - - - - EQUAL - 186 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6629 - - - - - - - - - - - - RFC binding displaces Pol Alpha - Once the RNA-DNA primer is synthesized, replication factor C (RFC) initiates a reaction called "polymerase switching"; pol delta, the processive enzyme replaces pol alpha, the priming enzyme. RFC binds to the 3'-end of the RNA-DNA primer on the Primosome, to displace the pol alpha primase complex. The binding of RFC triggers the binding of the primer recognition complex. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2008 - - - - - ENSP00000368161 - Ensembl - - - - - - Retinoblastoma binding protein 3 - RBBP-3 - PBR3 - Retinoblastoma-associated protein 1 - PRB-binding protein E2F-1 - Transcription factor E2F1 - RBAP-1 - E2F-1 - - - - - Reactome DB_ID: 68639 - http://www.reactome.org/biopax/46/48887#Protein3087 - E2F1 - - - - PSMD8 - HGNC Symbol - - - - - - - - - - - - RFC Heteropentamer:RNA primer-DNA primer:origin duplex - http://www.reactome.org/biopax/46/48887#Complex2633 - Reactome DB_ID: 68437 - - - - EQUAL - 32 - - - - 12438414 - Michael, WM - Van Hatten, RA - Holway, AH - Tutter, AV - Khederian, AM - Walter, JC - Pubmed - The Xenopus Xmus101 protein is required for the recruitment of Cdc45 to origins of DNA replication. - J Cell Biol 159:541-7 - 2002 - - - - - - MOD_RES 681 681 Phosphoserine. - - - - CHEBI:12056 - ChEBI - - - - - - TBP-1 - Proteasome subunit P50 - TAT-binding protein 1 - 26S protease regulatory subunit 6A - - - - - http://www.reactome.org/biopax/46/48887#Protein1067 - Reactome DB_ID: 68774 - PSMC3 - - - - ENSG00000110801 - Ensembl - - - - PSMD9 - HGNC Symbol - - - - - - MOD_RES 144 144 Phosphoserine. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1069 - - - - PSME3 - HGNC Symbol - - - - ENST00000378886 - Ensembl - - - - - - MOD_RES 14 14 Phosphoserine. - - - - XTWYTFMLZFPYCI-KQYNXXCUSA-N - InChIKey - - - - ENSP00000376325 - Ensembl - - - - P06493 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2228 - - - - - - 156564 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=156564 - - - - HGNC:9564 - HGNC - - - - ENSG00000198176 - Ensembl - - - - EQUAL - 589 - http://www.reactome.org/biopax/46/48887#SequenceSite4926 - - - - REACT_383 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_383.6 - - - - 68585 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68585 - - - - P09884 - UniProt - - - - - - - - - - - - RNA primer-DNA primer:origin duplex:PCNA - Reactome DB_ID: 68441 - http://www.reactome.org/biopax/46/48887#Complex2636 - - - - 15707891 - Danis, E - Mechali, M - Cuvier, O - Maiorano, D - Pubmed - MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation - Cell 120:315-28 - 2005 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4851 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1083 - - - - EQUAL - 307 - - - - ENST00000225426 - Ensembl - - - - 9312054 - Perkins, G - Diffley, JF - Drury, LS - Pubmed - The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast. - EMBO J 16:5966-76 - 1997 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6681 - - - - 9778043 - Nakamura, M - Ikeda, M - Ohtani, K - Tsujimoto, A - Pubmed - Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F. - Oncogene 17:1777-85 - 1998 - - - - 68437 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68437 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2121 - - - - - - HGNC:9558 - HGNC - - - - EQUAL - 73 - - - - A8K400 - UniProt - - - - 113582 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113582 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2483 - - - - - - - PP2A-subunit A alpha isoform - - - - - http://www.reactome.org/biopax/46/48887#Protein2615 - Reactome DB_ID: 165968 - PPP2R1A - - - - - - Replication protein C - RP-C - PPP2CA - PP2A-alpha - 3.1.3.16 - - - - - - - - - - - - - - - - PP2AA_HUMAN - Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform - FUNCTION: PP2A is the major phosphatase for microtubule-associated proteins (MAPs). PP2A can modulate the activity of phosphorylase B kinase casein kinase 2, mitogen-stimulated S6 kinase, and MAP-2 kinase. Cooperates with SGOL2 to protect centromeric cohesin from separase-mediated cleavage in oocytes specifically during meiosis I (By similarity). Can dephosphorylate SV40 large T antigen and p53/TP53. Activates RAF1 by dephosphorylating it at 'Ser-259'.CATALYTIC ACTIVITY: A phosphoprotein + H(2)O = a protein + phosphate.COFACTOR: Binds 1 iron ion per subunit (By similarity).COFACTOR: Binds 1 manganese ion per subunit (By similarity).SUBUNIT: PP2A consists of a common heterodimeric core enzyme, composed of PPP2CA a 36 kDa catalytic subunit (subunit C) and PPP2R1A a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B''/PR72/PR130/PR59 and R5/B'/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Interacts with NXN; the interaction is direct (By similarity). Interacts with TP53, SGOL1 and SGOL2. Interacts with AXIN1; the interaction dephosphorylates AXIN1. Interacts with PIM3; this interaction promotes dephosphorylation, ubiquitination and proteasomal degradation of PIM3. Interacts with RAF1. Interaction with IGBP1 protects unassembled PPP2CA from degradative ubiquitination. Interacts with GSK3B (via C2 domain).SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Chromosome, centromere. Cytoplasm, cytoskeleton, spindle pole. Note=In prometaphase cells, but not in anaphase cells, localizes at centromeres. During mitosis, also found at spindle poles. Centromeric localization requires the presence of SGOL2 (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=PP2Acalpha1; IsoId=P67775-1; Sequence=Displayed; Name=2; Synonyms=PP2Acalpha2; IsoId=P67775-2; Sequence=VSP_044320; Note=Catalytically inactive, shows enhanced binding to IGBP1, and does not interact with the scaffolding subunit PPP2R1A;PTM: Reversibly methyl esterified on Leu-309. Carboxyl methylation may play a role in holoenzyme assembly, enhancing the affinity of the PP2A core enzyme for some, but not all, regulatory subunits. It varies during the cell cycle.PTM: Phosphorylation of either threonine (by autophosphorylation- activated protein kinase) or tyrosine results in inactivation of the phosphatase. Auto-dephosphorylation has been suggested as a mechanism for reactivation.SIMILARITY: Belongs to the PPP phosphatase family. PP-1 subfamily. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 939868 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939868 - - - - ENST00000395284 - Ensembl - - - - Q96E27 - UniProt - - - - 5707 - NCBI Gene - - - - Q13773 - UniProt - - - - NM_018518 - RefSeq - - - - EQUAL - 249 - http://www.reactome.org/biopax/46/48887#SequenceSite1869 - - - - CDC45 - HGNC - - - - NP_002780 - RefSeq - - - - REACT_4563 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4563.2 - - - - EQUAL - 496 - http://www.reactome.org/biopax/46/48887#SequenceSite10886 - - - - - - MOD_RES 354 354 N6-acetyllysine. - - - - - - MOD_RES 146 146 Phosphoserine; by PKC. - - - - EQUAL - 55 - - - - EQUAL - 2 - - - - RPA4 - HGNC Symbol - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2509 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1081 - - - - Q9BRM7 - UniProt - - - - PSMD1 - HGNC - - - - 10205060 - Brewer, G - Schneider, RJ - Laroia, G - Cuesta, R - Pubmed - Control of mRNA decay by heat shock-ubiquitin-proteasome pathway - Science 284:499-502 - 1999 - - - - 11756551 - Wu, X - Yamane, K - Chen, J - Pubmed - A DNA damage-regulated BRCT-containing protein, TopBP1, is required for cell survival. - Mol Cell Biol 22:555-66 - 2001 - - - - ENST00000361611 - Ensembl - - - - 11864598 - Dutta, A - Prokhorova, TA - Wohlschlegel, JA - Walter, JC - Dhar, SK - Pubmed - Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45. - Mol Cell 9:233-40 - 2002 - - - - P49642 - UniProt - - - - - - MOD_RES 230 230 N6-acetyllysine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature823 - - - - - C10H16N5O14P3 - guanosine 5'-triphosphoric acid - guanosine 5'-(tetrahydrogen triphosphate) - H4gtp - guanosine triphosphate - 5'-GTP - - - - - - - - - 523.1806 - GTP - GTP - - - - NP_002805 - RefSeq - - - - EQUAL - 376 - http://www.reactome.org/biopax/46/48887#SequenceSite1821 - - - - 176958 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176958 - - - - MCM5 - HGNC - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2481 - - - - - - 2WVR - PROTEIN DATA BANK - - - - NM_001270482 - RefSeq - - - - REACT_4170 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4170.1 - - - - CHEBI:10494 - ChEBI - - - - PTHR11599:SF16 - PANTHER Family - - - - - - - 26S protease regulatory subunit 7 - MSS1 protein - - - - - Reactome DB_ID: 68771 - http://www.reactome.org/biopax/46/48887#Protein1078 - PSMC2 - - - - REACT_421 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_421.5 - - - - HGNC:3114 - HGNC - - - - Q6IBS1 - UniProt - - - - EQUAL - 229 - http://www.reactome.org/biopax/46/48887#SequenceSite1780 - - - - EQUAL - 309 - - - - - - - - - - - - Ubiquitinated AUF1 Tetramer: Destabilized mRNA Complex - http://www.reactome.org/biopax/46/48887#Complex409 - Reactome DB_ID: 450458 - - - - Q92530 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10614 - - - - 10872463 - Tye, BK - Pubmed - MCM proteins in DNA replication. - Annu Rev Biochem 68:649-86 - 2000 - - - - EQUAL - 307 - - - - EQUAL - 1 - - - - - - - - - - - - - - - - - - - UBIQ_HUMAN - - - - Reactome DB_ID: 68524 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein2471 - ubiquitin - - - - EQUAL - 791 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4956 - - - - - - MOD_RES 160 160 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval842 - - - - - - ENST00000546266 - Ensembl - - - - Q9BUT4 - UniProt - - - - NP_853556 - RefSeq - - - - EQUAL - 273 - - - - REACT_1408 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1408.4 - - - - - - CDKN1A - - - - - http://www.reactome.org/biopax/46/48887#Protein5536 - Reactome DB_ID: 182585 - p21 - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 165974 - http://www.reactome.org/biopax/46/48887#Protein2610 - PP2A-catalytic subunit C - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1051 - - - - ENSG00000138668 - Ensembl - - - - NM_002806 - RefSeq - - - - 8143180 - pubchem-substance - - - - 68401 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68401 - - - - HGNC:9178 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10883 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature866 - - - - EQUAL - 126 - - - - EQUAL - 1107 - http://www.reactome.org/biopax/46/48887#SequenceSite10912 - - - - EQUAL - 1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1047 - - - - ENST00000313639 - Ensembl - - - - NM_001111045 - RefSeq - - - - - - MOD_RES 77 77 N6-acetyllysine. - - - - ENST00000381897 - Ensembl - - - - - - MOD_RES 271 271 Phosphoserine. - - - - 8144170 - pubchem - - - - 2CCH - PROTEIN DATA BANK - - - - EQUAL - 234 - http://www.reactome.org/biopax/46/48887#SequenceSite1807 - - - - - - MOD_RES 39 39 Phosphoserine. - - - - NP_005796 - RefSeq - - - - P28066 - UniProt - - - - RPA2 - HGNC Symbol - - - - Q567Q5 - UniProt - - - - - - Replication factor C subunit 5 - Activator 1 36 kDa subunit - A1 36 kDa subunit - RF-C 36 kDa subunit - RFC36 - Activator 1 36 kDa subunit (Replication factor C 36 kDa subunit) (A1 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36) - Replication factor C 36 kDa subunit - - - - - Reactome DB_ID: 68427 - http://www.reactome.org/biopax/46/48887#Protein5564 - RFC5 - - - - 12200445 - Bambara, RA - Tom, S - Ranalli, TA - Pubmed - AP endonuclease 1 coordinates flap endonuclease 1 and DNA ligase I activity in long patch base excision repair. - J Biol Chem 277:41715-24 - 2002 - - - - REACT_2986 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2986.2 - - - - NM_002792 - RefSeq - - - - ENST00000595158 - Ensembl - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - 68948 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68948 - - - - 300339 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4991 - - - - - - EQUAL - 263 - http://www.reactome.org/biopax/46/48887#SequenceSite1879 - - - - - - MOD_RES 147 147 Phosphoserine. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval832 - - - - - - EQUAL - 27 - - - - ENST00000573234 - Ensembl - - - - RB1 - HGNC Symbol - - - - - - MOD_RES 102 102 N6-acetyllysine. - - - - - - - - - - - - - Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2029 - At the beginning of this reaction, 1 molecule of 'Orc4:Orc5:Orc3:Orc2:origin', and 1 molecule of 'Orc1' are present. At the end of this reaction, 1 molecule of 'Orc1:Orc4:Orc5:Orc3:Orc2:origin' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2646 - - - - - - EQUAL - 377 - - - - EQUAL - 875 - http://www.reactome.org/biopax/46/48887#SequenceSite10619 - - - - 69109 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69109 - - - - REACT_6963 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6963.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6622 - - - - ENST00000452185 - Ensembl - - - - 5424 - NCBI Gene - - - - EQUAL - 808 - http://www.reactome.org/biopax/46/48887#SequenceSite10641 - - - - - - MOD_RES 33 33 Phosphoserine; by PRKDC; in vitro. - - - - REACT_2111 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2111.3 - - - - O00495 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6654 - - - - EQUAL - 127 - - - - - - ubiquitin (UBA52) - - - - - http://www.reactome.org/biopax/46/48887#Protein2473 - Reactome DB_ID: 939844 - UBA52(1-76) - - - - REACT_2941 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2941.2 - - - - EQUAL - 928 - http://www.reactome.org/biopax/46/48887#SequenceSite10723 - - - - Q13156 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature151 - - - - ENSP00000412027 - Ensembl - - - - 5685 - NCBI Gene - - - - 7926735 - Lieber, MR - Harrington, JJ - Pubmed - Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. - Genes Dev 8:1344-55 - 1994 - - - - REACT_3630 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3630.2 - - - - REACT_3427 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3427.2 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2645 - - - - - - CHEBI:5234 - ChEBI - - - - ENST00000444284 - Ensembl - - - - EQUAL - 163 - - - - 1C3T - PROTEIN DATA BANK - - - - 9822671 - Podust, VN - Stephan, S - Tiwari, N - Pubmed - Replication factor C disengages from proliferating cell nuclear antigen (PCNA) upon sliding clamp formation, and PCNA itself tethers DNA polymerase delta to DNA. - J Biol Chem 273:31992-9 - 1998 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10895 - - - - REACT_315 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_315.3 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis630 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4972 - - - - - - REACT_4156 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4156.2 - - - - P28070 - UniProt - - - - ENST00000455660 - Ensembl - - - - - - MOD_RES 152 152 Phosphoserine. - - - - Q15008 - UniProt - - - - NP_859050 - RefSeq - - - - - - - - - - - CDKN1B - KIP1 - Cyclin-dependent kinase inhibitor p27 - p27Kip1 - - - - - - - - - - - - - - - - CDN1B_HUMAN - Cyclin-dependent kinase inhibitor 1B - FUNCTION: Important regulator of cell cycle progression. Involved in G1 arrest. Potent inhibitor of cyclin E- and cyclin A-CDK2 complexes. Forms a complex with cyclin type D-CDK4 complexes and is involved in the assembly, stability, and modulation of CCND1- CDK4 complex activation. Acts either as an inhibitor or an activator of cyclin type D-CDK4 complexes depending on its phosphorylation state and/or stoichometry.SUBUNIT: Forms a ternary compex with CCNE1/CDK2/CDKN1B. Interacts directly with CCNE1; the interaction is inhibited by CDK2- dependent phosphorylation on Thr-187. Interacts with COPS5, subunit of the COP9 signalosome complex; the interaction leads to CDKN1B degradation. Interacts with NUP50; the interaction leads to nuclear import and degradation of phosphorylated CDKN1B. Interacts with CCND1 and SNX6 (By similarity). Interacts (Thr-198- phosphorylated form) with 14-3-3 proteins, binds strongly YWHAQ, weakly YWHAE and YWHAH, but not YWHAB nor YWHAZ; the interaction with YWHAQ results in translocation to the cytoplasm. Interacts with AKT1 and LYN; the interactions lead to cytoplasmic mislocation, phosphorylation of CDKN1B and inhibition of cell cycle arrest. Interacts (unphosphorylated form) with CDK2. Forms a ternary complex, cyclin D/CDK4/CDKN1B. Interacts (phosphorylated on Tyr-88 and Tyr-89) with CDK4; the interaction is required for cyclin D/CDK4 complex assembly, induces nuclear translocation and activates the CDK4 kinase activity. Interacts with GRB2. Interacts with PIM1. Identified in a complex with SKP1, SKP2 and CKS1B. Interacts with UHMK1; the interaction leads to cytoplasmic mislocation, phosphorylation of CDKN1B and inhibition of cell cycle arrest. Interacts also with CDK1.SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Endosome (By similarity). Note=Nuclear and cytoplasmic in quiescent cells. AKT- or RSK-mediated phosphorylation on Thr-198, binds 14-3-3, translocates to the cytoplasm and promotes cell cycle progression. Mitogen-activated UHMK1 phosphorylation on Ser-10 also results in translocation to the cytoplasm and cell cycle progression. Phosphorylation on Ser-10 facilitates nuclear export. Translocates to the nucleus on phosphorylation of Tyr-88 and Tyr-89. Colocalizes at the endosome with SNX6; this leads to lysosomal degradation (By similarity).TISSUE SPECIFICITY: Expressed in all tissues tested. Highest levels in skeletal muscle, lowest in liver and kidney.INDUCTION: Maximal levels in quiescence cells and early G(1). Levels decrease after mitogen stimulation as cells progress toward S-phase.DOMAIN: A peptide sequence containing only AA 28-79 retains substantial Kip1 cyclin A/CDK2 inhibitory activity.PTM: Phosphorylated; phosphorylation occurs on serine, threonine and tyrosine residues. Phosphorylation on Ser-10 is the major site of phosphorylation in resting cells, takes place at the G(0)-G(1) phase and leads to protein stability. Phosphorylation on other sites is greatly enhanced by mitogens, growth factors, cMYC and in certain cancer cell lines. The phosphorylated form found in the cytoplasm is inactivate. Phosphorylation on Thr-198 is required for interaction with 14-3-3 proteins. Phosphorylation on Thr-187, by CDK2 leads to protein ubiquitination and proteasomal degradation. Tyrosine phosphorylation promotes this process. Phosphorylation by PKB/AKT1 can be suppressed by LY294002, an inhibitor of the catalytic subunit of PI3K. Phosphorylation on Tyr-88 and Tyr-89 has no effect on binding CDK2, but is required for binding CDK4. Dephosphorylated on tyrosine residues by G-CSF.PTM: Ubiquitinated; in the cytoplasm by the KPC complex (composed of RNF123/KPC1 and UBAC1/KPC2) and, in the nucleus, by SCF(SKP2). The latter requires prior phosphorylation on Thr-187. Ubiquitinated; by a TRIM21-containing SCF(SKP2)-like complex; leads to its degradation.PTM: Subject to degradation in the lysosome. Interaction with SNX6 promotes lysosomal degradation (By similarity).DISEASE: Multiple endocrine neoplasia 4 (MEN4) [MIM:610755]: Multiple endocrine neoplasia (MEN) syndromes are inherited cancer syndromes of the thyroid. MEN4 is a MEN-like syndrome with a phenotypic overlap of both MEN1 and MEN2. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: Decreased levels of p27Kip1, mainly due to proteasomal degradation, are found in various epithelial tumors originating from lung, breast, colon, ovary, esophagus, thyroid and prostate.SIMILARITY: Belongs to the CDI family.WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CDKN1BID116.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdkn1b/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - REACT_7043 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7043.2 - - - - ENSP00000385240 - Ensembl - - - - REACT_3326 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3326.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6435 - - - - EQUAL - 375 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6418 - - - - - - MOD_RES 165 165 N6-acetyllysine. - - - - EQUAL - 261 - http://www.reactome.org/biopax/46/48887#SequenceSite1859 - - - - EQUAL - 48 - - - - REACT_3922 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3922.2 - - - - ENSP00000225426 - Ensembl - - - - ORC3 - HGNC Symbol - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - REACT_26274 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26274.1 - - - - EQUAL - 2 - - - - - - Proteasome iota chain - 27 kDa prosomal protein - Proteasome subunit alpha type 6 - PSMA6 - Multicatalytic endopeptidase complex iota chain - PROS-27 - Macropain iota chain - - - - - Reactome DB_ID: 68734 - http://www.reactome.org/biopax/46/48887#Protein1063 - p27K - - - - - - - - - - - - - - - - - CDK-mediated phosphorylation and removal of Cdc6 - As cells enter S phase, HsCdc6p is phosphorylated by CDK promoting its export from the nucleus (see Bell and Dutta 2002). - http://www.reactome.org/biopax/46/48887#Pathway507 - - - - - NM_001256870 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10897 - - - - 2VT8 - PROTEIN DATA BANK - - - - CHEBI:15422 - ChEBI - - - - - - MOD_RES 450 450 N6-acetyllysine. - - - - ENST00000532097 - Ensembl - - - - ENSP00000266970 - Ensembl - - - - ENSP00000301019 - Ensembl - - - - - - RF-C 37 kDa subunit - A1 37 kDa subunit - RFC37 - Replication factor C 37 kDa subunit - Activator 1 37 kDa subunit - - - - - Reactome DB_ID: 68429 - http://www.reactome.org/biopax/46/48887#Protein5567 - RFC4 - - - - ENST00000523944 - Ensembl - - - - EQUAL - 233 - - - - - - MOD_RES 248 248 Phosphoserine. - - - - NP_002806 - RefSeq - - - - 8145706 - pubchem - - - - PSMD11 - HGNC Symbol - - - - PSME2 - HGNC - - - - NM_030928 - RefSeq - - - - HGNC:9565 - HGNC - - - - 602627 - omim - - - - NM_001025096 - RefSeq - - - - 11095689 - Yokoi, M - Mizuno, T - Izumi, M - Moon, KY - Kawasaki, Y - Yatagai, F - Hurwitz, J - Yanagi, K - Hanaoka, F - Pubmed - The human homolog of Saccharomyces cerevisiae Mcm10 interacts with replication factors and dissociates from nuclease-resistant nuclear structures in G(2) phase. - Nucleic Acids Res 28:4769-77 - 2000 - - - - D3DSY0 - UniProt - - - - NM_170750 - RefSeq - - - - 169509 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=169509 - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite4651 - - - - REACT_3011 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3011.2 - - - - HGNC:9971 - HGNC - - - - 54745 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=54745 - - - - 68563 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68563 - - - - EQUAL - 219 - http://www.reactome.org/biopax/46/48887#SequenceSite1827 - - - - 69140 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69140 - - - - EQUAL - 1 - - - - 8020968 - Kesti T - Riviere M - Turc-Carel C - Syvaoja JE - Szpirer J - Szpirer C - Pedeutour F - PubMed - Localization of the gene for DNA polymerase epsilon (POLE) to human chromosome 12q24.3 and rat chromosome 12 by somatic cell hybrid panels and fluorescence in situ hybridization. - Genomics 20(2);223-6 - 1994 - - - - Q13471 - UniProt - - - - - - MOD_RES 130 130 Phosphotyrosine. - - - - 600393 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4871 - - - - - - Q3SY03 - UniProt - - - - Q13143 - UniProt - - - - REACT_2244 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2244.4 - - - - REACT_984 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_984.3 - - - - InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 - InChI - - - - Q9H1Z1 - UniProt - - - - NP_003905 - RefSeq - - - - EQUAL - 206 - - - - - - MOD_RES 186 186 Phosphoserine. - - - - 68771 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68771 - - - - REACT_6018 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6018.1 - - - - PSMD3 - HGNC - - - - - - RBP1 - Retinoblastoma-associated protein - Rb-binding protein 1 - pRb - Retinoblastoma Protein 1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5634 - Reactome DB_ID: 68642 - RB1 - - - - 939184 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939184 - - - - ENSP00000466794 - Ensembl - - - - Q96H01 - UniProt - - - - 68649 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68649 - - - - - - UBA52(1-76) - ubiquitin (UBA52) - - - - - http://www.reactome.org/biopax/46/48887#Protein1045 - Reactome DB_ID: 939203 - UBA52 - - - - PSME1 - HGNC - - - - EQUAL - 928 - http://www.reactome.org/biopax/46/48887#SequenceSite10720 - - - - - - MOD_RES 250 250 Phosphoserine. - - - - - - RPS27A(1-76) - ubiquitin (RPS27A) - - - - - http://www.reactome.org/biopax/46/48887#Protein1044 - Reactome DB_ID: 939205 - RPS27A - - - - ENSP00000384493 - Ensembl - - - - NP_001238920 - RefSeq - - - - 607173 - omim - - - - EQUAL - 104 - - - - HGNC:24824 - HGNC - - - - 5699 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval830 - - - - - - NM_004526 - RefSeq - - - - - - MOD_RES 258 258 N6-acetyllysine. - - - - Q14181 - UniProt - - - - B2R5J4 - UniProt - - - - CDKN1B - HGNC Symbol - - - - EQUAL - 122 - - - - 116945 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4981 - - - - - - Q8TB30 - UniProt - - - - 17487135 - pubchem-substance - - - - 176740 - omim - - - - NM_002786 - RefSeq - - - - ENSG00000167513 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1057 - - - - REACT_6082 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6082.1 - - - - - - - - - - - - - - - - - - - Mcm10 associates with the pre-replicative complex, stabilizing Mcm2-7 - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1972 - MCM10 is required for human DNA replication. In S. cerevisiae, Mcm10, like Mcm2-7, is required for minichromosome maintenance, but Mcm10 has no sequence homology with these other proteins (Merchant et al., 1997). Genetic studies have demonstrated that Mcm10 is required for DNA replication in S. pombe (Aves et al., 1998) and S. cerevisiae cells (Homesley et al., 2000) and immunodepletion of XlMcm10 interferes with DNA replication in Xenopus egg extracts (Wohlschlegel et al., 2002). Human Mcm10 interacts with chromatin in G1 phase and then dissociates during G2 phase. In S. cerevisiae, Mcm10 has been shown to localize to origins during G1 (Ricke and Bielinsky, 2004), and it may stabilize the association of Mcm2-7 with the pre-replicative complex (Sawyer et al., 2004). This timing of association is consistent with studies that demonstrate that, in Xenopus egg extracts, Mcm10 is required for association of Cdc45, but not Mcm2-7 with chromatin. Biochemical evidence that Mcm10 plays a direct role in the activation of the pre-replicative complex includes the requirement for SpMcm10 in the phosphorylation of the Mcm2-7 complex by DDK (Lee et al., 2004) and the fact that SpMcm10 binds and stimulates DNA polymerase alpha activity (Fien et al., 2004). - - - - - EQUAL - 256 - http://www.reactome.org/biopax/46/48887#SequenceSite1819 - - - - Q53TI2 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1850 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7548 - - - - GMNN - HGNC - - - - REACT_1871 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1871.3 - - - - D3DP86 - UniProt - - - - EQUAL - 355 - http://www.reactome.org/biopax/46/48887#SequenceSite1795 - - - - 68774 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68774 - - - - MOD_RES Dimethylated arginine - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval831 - - - - - - - - Multicatalytic endopeptidase complex subunit MECl-1 - Proteasome MECl-1 - Proteasome subunit beta type 10 precursor - Macropain subunit MECl-1 - Proteasome subunit beta type 10 - - - - - http://www.reactome.org/biopax/46/48887#Protein1082 - Reactome DB_ID: 68741 - PSMB10 - - - - NP_001177811 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval829 - - - - - - 68655 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68655 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval845 - - - - - - 166000 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=166000 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature153 - - - - ENSP00000265728 - Ensembl - - - - REACT_1601 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1601.4 - - - - ENSP00000462495 - Ensembl - - - - - - Dbf4 - - - - - Reactome DB_ID: 68387 - http://www.reactome.org/biopax/46/48887#Protein5575 - DBF4 - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite2929 - - - - - - MOD_RES 163 163 Phosphothreonine. - - - - REACT_7007 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7007.1 - - - - ENST00000409682 - Ensembl - - - - 3146346 - Robinson-Hill RM - Hunting DJ - Dresler SL - Gowans BJ - PubMed - Involvement of DNA polymerase delta in DNA repair synthesis in human fibroblasts at late times after ultraviolet irradiation. - Biochemistry 27(17);6379-83 - 1988 - - - - EQUAL - 4 - - - - - - MOD_RES 24 24 Phosphoserine. - - - - ENSG00000170312 - Ensembl - - - - REACT_5400 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5400.2 - - - - HGNC:9536 - HGNC - - - - 68802 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68802 - - - - 312040 - omim - - - - RPS27A - HGNC - - - - EQUAL - 54 - - - - EQUAL - 77 - http://www.reactome.org/biopax/46/48887#SequenceSite4649 - - - - ENST00000599857 - Ensembl - - - - NM_002791 - RefSeq - - - - - - MOD_RES 25 25 Phosphothreonine (By similarity). - - - - 14766746 - Tappin, I - Cho, YS - Fien, K - Hurwitz, J - Lee, JK - Raychaudhuri, S - Pubmed - Primer utilization by DNA polymerase alpha-primase is influenced by its interaction with Mcm10p - J Biol Chem 279:16144-53 - 2004 - - - - ENST00000375812 - Ensembl - - - - NP_031396 - RefSeq - - - - ENST00000373635 - Ensembl - - - - NM_001237 - RefSeq - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5028 - - - - - - - - MOD_RES 407 407 Phosphoserine. - - - - ORC2 - HGNC - - - - - - MOD_RES 180 180 Phosphothreonine. - - - - 102579 - omim - - - - E9PAV2 - UniProt - - - - NM_002815 - RefSeq - - - - NM_181558 - RefSeq - - - - REACT_5197 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5197.2 - - - - REACT_3597 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3597.1 - - - - - - MOD_RES 420 420 Phosphoserine. - - - - - - MOD_RES 722 722 Phosphothreonine. - - - - NP_001243808 - RefSeq - - - - REACT_24747 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24747.2 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2505 - - - - - Q9UBU7 - UniProt - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10866 - - - - 164121 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=164121 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1155 - - - - 10213 - NCBI Gene - - - - 68536 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68536 - - - - 8253737 - Wang, TS - Copeland, WC - Pubmed - Enzymatic characterization of the individual mammalian primase subunits reveals a biphasic mechanism for initiation of DNA replication. - J Biol Chem 268:26179-89 - 1994 - - - - EQUAL - 2 - - - - REACT_4984 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4984.1 - - - - EQUAL - 318 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval879 - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2510 - - - - - - Origin recognition complex subunit 1 - Replication control protein 1 - Orc1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5582 - Reactome DB_ID: 68522 - ORC1 - - - - - - ACTIVATION - - - - http://www.reactome.org/biopax/46/48887#Catalysis628 - - - - EQUAL - 919 - http://www.reactome.org/biopax/46/48887#SequenceSite10918 - - - - EQUAL - 50 - http://www.reactome.org/biopax/46/48887#SequenceSite1882 - - - - ENSG00000150991 - Ensembl - - - - - - - - - - - - Cdt1:geminin - http://www.reactome.org/biopax/46/48887#Complex2669 - Reactome DB_ID: 68537 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10976 - - - - ENSP00000363993 - Ensembl - - - - ENSP00000256442 - Ensembl - - - - EQUAL - 340 - - - - Q5TEJ5 - UniProt - - - - PTHR10410:SF5 - PANTHER Family - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4848 - - - - - - 180200 - omim - - - - 116953 - omim - - - - D3DS43 - UniProt - - - - CCNB1 - HGNC Symbol - - - - - - MOD_RES 187 187 Phosphoserine; by CDK2. - - - - RPA3 - HGNC Symbol - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite4925 - - - - ENSG00000240065 - Ensembl - - - - ENST00000290541 - Ensembl - - - - ENSP00000430194 - Ensembl - - - - REACT_18992 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18992.1 - - - - Q53HU5 - UniProt - - - - P20618 - UniProt - - - - ENST00000264169 - Ensembl - - - - NM_001033930 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite2927 - - - - - - Proteasome subunit beta type 2 - Macropain subunit C7-I - Multicatalytic endopeptidase complex subunit C7-I - Proteasome component C7-I - - - - - Reactome DB_ID: 68744 - http://www.reactome.org/biopax/46/48887#Protein1077 - PSMB2 - - - - - - MOD_RES 51 51 Phosphoserine. - - - - CHEBI:24450 - ChEBI - - - - - - MOD_RES 139 139 Phosphoserine. - - - - 1AD6 - PROTEIN DATA BANK - - - - NP_853536 - RefSeq - - - - 68806 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68806 - - - - PSMD10 - 26S proteasome regulatory subunit p28 - p28(GANK) - Gankyrin - - - - - - - - - - - - - - - - - - - PSD10_HUMAN - 26S proteasome non-ATPase regulatory subunit 10 - FUNCTION: Acts as a chaperone during the assembly of the 26S proteasome, specifically of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD10:PSMC4:PSMC5:PAAF1 module which probably assembles with a PSMD5:PSMC2:PSMC1:PSMD2 module. Independently of the proteasome, regulates EGF-induced AKT activation through inhibition of the RHOA/ROCK/PTEN pahway, leading to prolonged AKT activation. Plays an important role in RAS-induced tumorigenesis.FUNCTION: Acts as an proto-oncoprotein by being involved in negative regulation of tumor suppressors RB1 and p53/TP53. Overexpression is leading to phosphorylation of RB1 and proteasomal degradation of RB1. Regulates CDK4-mediated phosphorylation of RB1 by competing with CDKN2A for binding with CDK4. Facilitates binding of MDM2 to p53/TP53 and the mono- and polyubiquitination of p53/TP53 by MDM2 suggesting a function in targeting the TP53:MDM2 complex to the 26S proteasome. Involved in p53-independent apoptosis. Involved in regulation of NF-kappa-B by retaining it in the cytoplasm. Binds to the NF-kappa-B component RELA and accelerates its XPO1/CRM1-mediated nuclear export.SUBUNIT: Part of transient complex containing PSMD10, PSMC4, PSMC5 and PAAF1 formed during the assembly of the 26S proteasome. Stays associated throughout the assembly of the PA700/19S RC and is released upon association with the 20S core. Interacts with PSMC4. Interacts with RB1. Interacts with CDK4. Interacts with MDM2. Interacts with RELA. Associates with a CDK4:CCND2 serine/threonine kinase complex. Interacts with ARHGDIA and increases the interaction between ARHGDIA and RHOA, hence promotes ARHGDIA inactivation of RHOA and ROCK.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O75832-1; Sequence=Displayed; Name=2; IsoId=O75832-2; Sequence=VSP_043043;TISSUE SPECIFICITY: Tends to be up-regulated in cancer cells with RAS mutations, including lung cancers and adenocarconimas (at protein level).SIMILARITY: Contains 7 ANK repeats.CAUTION: Was initially identified as a genuine component of the 26S proteasome. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P35250 - UniProt - - - - NP_004082 - RefSeq - - - - 5717 - NCBI Gene - - - - O75496 - UniProt - - - - REACT_4243 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4243.3 - - - - - - - - - - - - - - - - RAD2 - MF1 - Maturation factor 1 - 3.1.-.- - DNase IV - hFEN-1 - FEN-1 - Flap structure-specific endonuclease 1 - FEN1 - - - - - - - - - - - - - FEN1_HUMAN - Flap endonuclease 1 - FUNCTION: Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double- stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.COFACTOR: Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.SUBUNIT: Interacts with PCNA. Three molecules of FEN1 bind to one PCNA trimer with each molecule binding to one PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity. The C-terminal domain binds EP300. Can bind simultaneously to both PCNA and EP300. Interacts with DDX11.SUBCELLULAR LOCATION: Isoform 1: Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage.SUBCELLULAR LOCATION: Isoform FENMIT: Mitochondrion.ALTERNATIVE PRODUCTS: Event=Alternative initiation; Named isoforms=2; Name=1; IsoId=P39748-1; Sequence=Displayed; Name=FENMIT; IsoId=P39748-2; Sequence=VSP_047520; Note=No nuclease activity. Binds preferentially to RNA flap structures and R-loops;PTM: Acetylated by EP300. Acetylation inhibits both endonuclease and exonuclease activity. Acetylation also reduces DNA-binding activity but does not affect interaction with PCNA or EP300.PTM: Phosphorylation upon DNA damage induces relocalization to the nuclear plasma. Phosphorylation at Ser-187 by CDK2 occurs during late S-phase and results in dissociation from PCNA.PTM: Methylation at Arg-192 by PRMT5 impedes Ser-187 phosphorylation and increases interaction with PCNA.SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/fen1/";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/FEN1ID40543ch11q12.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - Processive synthesis on the leading strand - Polymerase switching is a key event that allows the processive synthesis of DNA by the pol delta and PCNA complex. Polymerase delta possesses polymerization and proofreading activities, which increases the overall fidelity of DNA replication. The pol delta holoenzyme is a heterotetrameric complex that contains p125, p66, p50, and p12 subunits, in human cells. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2012 - - - - - ENSG00000100297 - Ensembl - - - - ENSP00000397973 - Ensembl - - - - HGNC:2939 - HGNC - - - - REACT_5850 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5850.3 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2111 - - - - - - A8K763 - UniProt - - - - EQUAL - 40 - - - - 604452 - omim - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4908 - - - - - - REACT_24393 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24393.2 - - - - EQUAL - 535 - - - - CHEBI:2342 - ChEBI - - - - - - MOD_RES 125 125 N6-acetyllysine. - - - - - - MOD_RES 148 148 Phosphoserine. - - - - Q969W7 - UniProt - - - - 68482 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68482 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry7551 - - - - HGNC:30305 - HGNC - - - - - - ubiquitin (UBB 2) - - - - - Reactome DB_ID: 939213 - http://www.reactome.org/biopax/46/48887#Protein1047 - UBB(77-152) - - - - ENST00000441788 - Ensembl - - - - 69186 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69186 - - - - ENSP00000401802 - Ensembl - - - - HGNC:9557 - HGNC - - - - ENST00000301019 - Ensembl - - - - ENSG00000161057 - Ensembl - - - - P62987 - UniProt - - - - MOD_RES N6-methyllysine - - - - NM_181699 - RefSeq - - - - - - MOD_RES 138 138 Phosphoserine. - - - - - - - - - - - - Processive complex:Okazaki fragment complex - Reactome DB_ID: 68453 - http://www.reactome.org/biopax/46/48887#Complex2639 - - - - REACT_9299 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9299.1 - - - - ENST00000437685 - Ensembl - - - - PSMC6 - HGNC Symbol - - - - REACT_1471 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1471.3 - - - - NM_002553 - RefSeq - - - - EQUAL - 180 - - - - - - uridine 5'-triphosphate - Uridine triphosphate - - - - Reactome DB_ID: 113562 - http://www.reactome.org/biopax/46/48887#SmallMolecule201 - UTP - - - - 9405441 - Linn S - Patel VS - Li Y - Zhou S - Asahara H - PubMed - Purification, cDNA cloning, and gene mapping of the small subunit of human DNA polymerase epsilon. - J Biol Chem 272(51);32337-44 - 1997 - - - - 68459 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68459 - - - - ENST00000413643 - Ensembl - - - - 11006548 - Davey, MJ - O'Donnell, M - Pubmed - Mechanisms of DNA replication. - Curr Opin Chem Biol 4:581-6 - 2000 - - - - NP_001207707 - RefSeq - - - - HGNC:6950 - HGNC - - - - REACT_4286 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4286.2 - - - - EQUAL - 527 - http://www.reactome.org/biopax/46/48887#SequenceSite10865 - - - - POLD4 - HGNC Symbol - - - - B0YJ69 - UniProt - - - - REACT_3695 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3695.2 - - - - ENSP00000229854 - Ensembl - - - - ENSG00000134057 - Ensembl - - - - 16582612 - Enders, GH - Mitra, J - Lengel, KL - Azizkhan-Clifford, J - Pubmed - Dual regulation of the anaphase promoting complex in human cells by cyclin A-Cdk2 and cyclin A-Cdk1 complexes - Cell Cycle 5:661-6 - 2006 - - - - REACT_4584 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4584.1 - - - - MOD_RES Symmetric dimethylarginine - - - - ENSG00000014138 - Ensembl - - - - 113656 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113656 - - - - NP_055429 - RefSeq - - - - - - PSA7L_HUMAN - Proteasome subunit alpha type-7-like - - - - - Reactome DB_ID: 947610 - http://www.reactome.org/biopax/46/48887#Protein1072 - PSMA8 - - - - PSMD1 - HGNC Symbol - - - - - - MOD_RES 21 21 Phosphothreonine; by PRKDC; in vitro. - - - - A0AV55 - UniProt - - - - PSMA5 - HGNC Symbol - - - - 939258 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939258 - - - - 9620226 - Fox G - Thielmann HW - Popanda O - PubMed - Evidence for reduced copying fidelity of DNA polymerases alpha, delta, and epsilon from Novikoff hepatoma cells. - J Cancer Res Clin Oncol 123(11-12);659-68 - 1997 - - - - 68679 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68679 - - - - EQUAL - 363 - http://www.reactome.org/biopax/46/48887#SequenceSite10603 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10638 - - - - 68943 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68943 - - - - NM_148976 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10903 - - - - NP_002786 - RefSeq - - - - EQUAL - 220 - - - - REACT_2458 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2458.1 - - - - - - Cdh1 - - - - - Reactome DB_ID: 174099 - http://www.reactome.org/biopax/46/48887#Protein5719 - FZR1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature869 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1818 - - - - MOD_RES N-acetylalanine - - - - EQUAL - 226 - http://www.reactome.org/biopax/46/48887#SequenceSite1815 - - - - REACT_5587 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5587.1 - - - - Q6P1L7 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1806 - - - - Q14100 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1082 - - - - ENST00000541212 - Ensembl - - - - ENSP00000217958 - Ensembl - - - - REACT_4382 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4382.2 - - - - PSMB10 - HGNC Symbol - - - - 602177 - omim - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1059 - - - - EQUAL - 365 - - - - - - PP2A-catalytic subunit C alpha isoform - - - - - http://www.reactome.org/biopax/46/48887#Protein2611 - Reactome DB_ID: 165978 - PPP2CA - - - - 176844 - omim - - - - MCM3 - HGNC - - - - - - MOD_RES 2 2 N-acetylserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature1372 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval844 - - - - - - ENSP00000406046 - Ensembl - - - - 603480 - omim - - - - - - MOD_RES 76 76 Phosphotyrosine (By similarity). - - - - D3DPS0 - UniProt - - - - NM_001102668 - RefSeq - - - - ENSG00000136930 - Ensembl - - - - - - 26S proteasome non-ATPase regulatory subunit 10 - 26S proteasome regulatory subunit p28 - Gankyrin - - - - - http://www.reactome.org/biopax/46/48887#Protein1070 - Reactome DB_ID: 68788 - PSMD10 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4837 - - - - - - - - UBB(1-76) - ubiquitin (UBB 1) - - - - - http://www.reactome.org/biopax/46/48887#Protein2474 - Reactome DB_ID: 939847 - UBB - - - - - - DNA polymerase delta subunit 2 - DNA pol delta subunit 2 - - - - - http://www.reactome.org/biopax/46/48887#Protein5731 - Reactome DB_ID: 68443 - POLD2 - - - - - - Proteasome subunit XAPC7 - Proteasome subunit RC6-1 - Proteasome subunit alpha type 7 - - - - - Reactome DB_ID: 68736 - http://www.reactome.org/biopax/46/48887#Protein1103 - PSMA7 - - - - 603619 - omim - - - - EQUAL - 440 - http://www.reactome.org/biopax/46/48887#SequenceSite1841 - - - - - - ubiquitin (UBC 2) - - - - - Reactome DB_ID: 939164 - http://www.reactome.org/biopax/46/48887#Protein1050 - UBC(77-152) - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6695 - - - - CHEBI:46385 - ChEBI - - - - NM_021173 - RefSeq - - - - EQUAL - 417 - - - - - - - - - - - - Processive complex:Okazaki fragment:Flap - http://www.reactome.org/biopax/46/48887#Complex2640 - Reactome DB_ID: 68455 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4888 - - - - - - - - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule593 - Reactome DB_ID: 164121 - AMP - - - - 4999 - NCBI Gene - - - - EQUAL - 104 - - - - REACT_3748 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3748.1 - - - - Q15023 - UniProt - - - - REACT_1210 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1210.3 - - - - InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 - InChI - - - - ENSG00000154611 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6708 - - - - - - - - - - - - - - - - - - - - - - ORC complex bound to origin - Reactome DB_ID: 176958 - http://www.reactome.org/biopax/46/48887#Complex2816 - - - - 1026 - NCBI Gene - - - - - - MOD_RES 500 500 Phosphoserine. - - - - - - MOD_RES 381 381 Phosphoserine. - - - - 177045 - omim - - - - CHEBI:47450 - ChEBI - - - - - - MOD_RES 70 70 N6-acetyllysine. - - - - P12004 - UniProt - - - - - - - - - Cyclin - PCNA - - - - - - - - - - - - - - - - - - - - PCNA_HUMAN - Proliferating cell nuclear antigen - FUNCTION: Auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Induces a robust stimulatory effect on the 3'- 5' exonuclease and 3'-phosphodiesterase, but not apurinic- apyrimidinic (AP) endonuclease, APEX2 activities. Has to be loaded onto DNA in order to be able to stimulate APEX2. Plays a key role in DNA damage response (DDR) by being conveniently positioned at the replication fork to coordinate DNA replication with DNA repair and DNA damage tolerance pathways. Acts as a loading platform to recruit DDR proteins that allow completion of DNA replication after DNA damage and promote postreplication repair: Monoubiquitinated PCNA leads to recruitment of translesion (TLS) polymerases, while 'Lys-63'-linked polyubiquitination of PCNA is involved in error-free pathway and employs recombination mechanisms to synthesize across the lesion.SUBUNIT: Homotrimer (By similarity). Forms a complex with activator 1 heteropentamer in the presence of ATP. Interacts with EXO1, POLH, POLK, DNMT1, ERCC5, FEN1, CDC6 and POLDIP2. Interacts with APEX2; this interaction is triggered by reactive oxygen species and increased by misincorporation of uracil in nuclear DNA. Forms a ternary complex with DNTTIP2 and core histone. Interacts with KCTD10 and PPP1R15A (By similarity). Interacts with POLD1, POLD3 and POLD4. Interacts with BAZ1B; the interaction is direct. Interacts with HLTF and SHPRH. Interacts with NUDT15. Interaction is disrupted in response to UV irradiation and acetylation. Interacts with CDKN1A/p21(CIP1) and CDT1; interacts via their PIP-box which also recruits the DCX(DTL) complex. Interacts with DDX11. Interacts with EGFR; positively regulates PCNA. Interacts with PARPBP. Interacts (when ubiquitinated) with SPRTN; leading to enhance RAD18-mediated PCNA ubiquitination. Interacts (when polyubiquitinated) with ZRANB3. Interacts with SMARCAD1. Interacts with CDKN1C. Interacts with KIAA0101/PAF15 (via PIP-box).SUBCELLULAR LOCATION: Nucleus. Note=Forms nuclear foci representing sites of ongoing DNA replication and vary in morphology and number during S phase. Together with APEX2, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents.PTM: Following DNA damage, can be either monoubiquitinated to stimulate direct bypass of DNA lesions by specialized DNA polymerases or polyubiquitinated to promote recombination- dependent DNA synthesis across DNA lesions by template switching mechanisms. Following induction of replication stress, monoubiquitinated by the UBE2B-RAD18 complex on Lys-164, leading to recruit translesion (TLS) polymerases, which are able to synthesize across DNA lesions in a potentially error-prone manner. An error-free pathway also exists and requires non-canonical polyubiquitination on Lys-164 through 'Lys-63' linkage of ubiquitin moieties by the E2 complex UBE2N-UBE2V2 and the E3 ligases, HLTF, RNF8 and SHPRH. This error-free pathway, also known as template switching, employs recombination mechanisms to synthesize across the lesion, using as a template the undamaged, newly synthesized strand of the sister chromatid. Monoubiquitination at Lys-164 also takes place in undamaged proliferating cells, and is mediated by the DCX(DTL) complex, leading to enhance PCNA-dependent translesion DNA synthesis. Sumoylated during S phase.PTM: Acetylated in response to UV irradiation. Acetylation disrupts interaction with NUDT15 and promotes degradation.PTM: Phosphorylated. Phosphorylation at Tyr-211 by EGFR stabilizes chromatin-associated PCNA.MISCELLANEOUS: Antibodies against PCNA are present in sera from patients with systemic lupus erythematosus.SIMILARITY: Belongs to the PCNA family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pcna/";WEB RESOURCE: Name=Wikipedia; Note=PCNA entry; URL="http://en.wikipedia.org/wiki/PCNA";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PCNAID41670ch20p12.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 169515 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=169515 - - - - 8145524 - pubchem - - - - REACT_3140 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3140.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6705 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1078 - - - - NM_002813 - RefSeq - - - - - - - - - - - - - - - - DNA Replication - Authored: Bambara, RA, Catlett, M, Davey, MJ, Forsburg, S, O'Donnell, M, Tom, S, Tye, BK, 2003-01-06 00:00:00 - Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the binding of the replication initiator to the origin of replication. The replicative helicase is then assembled onto the origin, usually by a helicase assembly factor. Either shortly before or shortly after helicase assembly, some local unwinding of the origin of replication occurs in a region rich in adenine and thymine bases (often termed a DNA unwinding element, DUE). The unwound region provides the substrate for primer synthesis and initiation of DNA replication. The best-defined eukaryotic origins are those of S. cerevisiae, which have well-conserved sequence elements for initiator binding, DNA unwinding and binding of accessory proteins. In multicellular eukaryotes, unlike S. cerevisiae, these loci appear not to be defined by the presence of a DNA sequence motif. Indeed, choice of replication origins in a multicellular eukaryote may vary with developmental stage and tissue type. In cell-free models of metazoan DNA replication, such as the one provided by Xenopus egg extracts, there are only limited DNA sequence specificity requirements for replication initiation (Kelly & Brown 2000; Bell & Dutta 2002; Marahrens & Stillman 1992; Cimbora & Groudine 2001; Mahbubani et al 1992, Hyrien & Mechali 1993). - Reviewed: Mendez, J, Aladjem, M, 0000-00-00 00:00:00 - http://www.reactome.org/biopax/46/48887#Pathway1471 - Edited: D'Eustachio, P, Joshi-Tope, G, Nickerson, E, 0000-00-00 00:00:00 - - - - - ENSP00000364519 - Ensembl - - - - EQUAL - 350 - http://www.reactome.org/biopax/46/48887#SequenceSite1803 - - - - ENSP00000472545 - Ensembl - - - - ENSP00000393185 - Ensembl - - - - A8K3I7 - UniProt - - - - CHEBI:15713 - ChEBI - - - - 8144764 - pubchem-substance - - - - EQUAL - 127 - - - - REACT_5263 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5263.2 - - - - E7EQU7 - UniProt - - - - 1L1O - PROTEIN DATA BANK - - - - ENST00000373809 - Ensembl - - - - 68824 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68824 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6669 - - - - P25789 - UniProt - - - - 68493 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68493 - - - - PTHR13989:SF7 - PANTHER Family - - - - - REACT_3472 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3472.2 - - - - EQUAL - 147 - - - - 177046 - omim - - - - InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 - InChI - - - - NM_033379 - RefSeq - - - - ENSP00000378699 - Ensembl - - - - CHEBI:14076 - ChEBI - - - - NM_002592 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1644 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2658 - - - - - 165974 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=165974 - - - - - - DNA polymerase alpha catalytic subunit - POLA1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5702 - Reactome DB_ID: 68487 - p180 - - - - B4DDE6 - UniProt - - - - EQUAL - 1184 - - - - ENST00000409643 - Ensembl - - - - PPP2R1A - HGNC - - - - 68568 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68568 - - - - O00716 - UniProt - - - - NM_002788 - RefSeq - - - - 8044842 - Rowley, A - Dowell, SJ - Cocker, JH - Diffley, JF - Pubmed - Two steps in the assembly of complexes at yeast replication origins in vivo. - Cell 78:303-16 - 1994 - - - - 450444 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=450444 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature833 - - - - CDK2 - HGNC - - - - 68753 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68753 - - - - - - MOD_RES 359 359 Phosphoserine. - - - - LIG1 - HGNC Symbol - - - - EQUAL - 359 - - - - EQUAL - 1 - - - - 8145531 - pubchem - - - - EQUAL - 31 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10872 - - - - - - Proteasome subunit alpha type 2 - Multicatalytic endopeptidase complex subunit C3 - Proteasome component C3 - Macropain subunit C3 - - - - - Reactome DB_ID: 68726 - http://www.reactome.org/biopax/46/48887#Protein1066 - PSMA2 - - - - ENSG00000108671 - Ensembl - - - - ENSP00000157812 - Ensembl - - - - HGNC:12468 - HGNC - - - - 9837 - NCBI Gene - - - - ENST00000429645 - Ensembl - - - - EQUAL - 222 - - - - CCNA2 - HGNC Symbol - - - - CHEBI:3275 - ChEBI - - - - 176635 - omim - - - - CHEBI:29058 - ChEBI - - - - - - MOD_RES 45 45 Phosphoserine. - - - - ENST00000407835 - Ensembl - - - - RFC3 - HGNC - - - - ENST00000378883 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1061 - - - - - - Proteasome subunit p42 - PSMC6 - Conserved ATPase domain protein 44 - CADp44 - 26S protease regulatory subunit S10B - - - - - Reactome DB_ID: 68783 - http://www.reactome.org/biopax/46/48887#Protein1091 - p44 - - - - EQUAL - 69 - - - - PSMA6 - HGNC - - - - REACT_7704 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7704.1 - - - - 1763 - NCBI Gene - - - - B4E2V4 - UniProt - - - - CHEBI:40938 - ChEBI - - - - REACT_1838 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1838.5 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval847 - - - - - - 68403 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68403 - - - - REACT_3019 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3019.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4939 - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - 68542 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68542 - - - - NM_006263 - RefSeq - - - - ENST00000379143 - Ensembl - - - - ENSP00000473052 - Ensembl - - - - - - Multicatalytic endopeptidase complex subunit C9 - Proteasome subunit L - Macropain subunit C9 - Proteasome subunit alpha type 4 - Proteasome component C9 - - - - - Reactome DB_ID: 68730 - http://www.reactome.org/biopax/46/48887#Protein1092 - PSMA4 - - - - - - MOD_RES 365 365 Phosphoserine. - - - - EQUAL - 1940 - - - - - - MOD_RES 19 19 Phosphotyrosine. - - - - 68537 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68537 - - - - EQUAL - 380 - http://www.reactome.org/biopax/46/48887#SequenceSite1783 - - - - ENSP00000441543 - Ensembl - - - - CCNB1 - HGNC - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10675 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2459 - - - - 68722 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68722 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4855 - - - - NM_182776 - RefSeq - - - - NM_002808 - RefSeq - - - - - - Replication factor-A protein 4 - RP-A - RF-A - DNA Replication factor A protein 4 (30kD) - Replication protein A 30 kDa subunit - - - - - http://www.reactome.org/biopax/46/48887#Protein5705 - Reactome DB_ID: 68566 - RPA4 - - - - POLA1 - HGNC - - - - REACT_4705 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4705.4 - - - - - - MOD_RES 674 674 Phosphothreonine. - - - - - - - - - - Free CDT1 associates with CDC6:ORC:origin complexes - At the beginning of this reaction, 1 molecule of 'CDT1', and 1 molecule of 'CDC6:ORC:origin complex' are present. At the end of this reaction, 1 molecule of 'CDT1:CDC6:ORC:origin complex' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2148 - - - - - NM_006739 - RefSeq - - - - EQUAL - 356 - http://www.reactome.org/biopax/46/48887#SequenceSite10595 - - - - - - - - - - - - - - - 3.6.4.12 - P1-CDC21 - CDC21 - MCM4 - CDC21 homolog - - - - - - - - - - - - - - - - - - MCM4_HUMAN - DNA replication licensing factor MCM4 - FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6- MCM4-MCM7-MCM3-MCM5 (By simililarity). Interacts with MCMBP.SUBCELLULAR LOCATION: Nucleus (By similarity).DISEASE: Natural killer cell and glucocorticoid deficiency with DNA repair defect (NKGCD) [MIM:609981]: An autosomal recessive disorder characterized by severe intra- and extrauterine growth retardation, microcephaly, decreased numbers of natural killer cells, and recurrent viral infections, most often affecting the respiratory tract and leading to respiratory failure. Affected individuals also have adrenal insufficiency requiring corticosteroid replacement therapy and may have an increased susceptibility to cancer. Note=The disease is caused by mutations affecting the gene represented in this entry.MISCELLANEOUS: Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/mcm4/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - 3.6.4.12 - CDC46 homolog - P1-CDC46 - CDC46 - MCM5 - - - - - - - - - - - - - - - - MCM5_HUMAN - DNA replication licensing factor MCM5 - FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity (By similarity). Interacts with MCMBP.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6- MCM4-MCM7-MCM3-MCM5 (By simililarity).SUBCELLULAR LOCATION: Nucleus.MISCELLANEOUS: Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/mcm5/";WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/MCM5ID41321ch22q12.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - CHEBI:13342 - ChEBI - - - - ENST00000518671 - Ensembl - - - - 5701 - NCBI Gene - - - - - - - - 3.6.4.12 - MCM7 - P1.1-MCM3 - CDC47 - CDC47 homolog - MCM2 - - - - - - - - - - - - - - - - - - - - - - - - MCM7_HUMAN - DNA replication licensing factor MCM7 - FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Required for S-phase checkpoint activation upon UV-induced damage.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6- MCM4-MCM7-MCM3-MCM5 (By simililarity). Interacts with the ATR- ATRIP complex and with RAD17. Interacts with TIPIN. Interacts with MCMBP.SUBCELLULAR LOCATION: Nucleus (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=P33993-1; Sequence=Displayed; Name=2; IsoId=P33993-2; Sequence=VSP_003205; Note=No experimental confirmation available; Name=3; IsoId=P33993-3; Sequence=VSP_044310;PTM: O-glycosylated (O-GlcNAcylated), in a cell cycle-dependent manner.MISCELLANEOUS: Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - PSMD6 - HGNC Symbol - - - - 450458 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=450458 - - - - ENSP00000379178 - Ensembl - - - - REACT_2893 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2893.3 - - - - Q6P4G9 - UniProt - - - - 939205 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939205 - - - - - - ubiquitin (UBC 7) - - - - - Reactome DB_ID: 939184 - http://www.reactome.org/biopax/46/48887#Protein1055 - UBC(457-532) - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 165997 - http://www.reactome.org/biopax/46/48887#Protein2614 - PP2A-subunit A - - - - REACT_1975 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1975.3 - - - - - - Antisecretory factor-1 - ASF - Rpn10 - 26S proteasome regulatory subunit S5A - PSMD4 - Multiubiquitin chain binding protein - 26S proteasome non-ATPase regulatory subunit 4 - - - - - Reactome DB_ID: 68800 - http://www.reactome.org/biopax/46/48887#Protein1061 - AF - - - - - - MOD_RES 281 281 Phosphoserine. - - - - 8824221 - Barnes, CJ - Murante, RS - Rumbaugh, JA - Norton, JR - Bambara, RA - Pubmed - Calf RTH-1 nuclease can remove the initiator RNAs of Okazaki fragments by endonuclease activity. - J Biol Chem 271:25888-97 - 1996 - - - - ENST00000435978 - Ensembl - - - - 1542570 - Lee MY - Yang CL - Chang LS - Zhang P - Toomey NL - Hao H - Zhu L - PubMed - Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase delta. - Nucleic Acids Res 20(4);735-45 - 1992 - - - - - - ubiquitin (UBB 3) - - - - - Reactome DB_ID: 939230 - http://www.reactome.org/biopax/46/48887#Protein1048 - UBB(153-228) - - - - 189902 - omim - - - - POLD2 - HGNC Symbol - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature835 - - - - ENST00000271308 - Ensembl - - - - EQUAL - 53 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1816 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2090 - - - - EQUAL - 201 - http://www.reactome.org/biopax/46/48887#SequenceSite1829 - - - - ENST00000436627 - Ensembl - - - - - - MOD_RES 337 337 Phosphothreonine. - - - - EQUAL - 80 - - - - - - MOD_RES 321 321 Phosphothreonine. - - - - EQUAL - 1121 - - - - 113595 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113595 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10889 - - - - ENSG00000106588 - Ensembl - - - - REACT_24880 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24880.2 - - - - 610611 - omim - - - - REACT_149 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_149.4 - - - - - - MOD_RES 40 40 Phosphoserine; by CDC7. - - - - Q9BTR3 - UniProt - - - - 68443 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68443 - - - - InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 - InChI - - - - - - - - ACTIVATION - - 'RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex' positively regulates 'DNA polymerase epsilon binds at the origin' - http://www.reactome.org/biopax/46/48887#Control185 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2488 - - - - Q96EI2 - UniProt - - - - - - - - - Reactome DB_ID: 75031 - Converted from EntitySet in Reactome - http://www.reactome.org/biopax/46/48887#Protein5711 - Cyclin B - - - - 601324 - omim - - - - Proteasome subunit beta-5t - 3.4.25.1 - PSMB11 - - - - - - - - - - - PSB11_HUMAN - Proteasome subunit beta type-11 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. Incorporated instead of PSMB5 or PSMB8, this unit reduces the chymotrypsin-like activity of the proteasome (By similarity). Plays a pivotal role in development of CD8-positive T cells (By similarity).CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. Incorporated instead of PSMB5 and PSMB8.SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).SIMILARITY: Belongs to the peptidase T1B family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6688 - - - - NM_001199163 - RefSeq - - - - MOD_RES Phosphothreonine - - - - EQUAL - 35 - http://www.reactome.org/biopax/46/48887#SequenceSite1874 - - - - 11968016 - Liu J - Wills PW - Malkas LH - Jiang HY - Hickey RJ - Abdel-Aziz W - Tom TD - PubMed - Human cell DNA replication is mediated by a discrete multiprotein complex. - J Cell Biochem 85(4);762-74 - 2002 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4870 - - - - - - REACT_5615 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5615.3 - - - - - - MOD_RES 14 14 N6-acetyllysine. - - - - - - MOD_RES 10 10 Phosphoserine; by UHMK1. - - - - ENST00000352301 - Ensembl - - - - 939849 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939849 - - - - PSMC2 - HGNC - - - - EQUAL - 674 - - - - NM_003333 - RefSeq - - - - 68944 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68944 - - - - - - MOD_RES 26 26 Phosphoserine. - - - - Q96FV5 - UniProt - - - - PTHR10322:SF3 - PANTHER Family - - - - - 176636 - omim - - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature150 - - - - REACT_312 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_312.5 - - - - CHEBI:41312 - ChEBI - - - - Q6PI80 - UniProt - - - - cytosol - - - - - 1967833 - Stillman, B - Tsurimoto, T - Pubmed - Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4. - Proc Natl Acad Sci U S A 87:1023-7 - 1990 - - - - - - PROS-30 - Proteasome subunit alpha type 1 - Proteasome nu chain - Multicatalytic endopeptidase complex subunit C2 - Proteasome component C2 - Macropain subunit C2 - 30 kDa prosomal protein - - - - - Reactome DB_ID: 68724 - http://www.reactome.org/biopax/46/48887#Protein1062 - PSMA1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4950 - - - - - - MOD_RES 273 273 Phosphoserine. - - - - EQUAL - 252 - - - - ENSP00000263681 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2229 - - - - - - Q495R4 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6444 - - - - 68914 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68914 - - - - - - - - - - - - ORC:origin:cyclin B:cdk1 complex - Reactome DB_ID: 113637 - http://www.reactome.org/biopax/46/48887#Complex2616 - - - - REACT_135 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_135.3 - - - - - - - - - 3.6.4.12 - p105MCM - MCM6 - - - - - - - - - - - - - - - MCM6_HUMAN - DNA replication licensing factor MCM6 - FUNCTION: Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity.CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.SUBUNIT: Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6- MCM4-MCM7-MCM3-MCM5 (By simililarity). May interact with MCM10. Interacts with TIPIN. Interacts with CDT1. Interacts with MCMBP.SUBCELLULAR LOCATION: Nucleus. Note=Binds to chromatin during G1 and detach from it during S phase.PTM: O-glycosylated (O-GlcNAcylated), in a cell cycle-dependent manner.POLYMORPHISM: Intronic variations in MCM6 upstream from the LCT gene are associated with adult-type hypolactasia [MIM:223100] leading to lactose intolerance, or with lactase persistance. Lactose intolerance is a normal physiological phenomenon caused by developmental down-regulation of lactase activity during childhood or early adulthood. A non-coding variation in MCM6 affects the transcriptional regulation of the LCT gene resulting in down- regulation of lactase activity. However, the majority of Northern Europeans and some African populations have the ability to maintain lactase activity and digest lactose throughout life (lactase persistence).MISCELLANEOUS: Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY: Belongs to the MCM family.SIMILARITY: Contains 1 MCM domain.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/mcm6/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - EQUAL - 354 - - - - - - MOD_RES 109 109 N6-acetyllysine. - - - - EQUAL - 394 - - - - - - MOD_RES 150 150 Phosphoserine. - - - - REACT_6776 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6776.3 - - - - 68783 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68783 - - - - - nucleotide binding site - http://www.reactome.org/biopax/46/48887#EntityFeature33 - - - - P34062 - UniProt - - - - P13197 - UniProt - - - - EQUAL - 420 - - - - NM_001190882 - RefSeq - - - - 939239 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939239 - - - - ENST00000356126 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval5027 - - - - - - ENST00000234296 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6703 - - - - EQUAL - 457 - http://www.reactome.org/biopax/46/48887#SequenceSite1786 - - - - PSMB3 - HGNC - - - - - - MOD_RES 307 307 Phosphotyrosine (By similarity). - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature831 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4982 - - - - - - 7641697 - Nasmyth, K - Lengauer, C - Piatti, S - Pubmed - Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae. - EMBO J 14:3788-99 - 1995 - - - - ENSP00000355325 - Ensembl - - - - HGNC:28226 - HGNC - - - - - - MOD_RES 2 2 N-acetylalanine. - - - - NM_001254 - RefSeq - - - - 300767 - omim - - - - EQUAL - 184 - - - - B0YJ75 - UniProt - - - - 600306 - omim - - - - ENSP00000292644 - Ensembl - - - - ENST00000537407 - Ensembl - - - - - - - - - - 60S ribosomal protein L40 - Ubiquitin A-52 residue ribosomal protein fusion product 1 - CEP52 - UBA52 - UBCEP2 - Ubiquitin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - RL40_HUMAN - Ubiquitin-60S ribosomal protein L40 - FUNCTION: Ubiquitin: exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.FUNCTION: 60S ribosomal protein L40: component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, and especially for cap-dependent translation of vesicular stomatitis virus mRNAs.SUBUNIT: Ribosomal protein L40 is part of the 60S ribosomal subunit (By similarity).SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).SUBCELLULAR LOCATION: 60S ribosomal protein L40: Cytoplasm (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: For a better understanding, features related to ubiquitin are only indicated for the first chain.SIMILARITY: In the N-terminal section; belongs to the ubiquitin family.SIMILARITY: In the C-terminal section; belongs to the ribosomal protein L40e family.SIMILARITY: Contains 1 ubiquitin-like domain.SEQUENCE CAUTION: Sequence=AAK31162.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P33991 - UniProt - - - - NP_001248329 - RefSeq - - - - 68445 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68445 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2091 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature853 - - - - - - MOD_RES 142 142 Phosphoserine. - - - - GO:0016301 - GENE ONTOLOGY - - - - - NP_002683 - RefSeq - - - - NP_683877 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6702 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1775 - - - - E2F1 - HGNC - - - - - - - - - - SDI1 - PIC1 - MDA-6 - CDK-interacting protein 1 - CAP20 - p21 - WAF1 - CIP1 - CDKN1 - CDKN1A - Melanoma differentiation-associated protein 6 - MDA6 - - - - - - - - - - - - - - - - - - - - - - - - - CDN1A_HUMAN - Cyclin-dependent kinase inhibitor 1 - FUNCTION: May be the important intermediate by which p53/TP53 mediates its role as an inhibitor of cellular proliferation in response to DNA damage. Binds to and inhibits cyclin-dependent kinase activity, preventing phosphorylation of critical cyclin- dependent kinase substrates and blocking cell cycle progression. Functions in the nuclear localization and assembly of cyclin D- CDK4 complex and promotes its kinase activity towards RB1. At higher stoichiometric ratios, inhibits the kinase activity of the cyclin D-CDK4 complex.SUBUNIT: Interacts with HDAC1; the interaction is prevented by competitive binding of C10orf90/FATS to HDAC1 facilitating acetylation and protein stabilization of CDKN1A/p21 (By similarity). Interacts with MKRN1. Interacts with PSMA3. Interacts with PCNA. Component of the ternary complex, cyclin D-CDK4-CDKN1A. Interacts (via its N-terminal domain) with CDK4; the interaction promotes the assembly of the cyclin D-CDK4 complex, its nuclear translocation and promotes the cyclin D-dependent enzyme activity of CDK4. Binding to CDK2 leads to CDK2/cyclin E inactivation at the G1-S phase DNA damage checkpoint, thereby arresting cells at the G1-S transition during DNA repair. Interacts with PIM1.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.TISSUE SPECIFICITY: Expressed in all adult tissues, with 5-fold lower levels observed in the brain.INDUCTION: Activated by p53/TP53, mezerein (antileukemic compound) and IFNB1. Repressed by HDAC1.DOMAIN: The PIP-box K+4 motif mediates both the interaction with PCNA and the recuitment of the DCX(DTL) complex: while the PIP-box interacts with PCNA, the presence of the K+4 submotif, recruits the DCX(DTL) complex, leading to its ubiquitination.DOMAIN: The C-terminal is required for nuclear localization of the cyclin D-CDK4 complex.PTM: Phosphorylation of Thr-145 by Akt or of Ser-146 by PKC impairs binding to PCNA. Phosphorylation at Ser-114 by GSK3-beta enhances ubiquitination by the DCX(DTL) complex. Phosphorylation of Thr-145 by PIM2 enhances CDKN1A stability and inhibits cell proliferation. Phosphorylation of Thr-145 by PIM1 results in the relocation of CDKN1A to the cytoplasm and enhanced CDKN1A protein stability.PTM: Ubiquitinated by MKRN1; leading to polyubiquitination and 26S proteasome-dependent degradation. Ubiquitinated by the DCX(DTL) complex, also named CRL4(CDT2) complex, leading to its degradation during S phase or following UV irradiation. Ubiquitination by the DCX(DTL) complex is essential to control replication licensing and is PCNA-dependent: interacts with PCNA via its PIP-box, while the presence of the containing the 'K+4' motif in the PIP box, recruit the DCX(DTL) complex, leading to its degradation.PTM: Acetylation leads to protein stability. Acetylated in vitro on Lys-141, Lys-154, Lys-161 and Lys-163. Deacetylation by HDAC1 is prevented by competitive binding of C10orf90/FATS to HDAC1 (By similarity).SIMILARITY: Belongs to the CDI family.SEQUENCE CAUTION: Sequence=AAB59559.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAB59560.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CDKN1AID139.html";WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdkn1a/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q14997 - UniProt - - - - Q5JSB4 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6606 - - - - NM_001177562 - RefSeq - - - - ENSG00000076003 - Ensembl - - - - EQUAL - 216 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2470 - - - - - ENSP00000406797 - Ensembl - - - - - - Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - P2R3B_HUMAN - - - - - Reactome DB_ID: 3008955 - http://www.reactome.org/biopax/46/48887#Protein5638 - PPP2R3B - - - - EQUAL - 125 - - - - EQUAL - 150 - - - - 68424 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68424 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6697 - - - - 1N4M - PROTEIN DATA BANK - - - - EQUAL - 465 - http://www.reactome.org/biopax/46/48887#SequenceSite5800 - - - - EQUAL - 187 - - - - EQUAL - 609 - http://www.reactome.org/biopax/46/48887#SequenceSite1790 - - - - - - MOD_RES 57 57 Phosphoserine (By similarity). - - - - ENSG00000124762 - Ensembl - - - - - - - 40S ribosomal protein S27a - UBA80 - Ubiquitin carboxyl extension protein 80 - RPS27A - Ubiquitin - UBCEP1 - - - - - - - - - - - - - - - - - - - - - - - RS27A_HUMAN - Ubiquitin-40S ribosomal protein S27a - FUNCTION: Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.FUNCTION: Ribosomal protein S27a is a component of the 40S subunit of the ribosome.SUBUNIT: Ribosomal protein S27a is part of the 40S ribosomal subunit (By similarity).SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm (By similarity). Nucleus (By similarity).MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.MISCELLANEOUS: For a better understanding, features related to ubiquitin are only indicated for the first chain.SIMILARITY: In the N-terminal section; belongs to the ubiquitin family.SIMILARITY: In the C-terminal section; belongs to the ribosomal protein S27Ae family.SIMILARITY: Contains 1 ubiquitin-like domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENST00000418263 - Ensembl - - - - 2204063 - Barnes DE - Kodama K - Tomkinson AE - Lasko DD - Johnston LH - Lindahl T - PubMed - Human DNA ligase I cDNA: cloning and functional expression in Saccharomyces cerevisiae. - Proc Natl Acad Sci U S A 87(17);6679-83 - 1990 - - - - 1427831 - Lee MY - Ahn ER - Zhang P - Kemper RR - Rabin M - PubMed - Human DNA polymerase delta gene maps to region 19q13.3-q13.4 by in situ hybridization. - Genomics 14(1);205-6 - 1992 - - - - O75832 - UniProt - - - - O35563 - UniProt - - - - Q12932 - UniProt - - - - NP_005038 - RefSeq - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite1824 - - - - PPP2R3B - HGNC Symbol - - - - EQUAL - 435 - http://www.reactome.org/biopax/46/48887#SequenceSite10627 - - - - D3DXG3 - UniProt - - - - P51665 - UniProt - - - - NM_003914 - RefSeq - - - - - - - - Remaining Flap - Reactome DB_ID: 68467 - http://www.reactome.org/biopax/46/48887#PhysicalEntity258 - - - - - - MOD_RES 251 251 N6-acetyllysine. - - - - ENST00000373912 - Ensembl - - - - 10827190 - Vispe S - Satoh MS - PubMed - DNA repair patch-mediated double strand DNA break formation in human cells. - J Biol Chem 275(35);27386-92 - 2000 - - - - - - Adenosine 5'-triphosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule88 - Reactome DB_ID: 29358 - ATP - - - - 68570 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68570 - - - - - - - - mRNA Transcript Targeted by AUF1(hnRNP D0) - http://www.reactome.org/biopax/46/48887#PhysicalEntity49 - Reactome DB_ID: 450444 - - - - 68440 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68440 - - - - ENST00000255465 - Ensembl - - - - NP_002544 - RefSeq - - - - MOD_RES N6,N6,N6-trimethyllysine (By similarity) - - - - 29626 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29626 - - - - EQUAL - 76 - - - - EQUAL - 23 - - - - 1AVO - PROTEIN DATA BANK - - - - ENST00000539565 - Ensembl - - - - 68555 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68555 - - - - ORC4 - HGNC Symbol - - - - EQUAL - 102 - - - - - - MOD_RES 128 128 Phosphoserine. - - - - REACT_26356 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26356.1 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature854 - - - - EQUAL - 165 - - - - REACT_111616 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_111616.1 - - - - 2200738 - Fairman, MP - Din, S - Stillman, B - Brill, SJ - Pubmed - Cell-cycle-regulated phosphorylation of DNA replication factor A from human and yeast cells. - Genes Dev 4:968-77 - 1990 - - - - NP_001184188 - RefSeq - - - - 10714 - NCBI Gene - - - - P28065 - UniProt - - - - EQUAL - 273 - - - - ENSG00000236443 - Ensembl - - - - 605525 - omim - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature834 - - - - 68790 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68790 - - - - Q96J48 - UniProt - - - - 602331 - omim - - - - 68516 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68516 - - - - 5518 - NCBI Gene - - - - ENST00000383114 - Ensembl - - - - Q5T159 - UniProt - - - - REACT_5425 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5425.2 - - - - - - PP2A-subunit A beta isoform - - - - - Reactome DB_ID: 166000 - http://www.reactome.org/biopax/46/48887#Protein2616 - PPP2R1B - - - - 68510 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68510 - - - - HGNC:9559 - HGNC - - - - NP_002906 - RefSeq - - - - 69166 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69166 - - - - 1976634 - Hurwitz, J - Lee, SH - Kwong, AD - Pubmed - The in vitro replication of DNA containing the SV40 origin. - J Biol Chem 265:18043-6 - 1990 - - - - 9038340 - Bell, SP - Austin, RJ - Klemm, RD - Pubmed - Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex. - Cell 88:493-502 - 1997 - - - - NM_002715 - RefSeq - - - - 603113 - omim - - - - PSMB7 - HGNC Symbol - - - - CHEBI:18077 - ChEBI - - - - 939192 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939192 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6417 - - - - ENST00000223321 - Ensembl - - - - 947610 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=947610 - - - - EQUAL - 1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6707 - - - - HGNC:1771 - HGNC - - - - - - - - - Replication initiation regulation by Rb1/E2F1 - Authored: Gopinathrao, G, 2004-05-26 17:05:00 - This set of events is inferred from annotated events in Drosophila.<BR><BR>Rb1 is normally hyperphosphorylated by CycD/CDK4/CDK6 and Cyclin E/CDK2 for transition into S-phase. PP2A can then reverse this reaction, in this case, in response to DNA damage induced checkpoint. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1982 - - - - - ENSG00000243594 - Ensembl - - - - - - 2'-deoxyguanosine 5'-triphosphate - Deoxyguanosine 5'-triphosphate - Deoxyguanosine triphosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule591 - Reactome DB_ID: 29892 - dGTP - - - - NP_006222 - RefSeq - - - - REACT_5490 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5490.3 - - - - ENSG00000093009 - Ensembl - - - - HGNC:10289 - HGNC - - - - Q96H67 - UniProt - - - - P49014 - UniProt - - - - - - MOD_RES 194 194 Phosphotyrosine. - - - - CHEBI:19238 - ChEBI - - - - 1H27 - PROTEIN DATA BANK - - - - Q6P2P4 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1048 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6692 - - - - - - MOD_RES 1940 1940 Phosphoserine. - - - - 68485 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68485 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4917 - - - - - - 603146 - omim - - - - 5713 - NCBI Gene - - - - - - - - - - - Cytoplasmic phosphorylated Cdc6 is ubiquitinated by the anaphase-promoting complex - At the beginning of this reaction, 1 molecule of 'phosphorylated Cdc6', 1 molecule of 'ubiquitin', and 1 molecule of 'ATP' are present. At the end of this reaction, 1 molecule of 'ubiquitinated Cdc6' is present.<br><br> This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of 'anaphase-promoting complex (APC)'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2001 - - - - - 9759502 - Waga, S - Stillman, B - Pubmed - The DNA replication fork in eukaryotic cells. - Annu Rev Biochem 67:721-51 - 1998 - - - - P33993 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2426 - - - - - PSMA8 - HGNC - - - - 1579437 - Paull, T - Blow, JJ - Elder, JK - Mahbubani, HM - Pubmed - DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. - Nucleic Acids Res 20:1457-62 - 1992 - - - - 7623835 - Burgers, PM - Gary, SL - Yoder, BL - Impellizzeri, KJ - Ayyagari, R - Pubmed - A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. - Mol Cell Biol 15:4420-9 - 1995 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6715 - - - - 1P9C - PROTEIN DATA BANK - - - - 68814 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68814 - - - - Q9UNV3 - UniProt - - - - EQUAL - 439 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1062 - - - - NM_003503 - RefSeq - - - - ENST00000596304 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6709 - - - - EQUAL - 29 - - - - ENST00000216367 - Ensembl - - - - 68546 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68546 - - - - MOD_RES Phosphotyrosine (By similarity) - - - - ENST00000264156 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2474 - - - - - 69239 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69239 - - - - EQUAL - 397 - - - - HGNC:9569 - HGNC - - - - ENST00000338193 - Ensembl - - - - NM_001204747 - RefSeq - - - - ENSP00000355249 - Ensembl - - - - 9491 - NCBI Gene - - - - InChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 - InChI - - - - EQUAL - 1 - - - - P38936 - UniProt - - - - REACT_5497 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5497.1 - - - - Q9NS92 - UniProt - - - - - - - - anaphase-promoting complex (APC) - Reactome DB_ID: 69007 - http://www.reactome.org/biopax/46/48887#PhysicalEntity252 - - - - - - MOD_RES 195 195 N6-acetyllysine; by P300/CBP. - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval881 - - - - - - GO:0004386 - GENE ONTOLOGY - - - - - 68818 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68818 - - - - - - - - Okazaki fragment minus Flap - Reactome DB_ID: 68469 - http://www.reactome.org/biopax/46/48887#PhysicalEntity259 - - - - HGNC:9535 - HGNC - - - - EQUAL - 130 - http://www.reactome.org/biopax/46/48887#SequenceSite10752 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4998 - - - - - - NM_005914 - RefSeq - - - - 68551 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68551 - - - - EQUAL - 227 - - - - EQUAL - 209 - http://www.reactome.org/biopax/46/48887#SequenceSite10981 - - - - 939870 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939870 - - - - CHEBI:10491 - ChEBI - - - - P67775 - UniProt - - - - - - MOD_RES 100 100 Symmetric dimethylarginine; by PRMT5. - - - - 602017 - omim - - - - EQUAL - 345 - - - - EQUAL - 82 - - - - EQUAL - 310 - - - - ENSG00000095261 - Ensembl - - - - EQUAL - 309 - - - - P30154 - UniProt - - - - 939856 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939856 - - - - Q5TC50 - UniProt - - - - 2O95 - PROTEIN DATA BANK - - - - 174762 - omim - - - - 11257218 - Cimbora, DM - Groudine, M - Pubmed - The control of mammalian DNA replication: a brief history of space and timing. - Cell 104:643-6 - 2001 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature848 - - - - NM_016937 - RefSeq - - - - 68441 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68441 - - - - EQUAL - 684 - http://www.reactome.org/biopax/46/48887#SequenceSite4670 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4814 - - - - ENST00000261303 - Ensembl - - - - - - phospho-Rb - - - - - - http://www.reactome.org/biopax/46/48887#Protein5696 - Reactome DB_ID: 188389 - p-RB1 - - - - - - Mcm10 - - - - - http://www.reactome.org/biopax/46/48887#Protein5576 - Reactome DB_ID: 68403 - MCM10 - - - - - - Heterogeneous nuclear ribonucleoprotein D0 - Ubiquitinated AUF1 isoform p40 phosphorylated on Ser83 and Ser87 - HNRPD_HUMAN - p-S83,S87-Ub-HNRNPD-3 - - - - - - - - Reactome DB_ID: 451223 - http://www.reactome.org/biopax/46/48887#Protein1060 - HNRNPD - - - - EQUAL - 167 - - - - EQUAL - 10 - - - - ENST00000353341 - Ensembl - - - - MCM2 - HGNC - - - - NM_001271779 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4828 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2660 - - - - - - - MOD_RES 12 12 Phosphoserine (By similarity). - - - - EQUAL - 508 - - - - EQUAL - 39 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10618 - - - - - 2.7.7.7 - - - - - - - - The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1994 - At the beginning of this reaction, 1 molecule of 'dTTP', 1 molecule of 'dGTP', 1 molecule of 'dATP', 1 molecule of 'RNA primer:origin duplex:DNA polymerase alpha:primase complex', and 1 molecule of 'dCTP' are present. At the end of this reaction, 1 molecule of 'RNA primer-DNA primer:origin duplex' is present.<br><br> This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'DNA polymerase alpha:primase'.<br> - - - - - Q6P1Q7 - UniProt - - - - REACT_26884 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26884.2 - - - - - - ubiquitin (UBB 3) - - - - - http://www.reactome.org/biopax/46/48887#Protein2476 - Reactome DB_ID: 939854 - UBB(153-228) - - - - NP_002543 - RefSeq - - - - B7Z7E3 - UniProt - - - - REACT_1278 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1278.3 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10681 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1814 - - - - EQUAL - 263 - http://www.reactome.org/biopax/46/48887#SequenceSite1799 - - - - ENSG00000197170 - Ensembl - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite4648 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1050 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4921 - - - - REACT_3876 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3876.2 - - - - POLD3 - HGNC - - - - - - MOD_RES 2 2 N-acetylserine. - - - - NP_001127892 - RefSeq - - - - HGNC:13417 - HGNC - - - - EQUAL - 575 - http://www.reactome.org/biopax/46/48887#SequenceSite10731 - - - - XKMLYUALXHKNFT-UUOKFMHZSA-N - InChIKey - - - - Q4W5A1 - UniProt - - - - REACT_5333 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5333.2 - - - - Q14010 - UniProt - - - - ENST00000333082 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6710 - - - - EQUAL - 145 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4968 - - - - - - REACT_5529 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5529.2 - - - - REACT_907 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_907.3 - - - - - - MOD_RES 184 184 Phosphoserine; by CK2. - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - POLD4 - POLDS - DNA polymerase delta subunit p12 - - - - - - - - - - - - - - - - - - DPOD4_HUMAN - DNA polymerase delta subunit 4 - FUNCTION: Required for optimal DNA polymerase delta activity. May contribute to PCNA-dependent activity of DNA polymerase delta.SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with WRNIP1. Interacts with POLD4, POLD2, POLD1 and PCNA.SUBCELLULAR LOCATION: Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9HCU8-1; Sequence=Displayed; Name=2; IsoId=Q9HCU8-2; Sequence=VSP_046864; Note=No experimental confirmation available;SIMILARITY: Belongs to the DNA polymerase delta subunit 4 family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pold4/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature832 - - - - REACT_24129 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24129.2 - - - - NM_002947 - RefSeq - - - - GO:0006270 - GENE ONTOLOGY - - - - - NP_001228 - RefSeq - - - - CDKN1A - HGNC Symbol - - - - 29892 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29892 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6630 - - - - B4E025 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature873 - - - - EQUAL - 187 - - - - ENST00000296273 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10899 - - - - EQUAL - 577 - http://www.reactome.org/biopax/46/48887#SequenceSite10633 - - - - - - - - - Ubiquitinated Orc1 enters the cytosol - In this reaction, 1 molecule of 'ubiquitinated Orc1' is translocated from nucleoplasm to cytosol.<br><br>This movement of the molecule occurs through the 'nuclear pore'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1997 - - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2431 - - - - - REACT_5232 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5232.2 - - - - EQUAL - 283 - - - - 113648 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113648 - - - - - - MOD_RES 280 280 N6-acetyllysine. - - - - 2B9R - PROTEIN DATA BANK - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10915 - - - - PTHR11599:SF10 - PANTHER Family - - - - - EQUAL - 40 - http://www.reactome.org/biopax/46/48887#SequenceSite1838 - - - - ENSG00000240508 - Ensembl - - - - 939853 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939853 - - - - 7027 - NCBI Gene - - - - - - MOD_RES 150 150 Phosphotyrosine (By similarity). - - - - NP_003495 - RefSeq - - - - NM_181741 - RefSeq - - - - NP_859526 - RefSeq - - - - NP_066545 - RefSeq - - - - NP_006805 - RefSeq - - - - ENSP00000383981 - Ensembl - - - - CHEBI:16761 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2473 - - - - - - - MOD_RES 129 129 Phosphoserine (By similarity). - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1804 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4961 - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2482 - - - - - EQUAL - 145 - - - - - - MOD_RES 384 384 Phosphoserine. - - - - NM_001261400 - RefSeq - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6635 - - - - ENST00000596273 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4962 - - - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - EQUAL - 223 - http://www.reactome.org/biopax/46/48887#SequenceSite1837 - - - - EQUAL - 76 - http://www.reactome.org/biopax/46/48887#SequenceSite1765 - - - - - - MOD_RES 307 307 Phosphoserine. - - - - - - MOD_RES 116 116 N6-acetyllysine. - - - - 165968 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=165968 - - - - 3E0J - PROTEIN DATA BANK - - - - NP_002789 - RefSeq - - - - O75100 - UniProt - - - - - - MOD_RES 392 392 N6-acetyllysine. - - - - Q15045 - UniProt - - - - - - MOD_RES 117 117 N6-acetyllysine. - - - - - - MOD_RES 190 190 Phosphoserine. - - - - - - - - - - - - - Replication control protein 1 - ORC1 - ORC1L - PARC1 - - - - - - - - - - - - - - - - - - - - - ORC1_HUMAN - Origin recognition complex subunit 1 - FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.SUBUNIT: ORC is composed of six subunits. In human, ORC is cell cycle-dependent regulated: it is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase. Interacts with CDC6 and KAT7/HBO1.SUBCELLULAR LOCATION: Nucleus.DEVELOPMENTAL STAGE: Expression is cell-cycle regulated, it starts to accumulate in mid-G1 phase, reaches a peak at the G1/S boundary, and decreases to a basal level in S phase (at protein level).DOMAIN: The BAH domain mediates binding to dimethylated histone H4 'Lys-20' (H4K20me2), which is enriched at replication origins (By similarity).DISEASE: Meier-Gorlin syndrome 1 (MGORS1) [MIM:224690]: A syndrome characterized by bilateral microtia, aplasia/hypoplasia of the patellae, and severe intrauterine and postnatal growth retardation with short stature and poor weight gain. Additional clinical findings include anomalies of cranial sutures, microcephaly, apparently low-set and simple ears, microstomia, full lips, highly arched or cleft palate, micrognathia, genitourinary tract anomalies, and various skeletal anomalies. While almost all cases have primordial dwarfism with substantial prenatal and postnatal growth retardation, not all cases have microcephaly, and microtia and absent/hypoplastic patella are absent in some. Despite the presence of microcephaly, intellect is usually normal. Note=The disease is caused by mutations affecting the gene represented in this entry.SIMILARITY: Belongs to the ORC1 family.SIMILARITY: Contains 1 BAH domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - ENSG00000204264 - Ensembl - - - - HGNC:9538 - HGNC - - - - - - - - - ORC2L - ORC2 - - - - - - - - - - - - - - ORC2_HUMAN - Origin recognition complex subunit 2 - FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent, however specific DNA sequences that define origins of replication have not been identified so far. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication.SUBUNIT: ORC is composed of six subunits. In human, ORC is cell cycle-dependent regulated: it is sequentially assembled at the exit from anaphase of mitosis and disassembled as cells enter S phase. Interacts with DBF4 (By similarity). Interacts with MCM10.SUBCELLULAR LOCATION: Nucleus.SIMILARITY: Belongs to the ORC2 family.WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/orc2l/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P62195 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4988 - - - - - - 156502 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=156502 - - - - EQUAL - 141 - - - - EQUAL - 100 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4824 - - - - UBB - HGNC Symbol - - - - EQUAL - 406 - http://www.reactome.org/biopax/46/48887#SequenceSite1863 - - - - EQUAL - 209 - http://www.reactome.org/biopax/46/48887#SequenceSite10979 - - - - 176944 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176944 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10642 - - - - REACT_2826 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2826.1 - - - - Q01858 - UniProt - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2428 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4872 - - - - REACT_3120 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3120.1 - - - - ENST00000313899 - Ensembl - - - - EQUAL - 546 - http://www.reactome.org/biopax/46/48887#SequenceSite10849 - - - - - - MOD_RES 161 161 Phosphothreonine; by CAK. - - - - 68539 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68539 - - - - - - - - - - - - - - - - - - - DNA strand elongation - http://www.reactome.org/biopax/46/48887#Pathway508 - Authored: Tom, S, Bambara, RA, 2003-06-05 08:03:21 - Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, one of the new strands is synthesized continuously in the direction of fork movement. This strand is designated as the leading strand. The other strand grows in the direction away from fork movement, and is called the lagging strand. Several specific interactions among the various proteins involved in DNA replication underlie the mechanism of DNA synthesis, on both the leading and lagging strands, at a DNA replication fork. These interactions allow the replication enzymes to cooperate in the replication process (Hurwitz et al 1990; Brush et al 1996; Ayyagari et al 1995; Budd & Campbell 1997; Bambara et al 1997). - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6686 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6668 - - - - 123835 - omim - - - - Q9BWL8 - UniProt - - - - EQUAL - 128 - - - - EQUAL - 163 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4964 - - - - - - EQUAL - 2 - - - - HGNC:9970 - HGNC - - - - - - MOD_RES 57 57 Phosphoserine (By similarity). - - - - NP_002793 - RefSeq - - - - 113554 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113554 - - - - 8144688 - pubchem-substance - - - - ENSP00000261424 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite5797 - - - - EQUAL - 173 - - - - EQUAL - 24 - - - - EQUAL - 141 - - - - 10926 - NCBI Gene - - - - 157970 - omim - - - - REACT_5357 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5357.2 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6690 - - - - REACT_5402 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5402.1 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6625 - - - - P28340 - UniProt - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4865 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4958 - - - - - - MOD_RES 204 204 N6-acetyllysine. - - - - EQUAL - 307 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4994 - - - - - - 5426 - NCBI Gene - - - - ENSP00000297431 - Ensembl - - - - HGNC:10417 - HGNC - - - - ENSG00000041357 - Ensembl - - - - 68826 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68826 - - - - - - MOD_RES 130 130 Phosphoserine. - - - - - - phospho-p21(Ser 130) - - - - - - http://www.reactome.org/biopax/46/48887#Protein5649 - Reactome DB_ID: 187857 - p-S130-CDKN1A - - - - EQUAL - 381 - http://www.reactome.org/biopax/46/48887#SequenceSite1784 - - - - NM_031370 - RefSeq - - - - NP_001123584 - RefSeq - - - - HGNC:9175 - HGNC - - - - ENSP00000263201 - Ensembl - - - - ENST00000395839 - Ensembl - - - - POLA2 - HGNC - - - - NM_006503 - RefSeq - - - - - - - - - - - - Orc2:origin - Reactome DB_ID: 68511 - http://www.reactome.org/biopax/46/48887#Complex2667 - - - - EQUAL - 110 - - - - - - MOD_RES 356 356 Phosphothreonine. - - - - ENST00000343848 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4821 - - - - P31148 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2457 - - - - - NP_789839 - RefSeq - - - - 68874 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68874 - - - - REACT_1770 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1770.4 - - - - ENSP00000418268 - Ensembl - - - - PTHR10855:SF1 - PANTHER Family - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1160 - - - - 12730199 - Sitry-Shevah, D - Nakayama, K - Pagano, M - Bornstein, G - Bloom, J - Hershko, A - Pubmed - Role of the SCFSkp2 ubiquitin ligase in the degradation of p21Cip1 in S phase - J Biol Chem 278:25752-7 - 2003 - - - - EQUAL - 533 - http://www.reactome.org/biopax/46/48887#SequenceSite1788 - - - - 68509 - Reactome Database ID Release 46 - - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68509 - - - - - - MOD_RES 1 1 N-acetylmethionine. - - - - EQUAL - 255 - http://www.reactome.org/biopax/46/48887#SequenceSite1843 - - - - REACT_3758 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3758.2 - - - - NM_002138 - RefSeq - - - - HGNC:1784 - HGNC - - - - FEN1 - HGNC Symbol - - - - Q16242 - UniProt - - - - EQUAL - 305 - http://www.reactome.org/biopax/46/48887#SequenceSite1782 - - - - NM_001197331 - RefSeq - - - - Q8IZK9 - UniProt - - - - 68473 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68473 - - - - NP_001243778 - RefSeq - - - - 12045100 - Dutta, A - Bell, SP - Pubmed - DNA replication in eukaryotic cells. - Annu Rev Biochem 71:333-74 - 2002 - - - - REACT_3605 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3605.2 - - - - REACT_2427 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2427.1 - - - - Q96AG8 - UniProt - - - - F5H506 - UniProt - - - - RGWHQCVHVJXOKC-SHYZEUOFSA-N - InChIKey - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6425 - - - - - - MOD_RES 126 126 Phosphoserine; by CDK1. - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6665 - - - - 68465 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68465 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4825 - - - - ENSG00000092010 - Ensembl - - - - Q14186 - UniProt - - - - EQUAL - 396 - - - - - - Proteasome theta chain - Proteasome component C10-II - Proteasome subunit beta type 3 - Proteasome chain 13 - - - - - Reactome DB_ID: 68747 - http://www.reactome.org/biopax/46/48887#Protein1088 - PSMB3 - - - - NP_001177747 - RefSeq - - - - D3DW86 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1076 - - - - Q53XQ4 - UniProt - - - - - - MOD_RES 311 311 Phosphothreonine. - - - - EQUAL - 1 - - - - RPS27A - HGNC Symbol - - - - 609357 - omim - - - - InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 - InChI - - - - REACT_9093 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_9093.2 - - - - EQUAL - 153 - http://www.reactome.org/biopax/46/48887#SequenceSite1778 - - - - ENST00000265056 - Ensembl - - - - 5692 - NCBI Gene - - - - - - MOD_RES 88 88 Phosphotyrosine; by ABL, LYN, SRC and JAK2. - - - - ENSP00000219313 - Ensembl - - - - - - - - Detection of damage during initiation of DNA synthesis in S-phase - At the beginning of this reaction, 1 molecule of 'RNA primer-DNA primer:origin duplex' is present. At the end of this reaction, 1 molecule of 'DNA polymerase alpha:primase', and 1 molecule of 'RNA primer-DNA primer:origin duplex with DNA damage' are present.<br><br> This reaction takes place in the 'nucleus'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1980 - - - - - - REACT_24310 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24310.2 - - - - PSMA2 - HGNC - - - - CHEBI:42831 - ChEBI - - - - ENST00000527614 - Ensembl - - - - MCM4 - HGNC Symbol - - - - 157563 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=157563 - - - - 68422 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68422 - - - - REACT_5685 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5685.1 - - - - ENST00000440232 - Ensembl - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6621 - - - - REACT_207 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_207.3 - - - - 2V6Z - PROTEIN DATA BANK - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval2120 - - - - - - 68639 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68639 - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4883 - - - - ENSP00000216802 - Ensembl - - - - ENST00000453059 - Ensembl - - - - Q5T0F5 - UniProt - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6704 - - - - ENST00000549829 - Ensembl - - - - - - - - - Ubiquitinated Orc1 is degraded by the proteasome - At the beginning of this reaction, 1 molecule of 'ubiquitinated Orc1' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present.<br><br> This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1998 - - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1870 - - - - - - MOD_RES 256 256 Phosphoserine (By similarity). - - - - P25788 - UniProt - - - - NM_001204453 - RefSeq - - - - Q9UCE8 - UniProt - - - - REACT_27038 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27038.1 - - - - REACT_789 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_789.2 - - - - 69017 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=69017 - - - - - - MOD_RES 39 39 Phosphothreonine. - - - - B7Z3D0 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature859 - - - - ENST00000343023 - Ensembl - - - - - - - - - - - Orc4 associates with Orc5:Orc3:Orc2:origin complexes - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2143 - At the beginning of this reaction, 1 molecule of 'Orc4', and 1 molecule of 'Orc5:Orc3:Orc2:origin' are present. At the end of this reaction, 1 molecule of 'Orc4:Orc5:Orc3:Orc2:origin' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - - - - - 68524 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68524 - - - - E2F1 - HGNC Symbol - - - - MOD_RES Phosphoserine - - - - 10323868 - Draetta, GF - Pagano, M - Fiore, F - Carrano, AC - Eytan, E - Montagnoli, A - Hershko, A - Pubmed - Ubiquitination of p27 is regulated by Cdk-dependent phosphorylation and trimeric complex formation - Genes Dev 13:1181-9 - 1999 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6424 - - - - 939871 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939871 - - - - Q16307 - UniProt - - - - NM_006230 - RefSeq - - - - 10197 - NCBI Gene - - - - - C10H16N5O13P3 - 2'-deoxyguanosine 5'-(tetrahydrogen triphosphate) - - - - - - - - 507.1812 - dGTP - dGTP - A purine 2'-deoxyribonucleoside 5'-triphosphate having guanine as the nucleobase. - - - - REACT_1344 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1344.3 - - - - REACT_2928 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2928.2 - - - - - - Phosphate - Orthophosphate - Inorganic Phosphate - - - - http://www.reactome.org/biopax/46/48887#SmallMolecule202 - Reactome DB_ID: 113550 - Pi - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2662 - - - - EQUAL - 102 - - - - PTHR10660:SF4 - PANTHER Family - - - - NP_002129 - RefSeq - - - - Q9BWA8 - UniProt - - - - ENSP00000368174 - Ensembl - - - - ENSP00000368458 - Ensembl - - - - EQUAL - 711 - - - - CDKN1B - HGNC - - - - Q5TC49 - UniProt - - - - ENSG00000143106 - Ensembl - - - - O95268 - UniProt - - - - NP_115874 - RefSeq - - - - NM_148919 - RefSeq - - - - PSMB5 - HGNC Symbol - - - - ENST00000390665 - Ensembl - - - - Q15000 - UniProt - - - - REACT_4810 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4810.1 - - - - REACT_24503 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24503.2 - - - - Q99436 - UniProt - - - - REACT_2747 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2747.2 - - - - CHEBI:14381 - ChEBI - - - - EQUAL - 229 - - - - - - ubiquitin (UBC 4) - - - - - Reactome DB_ID: 939192 - http://www.reactome.org/biopax/46/48887#Protein1052 - UBC(229-304) - - - - ENST00000396682 - Ensembl - - - - EQUAL - 70 - - - - REACT_1994 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1994.3 - - - - - http://www.reactome.org/biopax/46/48887#ModificationFeature1159 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6428 - - - - ENSG00000112312 - Ensembl - - - - EQUAL - 254 - http://www.reactome.org/biopax/46/48887#SequenceSite1865 - - - - NM_001949 - RefSeq - - - - HGNC:10291 - HGNC - - - - Q6IBM2 - UniProt - - - - REACT_4028 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4028.3 - - - - ENST00000261712 - Ensembl - - - - ENSG00000230034 - Ensembl - - - - - - - - - - - - CDC6:ORC:origin complex - http://www.reactome.org/biopax/46/48887#Complex2548 - Reactome DB_ID: 68543 - - - - 939863 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939863 - - - - REACT_929 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_929.3 - - - - 1E9H - PROTEIN DATA BANK - - - - REACT_2948 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2948.3 - - - - HGNC:9552 - HGNC - - - - NM_016263 - RefSeq - - - - ENST00000292644 - Ensembl - - - - - Mcm4,6,7 trimer forms and associates with the replication fork - - - - - - - - - - - - - - - - Rearrangement and mobilization of Mcm2-7 - At the start of the elongation phase of DNA replication, the Mcm2-7 complex may re-arrange to function as the replicative helicase associated with the replication fork. In general, a replicative helicase is associated with the replication fork and unwinds DNA ahead of the polymerase. In yeast, the Mcm proteins associate with origin DNA in G1 phase and then exit the origin upon replication initiation, consistent with moving out of the origin with the replication fork. The Mcm2-7 complex is a ring-shaped hexamer. Complexes of Mcm4, Mcm6 and Mcm7 proteins from humans or S. pombe display a modest ATP-dependent helicase activity in vitro. Consistent with the hypothesis that eukaryotic Mcm complexes function as helicases, an archaeal Mcm homolog is a ring-shaped double hexamer that has a processive DNA unwinding activity. Mcm proteins may have additional functions during elongation, as uninterrupted function of all six is required for replication fork progression in budding yeast. Mcm4,6,7 helicase activity may be negatively regulated in two ways. Mcm2, Mcm4, Mcm6, and Mcm7 also form a stable complex which, however, has no helicase activity, suggesting that Mcm2 inhibits DNA unwinding by Mcm4,6,7. In addition, phosphorylation of human Mcm4,6,7 complex by CDK inhibits its helicase activity. - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2003 - - - - - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6667 - - - - NP_848693 - RefSeq - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10848 - - - - NM_002803 - RefSeq - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2618 - - - - PSMD5 - HGNC Symbol - - - - - - MOD_RES 206 206 N6-acetyllysine. - - - - REACT_3235 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3235.2 - - - - HGNC:9566 - HGNC - - - - 11395402 - Richardson, CC - Frick, DN - Pubmed - DNA primases. - Annu Rev Biochem 70:39-80 - 2002 - - - - A4D1D8 - UniProt - - - - ENST00000349703 - Ensembl - - - - 68586 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68586 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6419 - - - - Q9BQA4 - UniProt - - - - - - MOD_RES 287 287 Phosphoserine. - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature2095 - - - - ENST00000055077 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4647 - - - - NP_002938 - RefSeq - - - - NM_006591 - RefSeq - - - - ENST00000442744 - Ensembl - - - - EQUAL - 66 - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite1774 - - - - 9372948 - Bell, SP - Lee, DG - Pubmed - Architecture of the yeast origin recognition complex bound to origins of DNA replication. - Mol Cell Biol 17:7159-68 - 1997 - - - - ENST00000341980 - Ensembl - - - - 68450 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68450 - - - - EQUAL - 298 - http://www.reactome.org/biopax/46/48887#SequenceSite10845 - - - - - - MOD_RES 146 146 Phosphoserine. - - - - EQUAL - 204 - - - - - - - - - - - Formation of GINS complex - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2006 - At the beginning of this reaction, 1 molecule of 'PSF3p', 1 molecule of 'SLD5P', 1 molecule of 'PSF2p', and 1 molecule of 'PSF1p' are present. At the end of this reaction, 1 molecule of 'GINS complex' is present.<br><br> This reaction takes place in the 'nucleus'.<br> - - - - - REACT_24088 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24088.2 - - - - ENSG00000125818 - Ensembl - - - - 68738 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68738 - - - - ENSP00000264156 - Ensembl - - - - A4FU92 - UniProt - - - - 68734 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68734 - - - - REACT_3907 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3907.1 - - - - - - MOD_RES 36 36 Phosphoserine. - - - - Q6FHK5 - UniProt - - - - - - 26S proteasome subunit p112 - 26S proteasome non-ATPase regulatory subunit 1 - 26S proteasome regulatory subunit S1 - - - - - http://www.reactome.org/biopax/46/48887#Protein1080 - Reactome DB_ID: 68786 - PSMD1 - - - - Q8NEH1 - UniProt - - - - EQUAL - 2 - http://www.reactome.org/biopax/46/48887#SequenceSite10644 - - - - 939847 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=939847 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6680 - - - - EQUAL - 73 - http://www.reactome.org/biopax/46/48887#SequenceSite1832 - - - - O00233 - UniProt - - - - - - - 26S proteasome regulatory subunit p55 - PSMD12 - 26S proteasome regulatory subunit RPN5 - - - - - - - - - - - - - - - - - - - - PSD12_HUMAN - 26S proteasome non-ATPase regulatory subunit 12 - FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.SUBUNIT: Component of the PA700 complex.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O00232-1; Sequence=Displayed; Name=2; IsoId=O00232-2; Sequence=VSP_042718; Note=No experimental confirmation available;SIMILARITY: Belongs to the proteasome subunit p55 family.SIMILARITY: Contains 1 PCI domain.SEQUENCE CAUTION: Sequence=AAH65826.1; Type=Erroneous initiation; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - 26S proteasome regulatory subunit S9 - PSMD11 - 26S proteasome regulatory subunit p44.5 - 26S proteasome regulatory subunit RPN6 - - - - - - - - - - - - - - - - - - - - - PSD11_HUMAN - 26S proteasome non-ATPase regulatory subunit 11 - FUNCTION: Component of the lid subcomplex of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. In the complex, PSMD11 is required for proteasome assembly. Plays a key role in increased proteasome activity in embryonic stem cells (ESCs): its high expression in ESCs promotes enhanced assembly of the 26S proteasome, followed by higher proteasome activity.SUBUNIT: Component of the lid subcomplex of the 19S proteasome regulatory particle complex (also named PA700 complex). The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits.SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm, cytosol (By similarity).ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=O00231-1; Sequence=Displayed; Name=2; IsoId=O00231-2; Sequence=VSP_044400; Note=No experimental confirmation available;TISSUE SPECIFICITY: Highly expressed in embryonic stem cells (ESCs). Expression decreases as ESCs differentiate.INDUCTION: By FOXO4; expression in embryonic stem cells (ESCs) is mediated by FOXO4.PTM: Phosphorylated by AMPK.SIMILARITY: Belongs to the proteasome subunit S9 family.SIMILARITY: Contains 1 PCI domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - NP_002904 - RefSeq - - - - 8594377 - Kelly, TJ - Stillman, B - Brush, GS - Pubmed - Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system. - Methods Enzymol 262:522-48 - 1996 - - - - PSMD13 - HGNC Symbol - - - - EQUAL - 258 - - - - ENST00000263201 - Ensembl - - - - 9606 - taxonomy - - - - - 26S proteasome regulatory subunit p27 - PSMD9 - - - - - - - - - - - - - - - - - - - PSMD9_HUMAN - 26S proteasome non-ATPase regulatory subunit 9 - FUNCTION: Acts as a chaperone during the assembly of the 26S proteasome, specifically of the base subcomplex of the PA700/19S regulatory complex (RC). During the base subcomplex assembly is part of an intermediate PSMD9:PSMC6:PSMC3 module, also known as modulator trimer complex; PSMD9 is released during the further base assembly process.SUBUNIT: Interacts with PSMC3. Part of a transient complex (modulator) containing PSMD9, PSMC6 and PSMC3 formed during the assembly of the 26S proteasome.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=p27-L; IsoId=O00233-1; Sequence=Displayed; Name=p27-S; IsoId=O00233-2; Sequence=VSP_005300; Name=3; IsoId=O00233-3; Sequence=VSP_046004; Note=No experimental confirmation available;TISSUE SPECIFICITY: Expressed in all tissues tested, highly expressed in liver and kidney.SIMILARITY: Belongs to the proteasome subunit p27 family.SIMILARITY: Contains 1 PDZ (DHR) domain.CAUTION: Was initially identified as a component of the 26S proteasome. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval854 - - - - - - NM_002689 - RefSeq - - - - - - RF-C 38 kDa subunit - Replication factor C subunit 3 - Replication factor C 38 kDa subunit - A1 38 kDa subunit - RFC38 - Activator 1 38 kDa subunit - - - - - Reactome DB_ID: 68431 - http://www.reactome.org/biopax/46/48887#Protein5563 - RFC3 - - - - - - http://www.reactome.org/biopax/46/48887#PathwayStep2432 - - - - 68387 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68387 - - - - 11323433 - Simancek, P - Vashee, S - Kelly, TJ - Challberg, MD - Pubmed - Assembly of the human origin recognition complex. - J Biol Chem 276:26666-73 - 2001 - - - - - - MOD_RES 396 396 N6-acetyllysine. - - - - - - Origin recognition complex subunit 1 - Replication control protein 1 - Orc1 - - - - - http://www.reactome.org/biopax/46/48887#Protein5723 - Reactome DB_ID: 113840 - ORC1 - - - - - - - - - Association of Cyclin B/Cdk1 with replicative origin inhibits pre-RC formation - http://www.reactome.org/biopax/46/48887#BiochemicalReaction1984 - This event is inferred from the fission yeast. Cyclin B activity is thought to inhibit pre-RC formation by first associating with ORC during DNA replication. - Authored: Gopinathrao, G, 2004-06-16 18:53:38 - - - - - REACT_5627 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5627.1 - - - - ENST00000373711 - Ensembl - - - - PTHR11599:SF15 - PANTHER Family - - - - - EQUAL - 152 - http://www.reactome.org/biopax/46/48887#SequenceSite1771 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6699 - - - - InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 - InChI - - - - PSMB7 - HGNC - - - - EQUAL - 51 - - - - POLD3 - HGNC Symbol - - - - - - Cdt1 - - - - - Reactome DB_ID: 113788 - http://www.reactome.org/biopax/46/48887#Protein5769 - CDT1 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4985 - - - - - - - - MOD_RES 23 23 Phosphoserine. - - - - 68454 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=68454 - - - - 1U76 - PROTEIN DATA BANK - - - - EQUAL - 253 - - - - ORC1 - HGNC Symbol - - - - EQUAL - 194 - - - - ENSP00000304697 - Ensembl - - - - - - ubiquitin (UBC 6) - - - - - http://www.reactome.org/biopax/46/48887#Protein2482 - Reactome DB_ID: 939856 - UBC(381-456) - - - - RFC5 - HGNC Symbol - - - - PTHR11599:SF12 - PANTHER Family - - - - - P31147 - UniProt - - - - EQUAL - 1 - - - - ENSP00000396910 - Ensembl - - - - NP_001177810 - RefSeq - - - - 1U7B - PROTEIN DATA BANK - - - - 10656792 - Keller, RC - Mossi, R - Hubscher, U - Ferrari, E - Pubmed - DNA polymerase switching: II. Replication factor C abrogates primer synthesis by DNA polymerase alpha at a critical length. - J Mol Biol 295:803-14 - 2000 - - - - REACT_4051 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4051.2 - - - - 10656791 - Spadari, S - Hubscher, U - Maga, G - Stucki, M - Pubmed - DNA polymerase switching: I. Replication factor C displaces DNA polymerase alpha prior to PCNA loading. - J Mol Biol 295:791-801 - 2000 - - - - MI:0359 - Molecular Interactions Ontology - - - - Q9UNQ1 - UniProt - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4942 - - - - ENST00000044462 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite10887 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval846 - - - - - - Q6IBU3 - UniProt - - - - EQUAL - 27 - - - - 176970 - Reactome Database ID Release 46 - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176970 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry6615 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval4845 - - - - - - - - MOD_RES 21 21 Phosphoserine. - - - - ENST00000383234 - Ensembl - - - - REACT_555 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_555.3 - - - - - - TBP-7 - TAT-binding protein-7 - MIP224 - 26S protease regulatory subunit 6B - MB67 interacting protein - - - - - http://www.reactome.org/biopax/46/48887#Protein1098 - Reactome DB_ID: 68777 - PSMC4 - - - - - - Proteasome subunit Y - Proteasome delta chain - Multicatalytic endopeptidase complex delta chain - Proteasome subunit beta type 6 precursor - Macropain delta chain - Proteasome subunit beta type 6 - - - - - Reactome DB_ID: 68756 - http://www.reactome.org/biopax/46/48887#Protein1100 - PSMB6 - - - - - C9H15N2O15P3 - uridine 5'-(tetrahydrogen triphosphate) - uridine 5'-triphosphoric acid - 5'-UTP - H4utp - - - - - - - - 484.14117 - UTP - UTP - A pyrimidine ribonucleoside 5'-triphosphate having uracil as the nucleobase. - - - - ENSG00000112242 - Ensembl - - - - NM_014225 - RefSeq - - - - P49721 - UniProt - - - - REACT_24666 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24666.2 - - - - ENSP00000445058 - Ensembl - - - - - - - - - - - - Mcm10:active pre-replicative complex - Reactome DB_ID: 156564 - http://www.reactome.org/biopax/46/48887#Complex2546 - - - - ENST00000449823 - Ensembl - - - - EQUAL - 2286 - http://www.reactome.org/biopax/46/48887#SequenceSite10867 - - - - - 1.0 - http://www.reactome.org/biopax/46/48887#Stoichiometry1070 - - - - 600407 - omim - - - - ENST00000378714 - Ensembl - - - - NM_001135592 - RefSeq - - - - NM_002812 - RefSeq - - - - EQUAL - 401 - - - - NP_877577 - RefSeq - - - - REACT_5909 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5909.2 - - - - NM_078467 - RefSeq - - - - NP_859525 - RefSeq - - - - CHEBI:13736 - ChEBI - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature4835 - - - - ENST00000234626 - Ensembl - - - - EQUAL - 1 - http://www.reactome.org/biopax/46/48887#SequenceSite4643 - - - - - - - - - Phosphorylated Cdc6 is exported from the nucleus - In this reaction, 1 molecule of 'phosphorylated Cdc6' is translocated from nucleoplasm to cytosol.<br><br>This movement of the molecule occurs through the 'nuclear pore'.<br> - http://www.reactome.org/biopax/46/48887#BiochemicalReaction2000 - - - - - ENST00000445930 - Ensembl - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1375 - - - - - - Q2NKM1 - UniProt - - - - - - - - ligated okazaki fragment - Reactome DB_ID: 69172 - http://www.reactome.org/biopax/46/48887#PhysicalEntity260 - - - - 5710 - NCBI Gene - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval837 - - - - - - EQUAL - 161 - - - - PSMC2 - HGNC Symbol - - - - - - MOD_RES 65 65 Phosphoserine (By similarity). - - - - EQUAL - 290 - - - - 9520412 - Nevins, JR - DeGregori, J - Leone, G - Shohet, R - Yan, Z - Williams, RS - Stillman, B - Pubmed - Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells. - Proc Natl Acad Sci U S A 95:3603-8 - 1998 - - - - ENST00000343380 - Ensembl - - - - 9566895 - Lawlis, SJ - Dutta, A - Hou, ZH - Parvin, JD - Saha, P - Hendricks, M - Chen, J - Thome, KC - Pubmed - Human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase. - Mol Cell Biol 18:2758-67 - 1998 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval877 - - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature847 - - - - NM_002388 - RefSeq - - - - ENSP00000459827 - Ensembl - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature836 - - - - 10959839 - Tomkinson, AE - McKenna, AE - Matsumoto, Y - Motycka, TA - Levin, DS - Pubmed - Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. - Curr Biol 10:919-22 - 2000 - - - - - - MOD_RES 48 48 N6-acetyllysine; alternate (By similarity). - - - - ENSP00000406878 - Ensembl - - - - REACT_24882 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_24882.2 - - - - O00176 - UniProt - - - - EQUAL - 206 - - - - REACT_5885 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5885.1 - - - - UBA52 - HGNC Symbol - - - - - - Proteasome subunit XAPC7 - Proteasome subunit RC6-1 - 3.4.25.1 - PSMA7 - HSPC - - - - - - - - - - - - - - - - - - - - - - PSA7_HUMAN - Proteasome subunit alpha type-7 - FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. Plays an important role in the regulation of cell proliferation or cell cycle control, transcriptional regulation, immune and stress response, cell differentiation, and apoptosis. Interacts with some important proteins involved in transcription factor regulation, cell cycle transition, viral replication and even tumor initiation and progression. Inhibits the transactivation function of HIF-1A under both normoxic and hypoxia-mimicking conditions. The interaction with EMAP2 increases the proteasome-mediated HIF-1A degradation under the hypoxic conditions. Plays a role in hepatitis C virus internal ribosome entry site-mediated translation. Mediates nuclear translocation of the androgen receptor (AR) and thereby enhances androgen-mediated transactivation. Promotes MAVS degradation and thereby negatively regulates MAVS-mediated innate immune response.CATALYTIC ACTIVITY: Cleavage of peptide bonds with very broad specificity.SUBUNIT: The 26S proteasome consists of a 20S proteasome core and two 19S regulatory subunits. The 20S proteasome core is composed of 28 subunits that are arranged in four stacked rings, resulting in a barrel-shaped structure. The two end rings are each formed by seven alpha subunits, and the two central rings are each formed by seven beta subunits. The catalytic chamber with the active sites is on the inside of the barrel. PSMA7 interacts directly with the PSMG1-PSMG2 heterodimer which promotes 20S proteasome assembly. Interacts with HIV-1 TAT protein. Interacts with hepatitis B virus X protein (HBX). Interacts with HIF1A. Interacts with RAB7A. Interacts with PARK2. Interacts with ABL1 and ABL2. Interacts with EMAP2. Interacts with MAVS.SUBCELLULAR LOCATION: Cytoplasm. Nucleus.ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Comment=Experimental confirmation may be lacking for some isoforms; Name=1; IsoId=O14818-1; Sequence=Displayed; Name=2; IsoId=O14818-2; Sequence=VSP_005281; Name=3; IsoId=O14818-4; Sequence=VSP_046556, VSP_046557;INDUCTION: Down-regulated by the ribozyme Rz3'X. Up-regulated in colorectal cancer tissues.PTM: Phosphorylation by ABL1 or ABL2 leads to an inhibition of proteasomal activity and cell cycle transition blocks.SIMILARITY: Belongs to the peptidase T1A family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - http://www.reactome.org/biopax/46/48887#FragmentFeature824 - - - - http://www.reactome.org/biopax/46/48887#SequenceInterval1377 - - - - \ No newline at end of file diff --git a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/raf_map_kinase_cascade_reactome.owl b/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/raf_map_kinase_cascade_reactome.owl deleted file mode 100755 index 92f4040e0..000000000 --- a/paxtools-archetype/src/main/resources/archetype-resources/src/main/resources/raf_map_kinase_cascade_reactome.owl +++ /dev/null @@ -1,4386 +0,0 @@ - - - - - - - - REACT_1866 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1866.6 - - - - REACT_2741 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2741.1 - - - - CHEBI:13236 - chebi - - - - 112374 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112374 - - - - CHEBI:13342 - chebi - - - - Q14971 - uniprot - - - - 5781 - Entrez Gene - - - - - - Adenosine 5'-triphosphate - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#SmallMolecule5 - Reactome DB_ID: 113592 - ATP - - - - REACT_27630 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27630.1 - - - - - - Activated JAK2 - p-JAK2 (Y1007) - - - - - - Reactome DB_ID: 873799 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1639 - p(Y1007)-JAK2 - - - - 1112594 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112594 - - - - CDK1 - Cell division protein kinase 1 - Cell division control protein 2 homolog - p34 protein kinase - 2.7.11.23 - 2.7.11.22 - - - - - - - - - CDK1_HUMAN - Cyclin-dependent kinase 1 - FUNCTION: Plays a key role in the control of the eukaryotic cell cycle. It is required in higher cells for entry into S-phase and mitosis. p34 is a component of the kinase complex that phosphorylates the repetitive C-terminus of RNA polymerase II. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. CATALYTIC ACTIVITY: ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate. ENZYME REGULATION: Phosphorylation at Thr-14 or Tyr-15 inactivates the enzyme, while phosphorylation at Thr-161 activates it. SUBUNIT: Forms a stable but non-covalent complex with a regulatory subunit and with a cyclin. Interacts with DLGAP5. Isoform 2 is unable to complex with cyclin B1 and also fails to bind to the CDK inhibitor p21. Interacts with catalytically active CCNB1 and RALBP1 during mitosis to form an endocytotic complex during interphase. SUBCELLULAR LOCATION: Nucleus (By similarity). ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P06493-1; Sequence=Displayed; Name=2; Synonyms=CDC2deltaT; IsoId=P06493-2; Sequence=VSP_021375; TISSUE SPECIFICITY: Isoform 2 is found in breast cancer tissues. SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily. SIMILARITY: Contains 1 protein kinase domain. WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/cdc2/"; GENE SYNONYMS: CDC2. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 1112596 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112596 - - - - CHEBI:13222 - chebi - - - - 1112598 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112598 - - - - 7529 - Entrez Gene - - - - - - Adenosine 5'-diphosphate - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#SmallMolecule6 - Reactome DB_ID: 29370 - ADP - - - - Protein 1054 - 14-3-3 protein beta/alpha, N-terminally processed - Protein kinase C inhibitor protein 1 - KCIP-1 - - - - - - - - 1433B_HUMAN - 14-3-3 protein beta/alpha - FUNCTION: Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathway. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negative regulator of osteogenesis. SUBUNIT: Homodimer. Interacts with SSH1 and TORC2/CRTC2. Interacts with ABL1; the interaction results in cytoplasmic location of ABL1 and inhition of cABL-mediated apoptosis. Interacts with ROR2 (dimer); the interaction results in phosphorylation of YWHAB on tyrosine residues. Interacts with GAB2 and YAP1 (phosphorylated form). SUBCELLULAR LOCATION: Cytoplasm. Melanosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV. ALTERNATIVE PRODUCTS: Event=Alternative initiation; Named isoforms=2; Name=Long; IsoId=P31946-1; Sequence=Displayed; Name=Short; IsoId=P31946-2; Sequence=VSP_018632; Note=Acetylated on Met-1 (By similarity); PTM: The alpha, brain-specific form differs from the beta form in being phosphorylated (By similarity). PTM: Isoform Short contains a N-acetylmethionine at position 1 (By similarity). SIMILARITY: Belongs to the 14-3-3 family. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - InChI%3D1S%2FC10H16N5O14P3%2Fc11-10-13-7-4%288%2818%2914-10%2912-2-15%287%299-6%2817%295%2816%293%2827-9%291-26-31%2822%2C23%2929-32%2824%2C25%2928-30%2819%2C20%2921%2Fh2-3%2C5-6%2C9%2C16-17H%2C1H2%2C%28H%2C22%2C23%29%28H%2C24%2C25%29%28H2%2C19%2C20%2C21%29%28H3%2C11%2C13%2C14%2C18%29%2Ft3-%2C5-%2C6-%2C9-%2Fm1%2Fs1 - InChI - - - - REACT_5391 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5391.2 - - - - REACT_2607 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2607.1 - - - - - - - - - - - - - p21 RAS:GTP - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex1116 - Reactome DB_ID: 109783 - - - - P05231 - uniprot - - - - 447100 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=447100 - - - - 1067638 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1067638 - - - - - - Protein kinase C inhibitor protein-1 - Protein 1054 - 143B protein - 14-3-3 protein beta/alpha - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2357 - Reactome DB_ID: 48888 - KCIP-1 - - - - 112398 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112398 - - - - - - - - - Dissociation of phospho-ERK-2:MEK2 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction703 - Authored: Charalambous, M, 2005-02-04 06:50:22 - MEK2 dissociates from phospho-ERK2, allowing phospho-ERK2 to dimerise with another phospho-ERK2. - Reviewed: Gillespie, ME, 2010-11-24 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - NP_109587 - RefSeq - - - - Raf1 - HGNC - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep897 - - - - REACT_2275 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2275.1 - - - - - - - - - - - - - phospho-ERK-1:MEK1 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex679 - Reactome DB_ID: 109843 - - - - - - p44-MAPK - MAP kinase 1 - Microtubule- associated protein-2 kinase - p44-ERK1 - Activated ERK1 - Extracellular signal-regulated kinase 1 - phospho-ERK-1 - ERK-1 - MAPK 1 - Mitogen-activated protein kinase 3 - Insulin-stimulated MAP2 kinase - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1632 - Reactome DB_ID: 109842 - ERT2 - - - - Q02750 - uniprot - - - - REACT_143 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_143.6 - - - - 48888 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=48888 - - - - 62725 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=62725 - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep1231 - - - - - BSF-2 - CTL differentiation factor - IL-6 - B-cell stimulatory factor 2 - CDF - IFN-beta-2 - Hybridoma growth factor - Interferon beta-2 - - - - - - - - IL6_HUMAN - Interleukin-6 - FUNCTION: Cytokine with a wide variety of biological functions. It is a potent inducer of the acute phase response. Plays an essential role in the final differentiation of B-cells into Ig- secreting cells Involved in lymphocyte and monocyte differentiation. It induces myeloma and plasmacytoma growth and induces nerve cells differentiation Acts on B-cells, T-cells, hepatocytes, hematopoeitic progenitor cells and cells of the CNS. Also acts as a myokine. It is discharged into the bloodstream after muscle contraction and acts to increase the breakdown of fats and to improve insulin resistance. SUBCELLULAR LOCATION: Secreted. PTM: N- and O-glycosylated. POLYMORPHISM: Genetic variations in IL6 may be correlated with bone mineral density (BMD). Low BMD is a risk factor for osteoporotic fracture. Osteoporosis is characterized by reduced bone mineral density, disrutption of bone microarchitecture, and the alteration of the amount and variety of non-collagenous proteins in bone. Osteoporotic bones are more at risk of fracture. DISEASE: Genetic variations in IL6 are associated with susceptibility to rheumatoid arthritis systemic juvenile (RASJ) [MIM:604302]. An inflammatory articular disorder with systemic- onset beginning before the age of 16. It represents a subgroup of juvenile arthritis associated with severe extraarticular features and occasionally fatal complications. During active phases of the disorder, patients display a typical daily spiking fever, an evanescent macular rash, lymphadenopathy, hepatosplenomegaly, serositis, myalgia and arthritis. DISEASE: Note=A IL6 promoter polymorphism is associated with a lifetime risk of development of Kaposi sarcoma in HIV-infected men. SIMILARITY: Belongs to the IL-6 superfamily. WEB RESOURCE: Name=R&D Systems' cytokine mini-reviews: IL-6; URL="http://www.rndsystems.com/molecule_detail.aspx?m=1648"; WEB RESOURCE: Name=Wikipedia; Note=Interleukin-6 entry; URL="http://en.wikipedia.org/wiki/Interleukin_6"; WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/il6/"; WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=IL6"; WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/IL6ID519ch7p15.html"; GENE SYNONYMS: IFNB2. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 5894 - Entrez Gene - - - - CHEBI:22249 - chebi - - - - CHEBI:22244 - chebi - - - - 1112563 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112563 - - - - NP_002218 - RefSeq - - - - - - Interleukin-6 receptor subunit alpha long transmembrane form - IL6RA_HUMAN - IL6RA - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1636 - Reactome DB_ID: 1067672 - IL6R - - - - NP_001777 - RefSeq - - - - extracellular region - - cPath2-generated - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep887 - - - - - REACT_3571 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3571.1 - - - - 9632795 - PubMed - - - - Q5FWG2 - uniprot - - - - NP_852004 - RefSeq - - - - 1067661 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1067661 - - - - REACT_3932 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3932.1 - - - - REACT_3339 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3339.1 - - - - 8388392 - Guan, KL - Zheng, CF - PubMed - Cloning and characterization of two distinct human extracellular signal-regulated kinase activator kinases, MEK1 and MEK2. - J Biol Chem 268:11435-9 - 1993 - - - - - - p44-MAPK - MAP kinase 1 - Microtubule- associated protein-2 kinase - p44-ERK1 - Extracellular signal-regulated kinase 1 - phospho-ERK-1 - MAPK 1 - ERK-1 - Mitogen-activated protein kinase 3 - Insulin-stimulated MAP2 kinase - - - - - - - Reactome DB_ID: 112359 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1633 - ERT2 - - - - 5604 - Entrez Gene - - - - 5605 - Entrez Gene - - - - - 2.7.11 - - - - - - - - Inactivation of MEK1 by p34cdc2 - At the beginning of this reaction, 2 molecules of 'ATP', and 1 molecule of 'MEK1' are present. At the end of this reaction, 1 molecule of 'phospho_MEK1', and 2 molecules of 'ADP' are present.<br><br> This reaction takes place in the 'cytosol' and is mediated by the 'protein serine/threonine kinase activity' of 'phospho-Cdc2 (Thr 161)'.<br> - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction695 - - - - - - EQUAL - 365 - - - - InChI%3D1S%2FC10H15N5O10P2%2Fc11-8-5-9%2813-2-12-8%2915%283-14-5%2910-7%2817%296%2816%294%2824-10%291-23-27%2821%2C22%2925-26%2818%2C19%2920%2Fh2-4%2C6-7%2C10%2C16-17H%2C1H2%2C%28H%2C21%2C22%29%28H2%2C11%2C12%2C13%29%28H2%2C18%2C19%2C20%29%2Ft4-%2C6-%2C7-%2C10-%2Fm1%2Fs1 - InChI - - - - 1112580 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112580 - - - - A8K8Z5 - uniprot - - - - 1112585 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112585 - - - - 1112584 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112584 - - - - P01118 - uniprot - - - - REACT_3199 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3199.1 - - - - P31946 - uniprot - - - - - - - - - - Dimerisation of phospho-ERK-1 - Two phospho-ERK1 molecules dimerise and enter the nucleus, where they may phosphorylate downstream targets. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction699 - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - P01116 - uniprot - - - - REACT_4906 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4906.3 - - - - NP_002737 - RefSeq - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep888 - - - - - 1067672 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1067672 - - - - - - - - - - - - MEK activation - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Pathway270 - MEK is phosphorylated and activated by RAF. - Authored: Charalambous, M, 2004-04-29 09:21:24 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - - - - - 9606 - taxonomy - - - - EQUAL - 1 - - - - NP_002736 - RefSeq - - - - EQUAL - 1187 - - - - EQUAL - 23 - - - - NP_203698 - RefSeq - - - - EQUAL - 918 - - - - REACT_27429 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27429.1 - - - - EQUAL - 20 - - - - EQUAL - 1 - - - - P01112 - uniprot - - - - EQUAL - 186 - - - - P01111 - uniprot - - - - REACT_1482 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1482.4 - - - - EQUAL - 212 - - - - EQUAL - 1154 - - - - - - Guanosine 5'-triphosphate - - - - Reactome DB_ID: 29438 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#SmallMolecule84 - GTP - - - - EQUAL - 1 - - - - EQUAL - 468 - - - - EQUAL - 20 - - - - - - Transforming protein N-Ras - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2356 - Reactome DB_ID: 62725 - p21/N-Ras - - - - 1112570 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112570 - - - - REACT_4992 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4992.1 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep894 - - - - - REACT_3906 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3906.1 - - - - P04049 - uniprot - - - - REACT_4863 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4863.1 - - - - CHEBI:10841 - chebi - - - - - - ACTIVATION - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Catalysis485 - - - - 1067687 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1067687 - - - - NP_002746 - RefSeq - - - - EQUAL - 30 - - - - Q9UQ41 - uniprot - - - - - - IL6ST - Tyrosine phosphorylated Interleukin-6 receptor subunit beta long transmembrane form - IL6RB_HUMAN - - - - - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1641 - Reactome DB_ID: 1112580 - gp130 - - - - - - Tyrosine-protein kinase JAK1 - p(Y1034)-JAK1 - Janus kinase 1 - - - - - - - Reactome DB_ID: 1112543 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1638 - JAK1_HUMAN - - - - B5BUA0 - uniprot - - - - 17993263 - Dance, M - Salles, JP - Montagner, A - Raynal, P - Yart, A - PubMed - The molecular functions of Shp2 in the Ras/Mitogen-activated protein kinase (ERK1/2) pathway - Cell Signal 20:453-9 - 2008 - - - - REACT_27564 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27564.1 - - - - GO:0000189 - Gene Ontology - - - - GO:0000187 - Gene Ontology - - - - GO:0000186 - Gene Ontology - - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 1112596 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1637 - Activated JAK1, JAK2, TYK2 - - - - NP_002871 - RefSeq - - - - P28482 - uniprot - - - - REACT_634 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_634.5 - - - - REACT_2822 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2822.1 - - - - - - p21A (K-Ras 2A) - Transforming protein p21A - c-K-ras - K-Ras 2A - - - - - Reactome DB_ID: 62719 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2355 - Ki-Ras - - - - Il6 - HGNC - - - - 57600 - CHEBI - - - - REACT_2196 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2196.5 - - - - - - - - - - - Reactome DB_ID: 112336 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1624 - Converted from EntitySet in Reactome - MEK1 - - - - REACT_5485 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5485.2 - - - - REACT_2640 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2640.2 - - - - - - - - - - - - - Activated RAF1 complex:MEK - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex1117 - Reactome DB_ID: 112406 - - - - 59504 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=59504 - - - - 59502 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=59502 - - - - - - MAPK/ERK kinase 2 - ERK activator kinase 2 - phospho-MEK2 - Dual specificity mitogen-activated protein kinase kinase 2 - MAPKK 2 - MAP kinase kinase 2 - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1643 - Reactome DB_ID: 109848 - MEK2 - - - - 3265 - Entrez Gene - - - - 162573 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=162573 - - - - - - - - - - - phospho-ERK-1 dimer - Reactome DB_ID: 109845 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex681 - - - - NP_005334 - RefSeq - - - - Q15104 - uniprot - - - - 112411 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112411 - - - - 1112543 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112543 - - - - REACT_4782 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4782.1 - - - - 29438 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29438 - - - - NP_004976 - RefSeq - - - - cRaf - Proto-oncogene c-RAF - 2.7.11.1 - Raf-1 - - - - - - - - - RAF1_HUMAN - RAF proto-oncogene serine/threonine-protein kinase - FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. Part of the Ras-dependent signaling pathway from receptors to the nucleus. Protects cells from apoptosis mediated by STK3. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. COFACTOR: Binds 2 zinc ions per subunit. SUBUNIT: Forms a multiprotein complex with Ras (M-Ras/MRAS), SHOC2 and protein phosphatase 1 (PPP1CA, PPP1CB and PPP1CC). Interacts with Ras proteins; the interaction is antagonized by RIN1. Weakly interacts with RIT1 (By similarity). Interacts with STK3; the interaction inhibits its pro-apoptotic activity. Interacts (when phosphorylated at Ser-259) with YWHAZ (unphosphorylated at 'Thr- 232'). ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=6C; IsoId=P04049-1; Sequence=Displayed; Name=2; Synonyms=1A; IsoId=P04049-2; Sequence=VSP_034649; TISSUE SPECIFICITY: In skeletal muscle, isoform 1 is more abundant than isoform 2. PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. Phosphorylation at Thr-269 increases its kinase activity. Phosphorylation at Ser-259 induces the interaction with YWHAZ and inactivates kinase activity. Dephosphorylation of Ser-259 by the complex containing protein phosphatase 1, SHOC2 and M-Ras/MRAS relieves inactivation, leading to stimulate RAF1 activity. DISEASE: Defects in RAF1 are the cause of Noonan syndrome type 5 (NS5) [MIM:611553]. Noonan syndrome (NS) is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. It is a genetically heterogeneous and relatively common syndrome, with an estimated incidence of 1 in 1000-2500 live births. DISEASE: Defects in RAF1 are the cause of LEOPARD syndrome type 2 (LEOPARD2) [MIM:611554]. LEOPARD syndrome is an autosomal dominant disorder allelic with Noonan syndrome. The acronym LEOPARD stands for lentigines, electrocardiographic conduction abnormalities, ocular hypertelorism, pulmonic stenosis, abnormalities of genitalia, retardation of growth, and deafness. SIMILARITY: Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. RAF subfamily. SIMILARITY: Contains 1 phorbol-ester/DAG-type zinc finger. SIMILARITY: Contains 1 protein kinase domain. SIMILARITY: Contains 1 RBD (Ras-binding) domain. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/RAF1"; WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/raf1/"; WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/RAF1ID42032ch3p25.html"; GENE SYNONYMS: RAF. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - phospho-ERK-2:MEK2 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex691 - Reactome DB_ID: 109854 - - - - - - - - - - - phospho-ERK-2 dimer - Reactome DB_ID: 109855 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex692 - - - - - - Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.1.-) (MAP kinase kinase 1) (MAPKK 1) (ERK activator kinase 1) (MAPK/ERK kinase 1) (MEK1) - MAPK/ERK kinase 1 - ERK activator kinase 1 - Dual specificity mitogen-activated protein kinase kinase 1 - phospho-MEK1 - MAP kinase kinase 1 - MAPKK 1 - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1629 - Reactome DB_ID: 112374 - MEK1 - - - - Q9UCE2 - uniprot - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep886 - - - - - Shp2 - Protein-tyrosine phosphatase 1D - Protein-tyrosine phosphatase 2C - PTP-2C - SH-PTP2 - SHP-2 - SH-PTP3 - PTP-1D - 3.1.3.48 - - - - - - - PTN11_HUMAN - Tyrosine-protein phosphatase non-receptor type 11 - FUNCTION: Acts downstream of various receptor and cytoplasmic protein tyrosine kinases to participate in the signal transduction from the cell surface to the nucleus. CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate. SUBUNIT: Interacts with phosphorylated LIME1 and BCAR3. Interacts with SHB and INPP5D/SHIP1 (By similarity). Interacts with MCA32 (tyrosine-phosphorylated) (By similarity). Interacts with PTPNS1 and CD84. Interacts with phosphorylated SIT1 and MPZL1. Interacts with FCRL3, FCRL4, FCRL6 and ANKHD1. Interacts with KIR2DL1; the interaction is enhanced by ARRB2. Interacts with GAB2. Interacts with TERT; the interaction retains TERT in the nucleus. Interacts with PECAM1. SUBCELLULAR LOCATION: Cytoplasm. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=PTP2Ci; IsoId=Q06124-1; Sequence=Displayed; Name=2; Synonyms=PTP2C; IsoId=Q06124-2; Sequence=VSP_016672; Name=3; IsoId=Q06124-3; Sequence=VSP_016672, VSP_016673, VSP_016674; TISSUE SPECIFICITY: Widely expressed, with highest levels in heart, brain, and skeletal muscle. DOMAIN: The SH2 domains repress phosphatase activity. Binding of these domains to phosphotyrosine-containing proteins relieves this auto-inhibition, possibly by inducing a conformational change in the enzyme. PTM: Phosphorylated on Tyr-546 and Tyr-584 upon receptor protein tyrosine kinase activation; which creates a binding site for GRB2 and other SH2-containing proteins. DISEASE: Defects in PTPN11 are the cause of LEOPARD syndrome type 1 (LEOPARD1) [MIM:151100]. It is an autosomal dominant disorder allelic with Noonan syndrome. The acronym LEOPARD stands for lentigines, electrocardiographic conduction abnormalities, ocular hypertelorism, pulmonic stenosis, abnormalities of genitalia, retardation of growth, and deafness. DISEASE: Defects in PTPN11 are the cause of Noonan syndrome type 1 (NS1) [MIM:163950]. Noonan syndrome (NS) is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. Some patients with Noonan syndrome type 1 develop multiple giant cell lesions of the jaw or other bony or soft tissues, which are classified as pigmented villomoduolar synovitis (PVNS) when occurring in the jaw or joints. Note=Mutations in PTPN11 account for more than 50% of the cases. Rarely, NS is associated with juvenile myelomonocytic leukemia (JMML). NS1 inheritance is autosomal dominant. DISEASE: Defects in PTPN11 are a cause of juvenile myelomonocytic leukemia (JMML) [MIM:607785]. JMML is a pediatric myelodysplastic syndrome that constitutes approximately 30% of childhood cases of myelodysplastic syndrome (MDS) and 2% of leukemia. It is characterized by leukocytosis with tissue infiltration and in vitro hypersensitivity of myeloid progenitors to granulocyte- macrophage colony stimulating factor. DISEASE: Defects in PTPN11 are a cause of metachondromatosis (MC) [MIM:156250]. It is a skeletal disorder with radiologic fetarures of both multiple exostoses and Ollier disease, characterized by the presence of multiple enchondromas and osteochondroma-like lesions. SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Non-receptor class 2 subfamily. SIMILARITY: Contains 2 SH2 domains. SIMILARITY: Contains 1 tyrosine-protein phosphatase domain. WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PTPN11ID41910ch12q24.html"; WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PTPN11"; GENE SYNONYMS: PTP2C SHPTP2. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Nras - HGNC - - - - Q14080 - uniprot - - - - Tyk2 - HGNC - - - - CHEBI:5234 - chebi - - - - - - - - - - - IL6_HUMAN - Interleukin-6 - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1635 - Reactome DB_ID: 447100 - IL6 - - - - - - ACTIVATION - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Catalysis486 - - - - CHEBI:2342 - chebi - - - - 62719 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=62719 - - - - - - - - NP_002825 - RefSeq - - - - 112339 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112339 - - - - B0LPG3 - uniprot - - - - NP_004963 - RefSeq - - - - 62717 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=62717 - - - - REACT_1836 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1836.2 - - - - IL-6R-alpha - Membrane glycoprotein 80 - gp80 - IL-6R 1 - IL-6 receptor subunit alpha - IL-6R subunit alpha - IL-6RA - CD126 - - - - - - - - - - - - IL6RA_HUMAN - Interleukin-6 receptor subunit alpha - FUNCTION: Part of the receptor for interleukin 6. Binds to IL6 with low affinity, but does not transduce a signal. Signal activation necessitate an association with IL6ST. Activation may lead to the regulation of the immune response, acute-phase reactions and hematopoiesis. FUNCTION: Low concentration of a soluble form of IL6 receptor acts as an agonist of IL6 activity. SUBUNIT: Hexamer of two molecules each of IL6, IL6R and IL6ST. SUBCELLULAR LOCATION: Isoform 1: Basolateral cell membrane; Single-pass type I membrane protein. SUBCELLULAR LOCATION: Isoform 2: Secreted. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=Long; IsoId=P08887-1; Sequence=Displayed; Name=2; Synonyms=Short; IsoId=P08887-2; Sequence=VSP_001682, VSP_001683; TISSUE SPECIFICITY: Isoform 2 is expressed in peripheral blood mononuclear cells and weakly found in urine and serum. DOMAIN: The two fibronectin type-III-like domains, contained in the N-terminal part, form together a cytokine-binding domain. DOMAIN: The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell- surface receptor binding. PTM: A short soluble form may also be released from the membrane by proteolysis. SIMILARITY: Belongs to the type I cytokine receptor family. Type 3 subfamily. SIMILARITY: Contains 1 fibronectin type-III domain. SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - CHEBI:42934 - chebi - - - - 112336 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112336 - - - - - - - - - - - - - IL6:IL6RA - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex686 - Reactome DB_ID: 1067638 - - - - - Homo sapiens - - - - B0LPF9 - uniprot - - - - Q6QB10 - uniprot - - - - REACT_962 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_962.4 - - - - NP_002175 - RefSeq - - - - P36507 - uniprot - - - - REACT_2875 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2875.1 - - - - Il6r - HGNC - - - - 112340 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112340 - - - - - - - - - - - - RAF1 phosphorylates MEK2 - Active Raf-1 phosphorylates MEK-1/2 on Serine residues, converting ATP to ADP. The MEK-1/2 kinase is now active. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction981 - Authored: Charalambous, M, 2005-01-07 11:17:43 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - - 112342 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112342 - - - - 456216 - CHEBI - - - - 112343 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112343 - - - - - - - - - - - - - - REACT_1289 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1289.6 - - - - - - - - - - - - - - CHEBI:2359 - chebi - - - - - - - - - GO:0005576 - Gene Ontology - - - - - - Mitogen-activated protein kinase 1 (EC 2.7.1.-) (Extracellular signal- regulated kinase 2) (ERK-2) (Mitogen-activated protein kinase 2) (MAP kinase 2) (MAPK 2) (p42-MAPK) (ERT1) - MAP kinase 2 - Extracellular signal-regulated kinase 2 - ERK-2 - MAPK 2 - ERT1 - Mitogen-activated protein kinase 1 - p42-MAPK - Mitogen-activated protein kinase 2 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein207 - Reactome DB_ID: 59282 - ERK2 - - - - REACT_3346 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3346.1 - - - - A8K9K2 - uniprot - - - - - - - - - - - - - ERK activation - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Pathway192 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Activated MEK phosphorylates and activates ERK. - - - - - - - p44-MAPK - MAP kinase 1 - Mitogen-activated protein kinase 3 (EC 2.7.1.-) (Extracellular signal- regulated kinase 1) (ERK-1) (Insulin-stimulated MAP2 kinase) (MAP kinase 1) (MAPK 1) (p44-ERK1) (ERT2) (p44-MAPK) (Microtubule- associated protein-2 kinase) - Microtubule- associated protein-2 kinase - p44-ERK1 - Extracellular signal-regulated kinase 1 - ERK-1 - MAPK 1 - Mitogen-activated protein kinase 3 - Insulin-stimulated MAP2 kinase - ERT2 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1631 - Reactome DB_ID: 59284 - ERK1 - - - - CHEBI:24451 - chebi - - - - - - - - - - - - RAF phosphorylates MEK - Active Raf-1 phosphorylates MEK-1/2 on Serine residues, converting ATP to ADP. The MEK-1/2 kinase is now active. - Authored: Charalambous, M, 2005-01-07 11:17:43 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Pathway250 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - B2R6V4 - uniprot - - - - O75297 - uniprot - - - - GO:0070371 - Gene Ontology - - - - A8K1D9 - uniprot - - - - 112359 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112359 - - - - 7297 - Entrez Gene - - - - 112354 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112354 - - - - c-H-ras - GTPase HRas, N-terminally processed - H-Ras-1 - p21ras - Transforming protein p21 - Ha-Ras - - - - - - - - - - RASH_HUMAN - GTPase HRas - FUNCTION: Ras proteins bind GDP/GTP and possess intrinsic GTPase activity. ENZYME REGULATION: Alternate between an inactive form bound to GDP and an active form bound to GTP. Activated by a guanine nucleotide-exchange factor (GEF) and inactivated by a GTPase- activating protein (GAP). SUBUNIT: In its GTP-bound form interacts with PLCE1. Interacts with TBC1D10C. Interacts with RGL3. Interacts with HSPD1 (By similarity). Forms a signaling complex with RASGRP1 and DGKZ. Interacts with RASSF5. Interacts with HRAS. SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side. Golgi apparatus membrane; Lipid-anchor. Note=Shuttles between the plasma membrane and the Golgi apparatus. PTM: Palmitoylated by the ZDHHC9-GOLGA7 complex. A continuous cycle of de- and re-palmitoylation regulates rapid exchange between plasma membrane and Golgi. PTM: S-nitrosylated; critical for redox regulation. Important for stimulating guanine nucleotide exchange. No structural perturbation on nitrosylation. MASS SPECTROMETRY: Mass=6223; Mass_error=2; Method=Electrospray; Range=112-166; Source=PubMed:9020151; MASS SPECTROMETRY: Mass=6253; Mass_error=2; Method=Electrospray; Range=112-166; Note=Includes one nitric oxide molecule; Source=PubMed:9020151; DISEASE: Defects in HRAS are the cause of Costello syndrome (COSTS) [MIM:218040]; also known as faciocutaneoskeletal syndrome. Costello syndrome is a rare condition characterized by prenatally increased growth, postnatal growth deficiency, mental retardation, distinctive facial appearance, cardiovascular abnormalities (typically pulmonic stenosis, hypertrophic cardiomyopathy and/or atrial tachycardia), tumor predisposition, skin and musculoskeletal abnormalities. DISEASE: Defects in HRAS are the cause of congenital myopathy with excess of muscle spindles (CMEMS) [MIM:218040]. CMEMS is a variant of Costello syndrome. DISEASE: Defects in HRAS may be a cause of susceptibility to Hurthle cell thyroid carcinoma (HCTC) [MIM:607464]. Hurthle cell thyroid carcinoma accounts for approximately 3% of all thyroid cancers. Although they are classified as variants of follicular neoplasms, they are more often multifocal and somewhat more aggressive and are less likely to take up iodine than are other follicular neoplasms. DISEASE: Note=Mutations which change positions 12, 13 or 61 activate the potential of HRAS to transform cultured cells and are implicated in a variety of human tumors. DISEASE: Defects in HRAS are a cause of susceptibility to bladder cancer (BLC) [MIM:109800]. A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas. They begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. DISEASE: Note=Defects in HRAS are the cause of oral squamous cell carcinoma (OSCC). SIMILARITY: Belongs to the small GTPase superfamily. Ras family. WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/HRASID108.html"; WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HRAS"; GENE SYNONYMS: HRAS1. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Transforming protein N-Ras - - - - - - - - RASN_HUMAN - GTPase NRas - FUNCTION: Ras proteins bind GDP/GTP and possess intrinsic GTPase activity. ENZYME REGULATION: Alternate between an inactive form bound to GDP and an active form bound to GTP. Activated by a guanine nucleotide-exchange factor (GEF) and inactivated by a GTPase- activating protein (GAP). SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side. Golgi apparatus membrane; Lipid-anchor. Note=Shuttles between the plasma membrane and the Golgi apparatus. PTM: Palmitoylated by the ZDHHC9-GOLGA7 complex. A continuous cycle of de- and re-palmitoylation regulates rapid exchange between plasma membrane and Golgi. DISEASE: Defects in NRAS are a cause of juvenile myelomonocytic leukemia (JMML) [MIM:607785]. JMML is a pediatric myelodysplastic syndrome that constitutes approximately 30% of childhood cases of myelodysplastic syndrome (MDS) and 2% of leukemia. DISEASE: Defects in NRAS are the cause of Noonan syndrome type 6 (NS6) [MIM:613224]. A syndrome characterized by facial dysmorphic features such as hypertelorism, a downward eyeslant and low-set posteriorly rotated ears. Other features can include short stature, a short neck with webbing or redundancy of skin, cardiac anomalies, deafness, motor delay and variable intellectual deficits. MISCELLANEOUS: Mutations which change AA 12, 13 or 61 activate the potential of Ras to transform cultured cells and are implicated in a variety of human tumors. SIMILARITY: Belongs to the small GTPase superfamily. Ras family. WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/NRASID92.html"; WEB RESOURCE: Name=NRASbase; Note=NRAS mutation db; URL="http://bioinf.uta.fi/NRASbase/"; WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/nras/"; WEB RESOURCE: Name=Wikipedia; Note=RAS proteins entry; URL="http://en.wikipedia.org/wiki/RAS_proteins"; GENE SYNONYMS: HRAS1. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 50733 - CHEBI - - - - K-Ras 2 - c-Ki-ras - c-K-ras - GTPase KRas, N-terminally processed - Ki-Ras - - - - - - - - - - RASK_HUMAN - GTPase KRas - FUNCTION: Ras proteins bind GDP/GTP and possess intrinsic GTPase activity. ENZYME REGULATION: Alternate between an inactive form bound to GDP and an active form bound to GTP. Activated by a guanine nucleotide-exchange factor (GEF) and inactivated by a GTPase- activating protein (GAP). SUBUNIT: Interacts with PHLPP (By similarity). SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Comment=Isoforms differ in the C-terminal region which is encoded by two alternative exons (IVA and IVB); Name=2A; IsoId=P01116-1; Sequence=Displayed; Name=2B; IsoId=P01116-2, P01118-1; Sequence=VSP_011140, VSP_011141; Note=Variant in position: 153:D->V (in CFC syndrome and NS3), exhibits only minor alterations in its in vitro biochemical behavior compared to wild-type protein. Variant in position: 156: F->I (in NS3/CFC syndrome). Variant in position: 156: F->L (found in a patient with Costello syndrome), exhibits an increase in intrinsic and guanine nucleotide exchange factor catalyzed nucleotide exchange in combination with an impaired GTPase-activating protein-stimulated GTP hydrolysis but functional in interaction with effectors; DISEASE: Defects in KRAS are a cause of acute myelogenous leukemia (AML) [MIM:601626]. AML is a malignant disease in which hematopoietic precursors are arrested in an early stage of development. DISEASE: Defects in KRAS are a cause of juvenile myelomonocytic leukemia (JMML) [MIM:607785]. JMML is a pediatric myelodysplastic syndrome that constitutes approximately 30% of childhood cases of myelodysplastic syndrome (MDS) and 2% of leukemia. It is characterized by leukocytosis with tissue infiltration and in vitro hypersensitivity of myeloid progenitors to granulocyte- macrophage colony stimulating factor. DISEASE: Defects in KRAS are the cause of Noonan syndrome type 3 (NS3) [MIM:609942]. Noonan syndrome (NS) [MIM:163950] is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. It is a genetically heterogeneous and relatively common syndrome, with an estimated incidence of 1 in 1000-2500 live births. Rarely, NS is associated with juvenile myelomonocytic leukemia (JMML). NS3 inheritance is autosomal dominant. DISEASE: Defects in KRAS are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:115150]; also known as cardio-facio- cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant. DISEASE: Note=KRAS mutations are involved in cancer development. SIMILARITY: Belongs to the small GTPase superfamily. Ras family. WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/KRASID91.html"; WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/KRAS"; WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=KRAS"; GENE SYNONYMS: KRAS2 RASK2. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - Q6FHV9 - uniprot - - - - REACT_26044 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26044.2 - - - - REACT_3037 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3037.2 - - - - Il6st - HGNC - - - - 8144912 - PubChem - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep892 - - - - - GO:0000165 - Gene Ontology - - - - NP_001035145 - RefSeq - - - - REACT_2247 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2247.5 - - - - REACT_27964 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27964.1 - - - - NP_001123914 - RefSeq - - - - REACT_27963 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27963.1 - - - - B0LPH8 - uniprot - - - - P23458 - uniprot - - - - P08887 - uniprot - - - - - - MAP kinase 2 - Extracellular signal-regulated kinase 2 - MAPK 2 - ERK-2 - phospho-ERK-2 - Mitogen-activated protein kinase 1 - p42-MAPK - Mitogen-activated protein kinase 2 - - - - - - - Reactome DB_ID: 112354 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1644 - ERT1 - - - - - - MAPK/ERK kinase 1 - ERK activator kinase 1 - Dual specificity mitogen-activated protein kinase kinase 1 - phospho-MEK1 - MAP kinase kinase 1 - MAPKK 1 - - - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1628 - Reactome DB_ID: 112339 - MEK1 - - - - - 2.7.11 - - - - - - - - - MEK1 phosphorylates ERK-1 - MEK1 phosphorylates the critical Tyrosine and Threonine on ERK1, converting two ATP to ADP. Phosphorylation of ERK-1 activates its kinase activity. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction697 - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - GO:0016301 - Gene Ontology - - - - NP_786943 - RefSeq - - - - GO:0005654 - Gene Ontology - - - - REACT_136 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_136.4 - - - - REACT_3688 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3688.1 - - - - Q16202 - uniprot - - - - NP_003395 - RefSeq - - - - MEK 2 - ERK activator kinase 2 - MAPK/ERK kinase 2 - 2.7.12.2 - MAPKK 2 - MAP kinase kinase 2 - - - - - MP2K2_HUMAN - Dual specificity mitogen-activated protein kinase kinase 2 - FUNCTION: Catalyzes the concomitant phosphorylation of a threonine and a tyrosine residue in a Thr-Glu-Tyr sequence located in MAP kinases. Activates the ERK1 and ERK2 MAP kinases (By similarity). CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. SUBUNIT: Interacts with MORG1 (By similarity). PTM: MAPKK is itself dependent on Ser/Thr phosphorylation for activity catalyzed by MAP kinase kinase kinases (RAF or MEKK1). PTM: Acetylation of Ser-222 and Ser-226 by Yersinia yopJ prevents phosphorylation and activation, thus blocking the MAPK signaling pathway. DISEASE: Defects in MAP2K2 are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:115150]; also known as cardio-facio- cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant. SIMILARITY: Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase subfamily. SIMILARITY: Contains 1 protein kinase domain. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/MAP2K2"; GENE SYNONYMS: MEK2 MKK2 PRKMK2. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - P06493 - uniprot - - - - - - - - - - - - O60764 - uniprot - - - - - - - - - - - - - - - - - Dissociation of phospho-ERK-1:MEK1 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction698 - MEK1 dissociates from phospho-ERK1, allowing phospho-ERK1 to dimerise with another phospho-ERK1. - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Gillespie, ME, 2010-11-24 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - Q15278 - uniprot - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep885 - - - - - 873799 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=873799 - - - - CD130 - CDw130 - Membrane glycoprotein 130 - IL-6R subunit beta - Interleukin-6 signal transducer - IL-6R-beta - IL-6RB - gp130 - Oncostatin-M receptor subunit alpha - IL-6 receptor subunit beta - - - - - - - - IL6RB_HUMAN - Interleukin-6 receptor subunit beta - FUNCTION: Signal-transducing molecule. The receptor systems for IL6, LIF, OSM, CNTF, IL11, CTF1 and BSF3 can utilize gp130 for initiating signal transmission. Binds to IL6/IL6R (alpha chain) complex, resulting in the formation of high-affinity IL6 binding sites, and transduces the signal. Does not bind IL6. May have a role in embryonic development (By similarity). The type I OSM receptor is capable of transducing OSM-specific signaling events. SUBUNIT: Interacts with INPP5D/SHIP1 (By similarity). Forms heterodimers composed of LIPR and IL6ST (type I OSM receptor). Also forms heterodimers composed of OSMR and IL6ST (type II OSM receptor). Homodimer. The homodimer binds two molecules of herpes virus IL6. Component of a hexamer of two molecules each of IL6, IL6R and IL6ST. SUBCELLULAR LOCATION: Isoform 1: Cell membrane; Single-pass type I membrane protein. SUBCELLULAR LOCATION: Isoform 2: Secreted. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=P40189-1; Sequence=Displayed; Name=2; Synonyms=GP130-RAPS; IsoId=P40189-2; Sequence=VSP_001684, VSP_001685; TISSUE SPECIFICITY: Found in all the tissues and cell lines examined. Expression not restricted to IL6 responsive cells. INDUCTION: Leukemia inhibitory factor (LIF) and Oncostatin-M (OSM) activate the type I OSM receptor while only OSM can activate the type II OSM receptor. DOMAIN: The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell- surface receptor binding. DOMAIN: The box 1 motif is required for JAK interaction and/or activation. PTM: Phosphorylation of Ser-782 down-regulates cell surface expression. PTM: Heavily N-glycosylated. SIMILARITY: Belongs to the type I cytokine receptor family. Type 2 subfamily. SIMILARITY: Contains 5 fibronectin type-III domains. SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - CHEBI:15996 - chebi - - - - MAPK 2 - MAPK 1 - 2.7.11.24 - ERT1 - p42-MAPK - MAP kinase 1 - MAP kinase 2 - Extracellular signal-regulated kinase 2 - ERK-2 - MAP kinase isoform p42 - Mitogen-activated protein kinase 2 - - - - - - MK01_HUMAN - Mitogen-activated protein kinase 1 - FUNCTION: Involved in both the initiation and regulation of meiosis, mitosis, and postmitotic functions in differentiated cells by phosphorylating a number of transcription factors such as ELK1. Phosphorylates EIF4EBP1; required for initiation of translation. Phosphorylates microtubule-associated protein 2 (MAP2). Phosphorylates SPZ1 (By similarity). Phosphorylates heat shock factor protein 4 (HSF4) and ARHGEF2. FUNCTION: Acts as a transcriptional repressor. Binds to a [GC]AAA[GC] consensus sequence. Repress the expression of interferon gamma-induced genes. Seems to bind to the promoter of CCL5, DMP1, IFIH1, IFITM1, IRF7, IRF9, LAMP3, OAS1, OAS2, OAS3 and STAT1. Transcriptional activity is independent of kinase activity. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. COFACTOR: Magnesium (By similarity). ENZYME REGULATION: Activated by phosphorylation on tyrosine and threonine in response to insulin and NGF. Both phosphorylations are required for activity (By similarity). SUBUNIT: Interacts with MORG1 (By similarity). Binds to HIV-1 Nef through its SH3 domain. This interaction inhibits its tyrosine- kinase activity. Interacts with its substrates HSF4 and ARHGEF2. Interacts (phosphorylated form) with CAV2 ('Tyr-19'-phosphorylated form); the interaction, promoted by insulin, leads to nuclear location and MAPK1 activation (By similarity). Interacts with NISCH. Interacts with ARRB2. Interacts with ADAM15. SUBCELLULAR LOCATION: Nucleus. DOMAIN: The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. PTM: Dually phosphorylated on Thr-185 and Tyr-187, which activates the enzyme. Dephosphorylated by PTPRJ at Tyr-187. SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily. SIMILARITY: Contains 1 protein kinase domain. SEQUENCE CAUTION: Sequence=CAA77753.1; Type=Erroneous initiation; Note=Translation N-terminally extended; WEB RESOURCE: Name=Wikipedia; Note=Extracellular signal-regulated kinase entry; URL="http://en.wikipedia.org/wiki/Extracellular_signal-regulated_kinase"; GENE SYNONYMS: ERK2 PRKM1 PRKM2. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - Converted from EntitySet in Reactome - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2354 - Reactome DB_ID: 109782 - p21 RAS - - - - REACT_5701 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5701.2 - - - - 113592 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113592 - - - - A8K7C4 - uniprot - - - - - - C-RAF - RAF proto-oncogene serine/threonine-protein kinase - Raf-1 - phospho-Raf1 (multiple sites) - - - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2358 - Reactome DB_ID: 109792 - cRaf - - - - 3717 - Entrez Gene - - - - P27361 - uniprot - - - - 3716 - Entrez Gene - - - - - - - - - - - - - IL6:sIL6R - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex689 - Reactome DB_ID: 1067687 - - - - REACT_4223 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4223.3 - - - - Ptpn11 - HGNC - - - - O14636 - uniprot - - - - InChI%3D1S%2FC10H16N5O13P3%2Fc11-8-5-9%2813-2-12-8%2915%283-14-5%2910-7%2817%296%2816%294%2826-10%291-25-30%2821%2C22%2928-31%2823%2C24%2927-29%2818%2C19%2920%2Fh2-4%2C6-7%2C10%2C16-17H%2C1H2%2C%28H%2C21%2C22%29%28H%2C23%2C24%29%28H2%2C11%2C12%2C13%29%28H2%2C18%2C19%2C20%29%2Ft4-%2C6-%2C7-%2C10-%2Fm1%2Fs1 - InChI - - - - NP_620407 - RefSeq - - - - - - - - - - - MEK2 binds ERK-2 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction701 - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - In the cytoplasm activated MEK2 (Serine phosphorylated) may encounter monomeric, inactive ERK2. ERK2 in its inactive form is not phosphorylated on a critical Threonine (T183) and a critical Tyrosine (Y185). - - - - - - C10H16N5O13P3 - Adenosine triphosphate - H4atp - adenosine 5'-(tetrahydrogen triphosphate) - - - - - - - - - - - - ATP - ATP - - - - REACT_6097 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_6097.2 - - - - - - MAP kinase 2 - Extracellular signal-regulated kinase 2 - Activated ERK2 - MAPK 2 - ERK-2 - phospho-ERK-2 - Mitogen-activated protein kinase 1 - p42-MAPK - Mitogen-activated protein kinase 2 - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein208 - Reactome DB_ID: 109853 - ERT1 - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep884 - - - - REACT_27735 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27735.1 - - - - - - - - - 3845 - Entrez Gene - - - - - - - - - INHIBITION - - 'phospho_MEK1 [cytosol]' negatively regulates 'MEK1 phosphorylates ERK-1' - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Control46 - - - - 112341 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112341 - - - - REACT_5046 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5046.1 - - - - plasma membrane - - cPath2-generated - - - - GO:0004674 - Gene Ontology - - - - A0N0L4 - uniprot - - - - Q59GQ2 - uniprot - - - - - - - - - - - - - - - - - - - - ERK1 activation - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Pathway193 - Activated MEK1 phosphorylates and activates ERK1. - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - GO:0005886 - Gene Ontology - - - - Microtubule-associated protein 2 kinase - MAP kinase isoform p44 - MAPK 1 - 2.7.11.24 - MAPK 3 - Insulin-stimulated MAP2 kinase - ERT2 - p44-MAPK - MAP kinase 1 - MAP kinase 3 - p44-ERK1 - Extracellular signal-regulated kinase 1 - ERK-1 - Mitogen-activated protein kinase 1 - - - - - - - - MK03_HUMAN - Mitogen-activated protein kinase 3 - FUNCTION: Involved in both the initiation and regulation of meiosis, mitosis, and postmitotic functions in differentiated cells by phosphorylating a number of transcription factors such as ELK-1. Phosphorylates EIF4EBP1; required for initiation of translation. Phosphorylates microtubule-associated protein 2 (MAP2). Phosphorylates SPZ1 (By similarity). Phosphorylates heat shock factor protein 4 (HSF4). CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. COFACTOR: Magnesium (By similarity). ENZYME REGULATION: Activated by tyrosine phosphorylation in response to insulin and NGF. SUBUNIT: Interacts with MORG1 (By similarity). Binds to HIV-1 Nef. This interaction inhibits its kinase activity. Interacts with HSF4 and NISCH. Interacts with ARRB2. Interacts with ADAM15. DOMAIN: The TXY motif contains the threonine and tyrosine residues whose phosphorylation activates the MAP kinases. PTM: Dually phosphorylated on Thr-202 and Tyr-204, which activates the enzyme. Dephosphorylated by PTPRJ at Tyr-204. SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily. SIMILARITY: Contains 1 protein kinase domain. GENE SYNONYMS: ERK1 PRKM3. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - - - - 4893 - Entrez Gene - - - - 7871433 - Stahl, N - Darnell JE, Jr - Farruggella, TJ - Zhong, Z - Boulton, TG - Yancopoulos, GD - PubMed - Choice of STATs and other substrates specified by modular tyrosine-based motifs in cytokine receptors - Science 267:1349-53 - 1995 - - - - - 1.0 - - - - - 2.0 - - - - NP_203524 - RefSeq - - - - - 1.0 - - - - - 1.0 - - - - - 1.0 - - - - - 2.0 - - - - - - ACTIVATION - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Catalysis583 - - - - - 1.0 - - - - - 1.0 - - - - O60674 - uniprot - - - - 112406 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112406 - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep1230 - - - - - - - - - - - - - Reactome DB_ID: 162573 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1634 - Phosphorylated SHP2 - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep890 - - - - 112409 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112409 - - - - 112407 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112407 - - - - REACT_3953 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3953.2 - - - - REACT_3280 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3280.1 - - - - - 2.0 - - - - REACT_27855 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27855.1 - - - - - - - - - - - - - - - - ACTIVATION - - 'IL6:Tyrosine phosphorylated hexameric IL-6 receptor:Activated JAKs:p-SHP2 [plasma membrane]' positively regulates 'ERK2 activation' - IL-6-type receptor activation leads to induction of the MAPK cascade. Experiments using gp130 identified that the gp130 SHP2 (SH2-domain-containing tyrosine phosphatase)-binding site Tyr-759 (Stahl et al. 1995) is required for this activation. Mutation of gp130 Tyr-759 impairs IL-6 induced activation of the MAPK cascade (Kim et al. 1998). While there is a consensus that SHP2 is involved in IL-6-induced activation of the MAPK pathway, the molecular details are uncertain. One proposed mechanism suggests SHP2 acts as an adaptor for Grb2-Sos recruitment (Fukada et al. 1996, Kim & Baumann 1999). IL-6 induced SHP2 recruitment to p-Tyr-759 of gp130 was demonstrated but relatively little of the SHP2 remained associated with gp130, suggesting that SHP2 dissociates from the receptor when phosphorylated. This seems inconsistent with a Grb2-Sos recruitment role for SHP2, though it is possible that only low levels or transient recruitment are required. IL-6 induced ERK activation was not inhibited in cells transfected with a phosphatase inactive mutant of SHP2, whereas an SHP2 mutant missing the Grb2 interaction region significantly suppressed ERK activation. This suggests phosphatase activity is not required for ERK activation while SHP-2 interaction with Grb2 is important. However, overexpression studies can generate artefactual interactions and this interpretation has been questioned (Dance et al. 2008). An alternative proposal suggests that SHP2 and the adaptor protein Gab1 couple gp130 signalling to Erk activation. In this proposal phosphorylated SHP2 dissociates from gp130 and becomes associated with membrane associated Gab1 in a complex with PI3-kinase (Takahashi-Tezuka et al. 1998, Eulenfeld & Schaper 2009). SHP2 interaction is suggested to induce a conformational change in Gab1 that permits Gab1-PI3-kinase activation and enhancement of IL-6-induced Erk pathway activation. However this is speculative, the role of SHP2 phosphatase activity is unclear. Other possible mechanisms are outlined by Dance et al. (2008), extrapolated from growth factor receptor mechanisms but with unknown relevance to IL-6/gp130. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Control48 - - - - - - - - - - - - - Activated RAF1 complex:MEK1 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex1114 - Reactome DB_ID: 109794 - - - - - 2.0 - - - - - 2.0 - - - - - 2.0 - - - - - 1.0 - - - - - 1.0 - - - - CHEBI:15422 - chebi - - - - Janus kinase 2 - JAK-2 - 2.7.10.2 - - - - - - - JAK2_HUMAN - Tyrosine-protein kinase JAK2 - FUNCTION: Non-receptor tyrosine kinase involved in various processes such as cell cycle progression, apoptosis, mitotic recombination, genetic instability and histone modifications. In the cytoplasm, plays a pivotal role in signal transduction via its association with cytokine receptors, which constitutes an initiating step in signaling for many members of the cytokine receptor superfamily including the receptors for growth hormone (GHR), prolactin (PRLR), leptin (LEPR), erythropoietin (EPOR), granulocyte-macrophage colony-stimulating factor (CSF2), thrombopoietin (THPO) and multiple interleukins. Following stimulation with erythropoietin (EPO) during erythropoiesis, it is autophosphorylated and activated, leading to its association with erythropoietin receptor (EPOR) and tyrosine phosphorylation of residues in the EPOR cytoplasmic domain. Also involved in promoting the localization of EPOR to the plasma membrane. Also acts downstream of some G-protein coupled receptors. Plays a role in the control of body weight (By similarity). Mediates angiotensin-2-induced ARHGEF1 phosphorylation. In the nucleus, plays a key role in chromatin by specifically mediating phosphorylation of 'Tyr-41' of histone H3 (H3Y41ph), a specific tag that promotes exclusion of CBX5 (HP1 alpha) from chromatin. CATALYTIC ACTIVITY: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate. ENZYME REGULATION: Regulated by autophosphorylation, can both activate or decrease activity (By similarity). Heme regulates its activity by enhancing the phosphorylation on Tyr-1007 and Tyr- 1008. SUBUNIT: Interacts with EPOR, SIRPA and SH2B1 (By similarity). Interacts with IL23R, SKB1 and STAM2. SUBCELLULAR LOCATION: Endomembrane system; Peripheral membrane protein (By similarity). Nucleus. TISSUE SPECIFICITY: Expressed in blood, bone marrow and lymph node. DOMAIN: Possesses 2 protein kinase domains. The second one probably contains the catalytic domain, while the presence of slight differences suggest a different role for protein kinase 1 (By similarity). PTM: Autophosphorylated, leading to regulate its activity. Leptin promotes phosphorylation on tyrosine residues, including phosphorylation on Tyr-813. Autophosphorylation on Tyr-119 in response to EPO down-regulates its kinase activity. Autophosphorylation on Tyr-868, Tyr-966 and Tyr-972 in response to growth hormone (GH) are required for maximal kinase activity (By similarity). DISEASE: Note=Chromosomal aberrations involving JAK2 are found in both chronic and acute forms of eosinophilic, lymphoblastic and myeloid leukemia. Translocation t(8;9)(p22;p24) with PCM1 links the protein kinase domain of JAK2 to the major portion of PCM1. Translocation t(9;12)(p24;p13) with ETV6. DISEASE: Defects in JAK2 are a cause of susceptibility to Budd- Chiari syndrome (BCS) [MIM:600880]. It is a syndrome caused by obstruction of hepatic venous outflow involving either the hepatic veins or the terminal segment of the inferior vena cava. Obstructions are generally caused by thrombosis and lead to hepatic congestion and ischemic necrosis. Clinical manifestations observed in the majority of patients include hepatomegaly, right upper quadrant pain and abdominal ascites. Budd-Chiari syndrome is associated with a combination of disease states including primary myeloproliferative syndromes and thrombophilia due to factor V Leiden, protein C deficiency and antithrombin III deficiency. Budd-Chiari syndrome is a rare but typical complication in patients with polycythemia vera. DISEASE: Defects in JAK2 are a cause of polycythemia vera (PV) [MIM:263300]. A myeloproliferative disorder characterized by abnormal proliferation of all hematopoietic bone marrow elements, erythroid hyperplasia, an absolute increase in total blood volume, but also by myeloid leukocytosis, thrombocytosis and splenomegaly. DISEASE: Defects in JAK2 gene may be a cause of essential thrombocythemia (ET) [MIM:187950]. ET is characterized by elevated platelet levels due to sustained proliferation of megakaryocytes, and frequently lead to thrombotic and haemorrhagic complications. DISEASE: Defects in JAK2 are a cause of myelofibrosis (MYELOF) [MIM:254450]. Myelofibrosis is a disorder characterized by replacement of the bone marrow by fibrous tissue, occurring in association with a myeloproliferative disorder. Clinical manifestations may include anemia, pallor, splenomegaly, hypermetabolic state, petechiae, ecchymosis, bleeding, lymphadenopathy, hepatomegaly, portal hypertension. DISEASE: Defects in JAK2 are a cause of acute myelogenous leukemia (AML) [MIM:601626]. AML is a malignant disease in which hematopoietic precursors are arrested in an early stage of development. SIMILARITY: Belongs to the protein kinase superfamily. Tyr protein kinase family. JAK subfamily. SIMILARITY: Contains 1 FERM domain. SIMILARITY: Contains 1 protein kinase domain. SIMILARITY: Contains 1 SH2 domain. WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/JAK98.html"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - 983 - Entrez Gene - - - - - - MAPK/ERK kinase 1 - ERK activator kinase 1 - Dual specificity mitogen-activated protein kinase kinase 1 - phospho-MEK1 - MAP kinase kinase 1 - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1626 - Reactome DB_ID: 109837 - MAPKK 1 - - - - - - ACTIVATION - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Catalysis487 - - - - XTWYTFMLZFPYCI-KQYNXXCUSA-N - InChI - - - - REACT_1019 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1019.3 - - - - urn:miriam:taxonomy:9606 - auto-generated - auto-generated - - - - Q5VZ23 - uniprot - - - - A8KAE8 - uniprot - - - - - 2.0 - - - - - 1.0 - - - - - 2.0 - - - - REACT_27336 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27336.1 - - - - - 2.0 - - - - - 1.0 - - - - REACT_1740 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1740.3 - - - - 109795 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109795 - - - - P29597 - uniprot - - - - 109794 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109794 - - - - 1112753 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112753 - - - - 109793 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109793 - - - - 109792 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109792 - - - - REACT_1727 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1727.5 - - - - - - - - - - - - CHEBI:40938 - chebi - - - - Q53EQ7 - uniprot - - - - CHEBI:40553 - chebi - - - - - 1.0 - - - - - - - - - 1.0 - - - - ZKHQWZAMYRWXGA-KQYNXXCUSA-N - InChI - - - - - 2.0 - - - - - - - - - - - - C9J497 - uniprot - - - - - - - - - - - - XKMLYUALXHKNFT-UUOKFMHZSA-N - InChI - - - - - - - - - - - - - - - - - MEK1:ERK-1 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex678 - Reactome DB_ID: 109838 - - - - - - - - - - - phospho-ERK-2 dimer - Reactome DB_ID: 109856 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex693 - - - - nucleoplasm - - cPath2-generated - - - - - - - - - - - - - - - - - - - Activated RAF1 complex - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex1115 - Reactome DB_ID: 109793 - - - - Q15282 - uniprot - - - - - 1.0 - - - - - 2.0 - - - - - - - - - - Dimerisation of phospho-ERK-2 - Two phospho-ERK2 molecules dimerise and enter the nucleus, where they may phosphorylate downstream targets. - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction704 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - 2.0 - - - - - 2.0 - - - - - 1.0 - - - - - 1.0 - - - - - 1.0 - - - - - 1.0 - - - - 1112769 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112769 - - - - 1112768 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1112768 - - - - - - - - - - - - - IL6:sIL6R:Tyrosine phosphorylated IL6RB:Activated JAKs - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex688 - Reactome DB_ID: 1112570 - - - - Q96CH0 - uniprot - - - - NP_001103361 - RefSeq - - - - 109783 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109783 - - - - 109782 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109782 - - - - - - - - - - Nuclear translocation of phospho-ERK-2 dimer - Phospho-ERK-2 dimer is translocated from cytosol to nucleoplasm. - Authored: Charalambous, M, 2004-04-29 09:21:24 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction705 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - Kras - HGNC - - - - REACT_4795 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4795.1 - - - - NP_647539 - RefSeq - - - - - 1.0 - - - - - 1.0 - - - - REACT_28018 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_28018.1 - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep896 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep1415 - - - - - - - - - - - - - - - - - - - - - - - - - - - - MAPK/ERK kinase 2 - ERK activator kinase 2 - Dual specificity mitogen-activated protein kinase kinase 2 - Dual specificity mitogen-activated protein kinase kinase 2 (EC 2.7.1.-) (MAP kinase kinase 2) (MAPKK 2) (ERK activator kinase 2) (MAPK/ERK kinase 2) (MEK2) - MAPKK 2 - MAP kinase kinase 2 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2360 - Reactome DB_ID: 59504 - MEK2 - - - - Q9UCU3 - uniprot - - - - 19050043 - Eulenfeld, R - Schaper, F - PubMed - A new mechanism for the regulation of Gab1 recruitment to the plasma membrane - J Cell Sci 122:55-64 - 2009 - - - - Q9UCU4 - uniprot - - - - - - - - - - - - Q9UCU2 - uniprot - - - - - - - - Q9UC20 - uniprot - - - - 109834 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109834 - - - - REACT_4256 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4256.3 - - - - MOD:00048 - Protein Modification Ontology - - - - 10409724 - PubMed - - - - MOD:00046 - Protein Modification Ontology - - - - MOD:00047 - Protein Modification Ontology - - - - - - - - - - Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.1.-) (MAP kinase kinase 1) (MAPKK 1) (ERK activator kinase 1) (MAPK/ERK kinase 1) (MEK1) - MAPK/ERK kinase 1 - ERK activator kinase 1 - Dual specificity mitogen-activated protein kinase kinase 1 - MAP kinase kinase 1 - MAPKK 1 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1625 - Reactome DB_ID: 59502 - MEK1 - - - - - - - - 110056 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110056 - - - - - - - - - - Transforming protein p21/H-Ras-1 - p21/H-RAS-1 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2350 - Reactome DB_ID: 62717 - c-H-ras - - - - - - - - - - Nuclear translocation of phospho-ERK-1 dimer - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction700 - Phospho-ERK-1 dimer is translocated from cytosol to nucleoplasm. - Authored: Charalambous, M, 2004-04-29 09:21:24 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - - - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep889 - - - - - - - - - - - - - - - - - - - - - - - - REACT_21811 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21811.1 - - - - REACT_5435 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5435.1 - - - - - - - - REACT_27710 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27710.1 - - - - 109869 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109869 - - - - REACT_487 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_487.6 - - - - 109867 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109867 - - - - 109868 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109868 - - - - cytosol - - cPath2-generated - - - - 109865 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109865 - - - - NP_000591 - RefSeq - - - - 109866 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109866 - - - - 109863 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109863 - - - - 109864 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109864 - - - - 109862 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109862 - - - - - - - - 157415 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=157415 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep891 - - - - - 109860 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109860 - - - - NP_003322 - RefSeq - - - - 17487135 - PubChem - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 112340 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1627 - phospho_MEK1 - - - - - 2.7.11 - - - - - - - - - MEK2 phosphorylates ERK-2 - MEK2 phosphorylates the critical Tyrosine and Threonine on ERK2, converting two ATP to ADP. Phosphorylation of ERK-2 activates its kinase activity. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction702 - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - - - - - - - - - - MEK2:ERK-2 - Reactome DB_ID: 109849 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex690 - - - - P40189 - uniprot - - - - 5594 - Entrez Gene - - - - 5595 - Entrez Gene - - - - REACT_27516 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27516.1 - - - - - - - - - - - IL-6:Tyrosine phosphorylated hexameric IL-6 receptor:Activated JAKs - Reactome DB_ID: 1112594 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex683 - - - - B2R5N3 - uniprot - - - - HRAS - HGNC - - - - 109859 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109859 - - - - O4&apos;-phospho-L-tyrosine - - cPath2-generated - - - - 109854 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109854 - - - - 109855 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109855 - - - - REACT_4582 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4582.1 - - - - 109856 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109856 - - - - 109861 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109861 - - - - 109857 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109857 - - - - 109858 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109858 - - - - Map2k1 - HGNC - - - - - - - - - - Activated RAF1 complex binds MEK - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction1144 - Authored: Charalambous, M, 2005-01-07 11:17:43 - MEK-1/2 have a proline rich domain (P) and critical Serine residues (MEK-1 S218/222, MEK-2 unknown, S) upon which the molecules may be phosphorylated. MEK1/2 are found in the cytoplasm of unstimulated cells.<br>MEK-1/2 bind to active Raf-1 via the proline-rich domain. Active Raf-1 is able to phosphorylate target Serine and Threonine residues in the presence of ATP. - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - Map2k2 - HGNC - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep1416 - - - - - C10H16N5O14P3 - guanosine 5'-triphosphoric acid - guanosine 5'-(tetrahydrogen triphosphate) - H4gtp - guanosine triphosphate - 5'-GTP - - - - - - - - - 523.181 - GTP - GTP - - - - REACT_2812 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2812.1 - - - - 109852 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109852 - - - - REACT_27518 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27518.1 - - - - 109853 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109853 - - - - 110049 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110049 - - - - - - - - - - - - - - - - ACTIVATION - - 'IL6:Tyrosine phosphorylated hexameric IL-6 receptor:Activated JAKs:p-SHP2 [plasma membrane]' positively regulates 'ERK1 activation' - IL-6-type receptor activation leads to induction of the MAPK cascade. Experiments using gp130 identified that the gp130 SHP2 (SH2-domain-containing tyrosine phosphatase)-binding site Tyr-759 (Stahl et al. 1995) is required for this activation. Mutation of gp130 Tyr-759 impairs IL-6 induced activation of the MAPK cascade (Kim et al. 1998). While there is a consensus that SHP2 is involved in IL-6-induced activation of the MAPK pathway, the molecular details are uncertain. One proposed mechanism suggests SHP2 acts as an adaptor for Grb2-Sos recruitment (Fukada et al. 1996, Kim & Baumann 1999). IL-6 induced SHP2 recruitment to p-Tyr-759 of gp130 was demonstrated but relatively little of the SHP2 remained associated with gp130, suggesting that SHP2 dissociates from the receptor when phosphorylated. This seems inconsistent with a Grb2-Sos recruitment role for SHP2, though it is possible that only low levels or transient recruitment are required. IL-6 induced ERK activation was not inhibited in cells transfected with a phosphatase inactive mutant of SHP2, whereas an SHP2 mutant missing the Grb2 interaction region significantly suppressed ERK activation. This suggests phosphatase activity is not required for ERK activation while SHP-2 interaction with Grb2 is important. However, overexpression studies can generate artefactual interactions and this interpretation has been questioned (Dance et al. 2008). An alternative proposal suggests that SHP2 and the adaptor protein Gab1 couple gp130 signalling to Erk activation. In this proposal phosphorylated SHP2 dissociates from gp130 and becomes associated with membrane associated Gab1 in a complex with PI3-kinase (Takahashi-Tezuka et al. 1998, Eulenfeld & Schaper 2009). SHP2 interaction is suggested to induce a conformational change in Gab1 that permits Gab1-PI3-kinase activation and enhancement of IL-6-induced Erk pathway activation. However this is speculative, the role of SHP2 phosphatase activity is unclear. Other possible mechanisms are outlined by Dance et al. (2008), extrapolated from growth factor receptor mechanisms but with unknown relevance to IL-6/gp130. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Control47 - - - - 3570 - Entrez Gene - - - - 3572 - Entrez Gene - - - - NP_002515 - RefSeq - - - - 57299 - CHEBI - - - - 109845 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109845 - - - - REACT_1391 - Reactome - 3 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1391.3 - - - - 109843 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109843 - - - - O-phospho-L-threonine - - cPath2-generated - - - - O-phospho-L-serine - - cPath2-generated - - - - 109844 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109844 - - - - 109849 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109849 - - - - 109848 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109848 - - - - REACT_5539 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5539.1 - - - - REACT_3152 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3152.1 - - - - REACT_495 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_495.5 - - - - 109841 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109841 - - - - 109842 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109842 - - - - REACT_28015 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_28015.1 - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep895 - - - - 29370 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29370 - - - - REACT_2686 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2686.2 - - - - - - - - - - - - - MAP kinase cascade - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Pathway269 - The MAP kinase cascade describes a sequence of phosphorylation events involving serine/threonine-specific protein kinases. Used by various signal transduction pathways, this cascade constitutes a common 'module' in the transmission of an extracellular signal into the nucleus. - Authored: Charalambous, M, 2004-04-29 09:21:24 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - - - - - - - - - - - - - - - - - - - - ERK2 activation - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Pathway194 - Activated MEK2 phosphorylates and activates ERK2. - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - - - - - - - - - Tyrosine phosphorylated IL6RB:Activated JAKs - Reactome DB_ID: 1112563 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex687 - - - - REACT_27493 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27493.1 - - - - Q9UD26 - uniprot - - - - REACT_27784 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27784.1 - - - - CHEBI:10789 - chebi - - - - Q96HD7 - uniprot - - - - Reactome - Reactome - cPath2-generated. Data loaded from: - cPath2-generated. Data version: 20110323, March 23, 2011 - http://www.reactome.org - cPath2-generated. Data (internal) id: REACTOME_HUMAN - cPath2-generated. Data type: BIOPAX - - - - 3569 - Entrez Gene - - - - 109830 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109830 - - - - - - - - - - - - - - - - - - - - 109837 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109837 - - - - - - - - - - - - - - - IL6:Tyrosine phosphorylated trimeric IL-6 receptor:Activated JAKs - Converted from EntitySet in Reactome - Reactome DB_ID: 1112584 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex684 - - - - - - - - Jak2 - HGNC - - - - REACT_27853 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27853.1 - - - - REACT_4130 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4130.1 - - - - 109838 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109838 - - - - REACT_2796 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2796.1 - - - - Jak1 - HGNC - - - - - - - - - - - phospho-ERK-1 dimer - Reactome DB_ID: 109844 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex680 - - - - 8143180 - PubChem - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#PathwayStep893 - - - - - REACT_545 - Reactome - 5 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_545.5 - - - - - - - - - - - Converted from EntitySet in Reactome - Reactome DB_ID: 112398 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein2359 - MEK - - - - 8934572 - Hibi, M - Fukada, T - Fujitani, Y - Nakajima, K - Yamaguchi, T - Yamanaka, Y - Hirano, T - Takahashi-Tezuka, M - PubMed - Two signals are necessary for cell proliferation induced by a cytokine receptor gp130: involvement of STAT3 in anti-apoptosis - Immunity 5:449-60 - 1996 - - - - - - - - - - - - - IL6:IL6RA:Tyrosine phosphorylated IL6RB:Activated JAKs - Reactome DB_ID: 1112585 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex685 - - - - - - ACTIVATION - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Catalysis582 - - - - REACT_2688 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2688.1 - - - - - C10H15N5O10P2 - 5'-adenylphosphoric acid - H3adp - adenosine 5'-(trihydrogen diphosphate) - - - - - - - - - ADP - ADP - A purine ribonucleoside 5'-diphosphate having adenine as the nucleobase. - - - - REACT_1780 - Reactome - 6 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1780.6 - - - - GO:0005829 - Gene Ontology - - - - - 2.0 - - - - CHEBI:16761 - chebi - - - - - - - - - - - - RAF1 phosphorylates MEK1 - Active Raf-1 phosphorylates MEK-1/2 on Serine residues, converting ATP to ADP. The MEK-1/2 kinase is now active. - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction980 - Authored: Charalambous, M, 2005-01-07 11:17:43 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - - NP_000556 - RefSeq - - - - Cdk1 - HGNC - - - - REACT_614 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_614.4 - - - - E1P616 - uniprot - - - - - - p(Y1054)-TYK2 - Non-receptor tyrosine-protein kinase TYK2 - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1640 - Reactome DB_ID: 1112598 - TYK2_HUMAN - - - - 9488469 - Baumann, H - Hawley, TS - Kim, H - Hawley, RG - PubMed - Protein tyrosine phosphatase 2 (SHP-2) moderates signaling by gp130 but is not required for the induction of acute-phase plasma protein genes in hepatic cells - Mol Cell Biol 18:1525-33 - 1998 - - - - - - - - - - - MEK1 binds ERK-1 - In the cytoplasm activated MEK1 (Serine phosphorylated) may encounter monomeric, inactive ERK1. ERK1 in its inactive form is not phosphorylated on a critical Threonine (T) and a critical Tyrosine (Y). - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#BiochemicalReaction696 - Authored: Charalambous, M, 2005-02-04 06:50:22 - Reviewed: Greene, LA, 2007-11-08 15:39:37 - Edited: Schmidt, EE, 0000-00-00 00:00:00 - - - - - - 1.0 - - - - - 1.0 - - - - REACT_1183 - Reactome - 4 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_1183.4 - - - - - 1.0 - - - - REACT_3645 - Reactome - 2 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3645.2 - - - - Mapk3 - HGNC - - - - - 2.0 - - - - - 1.0 - - - - Mapk1 - HGNC - - - - - 1.0 - - - - - - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1630 - Reactome DB_ID: 157415 - phospho-Cdc2 (Thr 161) - - - - - 1.0 - - - - Q06124 - uniprot - - - - - 1.0 - - - - - 1.0 - - - - 2.7.10.2 - - - - - - - TYK2_HUMAN - Non-receptor tyrosine-protein kinase TYK2 - FUNCTION: Probably involved in intracellular signal transduction by being involved in the initiation of type I IFN signaling. Phosphorylates the interferon-alpha/beta receptor alpha chain. CATALYTIC ACTIVITY: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate. SUBUNIT: Interacts with JAKMIP1. TISSUE SPECIFICITY: Observed in all cell lines analyzed. Expressed in a variety of lymphoid and non-lymphoid cell lines. DOMAIN: The FERM domain mediates interaction with JAKMIP1. DISEASE: Defects in TYK2 are the cause of protein-tyrosine kinase 2 deficiency (TYK2 deficiency) [MIM:611521]; also known as autosomal recessive hyper-IgE syndrome (HIES) with atypical mycobacteriosis. TYK2 deficiency consists of a primary immunodeficiency characterized by recurrent skin abscesses, pneumonia, and highly elevated serum IgE. SIMILARITY: Belongs to the protein kinase superfamily. Tyr protein kinase family. JAK subfamily. SIMILARITY: Contains 1 FERM domain. SIMILARITY: Contains 1 protein kinase domain. SIMILARITY: Contains 1 SH2 domain. WEB RESOURCE: Name=TYK2base; Note=TYK2 mutation db; URL="http://bioinf.uta.fi/TYK2base/"; WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/tyk2/"; COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - MEK 1 - MKK1 - MAPK/ERK kinase 1 - ERK activator kinase 1 - 2.7.12.2 - MAP kinase kinase 1 - MAPKK 1 - - - - - MP2K1_HUMAN - Dual specificity mitogen-activated protein kinase kinase 1 - FUNCTION: Catalyzes the concomitant phosphorylation of a threonine and a tyrosine residue in a Thr-Glu-Tyr sequence located in MAP kinases. Activates ERK1 and ERK2 MAP kinases. CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein. ENZYME REGULATION: Activated by phosphorylation. SUBUNIT: Interacts with MORG1. Interacts with ARRB2 (By similarity). Interacts with Yersinia yopJ. ALTERNATIVE PRODUCTS: Event=Alternative splicing; Named isoforms=2; Name=1; Synonyms=MKK1a; IsoId=Q02750-1; Sequence=Displayed; Name=2; Synonyms=MKK1b; IsoId=Q02750-2; Sequence=VSP_040500; TISSUE SPECIFICITY: Widely expressed, with extremely low levels in brain. PTM: Phosphorylation on Ser/Thr by MAP kinase kinase kinases (RAF or MEKK1) regulates positively the kinase activity. PTM: Acetylation by Yersinia yopJ prevents phosphorylation and activation, thus blocking the MAPK signaling pathway. DISEASE: Defects in MAP2K1 are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:115150]; also known as cardio-facio- cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant. SIMILARITY: Belongs to the protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase subfamily. SIMILARITY: Contains 1 protein kinase domain. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/MAP2K1"; GENE SYNONYMS: MEK1 PRKMK1. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - 1.0 - - - - Janus kinase 1 - JAK-1 - 2.7.10.2 - - - - - - - JAK1_HUMAN - Tyrosine-protein kinase JAK1 - FUNCTION: Tyrosine kinase of the non-receptor type, involved in the IFN-alpha/beta/gamma signal pathway. Kinase partner for the interleukin (IL)-2 receptor. CATALYTIC ACTIVITY: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate. SUBUNIT: Interacts with IL31RA, IFNAR2, JAKMIP1 and SHB. SUBCELLULAR LOCATION: Endomembrane system; Peripheral membrane protein. Note=Wholly intracellular, possibly membrane associated. TISSUE SPECIFICITY: Expressed at higher levels in primary colon tumors than in normal colon tissue. The expression level in metastatic colon tumors is comparable to the expression level in normal colon tissue. DOMAIN: Possesses two phosphotransferase domains. The second one probably contains the catalytic domain (By similarity), while the presence of slight differences suggest a different role for domain 1. DOMAIN: The FERM domain mediates interaction with JAKMIP1. SIMILARITY: Belongs to the protein kinase superfamily. Tyr protein kinase family. JAK subfamily. SIMILARITY: Contains 1 FERM domain. SIMILARITY: Contains 1 protein kinase domain. SIMILARITY: Contains 1 SH2 domain. SEQUENCE CAUTION: Sequence=AAA36527.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAA36527.1; Type=Frameshift; Positions=858, 862; GENE SYNONYMS: JAK1A JAK1B. COPYRIGHT: Protein annotation is derived from the UniProt Consortium (http://www.uniprot.org/). Distributed under the Creative Commons Attribution-NoDerivs License. - - - - - - - - - - - - - - Activated RAF1 complex:MEK2 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex1118 - Reactome DB_ID: 109795 - - - - - - - - - - - - - IL6:Tyrosine phosphorylated hexameric IL-6 receptor:Activated JAKs:p-SHP2 - Reactome DB_ID: 1112753 - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Complex682 - - - - REACT_3918 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3918.1 - - - - Q96D10 - uniprot - - - - - - sIL6R - Interleukin-6 receptor subunit alpha short soluble form - IL6RA_HUMAN - - - - - - Original RDFId (before applying ReactomeCleaner): http://www.reactome.org/biopax/48887#Protein1642 - Reactome DB_ID: 1067661 - IL6R - - - - - 2.0 - - - - Ywhab - HGNC - - - - - 2.0 - - - - - 1.0 - - - - - 1.0 - - - - REACT_27647 - Reactome - 1 - Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27647.1 - - - - 59282 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=59282 - - - - 59284 - Reactome - Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=59284 - - \ No newline at end of file diff --git a/paxtools-archetype/src/test/resources/projects/basic/archetype.properties b/paxtools-archetype/src/test/resources/projects/basic/archetype.properties deleted file mode 100644 index cfc061405..000000000 --- a/paxtools-archetype/src/test/resources/projects/basic/archetype.properties +++ /dev/null @@ -1,5 +0,0 @@ -#Tue Mar 04 19:25:14 EST 2014 -package=it.pkg -version=0.2-SNAPSHOT -groupId=archetype.it -artifactId=basic diff --git a/paxtools-archetype/src/test/resources/projects/basic/goal.txt b/paxtools-archetype/src/test/resources/projects/basic/goal.txt deleted file mode 100644 index e69de29bb..000000000 diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java index 65ebdf736..61bba14cb 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/ProteinNameLister.java @@ -62,22 +62,10 @@ public static void main(String[] args) * (do not worry - those pathway steps that are part of * the pathway must be in the PATHWAY-COMPONENTS set) */ - Filter nextStepPropertyFilter = new Filter() - { - public boolean filter(PropertyEditor editor) - { - return !editor.getProperty().equals("NEXT-STEP"); - } - }; + Filter nextStepPropertyFilter = editor -> !editor.getProperty().equals("NEXT-STEP"); fetcher = new Fetcher(SimpleEditorMap.L2, nextStepPropertyFilter); - FilenameFilter filter = new FilenameFilter() - { - public boolean accept(File dir, String name) - { - return (name.endsWith("owl")); - } - }; + FilenameFilter filter = (dir, name) -> (name.endsWith("owl")); for (String s : testDir.list(filter)) { diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java index 4b6ec7eb5..c3eae846b 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CommandManagerTest.java @@ -7,12 +7,12 @@ import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.MolecularInteraction; import org.biopax.paxtools.model.level3.Protein; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.util.HashSet; import java.util.Set; -import static junit.framework.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.assertTrue; public class CommandManagerTest { diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java index d44da305a..26d561fdd 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/CompleterClonerTest.java @@ -6,33 +6,28 @@ import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.util.ClassFilterSet; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.util.Collection; import java.util.Collections; import java.util.Set; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; -public class CompleterClonerTest -{ - private Model model; - private String pwUri; +public class CompleterClonerTest { - @Before - public void init() { - MockFactory mock= new MockFactory(BioPAXLevel.L3); - model = mock.createModel(); + @Test + public void completeAndClone() { + MockFactory mock = new MockFactory(BioPAXLevel.L3); + Model model = mock.createModel(); Pathway pw = mock.create(model,Pathway.class,1)[0]; - pwUri = pw.getUri(); + String pwUri = pw.getUri(); BiochemicalReaction[] rx = mock.create(model, BiochemicalReaction.class,2); Control[] co = mock.create(model, Control.class,2); PathwayStep[] ps = mock.create(model,PathwayStep.class,2); Protein[] p = mock.create(model,Protein.class,2); SmallMolecule[] sm = mock.create(model,SmallMolecule.class,2); - pw.addPathwayComponent(co[0]); pw.addPathwayOrder(ps[0]); mock.bindArrays(mock.editor("controlled",Control.class),co,rx); @@ -41,16 +36,11 @@ public void init() { ps[0].addNextStep(ps[1]); mock.bindArrays(mock.editor("stepProcess",PathwayStep.class),ps,rx); mock.bindArrays(mock.editor("stepProcess",PathwayStep.class),ps,co); - } - @Test - public void testCompleteAndClone() - { Completer completer = new Completer(SimpleEditorMap.L3); Collection completed = completer.complete(Collections.singleton(model.getByID(pwUri))); assertTrue(completed.size()>1); - //PathwayStep1 should not be there if @AutoComplete(forward=false) has any effect on getNextStep() Set steps = new ClassFilterSet<>(completed,PathwayStep.class); assertEquals(1, steps.size()); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java index ccfebe25f..ebbaf6848 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/EditorMapImplTest.java @@ -3,18 +3,16 @@ import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.util.Set; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.*; public class EditorMapImplTest { @Test - public void testGetKnownSubClassesOf() throws Exception + public void getKnownSubClassesOf() throws Exception { Set> organism = SimpleEditorMap.L3 .getSubclassEditorsForProperty("organism", BioPAXElement.class); @@ -22,7 +20,7 @@ public void testGetKnownSubClassesOf() throws Exception } @Test - public void testSomePropertyRange() { + public void somePropertyRange() { PropertyEditor entityReferencePropEditor = SimpleEditorMap.L3.getEditorForProperty("entityReference", Protein.class); assertEquals(EntityReference.class, entityReferencePropEditor.getRange()); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/FetcherTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/FetcherTest.java index 15b76cfa9..0f12610ac 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/FetcherTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/FetcherTest.java @@ -4,21 +4,20 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.BeforeClass; -import org.junit.Test; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; import java.util.Set; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class FetcherTest { - private static Model model; + static Model model = BioPAXLevel.L3.getDefaultFactory().createModel(); - @BeforeClass - public static void setupTest() { + @BeforeAll + public static void init() { model = BioPAXLevel.L3.getDefaultFactory().createModel(); - //create/add 8 objects Pathway pw1 = model.addNew(Pathway.class, "pathway1"); Pathway pw2 = model.addNew(Pathway.class, "pathway2"); @@ -48,7 +47,7 @@ public static void setupTest() { } @Test - public final void testForEndlessLoopOrOutOfMemory() { + public void endlessLoopOrOutOfMemory() { Pathway pw1 = (Pathway) model.getByID("pathway1"); Fetcher fetcher = new Fetcher(SimpleEditorMap.L3); @@ -69,7 +68,7 @@ public final void testForEndlessLoopOrOutOfMemory() { } @Test - public final void testFetchDepth() { + public final void fetchDepth() { Pathway pw1 = (Pathway) model.getByID("pathway1"); Set elements; diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java index 687efb5f6..cface8928 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ModelUtilsTest.java @@ -9,20 +9,19 @@ import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.util.IllegalBioPAXArgumentException; -import org.junit.Assert; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.io.ByteArrayOutputStream; import java.io.File; import java.util.Arrays; import java.util.Map; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class ModelUtilsTest { @Test - public final void testMergeAndReplace() { + public final void mergeAndReplace() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model m = factory.createModel(); @@ -147,7 +146,7 @@ public final void printMetrics() @Test - public final void testRemoveObjectsIfDangling() { + public final void removeObjectsIfDangling() { Model model = (new SimpleIOHandler()).convertFromOWL( getClass().getClassLoader().getResourceAsStream("L3" + File.separator + "hcyc.owl")); assertEquals(6, model.getObjects().size()); @@ -184,7 +183,7 @@ public final void testRemoveObjectsIfDangling() { } @Test - public void testGenericNormalization() { + public void genericNormalization() { MockFactory mock = new MockFactory(BioPAXLevel.L3); Model model = mock.createModel(); Protein[] p = mock.create(model, Protein.class, 3); @@ -201,7 +200,7 @@ public void testGenericNormalization() { } @Test - public void testFixEquivalentFeatures() + public void fixEquivalentFeatures() { MockFactory mock = new MockFactory(BioPAXLevel.L3); Model model = mock.createModel(); @@ -225,7 +224,7 @@ public void testFixEquivalentFeatures() } @Test - public void testMergeEquivalentConversions() + public void mergeEquivalentConversions() { MockFactory mock = new MockFactory(BioPAXLevel.L3); Model model = mock.createModel(); @@ -251,7 +250,7 @@ public void testMergeEquivalentConversions() } @Test - public void testMergeEquivalentPhysicalEntities() + public void mergeEquivalentPhysicalEntities() { MockFactory mock = new MockFactory(BioPAXLevel.L3); Model model = mock.createModel(); @@ -298,12 +297,12 @@ public void testMergeEquivalentPhysicalEntities() } @Test - public void testBase62() { + public void base62() { final String longUri = "http://www.ctdbase.org/#process_RXN_%5BCFTR+protein+inhibits+the+reaction+%5B%5B" + "Colforsin+co-treated+with+Genistein%5D+results+in+increased+transport+of+Iodides%5D%5D"; String shortStr = ModelUtils.encodeBase62(longUri); - Assert.assertEquals("k9viXaDIiOW", shortStr); + assertEquals("k9viXaDIiOW", shortStr); String shortUri = ModelUtils.shortenUri("http://www.ctdbase.org/", longUri); - Assert.assertEquals("http://www.ctdbase.org/k9viXaDIiOW", shortUri); + assertEquals("http://www.ctdbase.org/k9viXaDIiOW", shortUri); } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java index ef7a68688..e51777fab 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/PathAccessorTest.java @@ -5,22 +5,19 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Set; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; -/** - * - */ public class PathAccessorTest { @Test - public void testPaths() + public void paths() { MockFactory mock= new MockFactory(BioPAXLevel.L3); final Model model = mock.createModel(); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ShallowCopyTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ShallowCopyTest.java index 2a6330015..35fb1d8a7 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/ShallowCopyTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/ShallowCopyTest.java @@ -1,21 +1,21 @@ package org.biopax.paxtools.controller; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; import org.biopax.paxtools.model.BioPAXFactory; import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.level3.*; -import org.junit.Before; -import org.junit.Test; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class ShallowCopyTest { - @Before + @BeforeEach public void setUp() throws Exception { } @Test - public final void testCopyTString() { + public final void copyTString() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Protein p1 = factory.create(Protein.class, "p1"); ProteinReference pr1 = factory.create(ProteinReference.class, "pr1"); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java index b2fcf30fc..48eb9c001 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleEditorMapTest.java @@ -13,16 +13,16 @@ import org.biopax.paxtools.model.level3.DeltaG; import org.biopax.paxtools.model.level3.Protein; import org.biopax.paxtools.model.level3.ProteinReference; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.util.Set; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class SimpleEditorMapTest { @Test - public void testSimpleEditorMap() throws Exception + public void simpleEditorMap() throws Exception { for (BioPAXLevel level : BioPAXLevel.values()) { @@ -40,7 +40,7 @@ public void testSimpleEditorMap() throws Exception * using the corresponding property editor */ @Test - public void testClearSingularProperty() { + public void clearSingularProperty() { BioPAXFactory fac = BioPAXLevel.L3.getDefaultFactory(); EditorMap em = SimpleEditorMap.L3; @@ -78,7 +78,7 @@ public void testClearSingularProperty() { } @Test - public final void testComments() { + public final void comments() { BioPAXFactory fac = BioPAXLevel.L3.getDefaultFactory(); EditorMap em = SimpleEditorMap.L3; ProteinReference pr1 = fac.create(ProteinReference.class, "pr1"); @@ -103,7 +103,7 @@ public final void testComments() { * with confidence. */ @Test - public void testClearInverseProperty() { + public void clearInverseProperty() { BioPAXFactory fac = BioPAXLevel.L3.getDefaultFactory(); EditorMap em = SimpleEditorMap.L3; diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java index 4a30688cf..75d9eaa55 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/SimpleMergerTest.java @@ -2,10 +2,10 @@ import org.biopax.paxtools.model.*; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; /** * @author rodche @@ -13,7 +13,7 @@ public class SimpleMergerTest { @Test - public final void testMergeModel() { + public final void mergeModel() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model model = factory.createModel(); Xref ref = model.addNew(UnificationXref.class, "Xref1"); @@ -69,7 +69,7 @@ public final void testMergeModel() { } @Test - public final void testMergeObject() { + public final void mergeObject() { SimpleMerger merger = new SimpleMerger(SimpleEditorMap.L3); BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model model = factory.createModel(); @@ -93,7 +93,7 @@ public final void testMergeObject() { } @Test - public final void testMergeToInconsistentModel() { + public final void mergeToInconsistentModel() { // Let's merge an object having one xref into a model that // implicitly "contains" a different xref with the same URI; // merged model will explicitly contain only the xref @@ -190,7 +190,7 @@ public final void testMergeToInconsistentModel() { } @Test - public final void testMergeWithoutFilter() { + public final void mergeWithoutFilter() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model model = factory.createModel(); //create a PR, BS, etc., in the (target) model @@ -238,7 +238,7 @@ public final void testMergeWithoutFilter() { @Test - public final void testMergeWithFilter() { + public final void mergeWithFilter() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); Model model = factory.createModel(); //create a PR, BS, etc., in the (target) model diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/TransitiveAccessorTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/TransitiveAccessorTest.java index 2dd15b45f..0224099be 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/TransitiveAccessorTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/TransitiveAccessorTest.java @@ -6,19 +6,18 @@ import org.biopax.paxtools.model.level3.Complex; import org.biopax.paxtools.model.level3.PhysicalEntity; import org.biopax.paxtools.model.level3.Protein; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.util.Set; -import static org.hamcrest.core.Is.is; -import static org.junit.Assert.assertThat; +import static org.junit.jupiter.api.Assertions.*; /** */ public class TransitiveAccessorTest { @Test - public void testTransitiveGet() + public void transitiveGet() { Model model = new MockFactory(BioPAXLevel.L3).createModel(); Complex outer = model.addNew(Complex.class, "outer"); @@ -35,10 +34,10 @@ public void testTransitiveGet() "component", Complex.class); TransitivePropertyAccessor ta = TransitivePropertyAccessor.create(pe); Set components = ta.getValueFromBean(outer); - assertThat(true, is(components.size() == 3)); - assertThat(true, is(components.contains(base))); - assertThat(true, is(components.contains(inner))); - assertThat(true, is(components.contains(innermost))); + assertEquals(3,components.size()); + assertTrue(components.contains(base)); + assertTrue(components.contains(inner)); + assertTrue(components.contains(innermost)); //create a loop (bad idea, but it does happen in real data, not only with 'component' prop.) @@ -47,10 +46,10 @@ public void testTransitiveGet() inner.addComponent(outer); ta = TransitivePropertyAccessor.create(pe); components = ta.getValueFromBean(outer); //should not fail or loop infinitely - assertThat(true, is(components.size() == 4)); - assertThat(true, is(components.contains(base))); - assertThat(true, is(components.contains(inner))); - assertThat(true, is(components.contains(innermost))); - assertThat(true, is(components.contains(outer))); + assertTrue(components.size() == 4); + assertTrue(components.contains(base)); + assertTrue(components.contains(inner)); + assertTrue(components.contains(innermost)); + assertTrue(components.contains(outer)); } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/controller/UnionPropertyAccessorTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/controller/UnionPropertyAccessorTest.java index b4e5f608a..957bcd7bb 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/controller/UnionPropertyAccessorTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/controller/UnionPropertyAccessorTest.java @@ -4,19 +4,19 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; import java.util.Arrays; import java.util.Set; -import static org.junit.Assert.assertTrue; /** */ public class UnionPropertyAccessorTest { @Test - public void testUnion() + public void union() { MockFactory factory = new MockFactory(BioPAXLevel.L3); @@ -45,9 +45,7 @@ public void testUnion() PathAccessor pa = new PathAccessor("Complex/component/entityReference/organism", BioPAXLevel.L3); Set valueFromBean = pa.getValueFromBean(complex); - assertTrue(valueFromBean.containsAll(Arrays.asList(human,alien))); - assertTrue(valueFromBean.size()==2); - - + Assertions.assertTrue(valueFromBean.containsAll(Arrays.asList(human,alien))); + Assertions.assertTrue(valueFromBean.size()==2); } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/converter/LevelUpgraderTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/converter/LevelUpgraderTest.java index ae83da904..c4ef86831 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/converter/LevelUpgraderTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/converter/LevelUpgraderTest.java @@ -8,42 +8,42 @@ import org.biopax.paxtools.model.level2.protein; import org.biopax.paxtools.model.level3.Protein; import org.biopax.paxtools.model.level3.SmallMolecule; -import org.junit.Test; -import static org.junit.Assert.*; +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; import java.io.*; public class LevelUpgraderTest { - @Test - public final void testGetLocalId() { + public final void getLocalId() { BioPAXElement bpe = BioPAXLevel.L2.getDefaultFactory().create("protein", "http://example.com#someid"); - assertEquals("someid",LevelUpgrader.getLocalId(bpe)); + assertEquals("someid", LevelUpgrader.getLocalId(bpe)); bpe = BioPAXLevel.L2.getDefaultFactory().create("protein", "http://example.com/someid"); - assertEquals("someid",LevelUpgrader.getLocalId(bpe)); + assertEquals("someid", LevelUpgrader.getLocalId(bpe)); } @Test - public final void testFilter() throws IOException { + public final void filter() throws IOException { SimpleIOHandler io = new SimpleIOHandler(); Model model = io.convertFromOWL( - getClass().getClassLoader() - .getResourceAsStream("L2/biopax-example-short-pathway.owl")); - + getClass().getClassLoader() + .getResourceAsStream("L2/biopax-example-short-pathway.owl")); + physicalEntityParticipant pep31 = (physicalEntityParticipant) model.getByID(model.getXmlBase() + "physicalEntityParticipant31"); assertTrue(pep31 instanceof physicalEntityParticipant); assertTrue(pep31.getPHYSICAL_ENTITY() instanceof protein); assertNotNull(pep31.getCELLULAR_LOCATION()); - + model = (new LevelUpgrader()).filter(model); - + if (model != null) { io.convertToOWL(model, new FileOutputStream( getClass().getClassLoader().getResource("").getFile() + File.separator + "converted.owl")); } - - + + SmallMolecule p9 = (SmallMolecule) model.getByID(model.getXmlBase() + "physicalEntityParticipant9"); Protein p31 = (Protein) model.getByID(model.getXmlBase() + "physicalEntityParticipant31"); assertTrue(p9 instanceof SmallMolecule); @@ -53,12 +53,12 @@ public final void testFilter() throws IOException { assertEquals(p9.getCellularLocation(), p31.getCellularLocation()); } - @Test - public final void testFilterBigger() throws IOException { + @Test + public final void filterBigger() throws IOException { SimpleIOHandler io = new SimpleIOHandler(); Model model = io.convertFromOWL( - getClass().getClassLoader() - .getResourceAsStream("L2/biopax-example-ecocyc-glycolysis.owl")); + getClass().getClassLoader() + .getResourceAsStream("L2/biopax-example-ecocyc-glycolysis.owl")); model = (new LevelUpgrader()).filter(model); if (model != null) { io.convertToOWL(model, new FileOutputStream( diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java index 49de4db0c..988b02e58 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EqualsEtcTest.java @@ -11,9 +11,9 @@ import org.biopax.paxtools.model.level3.Xref; import org.biopax.paxtools.util.BiopaxElements; import org.biopax.paxtools.util.BiopaxSafeSet; -import org.junit.Test; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class EqualsEtcTest { diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java index b3b3767ac..1e212e99b 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/EquivalenceImplTest.java @@ -9,14 +9,14 @@ import org.biopax.paxtools.model.level3.Evidence; import org.biopax.paxtools.model.level3.EvidenceCodeVocabulary; import org.biopax.paxtools.model.level3.UnificationXref; -import org.junit.Test; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class EquivalenceImplTest { @Test - public final void testSemanticallyEquivalent() { + public final void semanticallyEquivalent() { Model m = BioPAXLevel.L3.getDefaultFactory().createModel(); UnificationXref x = m.addNew(UnificationXref.class, "ExpType_MI_0492"); @@ -41,7 +41,7 @@ public final void testSemanticallyEquivalent() { @Test - public final void testBindingFeatureEquivalentNPE() { + public final void bindingFeatureEquivalentNPE() { BioPAXIOHandler io = new SimpleIOHandler(); Model m = io.convertFromOWL(getClass().getResourceAsStream("test_bf_isequivalent-npe.owl")); BindingFeature a = (BindingFeature) m.getByID(m.getXmlBase() + "id377153490_STAT3_p_bf3"); diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java index ae91228d3..a5f4fb5ff 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/impl/level3/ModelCoverageTest.java @@ -5,15 +5,14 @@ import org.biopax.paxtools.impl.MockFactory; import org.biopax.paxtools.model.BioPAXElement; import org.biopax.paxtools.model.BioPAXLevel; -import org.junit.Test; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.*; public class ModelCoverageTest { - @Test - public void testCreationMethods() { + @Test + public void creationMethods() { MockFactory factory = new MockFactory(BioPAXLevel.L3); //test reflectively create EditorMap map = SimpleEditorMap.L3; diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java index 57727bb5a..2fa34119a 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/io/SimpleIOHandlerTest.java @@ -6,332 +6,316 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; import java.io.*; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class SimpleIOHandlerTest { - private void outputModel(Model m, OutputStream out) { - (new SimpleIOHandler()).convertToOWL(m, out); - } - - @Test - public final void testExportL2() throws FileNotFoundException { - Model model = BioPAXLevel.L2.getDefaultFactory().createModel(); - FileOutputStream out = new FileOutputStream( - getClass().getResource("").getFile() - + File.separator + "simple.owl" - ); - outputModel(model, out); - } - - @Test - public final void testReadWriteL2() throws IOException - { - BioPAXIOHandler io = new SimpleIOHandler(); - io.fixReusedPEPs(false); - Model model = getL2Model(io); - assertNotNull(model); - assertFalse(model.getObjects().isEmpty()); - System.out.println("Model has " + model.getObjects().size() + " objects)"); - FileOutputStream out = - new FileOutputStream( - getClass().getResource("").getFile() - + File.separator + "simpleReadWrite.owl" - ); - io.convertToOWL(model, out); - } - - public static Model getL2Model(BioPAXIOHandler io) - { - String s = "L2" + File.separator + "biopax_id_557861_mTor_signaling.owl"; - System.out.println("file = " + s); - System.out.println("starting " + s); - InputStream in = SimpleIOHandlerTest.class.getClassLoader().getResourceAsStream(s); - assertNotNull(in); - return io.convertFromOWL(in); - } - - @Test - public final void testReadWriteL3() throws IOException - { - BioPAXIOHandler io = new SimpleIOHandler(); //auto-detects level - Model model = getL3Model(io); - assertNotNull(model); - assertFalse(model.getObjects().isEmpty()); - System.out.println("Model has " + model.getObjects().size() + " objects)"); - FileOutputStream out = new FileOutputStream(getClass().getResource("") - .getFile() + File.separator + "simpleReadWrite.owl"); - io.convertToOWL(model, out); - } - - public static Model getL3Model(BioPAXIOHandler io) - { - String s = "L3" + File.separator + "biopax3-short-metabolic-pathway.owl"; - InputStream in = SimpleIOHandlerTest.class.getClassLoader().getResourceAsStream(s); - return io.convertFromOWL(in); - } - - @Test - public final void testDuplicateNamesByExporter() throws IOException - { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - Protein p = factory.create(Protein.class, "myProtein"); - String name = "aDisplayName"; - p.setDisplayName(name); - p.addComment("Display Name should not be repeated again in the Name property!"); - Model m = factory.createModel(); - m.add(p); - - FileOutputStream out = - new FileOutputStream( // to the target test dir - getClass().getResource("").getFile() - + File.separator + "testDuplicateNamesByExporter.xml" - ); - - outputModel(m, out); - - // read - BufferedReader in = new BufferedReader( - new FileReader(getClass().getResource("").getFile() - + File.separator + "testDuplicateNamesByExporter.xml")); - char[] buf = new char[1000]; - in.read(buf); - String xml = new String(buf); - if (xml.indexOf(name) != xml.lastIndexOf(name)) - { - fail("displayName gets duplicated by the SimpleIOHandler!"); - } - - } - - - @Test - public final void testDuplicateConversionInBiochemicalPathwayStepByExporter() throws IOException - { - BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); - BiochemicalPathwayStep bps = factory.create(BiochemicalPathwayStep.class, "myStep"); - BiochemicalReaction reaction = factory.create(BiochemicalReaction.class, "myConversion"); - bps.setStepConversion(reaction); - bps.addComment("The Conversion should not occur in stepProcess property!"); - Model m = factory.createModel(); - m.add(bps); - m.add(reaction); - - FileOutputStream out = - new FileOutputStream( // to the target test dir - getClass().getResource("").getFile() - + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml" - ); - - outputModel(m, out); - - // read back - BufferedReader in = new BufferedReader( - new FileReader(getClass().getResource("").getFile() - + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml")); - char[] buf = new char[3000]; - in.read(buf); - String xml = new String(buf); - - assertTrue(xml.contains(" & % : + && #"; - System.out.println(s); - pr[0].getName().clear(); - pr[0].addName(s); - - // Write - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - io.convertToOWL(model, outputStream); - outputStream.flush(); - - // Read - ByteArrayInputStream inputStream = new ByteArrayInputStream(outputStream.toByteArray()); - outputStream.close(); - Model newModel = io.convertFromOWL(inputStream); - - Protein prot = (Protein) newModel.getObjects().iterator().next(); - assertTrue(prot.getName().iterator().next().equals(s)); - } + private void outputModel(Model m, OutputStream out) { + (new SimpleIOHandler()).convertToOWL(m, out); + } + + @Test + public void exportL2() throws FileNotFoundException { + Model model = BioPAXLevel.L2.getDefaultFactory().createModel(); + FileOutputStream out = new FileOutputStream( + getClass().getResource("").getFile() + + File.separator + "simple.owl" + ); + outputModel(model, out); + } + + @Test + public void readWriteL2() throws IOException { + BioPAXIOHandler io = new SimpleIOHandler(); + io.fixReusedPEPs(false); + Model model = getL2Model(io); + assertNotNull(model); + assertFalse(model.getObjects().isEmpty()); + System.out.println("Model has " + model.getObjects().size() + " objects)"); + FileOutputStream out = + new FileOutputStream( + getClass().getResource("").getFile() + + File.separator + "simpleReadWrite.owl" + ); + io.convertToOWL(model, out); + } + + public static Model getL2Model(BioPAXIOHandler io) { + String s = "L2" + File.separator + "biopax_id_557861_mTor_signaling.owl"; + System.out.println("file = " + s); + System.out.println("starting " + s); + InputStream in = SimpleIOHandlerTest.class.getClassLoader().getResourceAsStream(s); + assertNotNull(in); + return io.convertFromOWL(in); + } + + @Test + public void readWriteL3() throws IOException { + BioPAXIOHandler io = new SimpleIOHandler(); //auto-detects level + Model model = getL3Model(io); + assertNotNull(model); + assertFalse(model.getObjects().isEmpty()); + System.out.println("Model has " + model.getObjects().size() + " objects)"); + FileOutputStream out = new FileOutputStream(getClass().getResource("") + .getFile() + File.separator + "simpleReadWrite.owl"); + io.convertToOWL(model, out); + } + + public static Model getL3Model(BioPAXIOHandler io) { + String s = "L3" + File.separator + "biopax3-short-metabolic-pathway.owl"; + InputStream in = SimpleIOHandlerTest.class.getClassLoader().getResourceAsStream(s); + return io.convertFromOWL(in); + } + + @Test + public void duplicateNamesByExporter() throws IOException { + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + Protein p = factory.create(Protein.class, "myProtein"); + String name = "aDisplayName"; + p.setDisplayName(name); + p.addComment("Display Name should not be repeated again in the Name property!"); + Model m = factory.createModel(); + m.add(p); + + FileOutputStream out = + new FileOutputStream( // to the target test dir + getClass().getResource("").getFile() + + File.separator + "testDuplicateNamesByExporter.xml" + ); + + outputModel(m, out); + + // read + BufferedReader in = new BufferedReader( + new FileReader(getClass().getResource("").getFile() + + File.separator + "testDuplicateNamesByExporter.xml")); + char[] buf = new char[1000]; + in.read(buf); + String xml = new String(buf); + if (xml.indexOf(name) != xml.lastIndexOf(name)) { + fail("displayName gets duplicated by the SimpleIOHandler!"); + } + + } + + + @Test + public void duplicateConversionInBiochemicalPathwayStepByExporter() throws IOException { + BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); + BiochemicalPathwayStep bps = factory.create(BiochemicalPathwayStep.class, "myStep"); + BiochemicalReaction reaction = factory.create(BiochemicalReaction.class, "myConversion"); + bps.setStepConversion(reaction); + bps.addComment("The Conversion should not occur in stepProcess property!"); + Model m = factory.createModel(); + m.add(bps); + m.add(reaction); + + FileOutputStream out = + new FileOutputStream( // to the target test dir + getClass().getResource("").getFile() + + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml" + ); + + outputModel(m, out); + + // read back + BufferedReader in = new BufferedReader( + new FileReader(getClass().getResource("").getFile() + + File.separator + "testDuplicateConversionInBiochemicalPathwayStepByExporter.xml")); + char[] buf = new char[3000]; + in.read(buf); + String xml = new String(buf); + + assertTrue(xml.contains(" & % : + && #"; + //System.out.println(s); + pr[0].getName().clear(); + pr[0].addName(s); + + // Write + ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); + io.convertToOWL(model, outputStream); + outputStream.flush(); + + // Read + ByteArrayInputStream inputStream = new ByteArrayInputStream(outputStream.toByteArray()); + outputStream.close(); + Model newModel = io.convertFromOWL(inputStream); + + Protein prot = (Protein) newModel.getObjects().iterator().next(); + assertTrue(prot.getName().iterator().next().equals(s)); + } } diff --git a/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java b/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java index 64f4b1129..ca9b28dee 100644 --- a/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java +++ b/paxtools-core/src/test/java/org/biopax/paxtools/model/BioPAXFactoryTest.java @@ -2,9 +2,9 @@ import org.biopax.paxtools.model.level3.*; import org.biopax.paxtools.model.level3.Process; -import org.junit.Test; +import org.junit.jupiter.api.Test; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; /** * Created by igor on 06/04/17. diff --git a/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java b/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java index 4e8a84994..afc22b891 100644 --- a/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java +++ b/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java @@ -15,8 +15,8 @@ import org.biopax.paxtools.query.wrapperL3.Filter; import org.biopax.paxtools.query.wrapperL3.OrganismFilter; import org.biopax.paxtools.query.wrapperL3.UbiqueFilter; -import org.junit.Ignore; -import org.junit.Test; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; import java.io.FileOutputStream; import java.io.IOException; @@ -26,18 +26,17 @@ import java.util.HashSet; import java.util.Set; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; +import static org.junit.jupiter.api.Assertions.*; /** * @author Ozgun Babur */ public class QueryTest { - static BioPAXIOHandler handler = new SimpleIOHandler(); + static final BioPAXIOHandler handler = new SimpleIOHandler(); @Test - public void testQueries() throws Throwable + public void queries() { Model model = handler.convertFromOWL(QueryTest.class.getResourceAsStream( "raf_map_kinase_cascade_reactome.owl")); @@ -124,8 +123,8 @@ protected static Collection findElements(Model model, String... i } @Test - @Ignore - public void testQueryPerformance() throws IOException + @Disabled + public void queryPerformance() throws IOException { long time = System.currentTimeMillis(); @@ -157,7 +156,7 @@ public void testQueryPerformance() throws IOException } @Test - public void testFilters() + public void filters() { Model model = handler.convertFromOWL(this.getClass().getResourceAsStream( "raf_map_kinase_cascade_reactome.owl")); diff --git a/pom.xml b/pom.xml index 9a1816103..e86262fb0 100644 --- a/pom.xml +++ b/pom.xml @@ -30,7 +30,6 @@ sbgn-converter paxtools-console paxtools-query - paxtools-archetype json-converter pattern normalizer @@ -40,9 +39,10 @@ github UTF-8 UTF-8 - 1.7.25 - -Dfile.encoding=UTF-8 + 2.0.7 17 + 17 + 17 @@ -330,7 +330,7 @@ false -ea - + -ea --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED @@ -358,11 +358,23 @@ - junit - junit - 4.13.2 + org.junit.jupiter + junit-jupiter-api + 5.9.3 test + + org.junit.jupiter + junit-jupiter-params + 5.9.3 + test + + + + + + + net.sourceforge.collections collections-generic @@ -462,10 +474,17 @@ test - junit - junit - test + org.junit.jupiter + junit-jupiter-api + + + org.junit.jupiter + junit-jupiter-params + + + + javax.xml.bind jaxb-api diff --git a/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java b/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java index d35e3e04f..aa4504b25 100644 --- a/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java +++ b/psimi-converter/src/test/java/org/biopax/paxtools/converter/psi/TestMapping.java @@ -32,9 +32,10 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.Test; +import org.junit.jupiter.api.Test; + +import static org.junit.jupiter.api.Assertions.*; -import static org.junit.Assert.*; import psidev.psi.mi.tab.PsimiTabReader; import psidev.psi.mi.tab.converter.tab2xml.Tab2Xml; import psidev.psi.mi.tab.model.BinaryInteraction; @@ -82,7 +83,6 @@ public class TestMapping { @Test public void testApi() throws Exception { - // unmarshall the data, close the stream PsimiXmlReader reader = new PsimiXmlReader(); InputStream is = new GZIPInputStream(getClass().getClassLoader().getResourceAsStream(PSI_MI_TEST_FILE)); @@ -92,7 +92,7 @@ public void testApi() throws Exception { // we should only have 1 entry assertEquals(1, entries.size()); // get entry - Entry entry = (Entry)entries.iterator().next(); + Entry entry = entries.iterator().next(); assertTrue(entry.hasExperiments()); assertEquals(4, entry.getExperiments().size()); @@ -126,7 +126,6 @@ public void testApi() throws Exception { assertFalse(participant.hasInteractionRef()); assertFalse(participant.hasInteraction()); - //TODO assert experimentalRole.hasExperiments()==true always (if there're experiments); experimentalRole.hasExperimentRefs()==false } @@ -135,7 +134,7 @@ public void testApi() throws Exception { * Tests that a PSI document (level 2.5) is correctly mapped into a biopax model. */ @Test - public void testMapping() { + public void mapping() { Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); @@ -171,7 +170,7 @@ public void testMapping() { @Test - public void testMitabToMi() throws Exception { + public void mitabToMi() throws Exception { PsimiTabReader reader = new PsimiTabReader(); InputStream is = getClass().getClassLoader().getResourceAsStream(PSI_MITAB_TEST_FILE); Collection its = reader.read(is); @@ -189,7 +188,7 @@ public void testMitabToMi() throws Exception { } @Test - public void testParticipantsAreNotDuplicated() throws IOException { + public void participantsAreNotDuplicated() throws IOException { Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); // open file @@ -235,7 +234,7 @@ public void testParticipantsAreNotDuplicated() throws IOException { } @Test - public void testMappingIntAct() { + public void mappingIntAct() { Model bpModel = BioPAXLevel.L3.getDefaultFactory().createModel(); try { PsimiXmlReader reader = new PsimiXmlReader(); diff --git a/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java b/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java index 103cbe192..035e472f2 100644 --- a/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java +++ b/sbgn-converter/src/test/java/org/biopax/paxtools/io/sbgn/SBGNConverterTest.java @@ -7,8 +7,8 @@ import org.biopax.paxtools.model.BioPAXLevel; import org.biopax.paxtools.model.Model; import org.biopax.paxtools.model.level3.*; -import org.junit.BeforeClass; -import org.junit.Test; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; import org.sbgn.GlyphClazz; import org.sbgn.SbgnUtil; import org.sbgn.bindings.Arc; @@ -23,7 +23,7 @@ import java.util.*; import java.util.stream.Collectors; -import static org.junit.Assert.*; +import static org.junit.jupiter.api.Assertions.*; public class SBGNConverterTest { @@ -33,7 +33,7 @@ public class SBGNConverterTest private static Marshaller marshaller; private final String NOSPACE = "\\S+"; - @BeforeClass + @BeforeAll public static void setUp() throws JAXBException { blacklist = new ListUbiqueDetector(new HashSet<>(Arrays.asList( "http://pid.nci.nih.gov/biopaxpid_685", @@ -50,7 +50,7 @@ public static void setUp() throws JAXBException { } @Test - public void testSBGNConversion() throws Exception + public void toSBGNConversion() throws Exception { String input = "/AR-TP53"; InputStream in = getClass().getResourceAsStream(input + ".owl"); @@ -90,7 +90,7 @@ public void testSBGNConversion() throws Exception } @Test - public void testNestedComplexes() throws Exception + public void nestedComplexes() throws Exception { String input = "/translation-initiation-complex-formation"; InputStream in = getClass().getResourceAsStream(input + ".owl"); @@ -127,7 +127,7 @@ public void testNestedComplexes() throws Exception } @Test - public void testStoichiometry() throws Exception + public void stoichiometry() throws Exception { String input = "/Stoic"; InputStream in = getClass().getResourceAsStream(input + ".owl"); @@ -157,7 +157,7 @@ public void testStoichiometry() throws Exception } @Test - public void testConvertBmpPathway() throws Exception + public void convertBmpPathway() throws Exception { String input = "/signaling-by-bmp"; InputStream in = getClass().getResourceAsStream(input + ".owl"); @@ -204,7 +204,7 @@ public void testConvertBmpPathway() throws Exception // it's probably about an unknown/omitted sub-pathway with known in/out chemicals, // but it's expressed in BioPAX badly (a Pathway with one Interaction and PathwayStep, and no comments...) @Test - public void testConvertOmittedSmpdbPathway() throws Exception { + public void convertOmittedSmpdbPathway() throws Exception { String input = "/smpdb-beta-oxidation"; InputStream in = getClass().getResourceAsStream(input + ".owl"); Model level3 = handler.convertFromOWL(in); @@ -218,7 +218,7 @@ public void testConvertOmittedSmpdbPathway() throws Exception { } @Test - public void testConvertBadWikiPathway() throws Exception { + public void convertBadWikiPathway() throws Exception { String input = "/WP561"; InputStream in = getClass().getResourceAsStream(input + ".owl"); Model level3 = handler.convertFromOWL(in); @@ -234,7 +234,7 @@ public void testConvertBadWikiPathway() throws Exception { } @Test - public void testSbgnLayoutKegg51() throws Exception + public void sbgnLayoutKegg51() throws Exception { File sbgnFile = new File(getClass().getResource("/hsa00051.sbgn").getFile()); @@ -250,7 +250,7 @@ public void testSbgnLayoutKegg51() throws Exception } @Test - public void testConvertGIs() throws JAXBException { + public void convertGIs() throws JAXBException { String out = "target/test_gi.sbgn"; MockFactory f = new MockFactory(BioPAXLevel.L3); Model m = f.createModel(); @@ -272,7 +272,7 @@ public void testConvertGIs() throws JAXBException { } @Test - public void testConvertTRs() throws JAXBException { + public void convertTRs() throws JAXBException { String out = "target/test_tr.sbgn"; MockFactory f = new MockFactory(BioPAXLevel.L3); Model m = f.createModel(); @@ -306,7 +306,7 @@ public void testConvertTRs() throws JAXBException { } @Test - public void testConvertTfap2Pathway() throws Exception + public void convertTfap2Pathway() throws Exception { String input = "/TFAP2"; InputStream in = getClass().getResourceAsStream(input + ".owl"); @@ -328,7 +328,7 @@ public void testConvertTfap2Pathway() throws Exception } @Test - public void testConvertActivation() throws Exception { + public void convertActivation() throws Exception { String input = "/activation"; InputStream in = getClass().getResourceAsStream(input + ".owl"); Model m = handler.convertFromOWL(in); @@ -345,7 +345,7 @@ public void testConvertActivation() throws Exception { } @Test - public void testConvertModulation() throws Exception { + public void convertModulation() throws Exception { String input = "/modulation"; InputStream in = getClass().getResourceAsStream(input + ".owl"); Model level3 = handler.convertFromOWL(in); @@ -361,7 +361,7 @@ public void testConvertModulation() throws Exception { } @Test - public void testConvertControlsChain() throws Exception { + public void convertControlsChain() throws Exception { String input = "/controlchain"; InputStream in = getClass().getResourceAsStream(input + ".owl"); Model level3 = handler.convertFromOWL(in); From 87588a9b56f481fb82117b1348ac00bfcd1e2c0c Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 2 Jul 2023 04:44:06 -0400 Subject: [PATCH 09/20] Paxtools-6: changes - deleted the validator client/command from the paxtools-console app; set compiler release to java 17; modified synonyms: kegg ligand is kegg.compound; kegg organism - kegg.genome; --- .../biopax/paxtools/normalizer/Resolver.java | 1 - .../biopax/paxtools/normalizer/spellmap.json | 4 +- .../biopax/paxtools/normalizer/synonymap.json | 3 +- paxtools-console/pom.xml | 35 +-- .../java/org/biopax/paxtools/Commands.java | 92 +------ .../main/java/org/biopax/paxtools/Main.java | 10 +- .../client/BiopaxValidatorClient.java | 238 ------------------ .../biopax/paxtools/client/package-info.java | 4 - .../org/biopax/paxtools/examples/commands.sh | 11 +- .../main/resources/validator-response-2.0.xsd | 65 ----- pom.xml | 53 +--- 11 files changed, 19 insertions(+), 497 deletions(-) delete mode 100644 paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java delete mode 100644 paxtools-console/src/main/java/org/biopax/paxtools/client/package-info.java delete mode 100644 paxtools-console/src/main/resources/validator-response-2.0.xsd diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java index 6cf0fadda..2900269f9 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java @@ -84,7 +84,6 @@ protected Resolver() { * @param identifier internal identifier used by the data type * @param datatype name, synonym or URI of a data type * @return "true" if the identifier follows the regular expression, "false" otherwise - * @throws IllegalArgumentException when datatype not found */ public static boolean checkRegExp(String identifier, String datatype) { Namespace dt = getNamespace(datatype); diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json index d78bb6639..00009c06c 100644 --- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json @@ -41,8 +41,8 @@ "EMBLBANK": "insdc", "EMBL": "insdc", "PROTEINGENBANKIDENTIFIER": "genpept", - "COMPOUND": "kegg.compound", - "LIGAND": "kegg.ligand", + "KEGGCOMPOUND": "kegg.compound", + "KEGGLIGAND": "kegg.compound", "KEGGGENOMES": "kegg.genome", "KEGGORGANISM": "kegg.genome", "KEGGGENE": "kegg.genes", diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json index e349ff219..9a935ec41 100644 --- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json @@ -33,8 +33,9 @@ "EMBL": "insdc", "PROTEIN GENBANK IDENTIFIER": "genpept", "COMPOUND": "kegg.compound", - "LIGAND": "kegg.ligand", + "LIGAND": "kegg.compound", "KEGG GENOMES": "kegg.genome", + "KEGG ORGANISM": "kegg.genome", "KEGG GENE": "kegg.genes", "AFFYMETRIX": "affy.probeset", "REACTOME STABLE ID": "reactome", diff --git a/paxtools-console/pom.xml b/paxtools-console/pom.xml index 6ff906db7..8374dbac2 100644 --- a/paxtools-console/pom.xml +++ b/paxtools-console/pom.xml @@ -48,37 +48,6 @@ - - org.codehaus.mojo - jaxb2-maven-plugin - 1.6 - - - generate-sources - - xjc - - - - - false - org.biopax.validator.jaxb - true - ${basedir}/src/main/resources - - - - xerces - xercesImpl - 2.8.1 - - - com.sun.activation - javax.activation - 1.2.0 - - - @@ -121,7 +90,7 @@ org.apache.httpcomponents fluent-hc - 4.3.1 + 4.5.14 commons-logging @@ -132,7 +101,7 @@ org.apache.httpcomponents httpmime - 4.3.1 + 4.5.14 ch.qos.logback diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java index bf4990ae6..4237c2ed0 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java @@ -2,8 +2,6 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.mutable.MutableInt; -import org.biopax.paxtools.client.BiopaxValidatorClient; -import org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat; import org.biopax.paxtools.controller.*; import org.biopax.paxtools.converter.LevelUpgrader; import org.biopax.paxtools.converter.psi.PsiToBiopax3Converter; @@ -23,7 +21,6 @@ import org.biopax.paxtools.query.QueryExecuter; import org.biopax.paxtools.query.algorithm.Direction; import org.biopax.paxtools.util.ClassFilterSet; -import org.biopax.validator.jaxb.Behavior; import org.json.simple.JSONArray; import org.json.simple.JSONObject; import org.slf4j.Logger; @@ -275,93 +272,6 @@ static void toSbgn(String[] argv) throws IOException { l3ToSBGNPDConverter.writeSBGN(model, output); } - static void validate(String[] argv) throws IOException - { - String input = argv[1]; - String output = argv[2]; - // default options - RetFormat outf = RetFormat.HTML; - boolean fix = false; - Integer maxErrs = null; - Behavior level = null; //will report both errors and warnings - String profile = null; - - // match optional args - for (int i = 3; i < argv.length; i++) { - if ("html".equalsIgnoreCase(argv[i])) { - outf = RetFormat.HTML; - } else if ("xml".equalsIgnoreCase(argv[i])) { - outf = RetFormat.XML; - } else if ("biopax".equalsIgnoreCase(argv[i])) { - outf = RetFormat.OWL; - } else if ("auto-fix".equalsIgnoreCase(argv[i])) { - fix = true; - } else if ("only-errors".equalsIgnoreCase(argv[i])) { - level = Behavior.ERROR; - } else if ((argv[i]).toLowerCase().startsWith("maxerrors=")) { - String num = argv[i].substring(10); - maxErrs = Integer.valueOf(num); - } else if ("notstrict".equalsIgnoreCase(argv[i])) { - profile = "notstrict"; - } - } - - Collection files = new HashSet<>(); - File fileOrDir = new File(input); - if (!fileOrDir.canRead()) { - System.out.println("Cannot read " + input); - } - - // collect files - if (fileOrDir.isDirectory()) { - // validate all the OWL files in the folder - for (String s : fileOrDir.list((dir, name) -> (name.endsWith(".owl")))) { - files.add(new File(fileOrDir.getCanonicalPath() - + File.separator + s)); - } - } else { - files.add(fileOrDir); - } - - // upload and validate using the default URL: - // http://www.biopax.org/biopax-validator/check.html - OutputStream os = new FileOutputStream(output); - try { - if (!files.isEmpty()) { - BiopaxValidatorClient val = new BiopaxValidatorClient(); - val.validate(fix, profile, outf, level, maxErrs, null, files.toArray(new File[]{}), os); - } - } catch (Exception ex) { - // fall-back: not using the remote validator; trying to read files - String msg = "Unable to check with the biopax-validator web service: \n " + - ex + - "\n Fall-back: trying to parse the file(s) with paxtools " + - "(up to the first syntax error in each file)...\n"; - log.error(msg, ex); - os.write(msg.getBytes()); - - for (File f : files) { - try { - Model m = io.convertFromOWL(getInputStream(f.getPath())); - msg = "Model that contains " - + m.getObjects().size() - + " elements is successfully created from " - + f.getPath() - + " (check the console output for warnings).\n"; - os.write(msg.getBytes()); - } catch (Exception e) { - msg = "Error: " + e + - " in building a BioPAX Model from: " + - f.getPath() + "\n"; - os.write(msg.getBytes()); - e.printStackTrace(); - log.error(msg); - } - os.flush(); - } - } - } - static void toSifnx(String[] argv) throws IOException { boolean extended = false; //if it stays 'false', then andSif==true will be in effect automatically boolean andSif = false; //if extended==false, SIF will be generated as it would be andSif==true @@ -376,7 +286,7 @@ static void toSifnx(String[] argv) throws IOException { for(int i=3; i [-nolayout]\n" + "\t- converts model to the SBGN format and applies COSE layout unless optional -nolayout flag is set.") {public void run(String[] argv) throws IOException { toSbgn(argv); } }, - validate(" [xml|html|biopax] [auto-fix] [only-errors] [maxerrors=n] [notstrict]\n" + - "\t- validate BioPAX file/directory (up to ~25MB in total size, -\n" + - "\totherwise download and run the stand-alone validator)\n" + - "\tin the directory using the online validator service\n" + - "\t(generates html or xml report, or gets the processed biopax\n" + - "\t(cannot be perfect though) see http://www.biopax.org/validator)") - {public void run(String[] argv) throws IOException{validate(argv);} }, integrate(" \n" + "\t- integrates file2 into file1 and writes it into output (experimental)") {public void run(String[] argv) throws IOException{integrate(argv);} }, @@ -127,6 +120,7 @@ private static void help() { for (Command cmd : Command.values()) { System.out.println(cmd.name() + " " + cmd.getDescription()); } - System.out.println("Commands can also use compressed input files (only '.gz')."); + System.out.println("Commands can also use compressed inCput files (only '.gz')."); + System.out.println("Command: 'validate' was removed; use online biopax.org/validator or stand-alone biopax-validator.jar instead"); } } diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java b/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java deleted file mode 100644 index 530fc8989..000000000 --- a/paxtools-console/src/main/java/org/biopax/paxtools/client/BiopaxValidatorClient.java +++ /dev/null @@ -1,238 +0,0 @@ -package org.biopax.paxtools.client; - -/* - * #%L - * BioPAX Validator Client - * %% - * Copyright (C) 2008 - 2013 University of Toronto (baderlab.org) and Memorial Sloan-Kettering Cancer Center (cbio.mskcc.org) - * %% - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as - * published by the Free Software Foundation, either version 3 of the - * License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Lesser Public License for more details. - * - * You should have received a copy of the GNU General Lesser Public - * License along with this program. If not, see - * . - * #L% - */ - -import org.apache.http.Header; -import org.apache.http.HttpEntity; -import org.apache.http.HttpResponse; -import org.apache.http.client.ClientProtocolException; -import org.apache.http.client.ResponseHandler; -import org.apache.http.client.fluent.Executor; -import org.apache.http.client.fluent.Request; -import org.apache.http.entity.ContentType; -import org.apache.http.entity.mime.MultipartEntityBuilder; -import org.biopax.validator.jaxb.Behavior; -import org.biopax.validator.jaxb.ValidatorResponse; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import javax.xml.bind.JAXBContext; -import javax.xml.bind.JAXBException; -import javax.xml.bind.Unmarshaller; -import javax.xml.transform.Source; -import javax.xml.transform.stream.StreamSource; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.io.OutputStream; -import java.io.PrintWriter; -import java.io.StringReader; -import java.nio.charset.Charset; - -/** - * Simple (example) BioPAX Validator client - * to upload and check BioPAX OWL files. - * - * @author rodche - * - */ -public class BiopaxValidatorClient { - private static final Logger log = LoggerFactory.getLogger(BiopaxValidatorClient.class); - - /** - * Default BioPAX Validator's URL - */ - public static final String - DEFAULT_VALIDATOR_URL = "http://www.biopax.org/validator/check.html"; - - /** - * The Java Option to set a BioPAX Validator URL - * (if set, overrides the default and URL provided by the Constructor arg.) - */ - public static final String JVM_PROPERTY_URL = "biopax.validator.url"; - - public static enum RetFormat { - HTML,// errors as HTML/Javascript - XML, // errors as XML - OWL; // modified BioPAX only (when 'autofix' or 'normalize' is true) - } - - private String url; - - - /** - * Main Constructor - * - * It configures for the validator's URL - * (defined by DEFAULT_VALIDATOR_URL constant) - * and result format (). - * - * @param url - validator's file-upload form address - */ - public BiopaxValidatorClient(String url) { -// if(url == null || url.isEmpty()) -// this.url = System.getProperty(JVM_PROPERTY_URL, DEFAULT_VALIDATOR_URL); -// else -// this.url = url; -// - // 1) use the arg (if not empty/null) or the default URL - this.url = (url == null || url.isEmpty()) - ? DEFAULT_VALIDATOR_URL : url; - - // 2) override if the JVM option is set to another value - this.url = System.getProperty(JVM_PROPERTY_URL, this.url); - - // 3) get actual location (force through redirects, if any) - try { - this.url = location(this.url); -// System.out.println("Location: " + this.url); - } catch (IOException e) { - log.warn("Failed to resolve to actual web service " + - "URL using: " + url + " (if there is a 301/302/307 HTTP redirect, " + - "then validation requests (using HTTP POST method) will probably fail...)", e); - } - } - - - /** - * Default Constructor - * - * It configures for the default validator URL. - */ - public BiopaxValidatorClient() { - this(null); - } - - - /** - * Checks a BioPAX OWL file(s) or resource - * using the online BioPAX Validator - * and prints the results to the output stream. - * - * @param autofix true/false (experimental) - * @param profile validation profile name - * @param retFormat xml, html, or owl (no errors, just modified owl, if autofix=true) - * @param filterBy filter validation issues by the error/warning level - * @param maxErrs errors threshold - max no. critical errors to collect before quitting - * (warnings not counted; null/0/negative value means unlimited) - * @param biopaxUrl check the BioPAX at the URL - * @param biopaxFiles an array of BioPAX files to validate - * @param out validation report data output stream - * @throws IOException when there is an I/O error - */ - public void validate(boolean autofix, String profile, RetFormat retFormat, Behavior filterBy, - Integer maxErrs, String biopaxUrl, File[] biopaxFiles, OutputStream out) throws IOException - { - MultipartEntityBuilder meb = MultipartEntityBuilder.create(); - meb.setCharset(Charset.forName("UTF-8")); - - if(autofix) - meb.addTextBody("autofix", "true"); -//TODO: add options (normalizer.fixDisplayName, normalizer.inferPropertyOrganism, normalizer.inferPropertyDataSource, normalizer.xmlBase) - if(profile != null && !profile.isEmpty()) - meb.addTextBody("profile", profile); - if(retFormat != null) - meb.addTextBody("retDesired", retFormat.toString().toLowerCase()); - if(filterBy != null) - meb.addTextBody("filter", filterBy.toString()); - if(maxErrs != null && maxErrs > 0) - meb.addTextBody("maxErrors", maxErrs.toString()); - if(biopaxFiles != null && biopaxFiles.length > 0) - for (File f : biopaxFiles) //important: use MULTIPART_FORM_DATA content-type - meb.addBinaryBody("file", f, ContentType.MULTIPART_FORM_DATA, f.getName()); - else if(biopaxUrl != null) { - meb.addTextBody("url", biopaxUrl); - } else { - log.error("Nothing to do (no BioPAX data specified)!"); - return; - } - - //execute the query and get results as string - HttpEntity httpEntity = meb.build(); - String content = Executor.newInstance()//Executor.newInstance(httpClient) - .execute(Request.Post(url).body(httpEntity)) - .returnContent().asString(); - - //save: append to the output stream (file) - BufferedReader res = new BufferedReader(new StringReader(content)); - String line; - PrintWriter writer = new PrintWriter(out); - while((line = res.readLine()) != null) { - writer.println(line); - } - writer.flush(); - res.close(); - } - - public void setUrl(String url) { - this.url = url; - } - - public String getUrl() { - return url; - } - - /** - * Converts a biopax-validator XML response to the java object. - * - * @param xml input XML data - validation report - to import - * @return validation report object - * @throws JAXBException when there is an JAXB unmarshalling error - */ - public static ValidatorResponse unmarshal(String xml) throws JAXBException { - JAXBContext jaxbContext = JAXBContext.newInstance("org.biopax.validator.jaxb"); - Unmarshaller un = jaxbContext.createUnmarshaller(); - Source src = new StreamSource(new StringReader(xml)); - ValidatorResponse resp = un.unmarshal(src, ValidatorResponse.class).getValue(); - return resp; - } - - - private String location(final String url) throws IOException { - String location = url; //initially the same - // discover actual location, avoid going in circles: - int i=0; - for(String loc = url; loc != null && i<5; i++ ) - { - //do POST for location (Location header present if there's a 301/302/307 redirect on the way) - loc = Request.Post(loc).execute() - .handleResponse(new ResponseHandler() { - @Override - public String handleResponse(HttpResponse httpResponse) - throws ClientProtocolException, IOException { - Header header = httpResponse.getLastHeader("Location"); - return (header != null) ? header.getValue().trim() : null; - } - }); - - if(loc != null) { - location = loc; - log.info("BioPAX Validator location: " + loc); - } - } - - return location; - } - -} \ No newline at end of file diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/client/package-info.java b/paxtools-console/src/main/java/org/biopax/paxtools/client/package-info.java deleted file mode 100644 index 8bde2842c..000000000 --- a/paxtools-console/src/main/java/org/biopax/paxtools/client/package-info.java +++ /dev/null @@ -1,4 +0,0 @@ -/** -* A simple client for the BioPAX validator.. -*/ -package org.biopax.paxtools.client; \ No newline at end of file diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh b/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh index 785efded1..af32171c5 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh @@ -2,17 +2,16 @@ hg clone http://biopax.hg.sourceforge.net:8000/hgroot/biopax/paxtools --merge --to-sif ---to-sifnx prop1,prop2,etc... ---validate [xml|html] +--to-sifnx prop1,prop2,.. - converts a BioPAX file to the extended SIF format --integrate (experimental) --to-level3 --psimi-to ---to-GSEA " converts level 1 or 2 or 3 to GSEA output. Searches database for participant id or uses biopax rdf id if database is NONE. Cross species check ensures participant protein is from same species as pathway (set to true or false). ---fetch extracts a sub-model (id1,id2, etc. - new “root” elements) ---get-neighbors nearest neighborhood graph query +--to-GSEA - converts level 1 or 2 or 3 to GSEA output. Searches database for participant id or uses biopax rdf id if database is NONE. Cross species check ensures participant protein is from same species as pathway (set to true or false). +--fetch - extracts a sub-model (id1,id2, etc. - new root elements) +--get-neighbors - nearest neighborhood graph query java -jar paxtools.jar --merge file1.owl file2.owl output.owl java -Xmx2048M -jar paxtools.jar --merge file1.owl file2.owl output.owl -java -cp paxtools.jar org.biopax.paxtools.PaxtoolsMain --validate file.owl \ No newline at end of file +java -cp paxtools.jar org.biopax.paxtools.PaxtoolsMain --validate file.owl diff --git a/paxtools-console/src/main/resources/validator-response-2.0.xsd b/paxtools-console/src/main/resources/validator-response-2.0.xsd deleted file mode 100644 index f08d183b3..000000000 --- a/paxtools-console/src/main/resources/validator-response-2.0.xsd +++ /dev/null @@ -1,65 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/pom.xml b/pom.xml index e86262fb0..7e6f6724a 100644 --- a/pom.xml +++ b/pom.xml @@ -39,10 +39,6 @@ github UTF-8 UTF-8 - 2.0.7 - 17 - 17 - 17 @@ -369,12 +365,6 @@ 5.9.3 test - - - - - - net.sourceforge.collections collections-generic @@ -393,48 +383,31 @@ org.slf4j slf4j-api - ${slf4j.version} + 2.0.7 org.slf4j jcl-over-slf4j - ${slf4j.version} + 2.0.7 runtime org.slf4j jul-to-slf4j - ${slf4j.version} + 2.0.7 runtime org.slf4j log4j-over-slf4j - ${slf4j.version} + 2.0.7 ch.qos.logback logback-classic - 1.1.11 + 1.4.8 true - - javax.xml.bind - jaxb-api - 2.3.1 - - - com.sun.xml.bind - jaxb-core - 2.3.0 - runtime - - - com.sun.xml.bind - jaxb-impl - 2.3.0 - runtime - com.fasterxml.jackson.core jackson-core @@ -481,22 +454,6 @@ org.junit.jupiter junit-jupiter-params - - - - - - javax.xml.bind - jaxb-api - - - com.sun.xml.bind - jaxb-core - - - com.sun.xml.bind - jaxb-impl - From 2e388ccdca081dbb0b7690032dbcf8c7840576b1 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Mon, 3 Jul 2023 18:20:17 -0400 Subject: [PATCH 10/20] Paxtools-6: minor change to the log msg about Collections provider and biopax Set type system prop. --- .../java/org/biopax/paxtools/util/BPCollections.java | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java b/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java index 95da6d18f..0074f185d 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/util/BPCollections.java @@ -45,12 +45,11 @@ public Collection createCollection(int initSz) { BPCollections() { //if a custom collection provider was specified, try to use that String prop = System.getProperty("paxtools.CollectionProvider"); - log.info("System property: paxtools.CollectionProvider=" + prop); if (StringUtils.isNotBlank(prop)) { try { Class cProviderClass = (Class) Class.forName(prop); cProvider = cProviderClass.getDeclaredConstructor().newInstance(); - log.info("Custom CollectionProvider " + prop + " was successfully activated."); + log.info("Using custom paxtools.CollectionProvider=" + cProvider.getClass().getCanonicalName()); } catch (Exception e) { log.warn("Could not initialize the specified collection provider: " + prop + "; will use the default implementation; error: " + e); @@ -58,11 +57,11 @@ public Collection createCollection(int initSz) { } if(cProvider == null) { cProvider = new DefaultCollectionProvider(); - log.info("Using the default CollectionProvider."); + log.info("Using default paxtools.CollectionProvider=" + cProvider.getClass().getCanonicalName()); } safeSetOpt_ = System.getProperty("paxtools.model.safeset","map"); - log.info("System property: paxtools.model.safeset=" + safeSetOpt_); + log.info("Using paxtools.model.safeset=" + safeSetOpt_); } @@ -91,10 +90,10 @@ public Set createSet() public Set createSafeSet() { switch (safeSetOpt_) { case "list": - return new BiopaxElements<>();//Set based on Map (faster, more memory, for building/merging Models) + return new BiopaxElements<>(); //Set based on List (slower, less memory, for read-only analyses, queries) case "map": default: - return new BiopaxSafeSet<>();//Set based on List (slower, less memory, for read-only analyses, queries) + return new BiopaxSafeSet<>(); //Set based on Map (faster, more memory, for building/merging Models) } } From 5e17a9f66b7dfa74273430d0e0767a907301b6e3 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 9 Jul 2023 03:08:57 -0400 Subject: [PATCH 11/20] Paxtools-6: reverted back some of my previous refactoring - - using Set instead of Collection in the query and pattern methods --- .../org/biopax/paxtools/pattern/Pattern.java | 2 +- .../org/biopax/paxtools/pattern/Searcher.java | 20 +-- .../example/DeltaFeatureExtractor.java | 4 +- .../pattern/miner/BlacklistGenerator2.java | 22 +-- .../paxtools/pattern/miner/MinerAdapter.java | 29 ++-- .../pattern/util/ChemicalNameNormalizer.java | 2 +- .../biopax/paxtools/pattern/SPIKEParser.java | 4 +- .../biopax/paxtools/examples/Tutorial.java | 5 +- .../biopax/paxtools/controller/Completer.java | 2 +- .../biopax/paxtools/query/QueryExecuter.java | 151 +++++++++--------- .../biopax/paxtools/query/algorithm/BFS.java | 16 +- .../query/algorithm/CommonStreamQuery.java | 4 +- .../query/algorithm/CycleBreaker.java | 7 +- .../query/algorithm/NeighborhoodQuery.java | 9 +- .../query/algorithm/PathsBetweenQuery.java | 4 +- .../query/algorithm/PathsFromToQuery.java | 24 +-- .../paxtools/query/algorithm/Prune.java | 10 +- .../biopax/paxtools/query/model/Graph.java | 7 +- .../paxtools/query/wrapperL3/GraphL3.java | 6 +- .../GraphL3Undirected.java | 8 +- .../org/biopax/paxtools/query/QueryTest.java | 23 ++- 21 files changed, 167 insertions(+), 192 deletions(-) diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java b/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java index f49781f57..00cf42ded 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/Pattern.java @@ -38,7 +38,7 @@ public class Pattern private Pattern(Class startingClass) { this.startingClass = startingClass; - this.labelMap = new HashMap(); + this.labelMap = new HashMap<>(); this.constraints = new ArrayList<>(); this.lastIndex = 0; } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java b/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java index 764679032..a3a6da28d 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/Searcher.java @@ -171,7 +171,7 @@ public static Map> search(final Model model, final Pa final Map> map = new ConcurrentHashMap<>(); final ExecutorService exec = Executors.newFixedThreadPool(20); - Collection eles = model.getObjects(pattern.getStartingClass()); + Set eles = model.getObjects(pattern.getStartingClass()); if (prg != null) prg.setTotalTicks(eles.size()); for (final BioPAXElement ele : eles) @@ -243,7 +243,7 @@ public static Map> search( * @param c type of the element to collect * @return set of the elements at the specified index of the matching results */ - public static Collection searchAndCollect( + public static Set searchAndCollect( Model model, Pattern pattern, int index, Class c) { return searchAndCollect(model.getObjects(pattern.getStartingClass()), pattern, index, c); @@ -260,7 +260,7 @@ public static Collection searchAndCollect( * @param c type of the element to collect * @return set of the elements at the specified index of the matching results */ - public static Collection searchAndCollect( + public static Set searchAndCollect( Collection eles, Pattern pattern, int index, Class c) { Set set = new HashSet<>(); @@ -434,24 +434,12 @@ private static String getLeadingZeros(int i, int size) */ private static final SimpleEditorMap EM = SimpleEditorMap.L3; - /** - * Excises a model to the given elements. - * @param model model to excise (bogus parameter, in fact, deprecated) - * @param result elements to excise to - * @return excised model - * @deprecated use {@link #excise(Collection)} instead (parameter:model was not actually used at all) - */ - private static Model excise(Model model, Set result) - { - return excise(result); - } - /** * Excises a model to the given elements. * @param result elements to excise to * @return excised model */ - private static Model excise(Collection result) + private static Model excise(Set result) { Completer c = new Completer(EM); result = c.complete(result); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java b/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java index 90e64ffd2..f07d7d70d 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/example/DeltaFeatureExtractor.java @@ -113,7 +113,7 @@ public void writeResult(Map> matches, OutputStream ou { // record mediator ids to map these interactions to detailed data - if (!mediators.containsKey(s1s)) mediators.put(s1s, new HashMap>()); + if (!mediators.containsKey(s1s)) mediators.put(s1s, new HashMap<>()); if (!mediators.get(s1s).containsKey(s2s)) mediators.get(s1s).put(s2s, new HashSet<>()); List meds = m.get(getMediatorLabels(), getPattern()); @@ -141,7 +141,7 @@ public void writeResult(Map> matches, OutputStream ou private void collect(String s1, String s2, Set modificationFeatures, Map>> map) { - if (!map.containsKey(s1)) map.put(s1, new HashMap>()); + if (!map.containsKey(s1)) map.put(s1, new HashMap<>()); if (!map.get(s1).containsKey(s2)) map.get(s1).put(s2, new HashSet<>()); map.get(s1).get(s2).addAll(modificationFeatures); } diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java index 53b2107f8..5e086f28a 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/BlacklistGenerator2.java @@ -120,7 +120,7 @@ public Blacklist generateBlacklist(Model model) throws IOException Set upstr = upstrMap.get(name); Set dwstr = dwstrMap.get(name); - Set temp = new HashSet<>(upstr); + Set temp = new HashSet(upstr); upstr.removeAll(dwstr); dwstr.removeAll(temp); } @@ -164,7 +164,7 @@ private void writeTheGuideRankingToTuneTheDecider( // Sort to degree List names = new ArrayList<>(neighMap.keySet()); - Collections.sort(names, (o1, o2) -> new Integer(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size())); + Collections.sort(names, (o1, o2) -> Integer.valueOf(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size())); SIFSearcher searcher2 = new SIFSearcher(new Fetcher(nameMapping), new ChemicalAffectsThroughControlMiner()); @@ -220,7 +220,7 @@ private void generateNameMappingFileToCurate(Model model) throws IOException // Sort to degree List names = new ArrayList<>(neighMap.keySet()); - Collections.sort(names, (o1, o2) -> new Integer(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size())); + Collections.sort(names, (o1, o2) -> Integer.valueOf(neighMap.get(o2).size()).compareTo(neighMap.get(o1).size())); Set> bag = collectNameSets(model); Map>> nameToSets = getNameToSetsMap(bag); @@ -242,12 +242,12 @@ private void generateNameMappingFileToCurate(Model model) throws IOException name = name.toLowerCase(); remaining.remove(name); - Map[]> mappings = getMappingsAndBasis( + Map[]> mappings = getMappingsAndBasis( name, remaining, nameToSets, intersectionMap); for (String mapped : mappings.keySet()) { - Collection[] s = mappings.get(mapped); + Set[] s = mappings.get(mapped); writer.write(name + "\t" + mapped + "\t" + s[0] + "\t" + s[1] + "\t" + s[2] + "\n"); } } @@ -325,9 +325,9 @@ private Map>> getNameToSetsMap(Set> bag) return map; } - private Collection getCommon(Collection set1, Collection set2) + private Set getCommon(Set set1, Set set2) { - Collection comm = new HashSet<>(set1); + Set comm = new HashSet<>(set1); comm.retainAll(set2); return comm; } @@ -362,10 +362,10 @@ private Map, Set>> getIntersectionMap(Set> b return map; } - private Map[]> getMappingsAndBasis(String name, List consider, + private Map[]> getMappingsAndBasis(String name, List consider, Map>> nameToSets, Map, Set>> intersectionMap) { - Map[]> map = new HashMap<>(); + Map[]> map = new HashMap<>(); for (Set set : nameToSets.get(name)) { @@ -377,7 +377,7 @@ private Map[]> getMappingsAndBasis(String name, List< for (String target : common) { - map.put(target, new Collection[]{getCommon(set, other), set, other}); + map.put(target, new Set[]{getCommon(set, other), set, other}); } } } @@ -389,7 +389,7 @@ private Map readNameMapping() throws FileNotFoundException { if (!new File(MAPPING_FILE).exists()) return null; - Map map = new HashMap(); + Map map = new HashMap<>(); Scanner sc = new Scanner(new File(MAPPING_FILE)); while (sc.hasNextLine()) diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java index 2594f85c5..346b6d55f 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/miner/MinerAdapter.java @@ -274,23 +274,18 @@ public Set toStringSet(Set set) { List list = new ArrayList<>(set); - Collections.sort(list, new Comparator() - { - @Override - public int compare(ModificationFeature o1, ModificationFeature o2) - { - String t1 = getModificationTerm(o1); - String t2 = getModificationTerm(o2); - - Integer l1 = getPositionStart(o1); - Integer l2 = getPositionStart(o2); - - if (t1 == null && t2 == null) return l1.compareTo(l2); - if (t1 == null) return 1; - if (t2 == null) return -1; - if (t1.equals(t2)) return l1.compareTo(l2); - return t1.compareTo(t2); - } + Collections.sort(list, (o1, o2) -> { + String t1 = getModificationTerm(o1); + String t2 = getModificationTerm(o2); + + Integer l1 = getPositionStart(o1); + Integer l2 = getPositionStart(o2); + + if (t1 == null && t2 == null) return l1.compareTo(l2); + if (t1 == null) return 1; + if (t2 == null) return -1; + if (t1.equals(t2)) return l1.compareTo(l2); + return t1.compareTo(t2); }); return getInString(list); diff --git a/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java b/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java index 222b6abea..994fa0598 100644 --- a/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java +++ b/pattern/src/main/java/org/biopax/paxtools/pattern/util/ChemicalNameNormalizer.java @@ -152,7 +152,7 @@ else if (map.values().contains(match)) private Map> collectNames(boolean peLevel, Set... sets) { - Map> map = new HashMap<>(); + Map> map = new HashMap<>(); for (Set set : sets) { diff --git a/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java b/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java index b0a32ea69..3fa0e2578 100644 --- a/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java +++ b/pattern/src/test/java/org/biopax/paxtools/pattern/SPIKEParser.java @@ -20,8 +20,8 @@ public static void main(String[] args) throws IOException } public void parse(String inputFile, String outputFile) throws IOException { - Map id2gene = new HashMap(); - Map id2group = new HashMap(); + Map id2gene = new HashMap<>(); + Map id2group = new HashMap<>(); Set regs = new HashSet<>(); BufferedReader reader = new BufferedReader(new FileReader(inputFile)); diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java b/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java index fe81d1503..63711e29c 100644 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java +++ b/paxtools-console/src/main/java/org/biopax/paxtools/examples/Tutorial.java @@ -27,7 +27,6 @@ public class Tutorial { - public static void myFirstModel() { BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory(); @@ -212,7 +211,7 @@ private void recursivelyObtainMembers(Complex complex, public void graphQuery(Model model, PhysicalEntity entity3, PhysicalEntity entity2, PhysicalEntity entity1) { - Collection sourceSet = new HashSet<>(); + Set sourceSet = new HashSet<>(); // Add the related source PhysicalEntity (or children) objects to the // source set @@ -223,7 +222,7 @@ public void graphQuery(Model model, PhysicalEntity entity3, // Direction can be upstream, downstream, or bothstream. Direction direction = Direction.BOTHSTREAM; - Collection result = QueryExecuter.runNeighborhood(sourceSet, model, + Set result = QueryExecuter.runNeighborhood(sourceSet, model, limit, direction, null); Completer c = new Completer(SimpleEditorMap.get(BioPAXLevel.L3)); diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java index f48de1fc7..ff7fb3450 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/Completer.java @@ -47,7 +47,7 @@ public boolean filterInverse(PropertyEditor editor) } - public Collection complete(Collection elements) + public Set complete(Collection elements) { completed.clear(); diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java index 4620ac3b6..5deb77c8c 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/QueryExecuter.java @@ -32,8 +32,8 @@ public class QueryExecuter * @param filters for filtering graph elements * @return BioPAX elements in the result set */ - public static Collection runNeighborhood( - Collection sourceSet, + public static Set runNeighborhood( + Set sourceSet, Model model, int limit, Direction direction, @@ -55,13 +55,12 @@ public static Collection runNeighborhood( } else return Collections.emptySet(); - Collection source = prepareSingleNodeSet(sourceSet, graph); + Set source = prepareSingleNodeSet(sourceSet, graph); if (sourceSet.isEmpty()) return Collections.emptySet(); NeighborhoodQuery query = new NeighborhoodQuery(source, direction, limit); - Collection resultWrappers = query.run(); - + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -75,8 +74,8 @@ public static Collection runNeighborhood( * @param filters for filtering graph elements * @return BioPAX elements in the result set */ - public static Collection runNeighborhoodMultiSet( - Collection> sourceSets, + public static Set runNeighborhoodMultiSet( + Set> sourceSets, Model model, int limit, Direction direction, @@ -98,12 +97,12 @@ public static Collection runNeighborhoodMultiSet( } else return Collections.emptySet(); - Collection source = prepareSingleNodeSetFromSets(sourceSets, graph); + Set source = prepareSingleNodeSetFromSets(sourceSets, graph); if (sourceSets.isEmpty()) return Collections.emptySet(); NeighborhoodQuery query = new NeighborhoodQuery(source, direction, limit); - Collection resultWrappers = query.run(); + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -116,7 +115,7 @@ public static Collection runNeighborhoodMultiSet( * @param filters optional filters - for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runPathsBetween(Collection sourceSet, Model model, + public static Set runPathsBetween(Set sourceSet, Model model, int limit, Filter... filters) { Graph graph; @@ -132,8 +131,7 @@ public static Collection runPathsBetween(Collection resultWrappers = query.run(); - + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -146,8 +144,7 @@ public static Collection runPathsBetween(Collection runPathsBetweenMultiSet( - Collection> sourceSets, Model model, + public static Set runPathsBetweenMultiSet(Set> sourceSets, Model model, int limit, Filter... filters) { Graph graph; @@ -163,7 +160,7 @@ public static Collection runPathsBetweenMultiSet( if (sourceWrappers.size() < 2) return Collections.emptySet(); PathsBetweenQuery query = new PathsBetweenQuery(sourceWrappers, limit); - Collection resultWrappers = query.run(); + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -176,8 +173,8 @@ public static Collection runPathsBetweenMultiSet( * @return BioPAX elements in the result * @deprecated Use runPathsBetween instead */ - public static Collection runGOI( - Collection sourceSet, + public static Set runGOI( + Set sourceSet, Model model, int limit, Filter... filters) @@ -195,9 +192,9 @@ public static Collection runGOI( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runPathsFromTo( - Collection sourceSet, - Collection targetSet, + public static Set runPathsFromTo( + Set sourceSet, + Set targetSet, Model model, LimitType limitType, int limit, @@ -211,12 +208,11 @@ public static Collection runPathsFromTo( } else return Collections.emptySet(); - Collection source = prepareSingleNodeSet(sourceSet, graph); - Collection target = prepareSingleNodeSet(targetSet, graph); + Set source = prepareSingleNodeSet(sourceSet, graph); + Set target = prepareSingleNodeSet(targetSet, graph); PathsFromToQuery query = new PathsFromToQuery(source, target, limitType, limit, true); - Collection resultWrappers = query.run(); - + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -230,9 +226,9 @@ public static Collection runPathsFromTo( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runPathsFromToMultiSet( - Collection> sourceSets, - Collection> targetSets, + public static Set runPathsFromToMultiSet( + Set> sourceSets, + Set> targetSets, Model model, LimitType limitType, int limit, @@ -246,12 +242,11 @@ public static Collection runPathsFromToMultiSet( } else return Collections.emptySet(); - Collection source = prepareSingleNodeSetFromSets(sourceSets, graph); - Collection target = prepareSingleNodeSetFromSets(targetSets, graph); + Set source = prepareSingleNodeSetFromSets(sourceSets, graph); + Set target = prepareSingleNodeSetFromSets(targetSets, graph); PathsFromToQuery query = new PathsFromToQuery(source, target, limitType, limit, true); - Collection resultWrappers = query.run(); - + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, true); } @@ -264,8 +259,8 @@ public static Collection runPathsFromToMultiSet( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runCommonStream( - Collection sourceSet, + public static Set runCommonStream( + Set sourceSet, Model model, Direction direction, int limit, @@ -285,8 +280,7 @@ public static Collection runCommonStream( CommonStreamQuery query = new CommonStreamQuery(source, direction, limit); - Collection resultWrappers = query.run(); - + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, false); } @@ -299,8 +293,8 @@ public static Collection runCommonStream( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runCommonStreamMultiSet( - Collection> sourceSets, + public static Set runCommonStreamMultiSet( + Set> sourceSets, Model model, Direction direction, int limit, @@ -320,8 +314,7 @@ public static Collection runCommonStreamMultiSet( CommonStreamQuery query = new CommonStreamQuery(source, direction, limit); - Collection resultWrappers = query.run(); - + Set resultWrappers = query.run(); return convertQueryResult(resultWrappers, graph, false); } @@ -335,8 +328,8 @@ public static Collection runCommonStreamMultiSet( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runCommonStreamWithPOI( - Collection sourceSet, + public static Set runCommonStreamWithPOI( + Set sourceSet, Model model, Direction direction, int limit, @@ -367,8 +360,8 @@ public static Collection runCommonStreamWithPOI( * @param filters for filtering graph elements * @return BioPAX elements in the result */ - public static Collection runCommonStreamWithPOIMultiSet( - Collection> sourceSets, + public static Set runCommonStreamWithPOIMultiSet( + Set> sourceSets, Model model, Direction direction, int limit, @@ -389,21 +382,21 @@ public static Collection runCommonStreamWithPOIMultiSet( return runCommonStreamWithPOIContinued(nodes, direction, limit, graph); } - private static Collection runCommonStreamWithPOIContinued(Collection> sourceSets, + private static Set runCommonStreamWithPOIContinued(Collection> sourceSets, Direction direction, int limit, Graph graph) { // Run a common stream query CommonStreamQuery commStream = new CommonStreamQuery(sourceSets, direction, limit); - Collection resultWrappers = commStream.run(); + Set resultWrappers = commStream.run(); // Stop if they have no common stream. if (resultWrappers.isEmpty()) return Collections.emptySet(); // Extract nodes from the result - Collection target = new HashSet<>(); + Set target = new HashSet<>(); for (GraphObject go : resultWrappers) { @@ -412,8 +405,8 @@ private static Collection runCommonStreamWithPOIContinued(Collect // Take union of the sources - Collection source = new HashSet<>(); - for (Collection set : sourceSets) + Set source = new HashSet<>(); + for (Set set : sourceSets) { source.addAll(set); } @@ -443,12 +436,12 @@ private static Collection runCommonStreamWithPOIContinued(Collect * @param removeDisconnected whether to remove disconnected non-complex type physical entities * @return Set of elements in the result */ - private static Collection convertQueryResult( - Collection resultWrappers, Graph graph, boolean removeDisconnected) + private static Set convertQueryResult( + Set resultWrappers, Graph graph, boolean removeDisconnected) { - Collection result = graph.getWrappedSet(resultWrappers); + Set result = graph.getWrappedSet(resultWrappers); - Collection set = new HashSet<>(); + Set set = new HashSet<>(); for (Object o : result) { set.add((BioPAXElement) o); @@ -457,7 +450,7 @@ private static Collection convertQueryResult( // remove disconnected simple physical entities if (removeDisconnected) { - Collection remove = new HashSet<>(); + Set remove = new HashSet<>(); for (BioPAXElement ele : set) { @@ -473,7 +466,7 @@ private static Collection convertQueryResult( return set; } - private static boolean isDisconnected(SimplePhysicalEntity spe, Collection resultSet) + private static boolean isDisconnected(SimplePhysicalEntity spe, Set resultSet) { for (Interaction inter : spe.getParticipantOf()) { @@ -504,12 +497,12 @@ private static boolean isDisconnected(SimplePhysicalEntity spe, Collection prepareSingleNodeSet(Collection elements, Graph graph) + public static Set prepareSingleNodeSet(Set elements, Graph graph) { - Map> map = getRelatedPhysicalEntityMap(elements); + Map> map = getRelatedPhysicalEntityMap(elements); - Collection pes = new HashSet<>(); - for (Collection valueSet : map.values()) + Set pes = new HashSet<>(); + for (Set valueSet : map.values()) { pes.addAll(valueSet); } @@ -530,10 +523,10 @@ public static Set prepareSingleNodeSet(Collection elements, * @param graph Owner graph * @return Related wrappers in a set */ - public static Collection prepareSingleNodeSetFromSets(Collection> sets, Graph graph) + public static Set prepareSingleNodeSetFromSets(Set> sets, Graph graph) { - Collection elements = new HashSet<>(); - for (Collection set : sets) + Set elements = new HashSet<>(); + for (Set set : sets) { elements.addAll(set); } @@ -548,13 +541,13 @@ public static Collection prepareSingleNodeSetFromSets(Collection> prepareNodeSets(Collection elements, Graph graph) + private static Collection> prepareNodeSets(Set elements, Graph graph) { - Collection> sets = new HashSet<>(); + Set> sets = new HashSet<>(); - Map> map = getRelatedPhysicalEntityMap(elements); + Map> map = getRelatedPhysicalEntityMap(elements); - for (Collection pes : map.values()) + for (Set pes : map.values()) { Set set = graph.getWrapperSet(pes); if (!set.isEmpty()) sets.add(set); @@ -562,7 +555,7 @@ private static Collection> prepareNodeSets(Collection e // Add interactions in the seed as single node set - Collection inters = getSeedInteractions(elements, graph); + Set inters = getSeedInteractions(elements, graph); for (Node node : inters) { sets.add(Collections.singleton(node)); @@ -579,11 +572,11 @@ private static Collection> prepareNodeSets(Collection e * @param graph Owner graph * @return Related wrappers in individual sets */ - private static Collection> prepareNodeSetsFromSets(Collection> sets, Graph graph) + private static Collection> prepareNodeSetsFromSets(Set> sets, Graph graph) { - Collection> result = new HashSet<>(); + Set> result = new HashSet<>(); - for (Collection set : sets) + for (Set set : sets) { Set nodes = prepareSingleNodeSet(set, graph); if (!nodes.isEmpty()) result.add(nodes); @@ -598,15 +591,15 @@ private static Collection> prepareNodeSetsFromSets(Collection> getRelatedPhysicalEntityMap( + public static Map> getRelatedPhysicalEntityMap( Collection elements) { replaceXrefsWithRelatedER(elements); - Map> map = new HashMap<>(); + Map> map = new HashMap<>(); for (BioPAXElement ele : elements) { - Collection ents = getRelatedPhysicalEntities(ele, null); + Set ents = getRelatedPhysicalEntities(ele, null); if (!ents.isEmpty()) { map.put(ele, ents); @@ -623,8 +616,8 @@ public static Map> getRelatedPhysicalE protected static void replaceXrefsWithRelatedER( Collection elements) { - Collection ers = new HashSet<>(); - Collection xrefs = new HashSet<>(); + Set ers = new HashSet<>(); + Set xrefs = new HashSet<>(); for (BioPAXElement element : elements) { if (element instanceof Xref) @@ -654,8 +647,8 @@ protected static void replaceXrefsWithRelatedER( * @param pes Result set. If not supplied, a new set will be initialized. * @return Related PhysicalEntity objects */ - public static Collection getRelatedPhysicalEntities(BioPAXElement element, - Collection pes) + public static Set getRelatedPhysicalEntities(BioPAXElement element, + Set pes) { if (pes == null) pes = new HashSet<>(); @@ -708,7 +701,7 @@ else if (element instanceof EntityReference) * @param pe The PhysicalEntity to add its equivalents and complexes * @param pes Set to collect equivalents and complexes */ - private static void addEquivalentsComplexes(PhysicalEntity pe, Collection pes) + private static void addEquivalentsComplexes(PhysicalEntity pe, Set pes) { addEquivalentsComplexes(pe, true, pes); @@ -726,9 +719,9 @@ private static void addEquivalentsComplexes(PhysicalEntity pe, Collection pes) + Set pes) { - Collection set = outer ? + Set set = outer ? pe.getMemberPhysicalEntityOf() : pe.getMemberPhysicalEntity(); for (PhysicalEntity related : set) diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java index 310794c7d..151087e4e 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/BFS.java @@ -6,10 +6,10 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.util.Collection; import java.util.HashMap; import java.util.LinkedList; import java.util.Map; +import java.util.Set; /** * Implements breadth-first search. Takes a set of source nodes, distance limit and labels nodes @@ -35,12 +35,12 @@ public class BFS /** * BFS starts from source nodes. They get the label 0. */ - protected Collection sourceSet; + protected Set sourceSet; /** * BFS will not further traverse neighbors of any node in the stopSet. */ - protected Collection stopSet; + protected Set stopSet; /** * Whether the direction is FORWARD, it is REVERSE otherwise. @@ -64,7 +64,7 @@ public class BFS * @param direction Direction of the traversal * @param limit Distance limit */ - public BFS(Collection sourceSet, Collection stopSet, Direction direction, int limit) + public BFS(Set sourceSet, Set stopSet, Direction direction, int limit) { if (direction != Direction.UPSTREAM && direction != Direction.DOWNSTREAM) throw new IllegalArgumentException("Direction has to be either upstream or downstream"); @@ -78,7 +78,9 @@ public BFS(Collection sourceSet, Collection stopSet, Direction direc /** * Empty constructor for other possible uses. */ - public BFS() {} + public BFS() + { + } /** * Executes the algorithm. @@ -259,7 +261,7 @@ protected void labelEquivRecursive(Node node, boolean up, int dist, * @param set Node set * @return true if an equivalent is in the set */ - protected boolean isEquivalentInTheSet(Node node, Collection set) + protected boolean isEquivalentInTheSet(Node node, Set set) { return set.contains(node) || isEquivalentInTheSet(node, UPWARD, set) || isEquivalentInTheSet(node, DOWNWARD, set); @@ -272,7 +274,7 @@ protected boolean isEquivalentInTheSet(Node node, Collection set) * @param set Node set * @return true if an equivalent is in the set */ - protected boolean isEquivalentInTheSet(Node node, boolean direction, Collection set) + protected boolean isEquivalentInTheSet(Node node, boolean direction, Set set) { for (Node eq : direction == UPWARD ? node.getUpperEquivalent() : node.getLowerEquivalent()) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java index d93c360d1..ae94e40f8 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CommonStreamQuery.java @@ -87,7 +87,7 @@ public CommonStreamQuery(Collection> sourceStateSet, Direction directi * Method to run the query. * @return Common stream */ - public Collection run() + public Set run() { /** * Candidate contains all the graph objects that are the results of BFS. @@ -98,7 +98,7 @@ public Collection run() Set result = new HashSet<>(); //for each set of states of entity, run BFS separately - for (Collection source : sourceSet) + for (Set source : sourceSet) { //run BFS for set of states of each entity BFS bfs = new BFS (source, null, direction, limit); diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java index a3747f347..32b7ce461 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/CycleBreaker.java @@ -6,6 +6,7 @@ import java.util.ArrayList; import java.util.Collection; +import java.util.Set; /** * When an algorithm searches for a paths between multiple source nodes, or from a source to a @@ -20,12 +21,12 @@ public class CycleBreaker extends BFS /** * The result set to search for cycles. */ - Collection result; + Set result; /** * Source and (if exists) target nodes. */ - Collection ST; + Set ST; /** * Constructor with the objects in the result, source and target nodes, and search limit. @@ -33,7 +34,7 @@ public class CycleBreaker extends BFS * @param ST Source and target nodes * @param limit Search limit */ - public CycleBreaker(Collection result, Collection ST, int limit) + public CycleBreaker(Set result, Set ST, int limit) { this.result = result; this.ST = ST; diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java index 60fbf0bf3..800750bf9 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/NeighborhoodQuery.java @@ -3,7 +3,6 @@ import org.biopax.paxtools.query.model.GraphObject; import org.biopax.paxtools.query.model.Node; -import java.util.Collection; import java.util.HashSet; import java.util.Map; import java.util.Set; @@ -18,7 +17,7 @@ public class NeighborhoodQuery /** * Set of source nodes. */ - private Collection sourceNodes; + private Set sourceNodes; /** * Booleans to determine the directin of search. @@ -36,7 +35,7 @@ public class NeighborhoodQuery * @param direction Direction of the search * @param limit Distance limit */ - public NeighborhoodQuery(Collection sourceNodes, Direction direction, int limit) + public NeighborhoodQuery(Set sourceNodes, Direction direction, int limit) { if (direction == Direction.UNDIRECTED) throw new IllegalArgumentException("Direction cannot be undirected, " + @@ -51,10 +50,10 @@ public NeighborhoodQuery(Collection sourceNodes, Direction direction, int * Executes the query. * @return Neighborhood */ - public Collection run() + public Set run() { // result set of neighborhood query - Collection queryResult = new HashSet<>(); + Set queryResult = new HashSet<>(); // if upstream is selected if (direction == Direction.UPSTREAM || direction == Direction.BOTHSTREAM) diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java index b28470494..ccc64b026 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsBetweenQuery.java @@ -37,7 +37,7 @@ public PathsBetweenQuery(Collection> sourceSet, int limit) this.limit = limit; } - public Collection run() + public Set run() { /** * Distance labels of graph objects. Note that each source set may have a distinct label for @@ -46,7 +46,7 @@ public Collection run() Map, Integer>> fwdObj = new HashMap<>(); Map, Integer>> revObj = new HashMap<>(); - Collection result = new HashSet<>(); + Set result = new HashSet<>(); for (Set set : sourceSet) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java index 50bb1b9e0..d6c07b700 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/PathsFromToQuery.java @@ -4,10 +4,10 @@ import org.biopax.paxtools.query.model.GraphObject; import org.biopax.paxtools.query.model.Node; -import java.util.Collection; import java.util.HashMap; import java.util.HashSet; import java.util.Map; +import java.util.Set; /** * Finds the paths from a specified source set of states or entities to a @@ -25,12 +25,12 @@ public class PathsFromToQuery /** * The set of nodes from which the paths of interests should start. */ - private Collection sourceSet; + private Set sourceSet; /** * The set of nodes to which the paths of interests should arrive. */ - private Collection targetSet; + private Set targetSet; /** * True if length limit is used, false if shortes+k is used. @@ -66,11 +66,11 @@ public class PathsFromToQuery * @param stopDistance search limit * @param strict whether we want to extend and result path towards other source and targets */ - public PathsFromToQuery(Collection sourceSet, - Collection targetSet, - LimitType limitType, - int stopDistance, - boolean strict) + public PathsFromToQuery(Set sourceSet, + Set targetSet, + LimitType limitType, + int stopDistance, + boolean strict) { assert limitType != null : "limitType should be specified"; @@ -85,15 +85,15 @@ public PathsFromToQuery(Collection sourceSet, * Executes the algorithm. * @return paths from sources to targets */ - public Collection run() + public Set run() { /** * Candidate contains all the graph objects that are the results of BFS. * Eliminating nodes from candidate according to their labels will * yield result. */ - Map candidate = new HashMap(); - Collection result = new HashSet<>(); + Map candidate = new HashMap<>(); + Set result = new HashSet<>(); BFS bfsFwd = null; BFS bfsRev = null; @@ -176,7 +176,7 @@ else if (limitType == LimitType.SHORTEST_PLUS_K && strict) } } - Collection ST = new HashSet<>(sourceSet); + Set ST = new HashSet<>(sourceSet); ST.addAll(targetSet); CycleBreaker breaker = new CycleBreaker(result, ST, limit); diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java index 769637e01..61fb42cfa 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/algorithm/Prune.java @@ -4,8 +4,8 @@ import org.biopax.paxtools.query.model.GraphObject; import org.biopax.paxtools.query.model.Node; -import java.util.Collection; import java.util.HashSet; +import java.util.Set; /** * This algorithm is used internally by PathsBetween and PathsFromTo algorithms. It detects objects @@ -16,12 +16,12 @@ */ public class Prune { - private Collection result; + private Set result; /** * Source and targets merged. */ - private Collection ST; + private Set ST; /** @@ -30,7 +30,7 @@ public class Prune * @param result The result set * @param ST Source and target nodes */ - public Prune(Collection result, Collection ST) + public Prune(Set result, Set ST) { this.result = result; this.ST = ST; @@ -40,7 +40,7 @@ public Prune(Collection result, Collection ST) * Executes the algorithm. * @return the pruned graph */ - public Collection run() + public Set run() { for (GraphObject go : new HashSet<>(result)) { diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java index 7c281bbca..9c2ad693e 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/model/Graph.java @@ -1,6 +1,5 @@ package org.biopax.paxtools.query.model; -import java.util.Collection; import java.util.Map; import java.util.Set; @@ -23,21 +22,21 @@ public interface Graph * @param objects Wrapped objects * @return Related wrappers */ - Set getWrapperSet(Collection objects); + Set getWrapperSet(Set objects); /** * Gets a map from objects to their wrappers. * @param objects Wrapped objects * @return Object-to-wrapper map */ - Map getWrapperMap(Collection objects); + Map getWrapperMap(Set objects); /** * Gets the wrapped objects of the given wrapper set. * @param wrappers Wrappers * @return Wrapped objects */ - Collection getWrappedSet(Collection wrappers); + Set getWrappedSet(Set wrappers); /** * Should clear any analysis specific labeling on the graph. diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java index b8a82c964..6483a39d0 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3/GraphL3.java @@ -128,7 +128,7 @@ public String getKey(Object wrapped) * @param objects Wrapped objects * @return wrappers */ - public Set getWrapperSet(Collection objects) + public Set getWrapperSet(Set objects) { Set wrapped = new HashSet<>(); @@ -148,7 +148,7 @@ public Set getWrapperSet(Collection objects) * @param objects Wrapped objects * @return object-to-wrapper map */ - public Map getWrapperMap(Collection objects) + public Map getWrapperMap(Set objects) { Map map = new HashMap(); @@ -168,7 +168,7 @@ public Map getWrapperMap(Collection objects) * @param wrappers Wrappers * @return Wrapped objects */ - public Set getWrappedSet(Collection wrappers) + public Set getWrappedSet(Set wrappers) { Set objects = new HashSet<>(); diff --git a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java index 6307b29f8..4bb32c0bc 100644 --- a/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java +++ b/paxtools-query/src/main/java/org/biopax/paxtools/query/wrapperL3undirected/GraphL3Undirected.java @@ -125,7 +125,7 @@ public String getKey(Object wrapped) * @param objects Wrapped objects * @return wrappers */ - public Set getWrapperSet(Collection objects) + public Set getWrapperSet(Set objects) { Set wrapped = new HashSet<>(); @@ -145,9 +145,9 @@ public Set getWrapperSet(Collection objects) * @param objects Wrapped objects * @return object-to-wrapper map */ - public Map getWrapperMap(Collection objects) + public Map getWrapperMap(Set objects) { - Map map = new HashMap(); + Map map = new HashMap<>(); for (Object object : objects) { @@ -165,7 +165,7 @@ public Map getWrapperMap(Collection objects) * @param wrappers Wrappers * @return Wrapped objects */ - public Set getWrappedSet(Collection wrappers) + public Set getWrappedSet(Set wrappers) { Set objects = new HashSet<>(); diff --git a/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java b/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java index afc22b891..c50ad6e97 100644 --- a/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java +++ b/paxtools-query/src/test/java/org/biopax/paxtools/query/QueryTest.java @@ -22,7 +22,6 @@ import java.io.IOException; import java.io.InputStream; import java.util.Arrays; -import java.util.Collection; import java.util.HashSet; import java.util.Set; @@ -41,13 +40,13 @@ public void queries() Model model = handler.convertFromOWL(QueryTest.class.getResourceAsStream( "raf_map_kinase_cascade_reactome.owl")); - Collection source = findElements(model, + Set source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606"); //MEK2 - Collection target = findElements(model, + Set target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606"); //ERK1 - Collection result = QueryExecuter.runNeighborhood( + Set result = QueryExecuter.runNeighborhood( source, model, 1, Direction.BOTHSTREAM); assertTrue(result.size() > 0); @@ -95,7 +94,7 @@ public void queries() assertTrue(result.contains(check)); } - private Model excise(Collection result) + private Model excise(Set result) { Completer c = new Completer(SimpleEditorMap.L3); @@ -106,9 +105,9 @@ private Model excise(Collection result) return cln.clone(result); } - protected static Collection findElements(Model model, String... ids) + protected static Set findElements(Model model, String... ids) { - Collection set = new HashSet<>(); + Set set = new HashSet<>(); for (String id : ids) { @@ -139,11 +138,11 @@ public void queryPerformance() throws IOException BioPAXElement s1 = model.getByID("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN6022_1_9606"); BioPAXElement t1 = model.getByID("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN6020_1_9606"); - Collection source = new HashSet<>(); + Set source = new HashSet<>(); source.add(s1); source.add(t1); - Collection result = QueryExecuter.runCommonStreamWithPOI( + Set result = QueryExecuter.runCommonStreamWithPOI( source, model, Direction.DOWNSTREAM, 3, null); secs = (System.currentTimeMillis() - time); @@ -161,15 +160,15 @@ public void filters() Model model = handler.convertFromOWL(this.getClass().getResourceAsStream( "raf_map_kinase_cascade_reactome.owl")); - Collection source = findElements(model, + Set source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606"); //MEK2 - Collection target = findElements(model, + Set target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606"); //ERK1 // test organism filter Filter f = new OrganismFilter(new String[]{"Homo sapiens"}); - Collection result = QueryExecuter.runPathsFromTo( + Set result = QueryExecuter.runPathsFromTo( source, target, model, LimitType.NORMAL, 2, f); assertTrue(!result.isEmpty()); From d13ef1d2c8e3be1351f9bdd26d6d361566567f80 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 9 Jul 2023 03:50:46 -0400 Subject: [PATCH 12/20] Paxtools-6: added uniprotknowledgebase to spellmap.json --- .../main/resources/org/biopax/paxtools/normalizer/spellmap.json | 1 + 1 file changed, 1 insertion(+) diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json index 00009c06c..6a3d5762f 100644 --- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/spellmap.json @@ -25,6 +25,7 @@ "UNIPROTSWISSPROT": "uniprot", "UNIPROTKBSWISSPROT": "uniprot", "PROTEINKNOWLEDGEBASE": "uniprot", + "UNIPROTKNOWLEDGEBASE": "uniprot", "PIR": "uniprot", "PIRSSD": "uniprot", "UMBBD": "umbbd.compound", From 7650eb1caab05eb9fc5ed9b2266e475c3f98e401 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Mon, 24 Jul 2023 00:10:13 -0400 Subject: [PATCH 13/20] Paxtools-6: new methods in Normalizer --- .../paxtools/normalizer/Normalizer.java | 63 ++++++++++++------- 1 file changed, 39 insertions(+), 24 deletions(-) diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index bf5ae5441..29a2e5566 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -121,11 +121,12 @@ public Normalizer() { * (for CV or ProteinReference instead); so, this will also replace URIs of xrefs having bad 'db' or 'id'. * * @param model biopax model to update + * @param usePrefixAsDbName if possible, use CURIE prefix as xref.db instead of preferred name */ - private void normalizeXrefs(Model model) { + public void normalizeXrefs(Model model, boolean usePrefixAsDbName) { final NormalizerMap map = new NormalizerMap(model); final String xmlBase = getXmlBase(model); //current base, the default or model's one, if set. - + // use a copy of the xrefs set (to avoid concurrent exceptions) Set xrefs = new HashSet<>(model.getObjects(Xref.class)); for(Xref ref : xrefs) { @@ -134,10 +135,16 @@ private void normalizeXrefs(Model model) { continue; } - String quickFixDb = StringUtils - .replaceIgnoreCase(ref.getDb(),"uniprotkb", "uniprot") - .toLowerCase(); - ref.setDb(quickFixDb); + //normalize name first + Namespace ns = Resolver.getNamespace(ref.getDb()); //resolve a prefix, name, synonym or known spelling variants + if(ns != null) { + if (usePrefixAsDbName) { + ref.setDb(ns.getPrefix()); //use bioregistry collection prefix (already lowercase) + } else { + ref.setDb(ns.getName().toLowerCase()); //use the standard name + } + } + final String isoformName = (usePrefixAsDbName) ? "uniprot.isoform" : "uniprot isoform"; String idPart = ref.getId(); @@ -154,14 +161,14 @@ private void normalizeXrefs(Model model) { // fix 'uniprot' instead 'uniprot isoform' and vice versa mistakes if (ref.getDb().startsWith("uniprot")) { //auto-fix (guess) for possibly incorrect db/id (can be 'uniprot isoform' with/no idVersion, etc..) - if (isValidDbId("uniprot isoform", ref.getId()) + if (isValidDbId("uniprot.isoform", ref.getId()) && ref.getId().contains("-")) //the second condition is important { //then it's certainly an isoform id; so - fix the db name - ref.setDb("uniprot isoform"); //fix the db + ref.setDb(isoformName); //fix the db } else { //id does not end with "-\\d+", i.e., not a isoform id - //(idVersion is a different thing, but id db was "uniprot isoform" they probably misused idVersion) - if(ref.getDb().equals("uniprot isoform")) { + //(idVersion is a different thing, but if db was "uniprot isoform" they probably misused idVersion) + if(ref.getDb().equalsIgnoreCase(isoformName)) { if(ref.getIdVersion() != null && ref.getIdVersion().matches("^\\d+$")) { idPart = ref.getId() + "-" + ref.getIdVersion(); //guess idVersion is isoform number } @@ -176,15 +183,10 @@ else if(!isValidDbId(ref.getDb(), ref.getId())) { idPart = ref.getId(); } } - } else { //not an uniprot kind UX - //try to tell if it's a standard id type name - Namespace ns = Resolver.getNamespace(ref.getDb()); - if(ns != null) { - ref.setDb(ns.getName().toLowerCase()); //update to the standard name - } else { - if(ref.getIdVersion() != null) { + } else {//not any uniprot... + //if not standard and has idVersion, add that + if(ns == null && ref.getIdVersion() != null) { idPart += "_" + ref.getIdVersion(); - } } } } @@ -423,8 +425,9 @@ private UnificationXref findPreferredUnificationXref(XReferrable bpe) } else if(bpe instanceof NucleicAcidReference) { //that includes NucleicAcidRegionReference, etc. sub-classes; toReturn = findSingleUnificationXref(orderedUrefs, "entrez"); + //when xrefs were normalized to use either 'entrez gene' (the preferred name) or 'ncbigene' (the prefix) if(toReturn==null) - toReturn = findSingleUnificationXref(orderedUrefs, "ncbi gene"); //todo: impossible when xrefs already normalized?.. + toReturn = findSingleUnificationXref(orderedUrefs, "ncbigene"); } else { //for other XReferrable types (BioSource or ControlledVocabulary) //use if there's only one xref (return null if many) @@ -459,16 +462,29 @@ else if (ret.getDb().equalsIgnoreCase(x.getDb()) && !ret.getId().equals(x.getId( return ret; } + /** + * BioPAX normalization + * (modifies the original Model) + * + * @param model BioPAX model to normalize + * @throws NullPointerException if model is null + * @throws IllegalArgumentException if model is not Level3 BioPAX + */ + public void normalize(Model model) { + normalize(model, false); + } + /** * BioPAX normalization * (modifies the original Model) * * @param model BioPAX model to normalize + * @param usePrefixAsDbName if possible, use CURIE prefix as xref.db instead of preferred name * @throws NullPointerException if model is null * @throws IllegalArgumentException if model is not Level3 BioPAX */ - public void normalize(Model model) { + public void normalize(Model model, boolean usePrefixAsDbName) { if(model.getLevel() != BioPAXLevel.L3) throw new IllegalArgumentException("Not Level3 model. " + @@ -478,11 +494,10 @@ public void normalize(Model model) { if(xmlBase != null && !xmlBase.isEmpty()) model.setXmlBase(xmlBase); - // Normalize/merge xrefs, first, and then CVs - // (also because original xrefs might have "normalized" URIs - // that, in fact, must be used for other biopax types, such as CV or ProteinReference) + // Normalize/merge xrefs first and then - CVs + // (xrefs could have URIs that should be instead used for CV, PR, SMR or BS biopax types) log.info("Normalizing xrefs..." + description); - normalizeXrefs(model); + normalizeXrefs(model, usePrefixAsDbName); // fix displayName where possible if(fixDisplayName) { From 01c9874204d6fad26ce0c13a0b58a58838205d54 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 30 Jul 2023 15:56:13 -0400 Subject: [PATCH 14/20] Paxtools-6: changes - - fixed an old xmlns bug (writes shorter files now using xsd:string, etc.); - when normalizing xref.id, it will add banana+peel prefix if possible (e.g. "CHEBI:"); --- .../org/biopax/paxtools/normalizer/Normalizer.java | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index 29a2e5566..b603f5435 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -139,15 +139,21 @@ public void normalizeXrefs(Model model, boolean usePrefixAsDbName) { Namespace ns = Resolver.getNamespace(ref.getDb()); //resolve a prefix, name, synonym or known spelling variants if(ns != null) { if (usePrefixAsDbName) { - ref.setDb(ns.getPrefix()); //use bioregistry collection prefix (already lowercase) + ref.setDb(ns.getPrefix()); //use bioregistry collection prefix (already lowercase), e.g. 'uniprot' } else { - ref.setDb(ns.getName().toLowerCase()); //use the standard name + ref.setDb(ns.getName().toLowerCase()); //use the standard name, e.g. 'uniprot protein' + } + + //add banana and peel prefix to the ID if possible (improves index/search/id-mapping) + String banana = ns.getBanana(); + if(StringUtils.isNotBlank(banana) && !StringUtils.startsWith(ref.getId(), banana)) { + ref.setId(banana + ns.getBanana_peel() + ref.getId()); } } + final String isoformName = (usePrefixAsDbName) ? "uniprot.isoform" : "uniprot isoform"; String idPart = ref.getId(); - if(ref instanceof RelationshipXref) { //RXs might have the same db, id but different rel. type. RelationshipTypeVocabulary cv = ((RelationshipXref) ref).getRelationshipType(); From 42db8a951e1fb46eaec48000018573e863735c66 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sun, 30 Jul 2023 19:26:12 -0400 Subject: [PATCH 15/20] Removed obsolete/unnecessary step when normalizing ERs --- .../java/org/biopax/paxtools/normalizer/Normalizer.java | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index b603f5435..415fa9879 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -594,14 +594,7 @@ private void normalizeERs(Model model) { // process the rest of utility classes (selectively though) for (EntityReference bpe : model.getObjects(EntityReference.class)) { - - //skip those with already normalized URIs - if(bpe.getUri().contains("identifiers.org/")) { - log.info("Skip already normalized: " + bpe.getUri()); - continue; - } - - UnificationXref uref = findPreferredUnificationXref(bpe); + UnificationXref uref = findPreferredUnificationXref(bpe); if (uref != null) { // Create (with a new URI made from a unif. xref) // and save the replacement object, if possible, From a7593de19e47fdc934448f733d02d910fec4f027 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Mon, 31 Jul 2023 23:09:21 -0400 Subject: [PATCH 16/20] Added extra pubchem synonyms: CID and SID, and unit tests --- .../resources/org/biopax/paxtools/normalizer/synonymap.json | 2 ++ .../java/org/biopax/paxtools/normalizer/ResolverTest.java | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json index 9a935ec41..c50148337 100644 --- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/synonymap.json @@ -12,6 +12,8 @@ "GI": "ncbigi", "PUBCHEM": "pubchem.compound", "NCBI PUBCHEM": "pubchem.compound", + "CID": "pubchem.compound", + "SID": "pubchem.substance", "PMID": "pubmed", "MEDLINE": "pubmed", "SWISS-PROT": "uniprot", diff --git a/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java b/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java index 1c1d733f8..6b67d496c 100644 --- a/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java +++ b/normalizer/src/test/java/org/biopax/paxtools/normalizer/ResolverTest.java @@ -42,7 +42,10 @@ public final void getURI() { //old ns prefix (should auto-fix as "chebi") and id without "CHEBI:" banana... () -> Assertions.assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("identifiers.org/chebi/", "36927")), //similar, but using bioregistry.io/ base, with ending slash, and with banana... - () -> Assertions.assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("bioregistry.io/chebi", "CHEBI:36927")) + () -> Assertions.assertEquals("bioregistry.io/chebi:36927", Resolver.getURI("bioregistry.io/chebi", "CHEBI:36927")), + () -> Assertions.assertEquals("bioregistry.io/pubchem.compound:1", Resolver.getURI("CID", "1")), + () -> Assertions.assertEquals("bioregistry.io/pubchem.substance:1", Resolver.getURI("SID", "1")), + () -> Assertions.assertNull(Resolver.getURI("compound", "1")) //id pattern mismatch (kegg.compound) ); } From ed48955a4e50dbe850dc24ee7ab868f37f0fed57 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 5 Aug 2023 23:56:44 -0400 Subject: [PATCH 17/20] Fixed the maven site.xml, release configs, and set chilay-sbgn v3.1.0 --- pom.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 7e6f6724a..e99163459 100644 --- a/pom.xml +++ b/pom.xml @@ -297,7 +297,7 @@ org.apache.maven.wagon wagon-scm - 2.8 + 2.10 org.apache.maven.doxia @@ -449,10 +449,12 @@ org.junit.jupiter junit-jupiter-api + test org.junit.jupiter junit-jupiter-params + test From 3c8651cd0f844e72ed7ef69f0117ac80babd1cf6 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 26 Aug 2023 18:54:16 -0400 Subject: [PATCH 18/20] Updated registry.json, added "paxtools.normalizer.use-latest-registry" option; maven site related, etc. fix/polish --- README.md | 26 +- .../paxtools/normalizer/Normalizer.java | 7 +- .../biopax/paxtools/normalizer/Resolver.java | 26 +- .../org/biopax/paxtools/normalizer/readme.md | 10 +- .../biopax/paxtools/normalizer/registry.json | 10288 +++++++++++++--- .../org/biopax/paxtools/examples/commands.sh | 17 - .../paxtools/controller/ModelUtils.java | 43 +- pom.xml | 14 +- src/site/site.xml | 88 +- 9 files changed, 8551 insertions(+), 1968 deletions(-) delete mode 100644 paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh diff --git a/README.md b/README.md index 444313ae9..2697af513 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,15 @@ Paxtools provides, beyond the core and converters API, a console application tha `java -jar paxtools.jar` (add -Xmx option when processing large data files). -If you have [homebrew](http://brew.sh/) installed on your system (Mac OS X), you can install the latest release of Paxtools via the following brew command (there might be old version): +### JVM options + +Paxtools can be build and run with JDK-17 or newer, e.g. Temurin-20. Add these JVM options or set +`JDK_JAVA_OPTIONS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"` + + - `-Dpaxtools.model.safeset=list` for read-only BioPAX models/apps, which should consume less RAM. + - `-Dpaxtools.normalizer.use-latest-registry=true` (if using Normalizer/Resolver) to use the latest registry.json from bioregistry.io + +If you have [homebrew](http://brew.sh/) installed on your system (Mac OS X), you can install the latest release of Paxtools via the following brew command (could be old version): ```bash $ brew install homebrew/science/paxtools @@ -43,12 +51,14 @@ $ paxtools help ``` ## Availability -* The latest stable Paxtools modules are available in Maven Central -* [OSSRH public repository](https://oss.sonatype.org/content/groups/public/) (snapshots, since 4.3.1-SNAPSHOT, and releases) -* Older BioPAX [snapshots](http://www.biopax.org/m2repo/snapshots/) and [releases](http://www.biopax.org/m2repo/releases/) Maven2 repository -* [Downloads](http://www.biopax.org/downloads/paxtools/) +* Maven Central repository (only releases) +* [OSSRH public repository](https://oss.sonatype.org/content/groups/public/) (snapshots since 4.3.1, releases) +* [old BioPAX snapshots](http://www.biopax.org/m2repo/snapshots/) and [old BioPAX releases](http://www.biopax.org/m2repo/releases/) repositories +* [BioPAX Downloads](http://www.biopax.org/downloads/paxtools/) + +More information about Paxtools can be found in [the publication](http://dx.plos.org/10.1371/journal.pcbi.1003194), +[wiki archive](http://www.biopax.org/mediawiki/index.php/Paxtools), +and [BioPAX forum](https://groups.google.com/d/msg/biopax-discuss/zwtwDG23T1E/Vu1OK7iXBQAJ). + -More information about Paxtools can be found in [the publication](http://dx.plos.org/10.1371/journal.pcbi.1003194), [wiki archive](http://www.biopax.org/mediawiki/index.php/Paxtools), and [BioPAX forum](https://groups.google.com/d/msg/biopax-discuss/zwtwDG23T1E/Vu1OK7iXBQAJ). -UPDATE: can be now build and run with a JDK-18 (you might also need to add these command-line JVM options -or set _JAVA_OPTIONS env: --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED ) diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java index 415fa9879..3384883cf 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java @@ -616,10 +616,11 @@ private void normalizeERs(Model model) { if(uri != null) { map.put(bpe, uri); } - } else + } else { log.info("Cannot normalize EntityReference: " - + "no unification xrefs found in " + bpe.getUri() - + ". " + description); + + "no unification xrefs found in " + bpe.getUri() + + ". " + description); + } } // replace/update elements in the model diff --git a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java index 2900269f9..2b52cfaf8 100644 --- a/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java +++ b/normalizer/src/main/java/org/biopax/paxtools/normalizer/Resolver.java @@ -2,6 +2,7 @@ import java.io.IOException; import java.io.InputStream; +import java.net.URL; import java.util.*; import java.util.concurrent.ConcurrentSkipListMap; import java.util.regex.Pattern; @@ -19,7 +20,7 @@ */ public class Resolver { private static final Logger LOG = LoggerFactory.getLogger(Resolver.class); - private static final Map namespaces; + private static Map namespaces; private static Map spellmap; // compressed name -> prefix (combines custom spellmap.json and registry) private static Map synonymap;// synonym -> prefix (build from custom synonymap.json and registry) @@ -40,9 +41,26 @@ protected Resolver() { // load a custom map of synonyms is = Resolver.class.getResourceAsStream("synonymap.json"); synonymap = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>(){})); - // load registry.json - is = Resolver.class.getResourceAsStream("registry.json"); - namespaces = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>(){})); + + //load registry.json from URL if the system prop. is true + boolean useLatestBioregistry = Boolean.getBoolean("paxtools.normalizer.use-latest-registry"); + if(useLatestBioregistry) { + LOG.info("Getting registry.json from bioregistry.io (property: paxtools.normalizer.use-latest-registry=true)"); + try { + is = new URL("https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/registry/registry.json") + .openStream(); + namespaces = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>() { + })); + } catch (Exception e) { + LOG.warn("Failed loading registry.json from URL (fallback to the built-in, v2023-08-26)", e); + } + } + if(namespaces == null || namespaces.isEmpty()) { + is = Resolver.class.getResourceAsStream("registry.json"); + namespaces = new ConcurrentSkipListMap<>(om.readValue(is, new TypeReference>() { + })); + } + LOG.info("read registry.json to the namespaces map; size: " + namespaces.size()); //Post-process registry entries to add synonyms and spellings diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md index 4606ba090..df5f3c936 100644 --- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/readme.md @@ -1,14 +1,16 @@ # XRegistry resources ## registry.json -Extract the prefix, regexp, name, synonyms, etc. -bioregistry.io/chebi:12345 +The Consensus Registry JSON file downloaded from https://bioregistry.io/download, +https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/registry/registry.json +Contains the metadata about the collections of bio identifiers, such as the prefix, regexp, name, synonyms, etc. ## spellmap.json An additional mapping from identifier db/type name spelling variants (non-alphanumeric chars are removed) to the corresponding Prefix. All the keys and values should be upper case. In addition to the predefined map entries, -each registry prefix, name, synonym (removing non-alphanumeric chars) will be also auto-added. +each prefix, name, synonym (removing non-alphanumeric chars) in the registry +will be also auto-added to this map at run time. ## synonymap.json -An additional mapping from names/synonyms to Prefixes. +An additional mapping from names/synonyms to the Bioregistry Prefixes. diff --git a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json index fa070208b..6c1769414 100644 --- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json +++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json @@ -22,19 +22,28 @@ "name": "3D Metabolites", "pattern": "^B\\d{5}$", "preferred_prefix": "3dmet", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/3dmet:$1" + } + ], "publications": [ { "doi": "10.2142/biophysico.15.0_87", "pmc": "PMC5992871", "pubmed": "29892514", - "title": "Chemical curation to improve data accuracy: recent development of the 3DMET database.", + "title": "Chemical curation to improve data accuracy: recent development of the 3DMET database", "year": 2018 }, { "doi": "10.1021/ci300309k", "pmc": null, "pubmed": "23293959", - "title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures.", + "title": "Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures", "year": 2013 } ], @@ -58,12 +67,21 @@ "name": "4D Nucleome Data Portal Biosource", "pattern": "^4DN[A-Z]{2}[A-Z0-9]{7}$", "preferred_prefix": "4dn.biosource", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/4dn:$1" + } + ], "publications": [ { "doi": "10.1038/nature23884", "pmc": "PMC5617335", "pubmed": "28905911", - "title": "The 4D nucleome project.", + "title": "The 4D nucleome project", "year": 2017 } ], @@ -120,12 +138,21 @@ }, "name": "AAindex", "preferred_prefix": "aaindex", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/aaindex:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm998", "pmc": "PMC2238890", "pubmed": "17998252", - "title": "AAindex: amino acid index database, progress report 2008.", + "title": "AAindex: amino acid index database, progress report 2008", "year": 2007 } ], @@ -162,24 +189,48 @@ "name": "Amphibian gross anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "AAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/aao:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-5-21", "pmc": "PMC4089931", "pubmed": "25009735", - "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.", + "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon", "year": 2014 }, { "doi": "10.1142/9789812772435_0035", "pmc": null, "pubmed": "17992749", - "title": "An anatomical ontology for amphibians.", + "title": "An anatomical ontology for amphibians", "year": 2007 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/AAO_$1", "uri_format": "http://purl.obolibrary.org/obo/AAO_$1" }, + "abcam": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Vendor for assays, cells, and antibodies", + "example": "ab275461", + "homepage": "https://www.abcam.com", + "name": "Abcam", + "preferred_prefix": "abcam", + "uri_format": "https://www.abcam.com/$1.html" + }, "abcd": { "contributor": { "email": "cthoyt@gmail.com", @@ -206,13 +257,21 @@ "doi": "10.1093/nar/gkz714", "pmc": "PMC6943046", "pubmed": "31410491", - "title": "The ABCD database: a repository for chemically defined antibodies.", + "title": "The ABCD database: a repository for chemically defined antibodies", "year": 2020 } ], "uri_format": "https://web.expasy.org/abcd/ABCD_$1" }, "abm": { + "contributor_extras": [ + { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + } + ], "description": "Cell line collections", "example": "T0599", "homepage": "https://www.abmgood.com/Cell-Biology.html", @@ -221,7 +280,7 @@ }, "name": "Applied Biological Materials cell line products", "preferred_prefix": "abm", - "uri_format": "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1" + "uri_format": "https://www.abmgood.com/search?query=$1" }, "abs": { "contact": { @@ -250,12 +309,21 @@ "name": "Annotated Regulatory Binding Sites", "pattern": "^A\\d+$", "preferred_prefix": "abs", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/abs:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj116", "pmc": "PMC1347478", "pubmed": "16381947", - "title": "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.", + "title": "ABS: a database of Annotated regulatory Binding Sites from orthologous promoters", "year": 2006 } ], @@ -297,17 +365,65 @@ "name": "Aceview Worm", "pattern": "^[a-z0-9-]+$", "preferred_prefix": "aceview.worm", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/aceview.worm:$1" + } + ], "publications": [ { "doi": "10.1186/gb-2006-7-s1-s12", "pmc": "PMC1810549", "pubmed": "16925834", - "title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation.", + "title": "AceView: a comprehensive cDNA-supported gene and transcripts annotation", "year": 2006 } ], "uri_format": "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1" }, + "adcad": { + "contact": { + "email": "brycemecum@gmail.com", + "github": "amoeba", + "name": "Bryce Mecum", + "orcid": "0000-0002-0381-3766" + }, + "contributor": { + "email": "j.harry.caufield@gmail.com", + "github": "caufieldjh", + "name": "Harry Caufield", + "orcid": "0000-0001-5705-7831" + }, + "description": "An ontology to support disciplinary annotation of Arctic Data Center datasets.", + "download_owl": "http://aber-owl.net/media/ontologies/ADCAD/1/adcad.owl", + "download_rdf": "https://github.com/NCEAS/adc-disciplines/raw/main/ADCAD.ttl", + "example": "00000", + "github_request_issue": 827, + "homepage": "https://arcticdata.io/", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "ADCAD", + "bioportal": "ADCAD" + }, + "name": "Arctic Data Center Academic Disciplines Ontology", + "pattern": "^\\d{5}$", + "preferred_prefix": "adcad", + "repository": "https://github.com/NCEAS/adc-disciplines", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://purl.dataone.org/odo/ADCAD_$1" + }, "addexbio": { "description": "Cell line collections", "example": "C0020004/4992", @@ -337,32 +453,63 @@ "name": "Addgene Plasmid Repository", "pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$", "preferred_prefix": "addgene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/addgene:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gku893", "pmc": "PMC4384007", "pubmed": "25392412", - "title": "The Addgene repository: an international nonprofit plasmid and data resource.", + "title": "The Addgene repository: an international nonprofit plasmid and data resource", "year": 2014 }, { "doi": "10.1038/505272a", "pmc": null, "pubmed": "24429608", - "title": "Repositories share key research tools.", + "title": "Repositories share key research tools", "year": 2014 }, { "doi": "10.1038/nbt.2177", "pmc": null, "pubmed": "22491276", - "title": "Addgene provides an open forum for plasmid sharing.", + "title": "Addgene provides an open forum for plasmid sharing", "year": 2012 } ], "twitter": "Addgene", "uri_format": "http://addgene.org/$1" }, + "adms": { + "contact": { + "email": "bert.van.nuffelen@tenforce.com", + "github": "bertvannuffelen", + "name": "Bert Van Nuffelen", + "orcid": null + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).", + "example": "Asset", + "homepage": "http://www.w3.org/ns/adms", + "license": "CC-BY-4.0", + "name": "Asset Description Metadata Schema Vocabulary", + "preferred_prefix": "adms", + "repository": "https://github.com/SEMICeu/ADMS/", + "uri_format": "http://www.w3.org/ns/adms#$1" + }, "ado": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", @@ -399,13 +546,14 @@ "doi": "10.1016/j.jalz.2013.02.009", "pmc": null, "pubmed": "23830913", - "title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.", + "title": "ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ADO_$1", "repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", "uri_format": "http://purl.obolibrary.org/obo/ADO_$1", - "version": "2.0.0" + "version": "2022-06-11" }, "adw": { "contact": { @@ -437,6 +585,7 @@ "name": "Animal natural history and life history", "pattern": "^[A-Z_a-z]+$", "preferred_prefix": "ADW", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ADW_$1", "uri_format": "https://animaldiversity.org/accounts/$1" }, "aeo": { @@ -451,7 +600,7 @@ }, "deprecated": true, "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", - "download_obo": "https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo", + "download_obo": "http://purl.obolibrary.org/obo/aeo.obo", "download_owl": "http://purl.obolibrary.org/obo/aeo.owl", "example": "0001017", "homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology/", @@ -480,10 +629,11 @@ "doi": "10.3389/fgene.2012.00018", "pmc": "PMC3278863", "pubmed": "22347883", - "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs.", + "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/AEO_$1", "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", "synonyms": [ "AEO_RETIRED" @@ -551,11 +701,13 @@ "biocontext": "AERO", "bioportal": "AERO", "fairsharing": "FAIRsharing.rycy2x", - "obofoundry": "aero" + "obofoundry": "aero", + "ols": "aero" }, "name": "Adverse Event Reporting Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "AERO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/AERO_$1", "uri_format": "http://purl.obolibrary.org/obo/AERO_$1" }, "affy.probeset": { @@ -589,7 +741,7 @@ "orcid": null }, "description": "Allotrope Merged Ontology Suite", - "download_owl": "http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10", + "download_owl": "http://purl.allotrope.org/voc/afo/merged/REC/2023/03/merged-without-qudt-and-inferred", "homepage": "https://www.allotrope.org/", "keywords": [ "agricultural engineering", @@ -605,12 +757,13 @@ "aberowl": "AFO", "bioportal": "AFO", "fairsharing": "FAIRsharing.595710", - "ols": "afo" + "ols": "afo", + "ontobee": "AFO" }, "name": "Allotrope Merged Ontology Suite", "no_own_terms": true, "preferred_prefix": "afo", - "version": "2019-05-10" + "version": "2023/03" }, "aftol.taxonomy": { "contributor_extras": [ @@ -687,7 +840,7 @@ "doi": "10.1093/nar/gkz813", "pmc": "PMC6943066", "pubmed": "31552413", - "title": "Alliance of Genome Resources Portal: unified model organism research platform.", + "title": "Alliance of Genome Resources Portal: unified model organism research platform", "year": 2020 } ], @@ -781,9 +934,10 @@ "name": "Agronomy Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "AGRO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/AGRO_$1", "repository": "https://github.com/AgriculturalSemantics/agro", "uri_format": "http://purl.obolibrary.org/obo/AGRO_$1", - "version": "2021-11-05" + "version": "2022-11-02" }, "agrovoc": { "banana": "c_", @@ -822,6 +976,20 @@ "pattern": "^[a-z0-9]+$", "preferred_prefix": "agrovoc", "publications": [ + { + "doi": "https://doi.org/10.4060/cb2838en", + "pmc": null, + "pubmed": null, + "title": "AGROVOC – Semantic data interoperability on food and agriculture", + "year": null + }, + { + "doi": "https://doi.org/10.3390/engproc2021009017", + "pmc": null, + "pubmed": null, + "title": "How Agricultural Digital Innovation Can Benefit from Semantics: The Case of the AGROVOC Multilingual Thesaurus", + "year": null + }, { "doi": "10.4060/cb2838en", "pmc": null, @@ -844,6 +1012,7 @@ "year": 2022 } ], + "rdf_uri_format": "http://aims.fao.org/aos/agrovoc/$1", "references": [ "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_core.nt.zip", "http://agrovoc.uniroma2.it/latestAgrovoc/agrovoc_lod.nt.zip", @@ -868,6 +1037,15 @@ }, "name": "Animal Genome Size Database", "preferred_prefix": "agsd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/agsd:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -876,6 +1054,47 @@ }, "uri_format": "http://www.genomesize.com/result_species.php?id=$1" }, + "aio": { + "contact": { + "email": "MJoachimiak@lbl.gov", + "github": "realmarcin", + "name": "Marcin Pawel Joachimiak", + "orcid": "0000-0001-8175-045X" + }, + "contributor": { + "email": "lindsey.anderson@pnnl.gov", + "github": "lnanderson", + "name": "Lindsey N. Anderson", + "orcid": "0000-0002-8741-7823" + }, + "description": "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases.", + "download_json": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.json", + "download_obo": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.obo", + "download_owl": "https://raw.githubusercontent.com/berkeleybop/artificial-intelligence-ontology/main/aio.owl", + "example": "Causal_Graphical_Model", + "github_request_issue": 884, + "homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology", + "keywords": [ + "artificial intelligence", + "bioinformatics", + "ontology" + ], + "mappings": { + "aberowl": "AIO", + "bioportal": "AIO", + "fairsharing": "FAIRsharing.8d6247" + }, + "name": "The Artificial Intelligence Ontology", + "preferred_prefix": "aio", + "repository": "https://github.com/berkeleybop", + "reviewer": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "uri_format": "https://w3id.org/aio/$1" + }, "aism": { "appears_in": [ "colao", @@ -916,9 +1135,10 @@ "name": "Ontology for the Anatomy of the Insect SkeletoMuscular system", "pattern": "^\\d{7}$", "preferred_prefix": "AISM", + "rdf_uri_format": "http://purl.obolibrary.org/obo/AISM_$1", "repository": "https://github.com/insect-morphology/aism", "uri_format": "http://purl.obolibrary.org/obo/AISM_$1", - "version": "2022-06-27" + "version": "2023-04-14" }, "alfred": { "comment": "This resource doesn't exist on the web anymore", @@ -935,12 +1155,21 @@ }, "name": "The ALlele FREquency Database", "preferred_prefix": "alfred", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/alfred:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkg043", "pmc": "PMC165490", "pubmed": "12519999", - "title": "ALFRED: the ALelle FREquency Database. Update.", + "title": "ALFRED: the ALelle FREquency Database. Update", "year": 2003 } ], @@ -974,26 +1203,35 @@ "name": "Allergome", "pattern": "^\\d+$", "preferred_prefix": "allergome", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/allergome:$1" + } + ], "publications": [ { "doi": "10.1007/s11882-009-0055-9", "pmc": null, "pubmed": "19671381", - "title": "Allergen databases: current status and perspectives.", + "title": "Allergen databases: current status and perspectives", "year": 2009 }, { "doi": "10.1016/j.cellimm.2007.02.012", "pmc": null, "pubmed": "17434469", - "title": "Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model.", + "title": "Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model", "year": 2007 }, { "doi": null, "pmc": null, "pubmed": "17393720", - "title": "Allergome: a unifying platform.", + "title": "Allergome: a unifying platform", "year": 2006 } ], @@ -1033,12 +1271,21 @@ }, "name": "Alzheimer Gene Database", "preferred_prefix": "alzgene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/alzgene:$1" + } + ], "publications": [ { "doi": "10.1038/ng1934", "pmc": null, "pubmed": "17192785", - "title": "Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database.", + "title": "Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database", "year": 2007 } ], @@ -1070,12 +1317,21 @@ "name": "AmoebaDB", "pattern": "^EDI_\\d+$", "preferred_prefix": "amoebadb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/amoebadb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", - "title": "EuPathDB: a portal to eukaryotic pathogen databases.", + "title": "EuPathDB: a portal to eukaryotic pathogen databases", "year": 2009 } ], @@ -1112,6 +1368,7 @@ "name": "The Amphioxus Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "AMPHX", + "rdf_uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1", "repository": "https://github.com/EBISPOT/amphx_ontology", "uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1", "version": "2020-12-18" @@ -1151,17 +1408,53 @@ "name": "AntWeb", "pattern": "^casent\\d+(\\-D\\d+)?$", "preferred_prefix": "antweb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/antweb:$1" + } + ], "publications": [ { "doi": "10.1038/424242b", "pmc": null, "pubmed": "12867945", - "title": "Ants join online colony to boost conservation efforts.", + "title": "Ants join online colony to boost conservation efforts", "year": 2003 } ], "uri_format": "http://www.antweb.org/specimen.do?name=$1" }, + "anzctr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)", + "example": "ACTRN12623000498695", + "homepage": "https://anzctr.org.au", + "name": "Australian New Zealand Clinical Trials Registry", + "pattern": "^ACTRN\\d+$", + "preferred_prefix": "anzctr", + "providers": [ + { + "code": "", + "description": "", + "homepage": "", + "name": "", + "uri_format": "https://anzctr.org.au/ACTRN$1.aspx" + } + ], + "synonyms": [ + "ACTRN" + ], + "uri_format": "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1" + }, "aop": { "description": "International repository of Adverse Outcome Pathways.", "example": "98", @@ -1231,7 +1524,6 @@ "homepage": "https://bioportal.bioontology.org/ontologies/APAONTO", "keywords": [ "ontology", - "ontology and terminology", "psychology" ], "mappings": { @@ -1265,26 +1557,35 @@ "name": "Antimicrobial Peptide Database", "pattern": "^\\d{5}$", "preferred_prefix": "apd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/apd:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkv1278", "pmc": "PMC4702905", "pubmed": "26602694", - "title": "APD3: the antimicrobial peptide database as a tool for research and education.", + "title": "APD3: the antimicrobial peptide database as a tool for research and education", "year": 2015 }, { "doi": "10.1093/nar/gkn823", "pmc": "PMC2686604", "pubmed": "18957441", - "title": "APD2: the updated antimicrobial peptide database and its application in peptide design.", + "title": "APD2: the updated antimicrobial peptide database and its application in peptide design", "year": 2008 }, { "doi": "10.1093/nar/gkh025", "pmc": "PMC308759", "pubmed": "14681488", - "title": "APD: the Antimicrobial Peptide Database.", + "title": "APD: the Antimicrobial Peptide Database", "year": 2004 } ], @@ -1306,12 +1607,21 @@ "name": "AphidBase Transcript", "pattern": "^ACYPI\\d{6}(-RA)?$", "preferred_prefix": "aphidbase.transcript", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/aphidbase:$1" + } + ], "publications": [ { "doi": "10.1111/j.1365-2583.2009.00930.x", "pmc": "PMC4372297", "pubmed": "20482635", - "title": "AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.", + "title": "AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome", "year": 2010 } ], @@ -1368,14 +1678,15 @@ "doi": "10.1093/database/bap001", "pmc": "PMC2790299", "pubmed": "20157474", - "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database.", + "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/APO_$1", "repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology", "twitter": "yeastgenome", "uri_format": "https://www.yeastgenome.org/observable/APO:$1", - "version": "2022-07-06" + "version": "2023-04-27" }, "apollosv": { "appears_in": [ @@ -1387,7 +1698,7 @@ "name": "William Hogan", "orcid": "0000-0002-9881-1017" }, - "description": "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models", + "description": "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.", "download_owl": "http://purl.obolibrary.org/obo/apollo_sv.owl", "example": "00000443", "homepage": "https://github.com/ApolloDev/apollo-sv", @@ -1425,20 +1736,21 @@ "doi": "10.1186/s13326-016-0092-y", "pmc": "PMC4989460", "pubmed": "27538448", - "title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.", + "title": "The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation", "year": 2016 }, { "doi": null, "pmc": "PMC3900155", "pubmed": "24551417", - "title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services.", + "title": "Apollo: giving application developers a single point of access to public health models using structured vocabularies and Web services", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/APOLLO_SV_$1", "repository": "https://github.com/ApolloDev/apollo-sv", "uri_format": "http://purl.obolibrary.org/obo/APOLLO_SV_$1", - "version": "4.1.1" + "version": "2023-06-02" }, "arachnoserver": { "description": "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information.", @@ -1462,19 +1774,28 @@ "name": "ArachnoServer", "pattern": "^AS\\d{6}$", "preferred_prefix": "arachnoserver", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/arachnoserver:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btx661", "pmc": null, "pubmed": "29069336", - "title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins.", + "title": "ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins", "year": 2018 }, { "doi": "10.1093/nar/gkq1058", "pmc": "PMC3013666", "pubmed": "21036864", - "title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures.", + "title": "ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures", "year": 2010 } ], @@ -1497,7 +1818,7 @@ "doi": "10.1093/nar/gku1200", "pmc": "PMC4383980", "pubmed": "25414324", - "title": "Araport: the Arabidopsis information portal.", + "title": "Araport: the Arabidopsis information portal", "year": 2014 } ], @@ -1524,19 +1845,28 @@ }, "name": "ArchDB", "preferred_prefix": "archdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/archdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1189", "pmc": "PMC3964960", "pubmed": "24265221", - "title": "ArchDB 2014: structural classification of loops in proteins.", + "title": "ArchDB 2014: structural classification of loops in proteins", "year": 2013 }, { "doi": "10.1093/nar/gkh002", "pmc": "PMC308737", "pubmed": "14681390", - "title": "ArchDB: automated protein loop classification as a tool for structural genomics.", + "title": "ArchDB: automated protein loop classification as a tool for structural genomics", "year": 2004 } ], @@ -1597,6 +1927,7 @@ "miriam": "ark", "n2t": "ark" }, + "mastodon": "arks_org@fosstodon.org", "name": "Archival Resource Key", "namespace_in_lui": true, "pattern": "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", @@ -1643,10 +1974,11 @@ "doi": "10.1093/nar/gkz935", "pmc": "PMC7145624", "pubmed": "31665441", - "title": "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.", + "title": "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database", "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ARO_$1", "repository": "https://github.com/arpcard/aro", "uri_format": "http://purl.obolibrary.org/obo/ARO_$1" }, @@ -1673,6 +2005,13 @@ "pattern": "^[AEP]-\\w{4}-\\d+$", "preferred_prefix": "arrayexpress", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/arrayexpress:$1" + }, { "code": "omicsdi", "description": "ArrayExpress through OmicsDI", @@ -1686,21 +2025,21 @@ "doi": "10.1093/nar/gky964", "pmc": "PMC6323929", "pubmed": "30357387", - "title": "ArrayExpress update - from bulk to single-cell expression data.", + "title": "ArrayExpress update - from bulk to single-cell expression data", "year": 2019 }, { "doi": "10.1093/nar/gku1057", "pmc": "PMC4383899", "pubmed": "25361974", - "title": "ArrayExpress update--simplifying data submissions.", + "title": "ArrayExpress update--simplifying data submissions", "year": 2014 }, { "doi": "10.1093/nar/gkg091", "pmc": "PMC165538", "pubmed": "12519949", - "title": "ArrayExpress--a public repository for microarray gene expression data at the EBI.", + "title": "ArrayExpress--a public repository for microarray gene expression data at the EBI", "year": 2003 } ], @@ -1752,28 +2091,28 @@ "doi": "10.1093/nar/gkv1310", "pmc": "PMC4702916", "pubmed": "26615188", - "title": "The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.", + "title": "The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases", "year": 2015 }, { "doi": "10.1093/nar/gku1123", "pmc": "PMC4383937", "pubmed": "25428357", - "title": "arrayMap 2014: an updated cancer genome resource.", + "title": "arrayMap 2014: an updated cancer genome resource", "year": 2014 }, { "doi": "10.1186/1471-2164-15-82", "pmc": "PMC3909908", "pubmed": "24476156", - "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.", + "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens", "year": 2014 }, { "doi": "10.1371/journal.pone.0036944", "pmc": "PMC3356349", "pubmed": "22629346", - "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies.", + "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies", "year": 2012 } ], @@ -1805,6 +2144,13 @@ "name": "ar5iv", "uri_format": "https://ar5iv.org/abs/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/arxiv:$1" + }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", @@ -1839,19 +2185,28 @@ "name": "A Systematic Annotation Package for Community Analysis of Genomes", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "asap", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/asap:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj164", "pmc": "PMC1347526", "pubmed": "16381899", - "title": "ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.", + "title": "ASAP: a resource for annotating, curating, comparing, and disseminating genomic data", "year": 2006 }, { "doi": "10.1093/nar/gkg125", "pmc": "PMC165572", "pubmed": "12519969", - "title": "ASAP, a systematic annotation package for community analysis of genomes.", + "title": "ASAP, a systematic annotation package for community analysis of genomes", "year": 2003 } ], @@ -1950,19 +2305,28 @@ }, "name": "Arabidopsis Small RNA Project", "preferred_prefix": "asrp", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/asrp:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm997", "pmc": "PMC2238918", "pubmed": "17999994", - "title": "Update of ASRP: the Arabidopsis Small RNA Project database.", + "title": "Update of ASRP: the Arabidopsis Small RNA Project database", "year": 2007 }, { "doi": "10.1093/nar/gki127", "pmc": "PMC540081", "pubmed": "15608278", - "title": "ASRP: the Arabidopsis Small RNA Project Database.", + "title": "ASRP: the Arabidopsis Small RNA Project Database", "year": 2005 } ], @@ -1985,13 +2349,22 @@ }, "name": "ASTD", "preferred_prefix": "astd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/astd:$1" + } + ], "provides": "ensembl", "publications": [ { "doi": "10.1016/j.ygeno.2008.11.003", "pmc": null, "pubmed": "19059335", - "title": "ASTD: The Alternative Splicing and Transcript Diversity database.", + "title": "ASTD: The Alternative Splicing and Transcript Diversity database", "year": 2008 } ], @@ -2036,12 +2409,21 @@ "name": "Anatomical Therapeutic Chemical Classification System", "pattern": "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$", "preferred_prefix": "atc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/atc:$1" + } + ], "publications": [ { "doi": null, "pmc": null, "pubmed": "7368387", - "title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981].", + "title": "[New classification of drugs. The Medical list and the Drug catalogue are introduced in Anatomical--Therapeutic--Chemical classification code (ACT-code) in 1981]", "year": 1980 }, { @@ -2061,6 +2443,10 @@ "atcc": { "description": "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences.", "example": "11303", + "example_extras": [ + "ccl-1.4", + "ccl-1" + ], "homepage": "https://www.lgcstandards-atcc.org", "keywords": [ "epidemiology", @@ -2077,7 +2463,7 @@ "ncbi": "ATCC" }, "name": "American Type Culture Collection", - "pattern": "^([A-Z]+-)?\\d+$", + "pattern": "^([a-zA-Z]+-)?\\d+(\\.\\d)?$", "preferred_prefix": "atcc", "synonyms": [ "ATCC", @@ -2142,6 +2528,7 @@ "name": "Amphibian taxonomy", "pattern": "^\\d{7}$", "preferred_prefix": "ATO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ATO_$1", "uri_format": "http://purl.obolibrary.org/obo/ATO_$1" }, "atol": { @@ -2188,6 +2575,36 @@ "preferred_prefix": "autdb", "uri_format": "http://autism.mindspec.org/GeneDetail/$1" }, + "babelon": { + "contact": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nicolas Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "contributor": { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nicolas Matentzoglu", + "orcid": "0000-0002-7356-1779" + }, + "description": "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation.", + "example": "translation_language", + "github_request_issue": 903, + "homepage": "https://monarch-initiative.github.io/babelon/", + "license": "MIT", + "name": "Babelon", + "pattern": "^[a-z][a-z0-9_]+[a-z0-9]$", + "preferred_prefix": "babelon", + "repository": "https://github.com/monarch-initiative/babelon", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://w3id.org/babelon/$1" + }, "bacdive": { "contact": { "email": "contact@bacdive.de", @@ -2218,28 +2635,28 @@ "doi": "10.1093/nar/gky879", "pmc": "PMC6323973", "pubmed": "30256983", - "title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis.", + "title": "BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis", "year": 2019 }, { "doi": "10.1016/j.jbiotec.2017.05.004", "pmc": null, "pubmed": "28487186", - "title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase.", + "title": "Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase", "year": 2017 }, { "doi": "10.1093/nar/gkv983", "pmc": "PMC4702946", "pubmed": "26424852", - "title": "BacDive--The Bacterial Diversity Metadatabase in 2016.", + "title": "BacDive--The Bacterial Diversity Metadatabase in 2016", "year": 2015 }, { "doi": "10.1093/nar/gkt1058", "pmc": "PMC3965005", "pubmed": "24214959", - "title": "BacDive--the Bacterial Diversity Metadatabase.", + "title": "BacDive--the Bacterial Diversity Metadatabase", "year": 2013 } ], @@ -2294,19 +2711,28 @@ }, "name": "Bactibase", "preferred_prefix": "bactibase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bactibase:$1" + } + ], "publications": [ { "doi": "10.1186/1471-2180-10-22", "pmc": "PMC2824694", "pubmed": "20105292", - "title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization.", + "title": "BACTIBASE second release: a database and tool platform for bacteriocin characterization", "year": 2010 }, { "doi": "10.1186/1471-2180-7-89", "pmc": "PMC2211298", "pubmed": "17941971", - "title": "BACTIBASE: a new web-accessible database for bacteriocin characterization.", + "title": "BACTIBASE: a new web-accessible database for bacteriocin characterization", "year": 2007 } ], @@ -2363,28 +2789,35 @@ "doi": "10.1186/2041-1480-5-s1-s5", "pmc": "PMC4108877", "pubmed": "25093074", - "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications.", + "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications", "year": 2014 }, + { + "doi": "10.1186/2041-1480-5-S1-S5", + "pmc": "PMC4108877", + "pubmed": "25093074", + "title": "Evolving BioAssay Ontology (BAO): modularization, integration and applications", + "year": null + }, { "doi": "10.1371/journal.pone.0049198", "pmc": "PMC3498356", "pubmed": "23155465", - "title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).", + "title": "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)", "year": 2012 }, { "doi": "10.1186/1471-2105-12-257", "pmc": "PMC3149580", "pubmed": "21702939", - "title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results.", + "title": "BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results", "year": 2011 }, { "doi": "10:1371/journal.pone.0049198", "pmc": null, "pubmed": "10", - "title": "Digitoxin metabolism by rat liver microsomes.", + "title": "Digitoxin metabolism by rat liver microsomes", "year": 1975 } ], @@ -2393,7 +2826,7 @@ "BAO" ], "uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1", - "version": "2.7.2" + "version": "2.8.4" }, "bartoc": { "contact": { @@ -2440,6 +2873,7 @@ ], "pattern": "^[1-9][0-9]*$", "preferred_prefix": "bartoc", + "rdf_uri_format": "https://bartoc.org/en/node/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/783" ], @@ -2493,13 +2927,16 @@ "bioportal": "BCGO", "cellosaurus": "BCGO", "obofoundry": "bcgo", + "ols": "bcgo", "ontobee": "BCGO" }, "name": "Beta Cell Genomics Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BCGO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/BCGO_$1", "repository": "https://github.com/obi-bcgo/bcgo", - "uri_format": "http://purl.obolibrary.org/obo/BCGO_$1" + "uri_format": "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1", + "version": "2015-07-08" }, "bcio": { "contact": { @@ -2523,7 +2960,8 @@ "name": "The Behaviour Change Intervention Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "bcio", - "uri_format": "https://w3id.org/BCI-ontology#$1" + "uri_format": "https://w3id.org/BCI-ontology#$1", + "version": "2022-08-24" }, "bco": { "appears_in": [ @@ -2567,10 +3005,11 @@ "doi": "10.1371/journal.pone.0089606", "pmc": "PMC3940615", "pubmed": "24595056", - "title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.", + "title": "Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/BCO_$1", "repository": "https://github.com/BiodiversityOntologies/bco", "uri_format": "http://purl.obolibrary.org/obo/BCO_$1", "version": "2021-11-14" @@ -2599,7 +3038,7 @@ "bcrj": { "description": "Cell line collections", "example": "0278", - "homepage": "http://bcrj.org.br/celula/bcrj", + "homepage": "https://bcrj.org.br/pesquisa/", "mappings": { "cellosaurus": "BCRJ" }, @@ -2626,6 +3065,15 @@ "name": "Berkeley Drosophila Genome Project EST database", "pattern": "^\\w+(\\.)?(\\d+)?$", "preferred_prefix": "bdgp.est", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/flybase.est:$1" + } + ], "uri_format": "https://www.ncbi.nlm.nih.gov/nucest/$1" }, "bdgp.insertion": { @@ -2645,12 +3093,21 @@ "name": "BDGP insertion DB", "pattern": "^\\w+$", "preferred_prefix": "bdgp.insertion", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bdgp:$1" + } + ], "publications": [ { "doi": "10.1534/genetics.104.026427", "pmc": "PMC1470905", "pubmed": "15238527", - "title": "The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes.", + "title": "The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes", "year": 2004 } ], @@ -2690,12 +3147,21 @@ "name": "Tribolium Genome Database -- Insertion", "pattern": "^TC\\d+$", "preferred_prefix": "beetlebase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/beetlebase:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp807", "pmc": "PMC2808946", "pubmed": "19820115", - "title": "BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.", + "title": "BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum", "year": 2009 } ], @@ -2818,6 +3284,7 @@ "subject agnostic" ], "license": "CC-BY-4.0", + "logo": "https://avatars2.githubusercontent.com/u/12972134?v=3&s=200", "mappings": { "aberowl": "BFO", "agroportal": "BFO", @@ -2832,6 +3299,7 @@ "name": "Basic Formal Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "BFO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/BFO_$1", "repository": "https://github.com/BFO-ontology/BFO", "uri_format": "http://purl.obolibrary.org/obo/BFO_$1", "version": "2019-08-26" @@ -2851,9 +3319,23 @@ "uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1" }, "bgee.gene": { - "description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.", + "contact": { + "email": "sebastien.moretti@sib.swiss", + "github": "smoretti", + "name": "Sebastien Moretti", + "orcid": "0000-0003-3947-488X" + }, + "contributor_extras": [ + { + "email": "sebastien.moretti@sib.swiss", + "github": "smoretti", + "name": "Sebastien Moretti", + "orcid": "0000-0003-3947-488X" + } + ], + "description": "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee.", "example": "FBgn0000015", - "homepage": "https://bgee.org/", + "homepage": "https://www.bgee.org", "keywords": [ "gene expression" ], @@ -2864,9 +3346,21 @@ "prefixcommons": "bgee" }, "name": "Bgee gene", - "pattern": "^[A-Za-z]+\\d+$", + "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "bgee.gene", - "uri_format": "https://bgee.org/?page=gene&gene_id=$1" + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bgee:$1" + } + ], + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/890" + ], + "uri_format": "https://www.bgee.org/gene/$1" }, "bgee.organ": { "description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.", @@ -2962,7 +3456,7 @@ "uri_format": "http://bigg.ucsd.edu/compartments/$1" }, "bigg.metabolite": { - "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes.", + "description": "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites.", "example": "12dgr161", "homepage": "http://bigg.ucsd.edu/universal/metabolites", "mappings": { @@ -3006,9 +3500,9 @@ "bila": { "contact": { "email": "henrich@embl.de", - "github": null, - "name": "Thorsten Heinrich", - "orcid": null + "github": "ThorstenHen", + "name": "Thorsten Henrich", + "orcid": "0000-0002-1548-3290" }, "deprecated": true, "description": "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.", @@ -3025,21 +3519,33 @@ "biocontext": "BILA", "fairsharing": "FAIRsharing.eqgjeq", "obofoundry": "bila", + "ols": "bila", "prefixcommons": "4dxpress" }, "name": "Bilateria anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "BILA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/4dxpress:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm797", "pmc": "PMC2238840", "pubmed": "17916571", - "title": "4DXpress: a database for cross-species expression pattern comparisons.", + "title": "4DXpress: a database for cross-species expression pattern comparisons", "year": 2007 } ], - "uri_format": "http://purl.obolibrary.org/obo/BILA_$1" + "rdf_uri_format": "http://purl.obolibrary.org/obo/BILA_$1", + "uri_format": "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1", + "version": "2019-06-12" }, "bind": { "deprecated": true, @@ -3058,19 +3564,28 @@ }, "name": "BIND accession number", "preferred_prefix": "bind", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bind:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkg056", "pmc": "PMC165503", "pubmed": "12519993", - "title": "BIND: the Biomolecular Interaction Network Database.", + "title": "BIND: the Biomolecular Interaction Network Database", "year": 2003 }, { "doi": "10.1093/bioinformatics/16.5.465", "pmc": null, "pubmed": "10871269", - "title": "BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.", + "title": "BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways", "year": 2000 } ], @@ -3107,19 +3622,28 @@ "name": "BindingDB", "pattern": "^\\w\\d+$", "preferred_prefix": "bindingdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bindingdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkv1072", "pmc": "PMC4702793", "pubmed": "26481362", - "title": "BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.", + "title": "BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology", "year": 2015 }, { "doi": "10.1093/nar/gkl999", "pmc": "PMC1751547", "pubmed": "17145705", - "title": "BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.", + "title": "BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities", "year": 2006 } ], @@ -3155,12 +3679,21 @@ "name": "BioCatalogue Service", "pattern": "^\\d+$", "preferred_prefix": "biocatalogue.service", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biocatalogue:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkq394", "pmc": "PMC2896129", "pubmed": "20484378", - "title": "BioCatalogue: a universal catalogue of web services for the life sciences.", + "title": "BioCatalogue: a universal catalogue of web services for the life sciences", "year": 2010 } ], @@ -3187,19 +3720,28 @@ "name": "BioCyc collection of metabolic pathway databases", "pattern": "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$", "preferred_prefix": "biocyc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biocyc:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkv1164", "pmc": "PMC4702838", "pubmed": "26527732", - "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2015 }, { "doi": "10.1093/nar/gki892", "pmc": "PMC1266070", "pubmed": "16246909", - "title": "Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.", + "title": "Expansion of the BioCyc collection of pathway/genome databases to 160 genomes", "year": 2005 } ], @@ -3236,7 +3778,7 @@ "doi": "10.7554/elife.68292", "pmc": "PMC8683078", "pubmed": "34860157", - "title": "Author-sourced capture of pathway knowledge in computable form using Biofactoid.", + "title": "Author-sourced capture of pathway knowledge in computable form using Biofactoid", "year": 2021 } ], @@ -3283,40 +3825,49 @@ "name": "BioGRID", "pattern": "^\\d+$", "preferred_prefix": "biogrid", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biogrid:$1" + } + ], "publications": [ { "doi": "10.1002/pro.3978", "pmc": "PMC7737760", "pubmed": "33070389", - "title": "The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.", + "title": "The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions", "year": 2020 }, { "doi": "10.1093/nar/gky1079", "pmc": "PMC6324058", "pubmed": "30476227", - "title": "The BioGRID interaction database: 2019 update.", + "title": "The BioGRID interaction database: 2019 update", "year": 2019 }, { "doi": "10.1093/nar/gkq1116", "pmc": "PMC3013707", "pubmed": "21071413", - "title": "The BioGRID Interaction Database: 2011 update.", + "title": "The BioGRID Interaction Database: 2011 update", "year": 2010 }, { "doi": "10.1093/nar/gkj109", "pmc": "PMC1347471", "pubmed": "16381927", - "title": "BioGRID: a general repository for interaction datasets.", + "title": "BioGRID: a general repository for interaction datasets", "year": 2006 }, { "doi": "10.1186/gb-2003-4-3-r23", "pmc": "PMC153463", "pubmed": "12620108", - "title": "The GRID: the General Repository for Interaction Datasets.", + "title": "The GRID: the General Repository for Interaction Datasets", "year": 2003 } ], @@ -3350,6 +3901,18 @@ "twitter": "biogrid", "uri_format": "https://thebiogrid.org/interaction/$1" }, + "biokc": { + "description": "BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML).", + "example": "bkc640", + "homepage": "https://wwwen.uni.lu/lcsb", + "mappings": { + "miriam": "biokc" + }, + "name": "BioKC", + "pattern": "^bkc[0-9]*$", + "preferred_prefix": "biokc", + "uri_format": "https://biokb.lcsb.uni.lu/fact/$1" + }, "biolegend": { "contributor": { "email": "cthoyt@gmail.com", @@ -3416,6 +3979,15 @@ }, "name": "BioMagResBank", "preferred_prefix": "biomagresbank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biomagresbank:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -3463,6 +4035,13 @@ "name": "Caltech mirror", "uri_format": "http://biomodels.caltech.edu/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biomodels:$1" + }, { "code": "omicsdi", "description": "BioModels through OmicsDI", @@ -3476,7 +4055,7 @@ "doi": "10.1093/nar/gkj092", "pmc": "PMC1347454", "pubmed": "16381960", - "title": "BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.", + "title": "BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems", "year": 2006 } ], @@ -3522,6 +4101,13 @@ "pattern": "^\\d+$", "preferred_prefix": "biomodels.kisao", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kisao:$1" + }, { "code": "legacy", "description": "This is the URI scheme used in the ontology but it does not resolve.", @@ -3535,10 +4121,11 @@ "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", - "title": "Controlled vocabularies and semantics in systems biology.", + "title": "Controlled vocabularies and semantics in systems biology", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/KISAO_$1", "repository": "https://github.com/SED-ML/KiSAO", "synonyms": [ "biomodels.kisao", @@ -3579,12 +4166,21 @@ "name": "Terminology for Description of Dynamics", "pattern": "^\\d+$", "preferred_prefix": "biomodels.teddy", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/teddy:$1" + } + ], "publications": [ { "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", - "title": "Controlled vocabularies and semantics in systems biology.", + "title": "Controlled vocabularies and semantics in systems biology", "year": 2011 } ], @@ -3622,6 +4218,15 @@ "name": "BioNumbers", "pattern": "^\\d+$", "preferred_prefix": "bionumbers", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bionumbers:$1" + } + ], "uri_format": "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1" }, "biopixie": { @@ -3639,6 +4244,15 @@ }, "name": "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology", "preferred_prefix": "biopixie", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biopixie:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -3678,19 +4292,28 @@ "name": "BioPortal", "pattern": "^(\\d+)|(\\w+)$", "preferred_prefix": "bioportal", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bioportal:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr469", "pmc": "PMC3125807", "pubmed": "21672956", - "title": "BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.", + "title": "BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications", "year": 2011 }, { "doi": "10.1093/nar/gkp440", "pmc": "PMC2703982", "pubmed": "19483092", - "title": "BioPortal: ontologies and integrated data resources at the click of a mouse.", + "title": "BioPortal: ontologies and integrated data resources at the click of a mouse", "year": 2009 } ], @@ -3737,7 +4360,7 @@ "doi": "10.1093/nar/gkr1163", "pmc": "PMC3245069", "pubmed": "22139929", - "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.", + "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata", "year": 2011 } ], @@ -3771,6 +4394,7 @@ "bartoc": "18951", "fairsharing": "FAIRsharing.250a8c" }, + "mastodon": "bioregistry@fosstodon.org", "name": "Bioregistry", "preferred_prefix": "bioregistry", "publications": [ @@ -3895,6 +4519,7 @@ "uri_format": "https://scholia.toolforge.org/biorxiv/$1" } ], + "rdf_uri_format": "http://dx.doi.org/10.1101/$1", "uri_format": "https://www.biorxiv.org/content/10.1101/$1" }, "biosample": { @@ -3936,7 +4561,7 @@ "doi": "10.1093/nar/gkr1163", "pmc": "PMC3245069", "pubmed": "22139929", - "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.", + "title": "BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata", "year": 2011 } ], @@ -4027,14 +4652,14 @@ "doi": "10.1093/nar/gkx965", "pmc": "PMC5753238", "pubmed": "29069414", - "title": "The BioStudies database-one stop shop for all data supporting a life sciences study.", + "title": "The BioStudies database-one stop shop for all data supporting a life sciences study", "year": 2018 }, { "doi": "10.15252/msb.20156658", "pmc": "PMC4704487", "pubmed": "26700850", - "title": "The BioStudies database.", + "title": "The BioStudies database", "year": 2015 } ], @@ -4061,12 +4686,21 @@ "name": "BioSystems", "pattern": "^\\d+$", "preferred_prefix": "biosystems", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/biosystems:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp858", "pmc": "PMC2808896", "pubmed": "19854944", - "title": "The NCBI BioSystems database.", + "title": "The NCBI BioSystems database", "year": 2009 } ], @@ -4102,7 +4736,7 @@ "doi": "10.1093/nar/gkv1116", "pmc": "PMC4702812", "pubmed": "26538599", - "title": "Tools and data services registry: a community effort to document bioinformatics resources.", + "title": "Tools and data services registry: a community effort to document bioinformatics resources", "year": 2015 } ], @@ -4147,6 +4781,7 @@ "example": "2023", "homepage": "https://bioportal.bioontology.org/ontologies/BIRNLEX", "keywords": [ + "anatomy", "biomedical science", "ontology" ], @@ -4293,14 +4928,14 @@ "doi": "10.1007/s10858-008-9221-y", "pmc": "PMC2268728", "pubmed": "18288446", - "title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.", + "title": "BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions", "year": 2008 }, { "doi": "10.1093/nar/gkm957", "pmc": "PMC2238925", "pubmed": "17984079", - "title": "BioMagResBank.", + "title": "BioMagResBank", "year": 2007 } ], @@ -4344,12 +4979,21 @@ "name": "BOLD Systems taxon", "pattern": "^\\d+$", "preferred_prefix": "bold.taxonomy", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bold:$1" + } + ], "publications": [ { "doi": "10.1111/j.1471-8286.2007.01678.x", "pmc": "PMC1890991", "pubmed": "18784790", - "title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org).", + "title": "bold: The Barcode of Life Data System (http://www.barcodinglife.org)", "year": 2007 } ], @@ -4374,6 +5018,7 @@ }, "name": "Gene Regulation Ontology", "preferred_prefix": "BOOTSTREP", + "rdf_uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1", "uri_format": "http://purl.obolibrary.org/obo/BOOTSTREP_$1" }, "bpdb": { @@ -4416,84 +5061,107 @@ "name": "BRENDA Enzyme", "pattern": "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "preferred_prefix": "brenda", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/brenda:$1" + } + ], "provides": "eccode", "publications": [ - { - "doi": "s0168-1656(17)30183-9", - "pmc": null, - "pubmed": "28438579", - "title": "The BRENDA enzyme information system-From a database to an expert system.", - "year": null - }, { "doi": "10.1016/j.jbiotec.2017.04.020", "pmc": null, "pubmed": "28438579", - "title": "The BRENDA enzyme information system-From a database to an expert system.", + "title": "The BRENDA enzyme information system-From a database to an expert system", "year": 2017 }, { "doi": "10.1093/nar/gku1068", "pmc": "PMC4383907", "pubmed": "25378310", - "title": "BRENDA in 2015: exciting developments in its 25th year of existence.", + "title": "BRENDA in 2015: exciting developments in its 25th year of existence", "year": 2014 }, { "doi": "10.1093/nar/gks1049", "pmc": "PMC3531171", "pubmed": "23203881", - "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.", + "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA", "year": 2012 }, { "doi": "10.1093/nar/gkq1089", "pmc": "PMC3013686", "pubmed": "21062828", - "title": "BRENDA, the enzyme information system in 2011.", + "title": "BRENDA, the enzyme information system in 2011", "year": 2010 }, { "doi": "10.1093/nar/gkn820", "pmc": "PMC2686525", "pubmed": "18984617", - "title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.", + "title": "BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009", "year": 2008 }, { "doi": "10.1093/nar/gkl972", "pmc": "PMC1899097", "pubmed": "17202167", - "title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.", + "title": "BRENDA, AMENDA and FRENDA: the enzyme information system in 2007", "year": 2007 }, { "doi": "10.1093/nar/gkh081", "pmc": "PMC308815", "pubmed": "14681450", - "title": "BRENDA, the enzyme database: updates and major new developments.", + "title": "BRENDA, the enzyme database: updates and major new developments", "year": 2004 }, { "doi": "10.1016/s1096-7176(03)00008-9", "pmc": null, "pubmed": "12850129", - "title": "Review of the BRENDA Database.", + "title": "Review of the BRENDA Database", "year": 2003 }, { "doi": "10.1016/s0968-0004(01)02027-8", "pmc": null, "pubmed": "11796225", - "title": "BRENDA: a resource for enzyme data and metabolic information.", + "title": "BRENDA: a resource for enzyme data and metabolic information", "year": 2002 }, { "doi": "10.1093/nar/30.1.47", "pmc": "PMC99121", "pubmed": "11752250", - "title": "BRENDA, enzyme data and metabolic information.", + "title": "BRENDA, enzyme data and metabolic information", "year": 2002 + }, + { + "doi": "S0168-1656(17)30183-9", + "pmc": null, + "pubmed": null, + "title": "The BRENDA enzyme information system-From a database to an expert system.", + "year": null + }, + { + "doi": "10.1016/S1096-7176(03)00008-9", + "pmc": null, + "pubmed": null, + "title": "Review of the BRENDA Database.", + "year": null + }, + { + "doi": "10.1016/S0968-0004(01)02027-8", + "pmc": null, + "pubmed": null, + "title": "BRENDA: a resource for enzyme data and metabolic information.", + "year": null } ], "uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1" @@ -4537,6 +5205,23 @@ "preferred_prefix": "brenda.ligandgroup", "uri_format": "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1" }, + "bridgedb": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc.", + "example": "hasPrimaryUriPattern", + "homepage": "https://bridgedb.org", + "name": "BridgeDb Vocabulary", + "preferred_prefix": "bridgedb", + "references": [ + "https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl" + ], + "uri_format": "http://vocabularies.bridgedb.org/ops#$1" + }, "broad": { "description": "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae.", "example": "S7000002168151102", @@ -4616,13 +5301,14 @@ "doi": "10.1186/2041-1480-5-34", "pmc": "PMC4137724", "pubmed": "25140222", - "title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.", + "title": "Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/BSPO_$1", "repository": "https://github.com/obophenotype/biological-spatial-ontology", "uri_format": "http://purl.obolibrary.org/obo/BSPO_$1", - "version": "2022-06-28" + "version": "2023-05-27" }, "bto": { "banana": "BTO", @@ -4666,6 +5352,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "BTO", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bto:$1" + }, { "code": "miriam_obo_legacy", "description": "An old URI style for MIRIAM", @@ -4679,43 +5372,44 @@ "doi": "10.1093/nar/gky1048", "pmc": "PMC6323942", "pubmed": "30395242", - "title": "BRENDA in 2019: a European ELIXIR core data resource.", + "title": "BRENDA in 2019: a European ELIXIR core data resource", "year": 2019 }, { "doi": "10.1093/nar/gku1068", "pmc": "PMC4383907", "pubmed": "25378310", - "title": "BRENDA in 2015: exciting developments in its 25th year of existence.", + "title": "BRENDA in 2015: exciting developments in its 25th year of existence", "year": 2014 }, { "doi": "10.1093/nar/gks1049", "pmc": "PMC3531171", "pubmed": "23203881", - "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.", + "title": "BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA", "year": 2012 }, { "doi": "10.1093/nar/gkq968", "pmc": "PMC3013802", "pubmed": "21030441", - "title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.", + "title": "The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources", "year": 2010 }, { "doi": "10.1093/nar/gkh081", "pmc": "PMC308815", "pubmed": "14681450", - "title": "BRENDA, the enzyme database: updates and major new developments.", + "title": "BRENDA, the enzyme database: updates and major new developments", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/BTO_$1", "repository": "https://github.com/BRENDA-Enzymes/BTO", "synonyms": [ "BTO" ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1", + "uri_format": "https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1", "version": "2021-10-26" }, "bugbase.expt": { @@ -4766,34 +5460,43 @@ "name": "Bacterial Tyrosine Kinase Database", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "bykdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/bykdb:$1" + } + ], "provides": "uniprot", "publications": [ { "doi": "10.1016/s0378-1119(97)00554-4", "pmc": null, "pubmed": "9434192", - "title": "Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase.", + "title": "Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase", "year": 1997 }, { "doi": "10.1093/nar/gkr915", "pmc": "PMC3245071", "pubmed": "22080550", - "title": "BYKdb: the Bacterial protein tYrosine Kinase database.", + "title": "BYKdb: the Bacterial protein tYrosine Kinase database", "year": 2011 }, { "doi": "10.1007/s00726-009-0237-8", "pmc": null, "pubmed": "19189200", - "title": "Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes.", + "title": "Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes", "year": 2009 }, { "doi": "10.1093/bioinformatics/btn462", "pmc": null, "pubmed": "18772155", - "title": "Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.", + "title": "Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature", "year": 2008 } ], @@ -4870,14 +5573,14 @@ "doi": "10.1002/cfg.376", "pmc": "PMC2447341", "pubmed": "18629057", - "title": "Interoperability of CABRI Services and Biochemical Pathways Databases.", + "title": "Interoperability of CABRI Services and Biochemical Pathways Databases", "year": 2004 }, { "doi": "10.2165/00822942-200594030-00002", "pmc": null, "pubmed": "16231959", - "title": "The role of informatics in the coordinated management of biological resources collections.", + "title": "The role of informatics in the coordinated management of biological resources collections", "year": 2005 } ], @@ -4910,7 +5613,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins.", - "download_obo": "https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo", + "download_obo": "https://raw.githubusercontent.com/calipho-sib/controlled-vocabulary/master/caloha.obo", "example": "TS-0001", "homepage": "https://github.com/calipho-sib/controlled-vocabulary", "keywords": [ @@ -4967,7 +5670,7 @@ "doi": "10.1093/database/bat031", "pmc": "PMC3889916", "pubmed": "23624946", - "title": "The Protein Model Portal--a comprehensive resource for protein structure and model information.", + "title": "The Protein Model Portal--a comprehensive resource for protein structure and model information", "year": 2013 } ], @@ -5001,7 +5704,7 @@ "name": "Melissa Haendel", "orcid": "0000-0001-9114-8737" }, - "description": "None", + "description": "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.", "download_json": "http://purl.obolibrary.org/obo/caro.json", "download_obo": "http://purl.obolibrary.org/obo/caro.obo", "download_owl": "http://purl.obolibrary.org/obo/caro.owl", @@ -5045,9 +5748,10 @@ "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CARO_$1", "repository": "https://github.com/obophenotype/caro", "uri_format": "http://purl.obolibrary.org/obo/CARO_$1", - "version": "2022-02-18" + "version": "2023-03-15" }, "cas": { "description": "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information.", @@ -5074,6 +5778,20 @@ "pattern": "^\\d{1,7}\\-\\d{2}\\-\\d$", "preferred_prefix": "cas", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cas:$1" + }, + { + "code": "hoelzel", + "description": "Vendor page", + "homepage": "https://www.hoelzel-biotech.com", + "name": "Hölzel Diagnostika", + "uri_format": "https://www.hoelzel-biotech.com/de/casinfo/cas/index/number/$1" + }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", @@ -5087,7 +5805,7 @@ "doi": "10.1021/acs.jcim.2c00268", "pmc": "PMC9199008", "pubmed": "35559614", - "title": "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community.", + "title": "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community", "year": 2022 } ], @@ -5149,68 +5867,77 @@ "name": "CATH Protein Structural Domain Superfamily", "pattern": "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$", "preferred_prefix": "cath", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cath:$1" + } + ], "publications": [ { "doi": "10.1016/s0969-2126(97)00260-8", "pmc": null, "pubmed": "9309224", - "title": "CATH--a hierarchic classification of protein domain structures.", + "title": "CATH--a hierarchic classification of protein domain structures", "year": 1997 }, { "doi": "10.1093/nar/gkaa1079", "pmc": "PMC7778904", "pubmed": "33237325", - "title": "CATH: increased structural coverage of functional space.", + "title": "CATH: increased structural coverage of functional space", "year": 2021 }, { "doi": "10.1093/nar/gky1097", "pmc": "PMC6323983", "pubmed": "30398663", - "title": "CATH: expanding the horizons of structure-based functional annotations for genome sequences.", + "title": "CATH: expanding the horizons of structure-based functional annotations for genome sequences", "year": 2019 }, { "doi": "10.1093/nar/gkx1069", "pmc": "PMC5753370", "pubmed": "29112716", - "title": "Gene3D: Extensive prediction of globular domains in proteins.", + "title": "Gene3D: Extensive prediction of globular domains in proteins", "year": 2018 }, { "doi": "10.1093/nar/gkw1098", "pmc": "PMC5210570", "pubmed": "27899584", - "title": "CATH: an expanded resource to predict protein function through structure and sequence.", + "title": "CATH: an expanded resource to predict protein function through structure and sequence", "year": 2016 }, { "doi": "10.1093/bioinformatics/btw473", "pmc": "PMC5018379", "pubmed": "27477482", - "title": "Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.", + "title": "Functional classification of CATH superfamilies: a domain-based approach for protein function annotation", "year": 2016 }, { "doi": "10.1016/j.biochi.2015.08.004", "pmc": "PMC4678953", "pubmed": "26253692", - "title": "The history of the CATH structural classification of protein domains.", + "title": "The history of the CATH structural classification of protein domains", "year": 2015 }, { "doi": "10.1093/nar/gku947", "pmc": "PMC4384018", "pubmed": "25348408", - "title": "CATH: comprehensive structural and functional annotations for genome sequences.", + "title": "CATH: comprehensive structural and functional annotations for genome sequences", "year": 2014 }, { "doi": null, "pmc": null, "pubmed": "11788987", - "title": "The CATH protein family database: a resource for structural and functional annotation of genomes.", + "title": "The CATH protein family database: a resource for structural and functional annotation of genomes", "year": 2002 } ], @@ -5265,6 +5992,15 @@ "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "cattleqtldb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cattleqtldb:$1" + } + ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "cazy": { @@ -5290,19 +6026,28 @@ "name": "Carbohydrate Active EnZYmes", "pattern": "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$", "preferred_prefix": "cazy", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cazy:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1178", "pmc": "PMC3965031", "pubmed": "24270786", - "title": "The carbohydrate-active enzymes database (CAZy) in 2013.", + "title": "The carbohydrate-active enzymes database (CAZy) in 2013", "year": 2013 }, { "doi": "10.1093/nar/gkn663", "pmc": "PMC2686590", "pubmed": "18838391", - "title": "The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.", + "title": "The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics", "year": 2008 } ], @@ -5355,15 +6100,22 @@ "doi": "10.1126/scisignal.2004088", "pmc": "PMC4160307", "pubmed": "23550210", - "title": "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.", + "title": "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal", "year": 2013 }, { "doi": "10.1158/2159-8290.cd-12-0095", "pmc": "PMC3956037", "pubmed": "22588877", - "title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.", + "title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data", "year": 2012 + }, + { + "doi": "10.1158/2159-8290.CD-12-0095", + "pmc": null, + "pubmed": null, + "title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.", + "year": null } ], "repository": "https://github.com/cBioPortal/cbioportal", @@ -5402,17 +6154,68 @@ "name": "Consensus CDS", "pattern": "^CCDS\\d+\\.\\d+$", "preferred_prefix": "ccds", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ccds:$1" + } + ], "publications": [ { "doi": "10.1101/gr.080531.108", "pmc": "PMC2704439", "pubmed": "19498102", - "title": "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.", + "title": "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes", "year": 2009 } ], "uri_format": "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1" }, + "ccf": { + "contact": { + "email": "katy@indiana.edu", + "github": "katyb", + "name": "Katy Börner", + "orcid": "0000-0002-3321-6137" + }, + "contributor": { + "email": "benjamin_gyori@hms.harvard.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "description": "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA.", + "download_owl": "http://purl.org/ccf/releases/2.2.1/ccf.owl", + "example": "extraction_set", + "github_request_issue": 879, + "homepage": "https://bioportal.bioontology.org/ontologies/CCF", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "CCF", + "bioportal": "CCF", + "ols": "ccf", + "re3data": "r3d100012657" + }, + "name": "Human Reference Atlas Common Coordinate Framework Ontology", + "pattern": "^\\S+$", + "preferred_prefix": "ccf", + "rdf_uri_format": "http://purl.org/ccf/$1", + "repository": "https://github.com/hubmapconsortium/ccf-ontology", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1", + "version": "2.2.1" + }, "ccle": { "contributor": { "email": "cthoyt@gmail.com", @@ -5469,17 +6272,25 @@ "namespace_in_lui": true, "pattern": "^\\w+$", "preferred_prefix": "cco", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cco:$1" + } + ], "publications": [ { "doi": "10.1186/gb-2009-10-5-r58", "pmc": "PMC2718524", "pubmed": "19480664", - "title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.", + "title": "The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process", "year": 2009 } ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1", - "version": "2016-03-23" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1" }, "ccrid": { "contributor": { @@ -5539,13 +6350,14 @@ "doi": "10.4137/ebo.s2320", "pmc": "PMC2747124", "pubmed": "19812726", - "title": "Initial implementation of a comparative data analysis ontology.", + "title": "Initial implementation of a comparative data analysis ontology", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", "repository": "https://github.com/evoinfo/cdao", "uri_format": "http://purl.obolibrary.org/obo/CDAO_$1", - "version": "2019-06-26" + "version": "2022-11-30" }, "cdd": { "description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.", @@ -5572,26 +6384,28 @@ "name": "Conserved Domain Database at NCBI", "pattern": "^(cd)?\\d{5}$", "preferred_prefix": "cdd", - "publications": [ + "providers": [ { - "doi": "doi", - "pmc": "PMC4383992", - "pubmed": "25414356", - "title": null, - "year": null - }, + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cdd:$1" + } + ], + "publications": [ { "doi": "10.1093/nar/gku1221", "pmc": "PMC4383992", "pubmed": "25414356", - "title": "CDD: NCBI's conserved domain database.", + "title": "CDD: NCBI's conserved domain database", "year": 2014 }, { "doi": "10.1093/nar/gkn845", "pmc": "PMC2686570", "pubmed": "18984618", - "title": "CDD: specific functional annotation with the Conserved Domain Database.", + "title": "CDD: specific functional annotation with the Conserved Domain Database", "year": 2008 } ], @@ -5623,6 +6437,7 @@ "license": "CC-BY-3.0", "mappings": { "aberowl": "CDNO", + "agroportal": "CDNO", "bioportal": "CDNO", "obofoundry": "cdno", "ols": "cdno", @@ -5640,9 +6455,10 @@ "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", "repository": "https://github.com/Southern-Cross-Plant-Science/cdno", "uri_format": "http://purl.obolibrary.org/obo/CDNO_$1", - "version": "2022-06-23" + "version": "2022-12-23" }, "cdpd": { "description": "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN).", @@ -5668,8 +6484,8 @@ "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, - "description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.", - "download_owl": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl", + "description": "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D.", + "download_owl": "https://raw.githubusercontent.com/oral-health-and-disease-ontologies/ohd-ontology/f19378ff192b6f9ea16133e85671e8359fc371cd/src/ontology/archive/CDTCodes%20as%20Classes_pruned.owl", "example": "1000001", "homepage": "https://www.ada.org/publications/CDT", "keywords": [ @@ -5708,7 +6524,7 @@ "cellbank.australia": { "description": "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world.", "example": "ab-1-ha", - "homepage": "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/", + "homepage": "https://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/", "mappings": { "cellosaurus": "CBA" }, @@ -5736,12 +6552,21 @@ "name": "Cell Image Library", "pattern": "^\\d+$", "preferred_prefix": "cellimage", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cellimage:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gks1257", "pmc": "PMC3531121", "pubmed": "23203874", - "title": "The cell: an image library-CCDB: a curated repository of microscopy data.", + "title": "The cell: an image library-CCDB: a curated repository of microscopy data", "year": 2012 } ], @@ -5776,7 +6601,7 @@ "orcid": "0000-0003-2826-6444" }, "description": "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines.", - "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo", + "download_obo": "https://github.com/calipho-sib/cellosaurus/raw/master/cellosaurus.obo", "example": "0440", "homepage": "https://cellosaurus.org", "keywords": [ @@ -5792,6 +6617,7 @@ "re3data": "r3d100013293", "wikidata": "P3289" }, + "mastodon": "cellosaurus@fediscience.org", "name": "Cellosaurus", "pattern": "^[A-Z0-9]{4}$", "preferred_prefix": "cellosaurus", @@ -5816,17 +6642,18 @@ "doi": "10.1002/ijc.32639", "pmc": null, "pubmed": "31444973", - "title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication.", + "title": "CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication", "year": 2019 }, { "doi": "10.7171/jbt.18-2902-002", "pmc": "PMC5945021", "pubmed": "29805321", - "title": "The Cellosaurus, a Cell-Line Knowledge Resource.", + "title": "The Cellosaurus, a Cell-Line Knowledge Resource", "year": 2018 } ], + "repository": "https://github.com/calipho-sib/cellosaurus", "synonyms": [ "CVCL" ], @@ -5941,6 +6768,7 @@ "name": "Cephalopod Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CEPH", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "repository": "https://github.com/obophenotype/cephalopod-ontology", "uri_format": "http://purl.obolibrary.org/obo/CEPH_$1", "version": "2016-01-12" @@ -5969,26 +6797,35 @@ "name": "Candida Genome Database", "pattern": "^CAL\\d{7}$", "preferred_prefix": "cgd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cgd:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkw924", "pmc": "PMC5210628", "pubmed": "27738138", - "title": "The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.", + "title": "The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data", "year": 2016 }, { "doi": "10.1093/nar/gkr945", "pmc": "PMC3245171", "pubmed": "22064862", - "title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.", + "title": "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata", "year": 2011 }, { "doi": "10.1093/nar/gki003", "pmc": "PMC539957", "pubmed": "15608216", - "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.", + "title": "The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information", "year": 2005 } ], @@ -6025,12 +6862,21 @@ "name": "Chicken Gene Nomenclature Consortium", "pattern": "^\\d+$", "preferred_prefix": "cgnc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cgnc:$1" + } + ], "publications": [ { "doi": "10.1186/1471-2164-10-s2-s5", "pmc": "PMC2966335", "pubmed": "19607656", - "title": "The Chicken Gene Nomenclature Committee report.", + "title": "The Chicken Gene Nomenclature Committee report", "year": 2009 } ], @@ -6060,13 +6906,29 @@ "name": "Coli Genetic Stock Center", "pattern": "^\\d+$", "preferred_prefix": "cgsc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cgsc:$1" + } + ], "publications": [ { "doi": "10.1016/s0076-6879(06)21001-2", "pmc": null, "pubmed": "17352909", - "title": "Strain collections and genetic nomenclature.", + "title": "Strain collections and genetic nomenclature", "year": 2007 + }, + { + "doi": "10.1016/S0076-6879(06)21001-2", + "pmc": null, + "pubmed": null, + "title": "Strain collections and genetic nomenclature.", + "year": null } ], "uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1" @@ -6125,6 +6987,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png", "mappings": { "aberowl": "CHEBI", "bartoc": "558", @@ -6149,6 +7012,13 @@ "pattern": "^\\d+$", "preferred_prefix": "CHEBI", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chebi:$1" + }, { "code": "chebi-img", "description": "Image server from chebi", @@ -6162,38 +7032,39 @@ "doi": "10.1093/nar/gkv1031", "pmc": "PMC4702775", "pubmed": "26467479", - "title": "ChEBI in 2016: Improved services and an expanding collection of metabolites.", + "title": "ChEBI in 2016: Improved services and an expanding collection of metabolites", "year": 2015 }, { "doi": "10.1093/nar/gks1146", "pmc": "PMC3531142", "pubmed": "23180789", - "title": "The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.", + "title": "The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013", "year": 2012 }, { "doi": "10.1093/nar/gkp886", "pmc": "PMC2808869", "pubmed": "19854951", - "title": "Chemical Entities of Biological Interest: an update.", + "title": "Chemical Entities of Biological Interest: an update", "year": 2009 }, { "doi": "10.1002/0471250953.bi1409s26", "pmc": null, "pubmed": "19496059", - "title": "ChEBI: an open bioinformatics and cheminformatics resource.", + "title": "ChEBI: an open bioinformatics and cheminformatics resource", "year": 2009 }, { "doi": "10.1093/nar/gkm791", "pmc": "PMC2238832", "pubmed": "17932057", - "title": "ChEBI: a database and ontology for chemical entities of biological interest.", + "title": "ChEBI: a database and ontology for chemical entities of biological interest", "year": 2007 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CHEBI_$1", "repository": "https://github.com/ebi-chebi/ChEBI", "synonyms": [ "CHEBI", @@ -6202,7 +7073,7 @@ ], "twitter": "chebit", "uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1", - "version": "211" + "version": "222" }, "chembank": { "comment": "This resource doesn't exist on the web anymore", @@ -6221,12 +7092,21 @@ }, "name": "ChemBank", "preferred_prefix": "chembank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chembank:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm843", "pmc": "PMC2238881", "pubmed": "17947324", - "title": "ChemBank: a small-molecule screening and cheminformatics resource database.", + "title": "ChemBank: a small-molecule screening and cheminformatics resource database", "year": 2007 } ], @@ -6255,6 +7135,7 @@ "medicinal chemistry", "molecules" ], + "license": "CC-BY-4.0", "mappings": { "cheminf": "000412", "fairsharing": "FAIRsharing.m3jtpg", @@ -6266,33 +7147,42 @@ "name": "ChEMBL", "pattern": "^CHEMBL\\d+$", "preferred_prefix": "chembl", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chembl:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gky1075", "pmc": "PMC6323927", "pubmed": "30398643", - "title": "ChEMBL: towards direct deposition of bioassay data.", + "title": "ChEMBL: towards direct deposition of bioassay data", "year": 2019 }, { "doi": "10.1093/nar/gkw1074", "pmc": "PMC5210557", "pubmed": "27899562", - "title": "The ChEMBL database in 2017.", + "title": "The ChEMBL database in 2017", "year": 2016 }, { "doi": "10.1093/nar/gkt1031", "pmc": "PMC3965067", "pubmed": "24214965", - "title": "The ChEMBL bioactivity database: an update.", + "title": "The ChEMBL bioactivity database: an update", "year": 2013 }, { "doi": "10.1093/nar/gkr777", "pmc": "PMC3245175", "pubmed": "21948594", - "title": "ChEMBL: a large-scale bioactivity database for drug discovery.", + "title": "ChEMBL: a large-scale bioactivity database for drug discovery", "year": 2011 } ], @@ -6330,6 +7220,7 @@ }, "name": "ChEMBL database of bioactive drug-like small molecules - Cell lines section", "part_of": "chembl", + "pattern": "^CHEMBL\\d+$", "preferred_prefix": "chembl.cell", "synonyms": [ "ChEMBL-Cells" @@ -6346,6 +7237,7 @@ "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", "example": "CHEMBL465070", "homepage": "https://www.ebi.ac.uk/chembldb/", + "license": "CC-BY-4.0", "mappings": { "biocontext": "CHEMBL.COMPOUND", "edam": "2646", @@ -6373,6 +7265,7 @@ "uri_format": "https://rdf.ebi.ac.uk/resource/chembl/molecule/$1" } ], + "rdf_uri_format": "http://rdf.ebi.ac.uk/resource/chembl/molecule/$1", "uri_format": "https://www.ebi.ac.uk/chembl/compound/inspect/$1" }, "chembl.target": { @@ -6385,6 +7278,7 @@ "description": "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.", "example": "CHEMBL3467", "homepage": "https://www.ebi.ac.uk/chembldb/", + "license": "CC-BY-4.0", "mappings": { "biocontext": "CHEMBL.TARGET", "cellosaurus": "ChEMBL-Targets", @@ -6438,19 +7332,28 @@ "name": "ChemDB", "pattern": "^\\d+$", "preferred_prefix": "chemdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chemdb:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btm341", "pmc": null, "pubmed": "17599932", - "title": "ChemDB update--full-text search and virtual chemical space.", + "title": "ChemDB update--full-text search and virtual chemical space", "year": 2007 }, { "doi": "10.1093/bioinformatics/bti683", "pmc": null, "pubmed": "16174682", - "title": "ChemDB: a public database of small molecules and related chemoinformatics resources.", + "title": "ChemDB: a public database of small molecules and related chemoinformatics resources", "year": 2005 } ], @@ -6477,13 +7380,29 @@ "name": "ChemIDplus", "pattern": "^\\d+\\-\\d+\\-\\d+$", "preferred_prefix": "chemidplus", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chemidplus:$1" + } + ], "publications": [ { "doi": "10.1300/j115v21n01_04", "pmc": null, "pubmed": "11989279", - "title": "ChemIDplus-super source for chemical and drug information.", + "title": "ChemIDplus-super source for chemical and drug information", "year": 2002 + }, + { + "doi": "10.1300/J115v21n01_04", + "pmc": null, + "pubmed": null, + "title": "ChemIDplus-super source for chemical and drug information.", + "year": null } ], "synonyms": [ @@ -6539,10 +7458,11 @@ "doi": "10.1371/journal.pone.0025513", "pmc": "PMC3184996", "pubmed": "21991315", - "title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.", + "title": "The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CHEMINF_$1", "repository": "https://github.com/semanticchemistry/semanticchemistry", "uri_format": "https://semanticscience.org/resource/CHEMINF_$1", "version": "2.0" @@ -6605,6 +7525,15 @@ "name": "ChemSpider", "pattern": "^\\d+$", "preferred_prefix": "chemspider", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chemspider:$1" + } + ], "publications": [ { "doi": "10.1021/ed100697w", @@ -6614,6 +7543,7 @@ "year": 2010 } ], + "rdf_uri_format": "http://rdf.chemspider.com/$1", "synonyms": [ "ChemSpiderID", "Chemspider" @@ -6639,8 +7569,35 @@ "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "chickenqtldb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/chickenqtldb:$1" + } + ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, + "chictr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)", + "example": "ChiCTR2300070727", + "homepage": "https://www.chictr.org.cn", + "logo": "https://www.chictr.org.cn/images/top.jpg", + "name": "Chinese Clinical Trial Registry", + "pattern": "^ChiCTR\\d+$", + "preferred_prefix": "chictr", + "references": [ + "https://www.chictr.org.cn/showproj.html?proj=187605" + ] + }, "chiro": { "contact": { "email": "vasilevs@ohsu.edu", @@ -6685,6 +7642,7 @@ "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", "repository": "https://github.com/obophenotype/chiro", "uri_format": "http://purl.obolibrary.org/obo/CHIRO_$1", "version": "2015-11-23" @@ -6723,6 +7681,7 @@ "name": "Chemical Methods Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CHMO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "repository": "https://github.com/rsc-ontologies/rsc-cmo", "uri_format": "http://purl.obolibrary.org/obo/CHMO_$1", "version": "2022-04-19" @@ -6764,17 +7723,18 @@ "doi": "10.1186/s13326-022-00279-z", "pmc": "PMC9585694", "pubmed": "36271389", - "title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.", + "title": "A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology", "year": 2022 }, { "doi": "10.1038/s41597-020-0523-6", "pmc": "PMC7293349", "pubmed": "32533075", - "title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.", + "title": "CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis", "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CIDO_$1", "repository": "https://github.com/cido-ontology/cido", "uri_format": "http://purl.obolibrary.org/obo/CIDO_$1", "version": "1.0.337" @@ -6814,10 +7774,11 @@ "doi": "10.1093/database/bav043", "pmc": "PMC4425939", "pubmed": "25957950", - "title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.", + "title": "The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations", "year": 2015 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "repository": "https://github.com/BgeeDB/confidence-information-ontology", "uri_format": "http://purl.obolibrary.org/obo/CIO_$1", "version": "2015-03-10" @@ -6849,13 +7810,29 @@ }, "name": "CiteXplore", "preferred_prefix": "citexplore", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/citexplore:$1" + } + ], "publications": [ { "doi": "10.1097/mol.0b013e328362df13", "pmc": null, "pubmed": "23759795", - "title": "Cerebrotendinous xanthomatosis.", + "title": "Cerebrotendinous xanthomatosis", "year": 2013 + }, + { + "doi": "10.1097/MOL.0b013e328362df13", + "pmc": null, + "pubmed": "23759795", + "title": "Cerebrotendinous xanthomatosis", + "year": null } ], "references": [ @@ -6956,6 +7933,18 @@ "preferred_prefix": "civic.gid", "uri_format": "https://civicdb.org/links/gene/$1" }, + "civic.mpid": { + "description": "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.", + "example": "559", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.mpid" + }, + "name": "CIViC Molecular Profile", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.mpid", + "uri_format": "https://civicdb.org/links/molecular_profile/$1" + }, "civic.sid": { "description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.", "example": "62", @@ -6982,6 +7971,18 @@ "preferred_prefix": "civic.tid", "uri_format": "https://civicdb.org/links/drugs/$1" }, + "civic.vgid": { + "description": "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance", + "example": "16", + "homepage": "https://civicdb.org/", + "mappings": { + "miriam": "civic.vgid" + }, + "name": "CIViC Variant Group", + "pattern": "^[0-9]+$", + "preferred_prefix": "civic.vgid", + "uri_format": "https://civicdb.org/links/variant_group/$1" + }, "civic.vid": { "description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.", "example": "12", @@ -7037,6 +8038,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://obofoundry.org/images/CL-logo.jpg", "mappings": { "aberowl": "CL", "agroportal": "CL", @@ -7058,6 +8060,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "CL", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cl:$1" + }, { "code": "cellxgene", "description": "Explore single cell data through the CZ CELLxGENE portal", @@ -7071,21 +8080,22 @@ "doi": "10.1186/s13326-016-0088-7", "pmc": "PMC4932724", "pubmed": "27377652", - "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.", + "title": "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability", "year": 2016 }, { "doi": "10.1186/1471-2105-12-6", "pmc": "PMC3024222", "pubmed": "21208450", - "title": "Logical development of the cell ontology.", + "title": "Logical development of the cell ontology", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CL_$1", "repository": "https://github.com/obophenotype/cell-ontology", "twitter": "CellOntology", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1", - "version": "2022-12-15" + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http://purl.obolibrary.org/obo/$1", + "version": "2023-06-22" }, "clao": { "contact": { @@ -7117,6 +8127,7 @@ "name": "Collembola Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CLAO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "repository": "https://github.com/luis-gonzalez-m/Collembola", "uri_format": "http://purl.obolibrary.org/obo/CLAO_$1", "version": "2021-09-27" @@ -7167,6 +8178,9 @@ "name": "Cell Line Database", "pattern": "^(cl|tum)\\d+$", "preferred_prefix": "cldb", + "synonyms": [ + "hypercldb" + ], "uri_format": "http://bioinformatics.hsanmartino.it/hypercldb/$1.html" }, "clingene": { @@ -7226,6 +8240,13 @@ "pattern": "^NCT\\d{8}$", "preferred_prefix": "clinicaltrials", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/clinicaltrials:$1" + }, { "code": "smartpatients", "description": "Smart Patients is an online community for patients and their families. Join us to talk with other patients about the latest research for your condition.", @@ -7235,9 +8256,11 @@ } ], "synonyms": [ - "clinicaltrial" + "NCT", + "clinicaltrial", + "ctgov" ], - "uri_format": "https://clinicaltrials.gov/ct2/show/$1" + "uri_format": "https://www.clinicaltrials.gov/study/$1" }, "clinvar": { "description": "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier.", @@ -7268,7 +8291,7 @@ "doi": "10.1093/nar/gkt1113", "pmc": "PMC3965032", "pubmed": "24234437", - "title": "ClinVar: public archive of relationships among sequence variation and human phenotype.", + "title": "ClinVar: public archive of relationships among sequence variation and human phenotype", "year": 2013 } ], @@ -7363,6 +8386,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "CLO", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/clo:$1" + }, { "code": "bioportal", "description": "Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies in such a way that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. Our mission is to create software and support services for the application of principled ontologies in biomedical science and clinical care, ranging from tools for application developers to software for end-users.", @@ -7376,22 +8406,23 @@ "doi": "10.1186/2041-1480-5-37", "pmc": "PMC4387853", "pubmed": "25852852", - "title": "CLO: The cell line ontology.", + "title": "CLO: The cell line ontology", "year": 2014 }, { "doi": "10.1186/gb-2005-6-2-r21", "pmc": "PMC551541", "pubmed": "15693950", - "title": "An ontology for cell types.", + "title": "An ontology for cell types", "year": 2005 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CLO_$1", "repository": "https://github.com/CLO-Ontology/CLO", "synonyms": [ "CLO" ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/clo/terms?short_form=CLO_$1", + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/clo/terms?short_form=CLO_$1", "version": "2.1.178" }, "cls": { @@ -7437,6 +8468,7 @@ "name": "Clytia hemisphaerica Development and Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "CLYH", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "repository": "https://github.com/EBISPOT/clyh_ontology", "uri_format": "http://purl.obolibrary.org/obo/CLYH_$1", "version": "2020-05-29" @@ -7485,6 +8517,7 @@ }, "name": "CranioMaxilloFacial ontology", "preferred_prefix": "CMF", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CMF_$1", "uri_format": "http://purl.obolibrary.org/obo/CMF_$1" }, "cmo": { @@ -7510,6 +8543,7 @@ "preclinical studies" ], "license": "CC0-1.0", + "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "CMO", "biocontext": "CMO", @@ -7527,17 +8561,18 @@ "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", - "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", + "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", - "title": "Three ontologies to define phenotype measurement data.", + "title": "Three ontologies to define phenotype measurement data", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/CMO_$1", "repository": "https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/CMO_$1", @@ -7572,7 +8607,7 @@ "doi": "10.1186/s13326-016-0074-0", "pmc": "PMC4870745", "pubmed": "27195102", - "title": "The cellular microscopy phenotype ontology.", + "title": "The cellular microscopy phenotype ontology", "year": 2016 } ], @@ -7662,7 +8697,7 @@ "doi": "10.1093/aobpla/plq008", "pmc": "PMC3000699", "pubmed": "22476066", - "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature.", + "title": "Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature", "year": 2010 } ], @@ -8143,7 +9178,7 @@ "doi": "10.3389/fphys.2012.00326", "pmc": "PMC3429094", "pubmed": "22934074", - "title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice.", + "title": "Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice", "year": 2012 } ], @@ -8622,9 +9657,10 @@ "name": "Core Ontology for Biology and Biomedicine", "pattern": "^\\d{7}$", "preferred_prefix": "COB", + "rdf_uri_format": "http://purl.obolibrary.org/obo/COB_$1", "repository": "https://github.com/OBOFoundry/COB", "uri_format": "http://purl.obolibrary.org/obo/COB_$1", - "version": "2022-05-02" + "version": "2023-05-12" }, "coconut": { "comment": "@mSorok is the dev of the resource, hope I got it right!", @@ -8706,19 +9742,28 @@ "name": "Cluster of orthologous genes", "pattern": "^COG\\d+$", "preferred_prefix": "cog", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cog:$1" + } + ], "publications": [ { "doi": "10.1126/science.278.5338.631", "pmc": null, "pubmed": "9381173", - "title": "A genomic perspective on protein families.", + "title": "A genomic perspective on protein families", "year": 1997 }, { "doi": "10.1093/nar/gku1223", "pmc": "PMC4383993", "pubmed": "25428365", - "title": "Expanded microbial genome coverage and improved protein family annotation in the COG database.", + "title": "Expanded microbial genome coverage and improved protein family annotation in the COG database", "year": 2014 } ], @@ -8879,9 +9924,10 @@ "name": "Coleoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "COLAO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", "repository": "https://github.com/insect-morphology/colao", "uri_format": "http://purl.obolibrary.org/obo/COLAO_$1", - "version": "2022-06-18" + "version": "2023-04-08" }, "collagenmutdb": { "description": "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes.", @@ -8895,6 +9941,15 @@ }, "name": "Collagen Mutation Database", "preferred_prefix": "collagenmutdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cmd:$1" + } + ], "provides": "hgnc.symbol", "reviewer": { "email": "cthoyt@gmail.com", @@ -8947,6 +10002,15 @@ }, "name": "The Bioinorganic Motif Database", "preferred_prefix": "come", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/come:$1" + } + ], "uri_format": "https://www.flymine.org/come/entry?gn=$1" }, "commoncoreontology": { @@ -8997,7 +10061,7 @@ "doi": "10.1093/nar/gku975", "pmc": "PMC4384031", "pubmed": "25313161", - "title": "The complex portal--an encyclopaedia of macromolecular complexes.", + "title": "The complex portal--an encyclopaedia of macromolecular complexes", "year": 2014 } ], @@ -9038,9 +10102,37 @@ "name": "Compluyeast-2D-DB", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "compulyeast", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/compluyeast2dpage:$1" + } + ], "provides": "uniprot", "uri_format": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1" }, + "conference": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)", + "download_owl": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl", + "example": "isDocumentRelatedTo", + "homepage": "http://www.scholarlydata.org/ontology/doc/", + "keywords": [ + "ontology" + ], + "license": "CC-BY-3.0", + "name": "Conference Ontology", + "preferred_prefix": "conference", + "uri_format": "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1" + }, "confident.event": { "contact": { "email": "Philip.Stroemert@tib.eu", @@ -9126,35 +10218,35 @@ "doi": "10.1093/nar/gkr886", "pmc": "PMC3245185", "pubmed": "22058133", - "title": "ConoServer: updated content, knowledge, and discovery tools in the conopeptide database.", + "title": "ConoServer: updated content, knowledge, and discovery tools in the conopeptide database", "year": 2011 }, { "doi": "10.1016/j.toxicon.2010.03.002", "pmc": null, "pubmed": "20211197", - "title": "Conopeptide characterization and classifications: an analysis using ConoServer.", + "title": "Conopeptide characterization and classifications: an analysis using ConoServer", "year": 2010 }, { "doi": "10.1093/bioinformatics/btm596", "pmc": null, "pubmed": "18065428", - "title": "ConoServer, a database for conopeptide sequences and structures.", + "title": "ConoServer, a database for conopeptide sequences and structures", "year": 2007 }, { "doi": "10.1021/cb700091j", "pmc": null, "pubmed": "17649970", - "title": "Chemical modification of conotoxins to improve stability and activity.", + "title": "Chemical modification of conotoxins to improve stability and activity", "year": 2007 }, { "doi": "10.1152/physrev.00020.2003", "pmc": null, "pubmed": "14715910", - "title": "Conus venoms: a rich source of novel ion channel-targeted peptides.", + "title": "Conus venoms: a rich source of novel ion channel-targeted peptides", "year": 2004 } ], @@ -9288,12 +10380,21 @@ "name": "Comprehensive Resource of Mammalian protein complexes", "pattern": "^\\d+$", "preferred_prefix": "corum", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/corum:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gky973", "pmc": "PMC6323970", "pubmed": "30357367", - "title": "CORUM: the comprehensive resource of mammalian protein complexes-2019.", + "title": "CORUM: the comprehensive resource of mammalian protein complexes-2019", "year": 2019 } ], @@ -9323,28 +10424,28 @@ "doi": "10.1093/nar/gky1015", "pmc": "PMC6323903", "pubmed": "30371878", - "title": "COSMIC: the Catalogue Of Somatic Mutations In Cancer.", + "title": "COSMIC: the Catalogue Of Somatic Mutations In Cancer", "year": 2019 }, { "doi": "10.1093/nar/gku1075", "pmc": "PMC4383913", "pubmed": "25355519", - "title": "COSMIC: exploring the world's knowledge of somatic mutations in human cancer.", + "title": "COSMIC: exploring the world's knowledge of somatic mutations in human cancer", "year": 2014 }, { "doi": "10.1093/nar/gkq929", "pmc": "PMC3013785", "pubmed": "20952405", - "title": "COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.", + "title": "COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer", "year": 2010 }, { "doi": "10.1038/sj.bjc.6601894", "pmc": "PMC2409828", "pubmed": "15188009", - "title": "The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.", + "title": "The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website", "year": 2004 } ], @@ -9416,7 +10517,7 @@ "preferred_prefix": "covoc", "repository": "https://github.com/EBISPOT/covoc", "uri_format": "http://purl.obolibrary.org/obo/COVOC_$1", - "version": "2020-08-28" + "version": "2022-10-26" }, "cp": { "appears_in": [ @@ -9501,14 +10602,14 @@ "doi": "10.1136/neurintsurg-2014-011156", "pmc": null, "pubmed": "24589819", - "title": "Current procedural terminology; a primer.", + "title": "Current procedural terminology; a primer", "year": 2014 }, { "doi": "10.1016/j.jacr.2007.10.004", "pmc": null, "pubmed": "18359442", - "title": "CPT: an open system that describes all that you do.", + "title": "CPT: an open system that describes all that you do", "year": 2008 } ], @@ -9545,7 +10646,6 @@ "homepage": "https://casrai.org/credit/", "keywords": [ "data quality", - "ontology and terminology", "subject agnostic" ], "mappings": { @@ -9558,14 +10658,14 @@ "doi": "10.1038/d41586-019-01715-4", "pmc": null, "pubmed": "31164773", - "title": "Credit data generators for data reuse.", + "title": "Credit data generators for data reuse", "year": 2019 }, { "doi": "10.1038/508312a", "pmc": null, "pubmed": "24745070", - "title": "Publishing: Credit where credit is due.", + "title": "Publishing: Credit where credit is due", "year": 2014 }, { @@ -9619,21 +10719,21 @@ "doi": "10.1093/nar/gkn228", "pmc": "PMC2447796", "pubmed": "18442988", - "title": "CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.", + "title": "CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats", "year": 2008 }, { "doi": "10.1093/nar/gkm360", "pmc": "PMC1933234", "pubmed": "17537822", - "title": "CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.", + "title": "CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats", "year": 2007 }, { "doi": "10.1186/1471-2105-8-172", "pmc": "PMC1892036", "pubmed": "17521438", - "title": "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.", + "title": "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats", "year": 2007 } ], @@ -9667,6 +10767,7 @@ "name": "Contributor Role Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CRO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CRO_$1", "repository": "https://github.com/data2health/contributor-role-ontology", "uri_format": "http://purl.obolibrary.org/obo/CRO_$1", "version": "2019-12-11" @@ -9737,19 +10838,28 @@ "name": "CryptoDB", "pattern": "^\\w+$", "preferred_prefix": "cryptodb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cryptodb:$1" + } + ], "publications": [ { "doi": "10.1007/978-1-4939-9748-0_10", "pmc": null, "pubmed": "31452162", - "title": "Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.", + "title": "Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org", "year": 2020 }, { "doi": "10.1093/nar/gkj078", "pmc": "PMC1347441", "pubmed": "16381902", - "title": "CryptoDB: a Cryptosporidium bioinformatics resource update.", + "title": "CryptoDB: a Cryptosporidium bioinformatics resource update", "year": 2006 } ], @@ -9781,19 +10891,28 @@ "name": "Catalytic Site Atlas", "pattern": "^[0-9][A-Za-z0-9]{3}$", "preferred_prefix": "csa", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/csa:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1243", "pmc": "PMC3964973", "pubmed": "24319146", - "title": "The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.", + "title": "The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes", "year": 2013 }, { "doi": "10.1093/nar/gkh028", "pmc": "PMC308762", "pubmed": "14681376", - "title": "The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.", + "title": "The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data", "year": 2004 } ], @@ -9828,15 +10947,29 @@ "doi": "10.1107/s2052520616003954", "pmc": "PMC4822653", "pubmed": "27048719", - "title": "The Cambridge Structural Database.", + "title": "The Cambridge Structural Database", "year": 2016 }, { "doi": "10.1107/s0108768102003890", "pmc": null, "pubmed": "12037359", - "title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising.", + "title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising", "year": 2002 + }, + { + "doi": "10.1107/S2052520616003954", + "pmc": null, + "pubmed": null, + "title": "The Cambridge Structural Database.", + "year": null + }, + { + "doi": "10.1107/S0108768102003890", + "pmc": null, + "pubmed": null, + "title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising", + "year": null } ], "twitter": "ccdc_cambridge", @@ -9875,7 +11008,7 @@ "doi": null, "pmc": null, "pubmed": "8718842", - "title": "Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database.", + "title": "Taking a bite out of CRISP. Strategies on using and conducting searches in the Computer Retrieval of Information on Scientific Projects database", "year": 1996 } ], @@ -9923,8 +11056,29 @@ "name": "Cell Signaling Technology Antibody", "pattern": "^\\d+$", "preferred_prefix": "cst.ab", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cst:$1" + } + ], "uri_format": "http://www.cellsignal.com/products/$1.html" }, + "cstr": { + "description": "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. ", + "example": "31253.11.sciencedb.j00001.00123", + "homepage": "https://www.cstr.cn/en/", + "mappings": { + "miriam": "cstr" + }, + "name": "Common Science and Technology Resources", + "pattern": "^\\w{5}\\.\\d{2}\\..*$", + "preferred_prefix": "cstr", + "uri_format": "https://cstr.cn/$1" + }, "ctcae": { "appears_in": [ "oae" @@ -9961,7 +11115,7 @@ "doi": null, "pmc": "PMC5977606", "pubmed": "29854250", - "title": "Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.", + "title": "Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs", "year": 2018 } ], @@ -10028,7 +11182,7 @@ "doi": "10.1093/nar/gkaa891", "pmc": "PMC7779006", "pubmed": "33068428", - "title": "Comparative Toxicogenomics Database (CTD): update 2021.", + "title": "Comparative Toxicogenomics Database (CTD): update 2021", "year": 2021 } ], @@ -10069,10 +11223,26 @@ "name": "Ctenophore Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTENO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "repository": "https://github.com/obophenotype/ctenophore-ontology", "uri_format": "http://purl.obolibrary.org/obo/CTENO_$1", "version": "2016-10-19" }, + "ctis": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)", + "example": "2023-503698-40-00", + "homepage": "https://euclinicaltrials.eu/", + "name": "Clinical Trials Information System", + "pattern": "^\\d{4}-\\d+-\\d+-\\d+$", + "preferred_prefix": "ctis", + "uri_format": "https://euclinicaltrials.eu/app/#/view/$1" + }, "cto": { "contact": { "email": "alpha.tom.kodamullil@scai.fraunhofer.de", @@ -10103,10 +11273,28 @@ "name": "Clinical Trials Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CTO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "repository": "https://github.com/ClinicalTrialOntology/CTO", "uri_format": "http://purl.obolibrary.org/obo/CTO_$1", "version": "1.0.0" }, + "ctri": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages", + "example": "CTRI/2023/04/052053", + "homepage": "https://ctri.nic.in", + "name": "India Clinical Trials Registry", + "pattern": "^CTRI/\\d{4}/\\d{2}/\\d+$", + "preferred_prefix": "ctri", + "references": [ + "https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487" + ] + }, "cubedb": { "comment": "website down as of 2021-10-04", "deprecated": true, @@ -10136,6 +11324,15 @@ }, "name": "Codon Usage Tabulated from GenBank", "preferred_prefix": "cutg", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/cutg:$1" + } + ], "provides": "ncbitaxon", "reviewer": { "email": "cthoyt@gmail.com", @@ -10174,6 +11371,7 @@ "name": "Cardiovascular Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "CVDO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "repository": "https://github.com/OpenLHS/CVDO", "uri_format": "http://purl.obolibrary.org/obo/CVDO_$1", "version": "2020-03-05" @@ -10222,6 +11420,15 @@ "name": "DailyMed", "pattern": "^[A-Za-z0-9-]+$", "preferred_prefix": "dailymed", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dailymed:$1" + } + ], "uri_format": "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1" }, "dandi": { @@ -10270,7 +11477,7 @@ "doi": "10.1093/nar/gkr824", "pmc": "PMC3245104", "pubmed": "22009674", - "title": "The DARC site: a database of aligned ribosomal complexes.", + "title": "The DARC site: a database of aligned ribosomal complexes", "year": 2011 } ], @@ -10303,7 +11510,7 @@ "doi": "10.1093/nar/gkv1188", "pmc": "PMC4702848", "pubmed": "26553799", - "title": "DASHR: database of small human noncoding RNAs.", + "title": "DASHR: database of small human noncoding RNAs", "year": 2015 } ], @@ -10434,6 +11641,15 @@ "name": "Database of Arabidopsis Transcription Factors", "pattern": "^AT[1-5]G\\d{5}(\\.\\d+)?$", "preferred_prefix": "datf", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/datf:$1" + } + ], "uri_format": "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1" }, "dbd": { @@ -10454,6 +11670,15 @@ "name": "Transcription Factor Database", "pattern": "^\\d+$", "preferred_prefix": "dbd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dbd:$1" + } + ], "uri_format": "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD" }, "dbest": { @@ -10486,6 +11711,13 @@ "name": "dbEST through DNA Data Bank of Japan (DDBJ)", "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry/na/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dbest:$1" + }, { "code": "ebi", "description": "dbEST through European Nucleotide Archive (ENA)", @@ -10499,7 +11731,7 @@ "doi": "10.1038/ng0893-332", "pmc": null, "pubmed": "8401577", - "title": "dbEST--database for \"expressed sequence tags\".", + "title": "dbEST--database for \"expressed sequence tags\"", "year": 1993 } ], @@ -10521,12 +11753,21 @@ "name": "DBG2 Introns", "pattern": "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$", "preferred_prefix": "dbg2introns", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mgiid:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr1043", "pmc": "PMC3245105", "pubmed": "22080509", - "title": "Database for bacterial group II introns.", + "title": "Database for bacterial group II introns", "year": 2011 } ], @@ -10556,14 +11797,14 @@ "doi": "10.1093/nar/gkt1211", "pmc": "PMC3965052", "pubmed": "24297256", - "title": "NCBI's Database of Genotypes and Phenotypes: dbGaP.", + "title": "NCBI's Database of Genotypes and Phenotypes: dbGaP", "year": 2013 }, { "doi": "10.1038/ng1007-1181", "pmc": "PMC2031016", "pubmed": "17898773", - "title": "The NCBI dbGaP database of genotypes and phenotypes.", + "title": "The NCBI dbGaP database of genotypes and phenotypes", "year": 2007 } ], @@ -10621,6 +11862,15 @@ "name": "NCBI Probe database Public registry of nucleic acid reagents", "pattern": "^\\d+$", "preferred_prefix": "dbprobe", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dbprobe:$1" + } + ], "uri_format": "https://www.ncbi.nlm.nih.gov/probe/?term=$1" }, "dbsnp": { @@ -10650,6 +11900,13 @@ "pattern": "^rs\\d+$", "preferred_prefix": "dbsnp", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dbsnp:$1" + }, { "code": "sib", "description": "SNP2TFBS", @@ -10663,14 +11920,14 @@ "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 }, { "doi": "10.1093/nar/29.1.308", "pmc": "PMC29783", "pubmed": "11125122", - "title": "dbSNP: the NCBI database of genetic variation.", + "title": "dbSNP: the NCBI database of genetic variation", "year": 2001 } ], @@ -10726,7 +11983,7 @@ }, "deprecated": true, "description": "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3)).", - "download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl", + "download_owl": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf", "example": "contributor", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ @@ -10739,7 +11996,8 @@ "aberowl": "dcelements", "biocontext": "dc", "bioportal": "DC", - "fairsharing": "FAIRsharing.3nx7t" + "fairsharing": "FAIRsharing.3nx7t", + "ols": "dc" }, "name": "Dublin Core Elements (1.1)", "preferred_prefix": "dc", @@ -10771,6 +12029,7 @@ "name": "Dendritic cell", "pattern": "^\\d{7}$", "preferred_prefix": "DC_CL", + "rdf_uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1", "uri_format": "http://purl.obolibrary.org/obo/DC_CL_$1" }, "dcat": { @@ -10821,7 +12080,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.", - "download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl", + "download_owl": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf", "example": "title", "homepage": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/", "keywords": [ @@ -10833,7 +12092,8 @@ "biocontext": "dcterms", "biolink": "dct", "bioportal": "DCTERMS", - "fairsharing": "FAIRsharing.9vtwjs" + "fairsharing": "FAIRsharing.9vtwjs", + "ols": "dcterms" }, "name": "Dublin Core Metadata Initiative Terms", "preferred_prefix": "dcterms", @@ -10894,15 +12154,25 @@ "name": "Dictyostelium discoideum anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "DDANAT", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ddanat:$1" + } + ], "publications": [ { "doi": "10.1186/1471-2164-9-130", "pmc": "PMC2323390", "pubmed": "18366659", - "title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum.", + "title": "An anatomy ontology to represent biological knowledge in Dictyostelium discoideum", "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1", "repository": "https://github.com/dictyBase/migration-data", "twitter": "dictybase", "uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1", @@ -11007,21 +12277,22 @@ "doi": "10.1387/ijdb.190226pf", "pmc": "PMC7409682", "pubmed": "31840793", - "title": "dictyBase and the Dicty Stock Center (version 2.0) - a progress report.", + "title": "dictyBase and the Dicty Stock Center (version 2.0) - a progress report", "year": 2019 }, { "doi": "10.1007/978-1-62703-302-2_4", "pmc": "PMC3762881", "pubmed": "23494302", - "title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.", + "title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1", "repository": "https://github.com/obophenotype/dicty-phenotype-ontology", "twitter": "dictybase", "uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1", - "version": "2020-06-19" + "version": "2023-02-19" }, "debio": { "contact": { @@ -11085,14 +12356,14 @@ "doi": "10.1093/nar/gkt937", "pmc": "PMC3965078", "pubmed": "24150940", - "title": "DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.", + "title": "DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation", "year": 2013 }, { "doi": "10.1016/j.ajhg.2009.03.010", "pmc": "PMC2667985", "pubmed": "19344873", - "title": "DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.", + "title": "DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources", "year": 2009 } ], @@ -11137,6 +12408,13 @@ "name": "Discourse Elements Ontology", "preferred_prefix": "DEO", "publications": [ + { + "doi": "https://doi.org/10.3233/SW-150177", + "pmc": null, + "pubmed": null, + "title": "The Document Components Ontology (DoCO)", + "year": null + }, { "doi": "10.3233/sw-150177", "pmc": null, @@ -11193,32 +12471,25 @@ "preferred_prefix": "depod", "provides": "hgnc.symbol", "publications": [ - { - "doi": "doi", - "pmc": "PMC6911163", - "pubmed": "31836896", - "title": null, - "year": null - }, { "doi": "10.1093/database/baz133", "pmc": "PMC6911163", "pubmed": "31836896", - "title": "The human DEPhOsphorylation Database DEPOD: 2019 update.", + "title": "The human DEPhOsphorylation Database DEPOD: 2019 update", "year": 2019 }, { "doi": "10.1093/nar/gku1009", "pmc": "PMC4383878", "pubmed": "25332398", - "title": "The human DEPhOsphorylation database DEPOD: a 2015 update.", + "title": "The human DEPhOsphorylation database DEPOD: a 2015 update", "year": 2014 }, { "doi": "10.1126/scisignal.2003203", "pmc": null, "pubmed": "23674824", - "title": "Elucidating human phosphatase-substrate networks.", + "title": "Elucidating human phosphatase-substrate networks", "year": 2013 } ], @@ -11258,7 +12529,7 @@ "doi": "10.1186/s13326-016-0085-x", "pmc": "PMC4907256", "pubmed": "27296450", - "title": "DermO; an ontology for the description of dermatologic disease.", + "title": "DermO; an ontology for the description of dermatologic disease", "year": 2016 } ], @@ -11412,19 +12683,19 @@ "doi": "10.1007/s10278-013-9577-8", "pmc": "PMC3705029", "pubmed": "23404629", - "title": "Multi-series DICOM: an extension of DICOM that stores a whole study in a single object.", + "title": "Multi-series DICOM: an extension of DICOM that stores a whole study in a single object", "year": 2013 }, { "doi": "10.1016/j.crad.2005.07.003", "pmc": null, "pubmed": "16223609", - "title": "DICOM demystified: a review of digital file formats and their use in radiological practice.", + "title": "DICOM demystified: a review of digital file formats and their use in radiological practice", "year": 2005 } ], "uri_format": "http://dicom.nema.org/resources/ontology/DCM/$1", - "version": "2021e_20211122" + "version": "2023b_20230403" }, "dictybase": { "description": "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics", @@ -11447,26 +12718,35 @@ }, "name": "dictyBase", "preferred_prefix": "dictybase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dictybase:$1" + } + ], "publications": [ { "doi": "10.1007/978-1-62703-302-2_4", "pmc": "PMC3762881", "pubmed": "23494302", - "title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.", + "title": "One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012", "year": 2013 }, { "doi": "10.1093/nar/gks1064", "pmc": "PMC3531180", "pubmed": "23172289", - "title": "DictyBase 2013: integrating multiple Dictyostelid species.", + "title": "DictyBase 2013: integrating multiple Dictyostelid species", "year": 2012 }, { "doi": "10.1093/nar/gkh138", "pmc": "PMC308872", "pubmed": "14681427", - "title": "dictyBase: a new Dictyostelium discoideum genome database.", + "title": "dictyBase: a new Dictyostelium discoideum genome database", "year": 2004 } ], @@ -11554,14 +12834,14 @@ "doi": "10.1186/s13326-018-0183-z", "pmc": "PMC5944177", "pubmed": "29743102", - "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.", + "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse", "year": 2018 }, { "doi": null, "pmc": "PMC5765984", "pubmed": "29295242", - "title": "Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation.", + "title": "Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation", "year": 2017 }, { @@ -11572,6 +12852,7 @@ "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DIDEO_$1", "repository": "https://github.com/DIDEO/DIDEO", "uri_format": "http://purl.obolibrary.org/obo/DIDEO_$1", "version": "2022-06-14" @@ -11606,10 +12887,11 @@ "doi": "10.1021/acs.jcim.5b00119", "pmc": null, "pubmed": "26147071", - "title": "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms.", + "title": "DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms", "year": 2015 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DINTO_$1", "repository": "https://github.com/labda/DINTO", "uri_format": "http://purl.obolibrary.org/obo/DINTO_$1" }, @@ -11635,33 +12917,42 @@ "name": "Database of Interacting Proteins", "pattern": "^DIP(\\:)?\\-\\d{1,}[ENXS]$", "preferred_prefix": "dip", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dip:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh086", "pmc": "PMC308820", "pubmed": "14681454", - "title": "The Database of Interacting Proteins: 2004 update.", + "title": "The Database of Interacting Proteins: 2004 update", "year": 2004 }, { "doi": "10.1093/nar/30.1.303", "pmc": "PMC99070", "pubmed": "11752321", - "title": "DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.", + "title": "DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions", "year": 2002 }, { "doi": "10.1093/nar/29.1.239", "pmc": "PMC29798", "pubmed": "11125102", - "title": "DIP: The Database of Interacting Proteins: 2001 update.", + "title": "DIP: The Database of Interacting Proteins: 2001 update", "year": 2001 }, { "doi": "10.1093/nar/28.1.289", "pmc": "PMC102387", "pubmed": "10592249", - "title": "DIP: the database of interacting proteins.", + "title": "DIP: the database of interacting proteins", "year": 2000 } ], @@ -11704,6 +12995,7 @@ "name": "Disease Drivers Ontology", "pattern": "^\\d+$", "preferred_prefix": "DISDRIV", + "rdf_uri_format": "http://purl.obolibrary.org/obo/DISDRIV_$1", "repository": "https://github.com/DiseaseOntology/DiseaseDriversOntology", "twitter": "diseaseontology", "uri_format": "http://purl.obolibrary.org/obo/DISDRIV_$1" @@ -11779,40 +13071,49 @@ "name": "DisProt", "pattern": "^DP\\d{5}$", "preferred_prefix": "disprot", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/disprot:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1082", "pmc": "PMC8728214", "pubmed": "34850135", - "title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.", + "title": "DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation", "year": 2022 }, { "doi": "10.1093/nar/gkz975", "pmc": "PMC7145575", "pubmed": "31713636", - "title": "DisProt: intrinsic protein disorder annotation in 2020.", + "title": "DisProt: intrinsic protein disorder annotation in 2020", "year": 2020 }, { "doi": "10.1093/nar/gkw1056", "pmc": "PMC5210544", "pubmed": "27899601", - "title": "DisProt 7.0: a major update of the database of disordered proteins.", + "title": "DisProt 7.0: a major update of the database of disordered proteins", "year": 2016 }, { "doi": "10.1093/nar/gkl893", "pmc": "PMC1751543", "pubmed": "17145717", - "title": "DisProt: the Database of Disordered Proteins.", + "title": "DisProt: the Database of Disordered Proteins", "year": 2006 }, { "doi": "10.1093/bioinformatics/bth476", "pmc": null, "pubmed": "15310560", - "title": "DisProt: a database of protein disorder.", + "title": "DisProt: a database of protein disorder", "year": 2004 } ], @@ -11939,6 +13240,13 @@ "pubmed": null, "title": "The Document Components Ontology (DoCO)", "year": 2016 + }, + { + "doi": "10.3233/SW-150177", + "pmc": null, + "pubmed": null, + "title": "The Document Components Ontology (DoCO)", + "year": null } ], "repository": "https://github.com/sparontologies/doco", @@ -11992,6 +13300,13 @@ "pattern": "^10.\\d{2,9}/.*$", "preferred_prefix": "doi", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/doi:$1" + }, { "code": "doi_http", "description": "An alternate provider from the DOI website using HTTP", @@ -12028,6 +13343,7 @@ "uri_format": "https://scholia.toolforge.org/doi/$1" } ], + "rdf_uri_format": "http://dx.doi.org/$1", "references": [ "https://github.com/biopragmatics/bioregistry/issues/287", "https://github.com/biopragmatics/bioregistry/pull/316" @@ -12061,6 +13377,7 @@ "ontology" ], "license": "CC0-1.0", + "logo": "http://www.disease-ontology.org/media/images/DO_logo.jpg", "mappings": { "aberowl": "DOID", "bartoc": "576", @@ -12080,6 +13397,13 @@ "pattern": "^\\d+$", "preferred_prefix": "DOID", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/do:$1" + }, { "code": "hdo", "description": "Human Disease Ontology at Northwestern University", @@ -12100,108 +13424,146 @@ "doi": "10.1093/nar/gkab1063", "pmc": "PMC8728220", "pubmed": "34755882", - "title": "The Human Disease Ontology 2022 update.", + "title": "The Human Disease Ontology 2022 update", "year": 2022 }, { "doi": "10.1093/bib/bbab191", "pmc": "PMC8195003", "pubmed": "34015823", - "title": "COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model.", + "title": "COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model", "year": 2021 }, { "doi": "10.7554/elife.52614", "pmc": "PMC7077981", "pubmed": "32180547", - "title": "Wikidata as a knowledge graph for the life sciences.", + "title": "Wikidata as a knowledge graph for the life sciences", "year": 2020 }, + { + "doi": "10.7554/eLife.52614", + "pmc": "PMC7077981", + "pubmed": "32180547", + "title": "Wikidata as a knowledge graph for the life sciences", + "year": null + }, { "doi": "10.1093/nar/gky1036", "pmc": "PMC6323956", "pubmed": "30407590", - "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information.", + "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information", "year": 2019 }, { "doi": "10.1093/nar/gky1032", "pmc": "PMC6323977", "pubmed": "30407550", - "title": "Human Disease Ontology 2018 update: classification, content and workflow expansion.", + "title": "Human Disease Ontology 2018 update: classification, content and workflow expansion", "year": 2019 }, { "doi": "10.1242/dmm.032839", "pmc": "PMC5897730", "pubmed": "29590633", - "title": "Disease Ontology: improving and unifying disease annotations across species.", + "title": "Disease Ontology: improving and unifying disease annotations across species", "year": 2018 }, { "doi": "10.1093/database/baw015", "pmc": "PMC4795929", "pubmed": "26989148", - "title": "Wikidata as a semantic framework for the Gene Wiki initiative.", + "title": "Wikidata as a semantic framework for the Gene Wiki initiative", "year": 2016 }, { "doi": "10.1016/j.ajhg.2015.05.020", "pmc": "PMC4572507", "pubmed": "26119816", - "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.", + "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease", "year": 2015 }, { "doi": "10.1007/s00335-015-9576-9", "pmc": "PMC4602048", "pubmed": "26093607", - "title": "The Disease Ontology: fostering interoperability between biological and clinical human disease-related data.", + "title": "The Disease Ontology: fostering interoperability between biological and clinical human disease-related data", "year": 2015 }, { "doi": "10.1093/database/bav032", "pmc": "PMC4385274", "pubmed": "25841438", - "title": "Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.", + "title": "Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis", "year": 2015 }, { "doi": "10.1093/nar/gku1011", "pmc": "PMC4383880", "pubmed": "25348409", - "title": "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.", + "title": "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data", "year": 2014 }, { "doi": "10.1093/nar/gkr972", "pmc": "PMC3245088", "pubmed": "22080554", - "title": "Disease Ontology: a backbone for disease semantic integration.", + "title": "Disease Ontology: a backbone for disease semantic integration", "year": 2011 }, { "doi": "10.1186/1471-2164-10-s1-s6", "pmc": "PMC2709267", "pubmed": "19594883", - "title": "Annotating the human genome with Disease Ontology.", + "title": "Annotating the human genome with Disease Ontology", "year": 2009 }, + { + "doi": "10.1186/1471-2164-10-S1-S6", + "pmc": "PMC2709267", + "pubmed": "19594883", + "title": "Annotating the human genome with Disease Ontology", + "year": null + }, { "doi": "10.1093/bioinformatics/btp193", "pmc": "PMC2687947", "pubmed": "19478018", - "title": "From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.", + "title": "From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DOID_$1", "repository": "https://github.com/DiseaseOntology/HumanDiseaseOntology", "synonyms": [ "do" ], "twitter": "diseaseontology", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1", - "version": "2022-09-29" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/doid/terms?obo_id=DOID:$1", + "version": "2023-05-31" + }, + "dolce": { + "comment": "This resource doesn't exist anymore", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use.", + "homepage": "http://www.loa.istc.cnr.it/dolce/overview.html", + "keywords": [ + "computer science", + "knowledge and information systems", + "linguistics", + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.ae8hpt" + }, + "name": "Descriptive Ontology for Linguistic and Cognitive Engineering", + "preferred_prefix": "dolce" }, "dommino": { "description": "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.", @@ -12234,6 +13596,15 @@ "name": "Database for Prokaryotic Operons", "pattern": "^\\d+$", "preferred_prefix": "door", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/door:$1" + } + ], "uri_format": "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1" }, "doqcs.model": { @@ -12253,12 +13624,21 @@ "part_of": "doqcs", "pattern": "^\\d+$", "preferred_prefix": "doqcs.model", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/doqcs.model:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btf860", "pmc": null, "pubmed": "12584128", - "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.", + "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks", "year": 2003 } ], @@ -12281,12 +13661,21 @@ "part_of": "doqcs", "pattern": "^\\d+$", "preferred_prefix": "doqcs.pathway", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/doqcs.pathway:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btf860", "pmc": null, "pubmed": "12584128", - "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.", + "title": "The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks", "year": 2003 } ], @@ -12326,13 +13715,14 @@ "doi": "10.1186/2041-1480-4-30", "pmc": "PMC3816596", "pubmed": "24138933", - "title": "The Drosophila phenotype ontology.", + "title": "The Drosophila phenotype ontology", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", "repository": "https://github.com/FlyBase/drosophila-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", - "version": "2022-08-11" + "version": "2023-05-03" }, "dpv": { "description": "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene.", @@ -12351,12 +13741,21 @@ "name": "Description of Plant Viruses", "pattern": "^\\d+$", "preferred_prefix": "dpv", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/dpvweb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj023", "pmc": "PMC1347386", "pubmed": "16381892", - "title": "DPVweb: a comprehensive database of plant and fungal virus genes and genomes.", + "title": "DPVweb: a comprehensive database of plant and fungal virus genes and genomes", "year": 2006 } ], @@ -12441,6 +13840,37 @@ "preferred_prefix": "drduke", "uri_format": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1" }, + "drks": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)", + "example": "DRKS00031815", + "homepage": "http://drks.de", + "name": "German Clinical Trials Register", + "pattern": "^DRKS\\d+$", + "preferred_prefix": "drks", + "providers": [ + { + "code": "alt1", + "description": "German Language Provider", + "homepage": "http://drks.de", + "name": "German Language Provider", + "uri_format": "https://drks.de/search/de/trial/$1" + }, + { + "code": "alt2", + "description": "Legacy Provider", + "homepage": "http://drks.de", + "name": "Legacy Provider", + "uri_format": "http://drks.de/en/trial/$1" + } + ], + "uri_format": "https://drks.de/search/en/trial/$1" + }, "dron": { "appears_in": [ "scdo" @@ -12480,27 +13910,40 @@ "doi": "10.1186/s13326-017-0121-5", "pmc": "PMC5335794", "pubmed": "28253937", - "title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.", + "title": "Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request", "year": 2017 }, { "doi": "10.1186/s13326-016-0048-2", "pmc": "PMC4836073", "pubmed": "27096073", - "title": "An accurate and precise representation of drug ingredients.", + "title": "An accurate and precise representation of drug ingredients", "year": 2016 }, { "doi": "10.1186/2041-1480-4-44", "pmc": "PMC3931349", "pubmed": "24345026", - "title": "Building a drug ontology based on RxNorm and other sources.", + "title": "Building a drug ontology based on RxNorm and other sources", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DRON_$1", "repository": "https://github.com/ufbmi/dron", "uri_format": "http://purl.obolibrary.org/obo/DRON_$1", - "version": "2022-04-22" + "version": "2023-06-11" + }, + "drsanv0": { + "description": "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. ", + "example": "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082", + "homepage": "https://www.genome.gov/", + "mappings": { + "miriam": "drs.anv0" + }, + "name": "AnVIL DRS", + "pattern": "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$", + "preferred_prefix": "drsanv0", + "uri_format": "https://data.terra.bio/ga4gh/drs/v1/objects/$1" }, "drsc": { "description": "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene.", @@ -12549,33 +13992,42 @@ "name": "DrugBank", "pattern": "^DB\\d{5}$", "preferred_prefix": "drugbank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/drugbank:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1068", "pmc": "PMC3965102", "pubmed": "24203711", - "title": "DrugBank 4.0: shedding new light on drug metabolism.", + "title": "DrugBank 4.0: shedding new light on drug metabolism", "year": 2013 }, { "doi": "10.1093/nar/gkq1126", "pmc": "PMC3013709", "pubmed": "21059682", - "title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.", + "title": "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs", "year": 2010 }, { "doi": "10.1093/nar/gkm958", "pmc": "PMC2238889", "pubmed": "18048412", - "title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets.", + "title": "DrugBank: a knowledgebase for drugs, drug actions and drug targets", "year": 2007 }, { "doi": "10.1093/nar/gkj067", "pmc": "PMC1347430", "pubmed": "16381955", - "title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration.", + "title": "DrugBank: a comprehensive resource for in silico drug discovery and exploration", "year": 2006 } ], @@ -12669,6 +14121,7 @@ "pharmacology", "pharmacy" ], + "license": "CC-BY-SA-4.0", "mappings": { "biolink": "DrugCentral", "fairsharing": "FAIRsharing.3me82d", @@ -12684,14 +14137,14 @@ "doi": "10.1093/nar/gky963", "pmc": "PMC6323925", "pubmed": "30371892", - "title": "DrugCentral 2018: an update.", + "title": "DrugCentral 2018: an update", "year": 2019 }, { "doi": "10.1093/nar/gkw993", "pmc": "PMC5210665", "pubmed": "27789690", - "title": "DrugCentral: online drug compendium.", + "title": "DrugCentral: online drug compendium", "year": 2016 } ], @@ -12763,7 +14216,11 @@ "re3data": "r3d100010219" }, "name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen", + "pattern": "^ACC-\\d+$", "preferred_prefix": "dsmz", + "synonyms": [ + "DSMZCellDive" + ], "uri_format": "https://www.dsmz.de/collection/catalogue/details/culture/$1" }, "dso": { @@ -12829,7 +14286,7 @@ "doi": "10.1186/s13326-017-0161-x", "pmc": "PMC5679337", "pubmed": "29122012", - "title": "Drug target ontology to classify and integrate drug discovery data.", + "title": "Drug target ontology to classify and integrate drug discovery data", "year": 2017 } ], @@ -12878,10 +14335,11 @@ "doi": "10.1016/j.xgen.2021.100028", "pmc": "PMC8591903", "pubmed": "34820659", - "title": "The Data Use Ontology to streamline responsible access to human biomedical datasets.", + "title": "The Data Use Ontology to streamline responsible access to human biomedical datasets", "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/DUO_$1", "repository": "https://github.com/EBISPOT/DUO", "uri_format": "http://purl.obolibrary.org/obo/DUO_$1", "version": "2021-02-23" @@ -12944,11 +14402,15 @@ "ebisc": { "description": "Cell line collections", "example": "ESi007-A", + "example_extras": [ + "EDi008-B" + ], "homepage": "https://www.ebisc.org", "mappings": { "cellosaurus": "EBiSC" }, "name": "European Bank for induced pluripotent Stem Cells", + "pattern": "^E(S|D)i\\d+-\\w$", "preferred_prefix": "ebisc", "uri_format": "https://cells.ebisc.org/$1" }, @@ -13002,6 +14464,7 @@ "name": "The Echinoderm Anatomy and Development Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ECAO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ECAO_$1", "repository": "https://github.com/echinoderm-ontology/ecao_ontology", "uri_format": "http://purl.obolibrary.org/obo/ECAO_$1", "version": "2020-05-22" @@ -13063,6 +14526,13 @@ "name": "KEGG Ligand Database for Enzyme Nomenclature", "uri_format": "https://www.genome.jp/dbget-bin/www_bget?ec:$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/intenz:$1" + }, { "code": "enzymeportal", "description": "Enzyme Portal through EMBL-EBI", @@ -13090,7 +14560,7 @@ "doi": "10.1093/nar/28.1.304", "pmc": "PMC102465", "pubmed": "10592255", - "title": "The ENZYME database in 2000.", + "title": "The ENZYME database in 2000", "year": 2000 } ], @@ -13142,7 +14612,7 @@ "doi": "10.1016/j.jbi.2010.08.007", "pmc": null, "pubmed": "20800107", - "title": "Using an ECG reference ontology for semantic interoperability of ECG data.", + "title": "Using an ECG reference ontology for semantic interoperability of ECG data", "year": 2010 } ], @@ -13151,6 +14621,21 @@ ], "uri_format": "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1" }, + "echinobase": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species.", + "example": "23159291", + "homepage": "https://www.echinobase.org", + "name": "Echinobase", + "pattern": "^\\d+$", + "preferred_prefix": "echinobase", + "uri_format": "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1" + }, "echobase": { "description": "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products.", "example": "EB0170", @@ -13171,12 +14656,21 @@ "name": "EchoBASE post-genomic database for Escherichia coli", "pattern": "^EB\\d+$", "preferred_prefix": "echobase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/echobase:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gki028", "pmc": "PMC539982", "pubmed": "15608209", - "title": "EchoBASE: an integrated post-genomic database for Escherichia coli.", + "title": "EchoBASE: an integrated post-genomic database for Escherichia coli", "year": 2005 } ], @@ -13242,6 +14736,7 @@ "ontology" ], "license": "CC0-1.0", + "logo": "https://avatars1.githubusercontent.com/u/12802432", "mappings": { "aberowl": "ECO", "bartoc": "1028", @@ -13261,46 +14756,56 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "ECO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/eco:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1025", "pmc": "PMC8728134", "pubmed": "34986598", - "title": "ECO: the Evidence and Conclusion Ontology, an update for 2022.", + "title": "ECO: the Evidence and Conclusion Ontology, an update for 2022", "year": 2022 }, { "doi": "10.1093/nar/gky1036", "pmc": "PMC6323956", "pubmed": "30407590", - "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information.", + "title": "ECO, the Evidence & Conclusion Ontology: community standard for evidence information", "year": 2019 }, { "doi": "10.1007/978-1-4939-3743-1_18", "pmc": "PMC6377151", "pubmed": "27812948", - "title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.", + "title": "The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations", "year": 2017 }, { "doi": "10.1093/database/bau075", "pmc": "PMC4105709", "pubmed": "25052702", - "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO).", + "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)", "year": 2014 }, { "doi": "10.1142/9789812704856_0019", "pmc": null, "pubmed": "14992503", - "title": "An evidence ontology for use in pathway/genome databases.", + "title": "An evidence ontology for use in pathway/genome databases", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ECO_$1", "repository": "https://github.com/evidenceontology/evidenceontology", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1", - "version": "2022-08-05" + "uri_format": "http://www.evidenceontology.org/browse/#ECO_$1", + "version": "2023-04-07" }, "ecocore": { "contact": { @@ -13342,6 +14847,7 @@ "name": "An ontology of core ecological entities", "pattern": "^\\d+$", "preferred_prefix": "ECOCORE", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1", "repository": "https://github.com/EcologicalSemantics/ecocore", "uri_format": "http://purl.obolibrary.org/obo/ECOCORE_$1", "version": "2022-03-09" @@ -13374,29 +14880,36 @@ "doi": "10.3389/fmicb.2021.711077", "pmc": "PMC8357350", "pubmed": "34394059", - "title": "The EcoCyc Database in 2021.", + "title": "The EcoCyc Database in 2021", "year": 2021 }, { "doi": "10.1093/nar/gkw1003", "pmc": "PMC5210515", "pubmed": "27899573", - "title": "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.", + "title": "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12", "year": 2016 }, { "doi": "10.1128/ecosalplus.esp-0009-2013", "pmc": "PMC4243172", "pubmed": "26442933", - "title": "The EcoCyc Database.", + "title": "The EcoCyc Database", "year": 2014 }, { "doi": "10.1093/nar/gks1027", "pmc": "PMC3531154", "pubmed": "23143106", - "title": "EcoCyc: fusing model organism databases with systems biology.", + "title": "EcoCyc: fusing model organism databases with systems biology", "year": 2012 + }, + { + "doi": "10.1128/ecosalplus.ESP-0009-2013", + "pmc": null, + "pubmed": null, + "title": "The EcoCyc Database.", + "year": null } ], "uri_format": "https://ecocyc.org/gene?id=$1" @@ -13421,12 +14934,21 @@ "name": "Database of Escherichia coli Sequence and Function", "pattern": "^EG\\d+$", "preferred_prefix": "ecogene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ecogene:$1" + } + ], "publications": [ { "doi": "10.1093/nar/28.1.60", "pmc": "PMC102481", "pubmed": "10592181", - "title": "EcoGene: a genome sequence database for Escherichia coli K-12.", + "title": "EcoGene: a genome sequence database for Escherichia coli K-12", "year": 2000 } ], @@ -13475,12 +14997,39 @@ "doi": "10.1016/j.tim.2009.04.004", "pmc": "PMC3575750", "pubmed": "19576778", - "title": "What we can learn about Escherichia coli through application of Gene Ontology.", + "title": "What we can learn about Escherichia coli through application of Gene Ontology", "year": 2009 } ], "uri_format": "http://ecoliwiki.net/colipedia/index.php/$1:Gene" }, + "ecso": { + "contact": { + "email": "brycemecum@gmail.com", + "github": "amoeba", + "name": "Bryce Mecum", + "orcid": "0000-0002-0381-3766" + }, + "description": "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases", + "download_owl": "https://raw.githubusercontent.com/DataONEorg/sem-prov-ontologies/run4/observation/d1-ECSO.owl", + "example": "00000532", + "homepage": "http://bioportal.bioontology.org/ontologies/ECSO", + "keywords": [ + "earth science", + "ecosystem science", + "ontology" + ], + "mappings": { + "aberowl": "ECSO", + "bioportal": "ECSO", + "fairsharing": "FAIRsharing.a4ww64" + }, + "name": "The Ecosystem Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "ecso", + "repository": "https://github.com/DataONEorg/sem-prov-ontologies", + "uri_format": "http://purl.dataone.org/odo/ECSO_$1" + }, "ecto": { "contact": { "email": "annethessen@gmail.com", @@ -13514,6 +15063,7 @@ "ontology" ], "license": "CC0-1.0", + "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png", "mappings": { "aberowl": "ECTO", "biolink": "ECTO", @@ -13525,9 +15075,10 @@ "name": "Environmental conditions, treatments and exposures ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ECTO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ECTO_$1", "repository": "https://github.com/EnvironmentOntology/environmental-exposure-ontology", "uri_format": "http://purl.obolibrary.org/obo/ECTO_$1", - "version": "2022-12-12" + "version": "2023-02-14" }, "ecyano.entity": { "description": "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities.", @@ -13616,22 +15167,31 @@ "ontobee": "EDAM", "prefixcommons": "edam" }, - "name": "Bioinformatics operations, data types, formats, identifiers and topics", + "name": "EDAM Ontology", "pattern": "^(data|topic|operation|format)\\_\\d{4}$", "preferred_prefix": "edam", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/edam:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btt113", "pmc": "PMC3654706", "pubmed": "23479348", - "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.", + "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats", "year": 2013 } ], + "rdf_uri_format": "http://edamontology.org/$1", "repository": "https://github.com/edamontology/edamontology", "twitter": "edamontology", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1", - "version": "2019-07-17" + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1" }, "edam.data": { "contact": { @@ -13797,6 +15357,7 @@ "functional genomics", "ontology" ], + "license": "Apache-2.0", "mappings": { "aberowl": "EFO", "agroportal": "EFO", @@ -13808,7 +15369,8 @@ "miriam": "efo", "n2t": "efo", "ols": "efo", - "ontobee": "EFO" + "ontobee": "EFO", + "wikidata": "P11956" }, "name": "Experimental Factor Ontology", "owners": [ @@ -13835,13 +15397,13 @@ "doi": "10.1093/bioinformatics/btq099", "pmc": "PMC2853691", "pubmed": "20200009", - "title": "Modeling sample variables with an Experimental Factor Ontology.", + "title": "Modeling sample variables with an Experimental Factor Ontology", "year": 2010 } ], "repository": "https://github.com/EBISPOT/efo/", "uri_format": "http://www.ebi.ac.uk/efo/EFO_$1", - "version": "3.49.0" + "version": "3.55.0" }, "ega.dataset": { "description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.", @@ -13886,14 +15448,14 @@ "doi": "10.1093/nar/gkab1059", "pmc": "PMC8728218", "pubmed": "34791407", - "title": "The European Genome-phenome Archive in 2021.", + "title": "The European Genome-phenome Archive in 2021", "year": 2022 }, { "doi": "10.1038/ng.3312", "pmc": "PMC5426533", "pubmed": "26111507", - "title": "The European Genome-phenome Archive of human data consented for biomedical research.", + "title": "The European Genome-phenome Archive of human data consented for biomedical research", "year": 2015 } ], @@ -13933,19 +15495,28 @@ "name": "eggNOG", "pattern": "^\\w+$", "preferred_prefix": "eggnog", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/eggnog:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp951", "pmc": "PMC2808932", "pubmed": "19900971", - "title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.", + "title": "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations", "year": 2009 }, { "doi": "10.1093/nar/gkm796", "pmc": "PMC2238944", "pubmed": "17942413", - "title": "eggNOG: automated construction and annotation of orthologous groups of genes.", + "title": "eggNOG: automated construction and annotation of orthologous groups of genes", "year": 2007 } ], @@ -13980,6 +15551,16 @@ "name": "Human developmental anatomy, timed version", "pattern": "^\\d+$", "preferred_prefix": "EHDA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ehda:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EHDA_$1", "uri_format": "http://purl.obolibrary.org/obo/EHDA_$1" }, "ehdaa": { @@ -14011,6 +15592,16 @@ "name": "Human developmental anatomy, abstract version", "pattern": "^\\d+$", "preferred_prefix": "EHDAA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ehdaa:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1", "uri_format": "http://purl.obolibrary.org/obo/EHDAA_$1" }, "ehdaa2": { @@ -14056,10 +15647,11 @@ "doi": "10.1111/j.1469-7580.2012.01566.x", "pmc": "PMC3482348", "pubmed": "22973865", - "title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20).", + "title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EHDAA2_$1", "repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology", "synonyms": [ "EHDAA2_RETIRED", @@ -14091,28 +15683,28 @@ "doi": "10.1093/nar/gkz1030", "pmc": "PMC7145657", "pubmed": "31680160", - "title": "ELM-the eukaryotic linear motif resource in 2020.", + "title": "ELM-the eukaryotic linear motif resource in 2020", "year": 2020 }, { "doi": "10.1093/nar/gkv1291", "pmc": "PMC4702912", "pubmed": "26615199", - "title": "ELM 2016--data update and new functionality of the eukaryotic linear motif resource.", + "title": "ELM 2016--data update and new functionality of the eukaryotic linear motif resource", "year": 2015 }, { "doi": "10.1093/nar/gkr1064", "pmc": "PMC3245074", "pubmed": "22110040", - "title": "ELM--the database of eukaryotic linear motifs.", + "title": "ELM--the database of eukaryotic linear motifs", "year": 2011 }, { "doi": "10.1093/nar/gkg545", "pmc": "PMC168952", "pubmed": "12824381", - "title": "ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.", + "title": "ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins", "year": 2003 } ], @@ -14141,12 +15733,24 @@ "biocontext": "EMAP", "bioportal": "EMAP", "obofoundry": "emap", + "ols": "emap", "prefixcommons": "emap.ontology" }, "name": "Mouse gross anatomy and development, timed", "pattern": "^\\d+$", "preferred_prefix": "EMAP", - "uri_format": "http://purl.obolibrary.org/obo/EMAP_$1" + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/emap.ontology:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EMAP_$1", + "uri_format": "http://purl.obolibrary.org/obo/EMAP_$1", + "version": "2020-04-13" }, "emapa": { "contact": { @@ -14186,21 +15790,21 @@ "doi": "10.1016/s0925-4773(98)00069-0", "pmc": null, "pubmed": "9651497", - "title": "An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature.", + "title": "An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature", "year": 1998 }, { "doi": "10.1007/s00335-015-9584-9", "pmc": "PMC4602063", "pubmed": "26208972", - "title": "Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.", + "title": "Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data", "year": 2015 }, { "doi": "10.1186/2041-1480-4-15", "pmc": "PMC3851555", "pubmed": "23972281", - "title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update.", + "title": "EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update", "year": 2013 }, { @@ -14211,12 +15815,13 @@ "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EMAPA_$1", "repository": "https://github.com/obophenotype/mouse-anatomy-ontology", "synonyms": [ "EMAPA_RETIRED" ], "uri_format": "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1", - "version": "2022-07-14" + "version": "2023-05-05" }, "emaps": { "contact": { @@ -14288,26 +15893,83 @@ "doi": "10.1093/nar/gkv1126", "pmc": "PMC4702818", "pubmed": "26578576", - "title": "EMDataBank unified data resource for 3DEM.", + "title": "EMDataBank unified data resource for 3DEM", "year": 2015 }, { "doi": "10.1093/nar/gkq880", "pmc": "PMC3013769", "pubmed": "20935055", - "title": "EMDataBank.org: unified data resource for CryoEM.", + "title": "EMDataBank.org: unified data resource for CryoEM", "year": 2010 }, { "doi": "10.1016/s0968-0004(02)02176-x", "pmc": null, "pubmed": "12417136", - "title": "New electron microscopy database and deposition system.", + "title": "New electron microscopy database and deposition system", "year": 2002 + }, + { + "doi": "10.1016/S0968-0004(02)02176-X", + "pmc": null, + "pubmed": null, + "title": "New electron microscopy database and deposition system", + "year": null } ], "uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1" }, + "emmo": { + "banana": "EMMO", + "banana_peel": "_", + "contact": { + "email": "jesper.friis@sintef.no", + "github": "jesper-friis", + "name": "Jesper Friis", + "orcid": "0000-0002-1560-809X" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)", + "download_rdf": "https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl", + "example": "03212fd7_abfd_4828_9c8e_62c293052d4b", + "homepage": "https://emmo-repo.github.io", + "license": "CC-BY-4.0", + "name": "Elementary Multiperspective Material Ontology", + "preferred_prefix": "emmo", + "repository": "https://github.com/emmo-repo/EMMO", + "uri_format": "http://emmo.info/emmo#EMMO_$1" + }, + "emmo.cif": { + "contact": { + "email": "jesper.friis@sintef.no", + "github": "jesper-friis", + "name": "Jesper Friis", + "orcid": "0000-0002-1560-809X" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)", + "download_rdf": "https://raw.githubusercontent.com/emmo-repo/CIF-ontology/main/ontology/cif-core.ttl", + "example": "_space_group_symop.operation_xyz", + "example_extras": [ + "o12" + ], + "homepage": "https://www.iucr.org/resources/cif", + "name": "Crystallographic Information Framework", + "preferred_prefix": "emmo.cif", + "repository": "https://github.com/emmo-repo/CIF-ontology", + "uri_format": "http://emmo.info/emmo/cif-core#$1" + }, "emolecules": { "contributor": { "email": "cthoyt@gmail.com", @@ -14364,12 +16026,40 @@ "doi": "10.1038/nmeth.3806", "pmc": null, "pubmed": "27067018", - "title": "EMPIAR: a public archive for raw electron microscopy image data.", + "title": "EMPIAR: a public archive for raw electron microscopy image data", "year": 2016 } ], "uri_format": "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1" }, + "emsl.project": { + "contact": { + "email": "montana.smith@pnnl.gov", + "github": "mslarae13", + "name": "Montana Smith", + "orcid": "0000-0002-8683-0050" + }, + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type", + "example": "60141", + "github_request_issue": 835, + "homepage": "https://www.emsl.pnnl.gov/projects", + "name": "Environmental Molecular Sciences Laboratory Project", + "pattern": "^\\d+$", + "preferred_prefix": "emsl.project", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://www.emsl.pnnl.gov/project/$1" + }, "ena.embl": { "contact": { "email": "datasubs@ebi.ac.uk", @@ -14418,6 +16108,13 @@ "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", "name": "ENA through GenBank", "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ena:$1" } ], "publications": [ @@ -14425,49 +16122,49 @@ "doi": "10.1093/nar/gkaa1028", "pmc": "PMC7778925", "pubmed": "33175160", - "title": "The European Nucleotide Archive in 2020.", + "title": "The European Nucleotide Archive in 2020", "year": 2021 }, { "doi": "10.1093/nar/gkw1106", "pmc": "PMC5210577", "pubmed": "27899630", - "title": "European Nucleotide Archive in 2016.", + "title": "European Nucleotide Archive in 2016", "year": 2016 }, { "doi": "10.1093/nar/gkv1323", "pmc": "PMC4702924", "pubmed": "26657633", - "title": "The International Nucleotide Sequence Database Collaboration.", + "title": "The International Nucleotide Sequence Database Collaboration", "year": 2015 }, { "doi": "10.1093/nar/gkv1311", "pmc": "PMC4702917", "pubmed": "26615190", - "title": "Biocuration of functional annotation at the European nucleotide archive.", + "title": "Biocuration of functional annotation at the European nucleotide archive", "year": 2015 }, { "doi": "10.1093/nar/gku1129", "pmc": "PMC4383942", "pubmed": "25404130", - "title": "Content discovery and retrieval services at the European Nucleotide Archive.", + "title": "Content discovery and retrieval services at the European Nucleotide Archive", "year": 2014 }, { "doi": "10.1093/nar/gks1175", "pmc": "PMC3531187", "pubmed": "23203883", - "title": "Facing growth in the European Nucleotide Archive.", + "title": "Facing growth in the European Nucleotide Archive", "year": 2012 }, { "doi": "10.1093/nar/gkh120", "pmc": "PMC308854", "pubmed": "14681351", - "title": "The EMBL Nucleotide Sequence Database.", + "title": "The EMBL Nucleotide Sequence Database", "year": 2004 } ], @@ -14507,105 +16204,105 @@ "doi": "10.1038/s41586-020-2493-4", "pmc": "PMC7410828", "pubmed": "32728249", - "title": "Expanded encyclopaedias of DNA elements in the human and mouse genomes.", + "title": "Expanded encyclopaedias of DNA elements in the human and mouse genomes", "year": 2020 }, { "doi": "10.1038/s41586-020-2449-8", "pmc": "PMC7410827", "pubmed": "32728248", - "title": "Perspectives on ENCODE.", + "title": "Perspectives on ENCODE", "year": 2020 }, { "doi": "10.1002/cpbi.89", "pmc": "PMC7307447", "pubmed": "31751002", - "title": "The ENCODE Portal as an Epigenomics Resource.", + "title": "The ENCODE Portal as an Epigenomics Resource", "year": 2019 }, { "doi": "10.1093/nar/gkz1062", "pmc": "PMC7061942", "pubmed": "31713622", - "title": "New developments on the Encyclopedia of DNA Elements (ENCODE) data portal.", + "title": "New developments on the Encyclopedia of DNA Elements (ENCODE) data portal", "year": 2020 }, { "doi": "10.1093/nar/gkx1081", "pmc": "PMC5753278", "pubmed": "29126249", - "title": "The Encyclopedia of DNA elements (ENCODE): data portal update.", + "title": "The Encyclopedia of DNA elements (ENCODE): data portal update", "year": 2018 }, { "doi": "10.1371/journal.pone.0175310", "pmc": "PMC5389787", "pubmed": "28403240", - "title": "SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.", + "title": "SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata", "year": 2017 }, { "doi": "10.1093/database/baw001", "pmc": "PMC4792520", "pubmed": "26980513", - "title": "Principles of metadata organization at the ENCODE data coordination center.", + "title": "Principles of metadata organization at the ENCODE data coordination center", "year": 2016 }, { "doi": "10.1093/nar/gkv1160", "pmc": "PMC4702836", "pubmed": "26527727", - "title": "ENCODE data at the ENCODE portal.", + "title": "ENCODE data at the ENCODE portal", "year": 2015 }, { "doi": "10.1093/database/bav010", "pmc": "PMC4360730", "pubmed": "25776021", - "title": "Ontology application and use at the ENCODE DCC.", + "title": "Ontology application and use at the ENCODE DCC", "year": 2015 }, { "doi": "10.1093/nar/gks1172", "pmc": "PMC3531152", "pubmed": "23193274", - "title": "ENCODE data in the UCSC Genome Browser: year 5 update.", + "title": "ENCODE data in the UCSC Genome Browser: year 5 update", "year": 2012 }, { "doi": "10.1093/nar/gkr1012", "pmc": "PMC3245183", "pubmed": "22075998", - "title": "ENCODE whole-genome data in the UCSC Genome Browser: update 2012.", + "title": "ENCODE whole-genome data in the UCSC Genome Browser: update 2012", "year": 2011 }, { "doi": "10.1093/nar/gkq1017", "pmc": "PMC3013645", "pubmed": "21037257", - "title": "ENCODE whole-genome data in the UCSC genome browser (2011 update).", + "title": "ENCODE whole-genome data in the UCSC genome browser (2011 update)", "year": 2010 }, { "doi": "10.1093/nar/gkp961", "pmc": "PMC2808953", "pubmed": "19920125", - "title": "ENCODE whole-genome data in the UCSC Genome Browser.", + "title": "ENCODE whole-genome data in the UCSC Genome Browser", "year": 2009 }, { "doi": "10.1093/nar/gkl1017", "pmc": "PMC1781110", "pubmed": "17166863", - "title": "The ENCODE Project at UC Santa Cruz.", + "title": "The ENCODE Project at UC Santa Cruz", "year": 2006 }, { "doi": "10.1126/science.1105136", "pmc": null, "pubmed": "15499007", - "title": "The ENCODE (ENCyclopedia Of DNA Elements) Project.", + "title": "The ENCODE (ENCyclopedia Of DNA Elements) Project", "year": 2004 } ], @@ -14618,8 +16315,8 @@ "name": "Egon Willighagen", "orcid": "0000-0001-7542-0286" }, - "description": "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. ", - "download_owl": "http://enanomapper.github.io/ontologies/enanomapper.owl", + "description": "The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO.", + "download_owl": "http://enanomapper.github.io/ontologies/releases/9.0/enanomapper.owl", "example": "8000221", "homepage": "http://www.enanomapper.net/", "keywords": [ @@ -14632,7 +16329,7 @@ "fairsharing": "FAIRsharing.2gpf81", "ols": "enm" }, - "name": "eNanoMapper Ontology", + "name": "eNanoMapper ontology", "pattern": "^\\d+$", "preferred_prefix": "enm", "publications": [ @@ -14640,12 +16337,12 @@ "doi": "10.1186/s13326-015-0005-5", "pmc": "PMC4374589", "pubmed": "25815161", - "title": "eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.", + "title": "eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment", "year": 2015 } ], "uri_format": "http://purl.enanomapper.org/onto/ENM_$1", - "version": "7.4" + "version": "9.0" }, "ensembl": { "description": "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.", @@ -14677,6 +16374,7 @@ "uniprot": "DB-0023", "wikidata": "P594" }, + "mastodon": "ensembl@genomic.social", "name": "Ensembl Gene", "pattern": "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$", "preferred_prefix": "ensembl", @@ -14709,6 +16407,13 @@ "name": "Bgee", "uri_format": "https://bgee.org/?page=gene&gene_id=$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ensembl:$1" + }, { "code": "gnomad", "description": "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.", @@ -14729,339 +16434,340 @@ "doi": "10.1093/nar/gkab1049", "pmc": "PMC8728283", "pubmed": "34791404", - "title": "Ensembl 2022.", + "title": "Ensembl 2022", "year": 2022 }, { "doi": "10.1093/nar/gkz966", "pmc": "PMC7145704", "pubmed": "31691826", - "title": "Ensembl 2020.", + "title": "Ensembl 2020", "year": 2020 }, { "doi": "10.1093/nar/gky1113", "pmc": "PMC6323964", "pubmed": "30407521", - "title": "Ensembl 2019.", + "title": "Ensembl 2019", "year": 2019 }, { "doi": "10.1093/nar/gkw1104", "pmc": "PMC5210575", "pubmed": "27899575", - "title": "Ensembl 2017.", + "title": "Ensembl 2017", "year": 2016 }, { "doi": "10.1093/database/baw093", "pmc": "PMC4919035", "pubmed": "27337980", - "title": "The Ensembl gene annotation system.", + "title": "The Ensembl gene annotation system", "year": 2016 }, { "doi": "10.1186/s13059-016-0974-4", "pmc": "PMC4893825", "pubmed": "27268795", - "title": "The Ensembl Variant Effect Predictor.", + "title": "The Ensembl Variant Effect Predictor", "year": 2016 }, { "doi": "10.1093/database/baw053", "pmc": "PMC4852398", "pubmed": "27141089", - "title": "Ensembl comparative genomics resources.", + "title": "Ensembl comparative genomics resources", "year": 2016 }, { "doi": "10.1093/database/bav127", "pmc": "PMC4792531", "pubmed": "26980512", - "title": "ncRNA orthologies in the vertebrate lineage.", + "title": "ncRNA orthologies in the vertebrate lineage", "year": 2016 }, { "doi": "10.1093/database/bav096", "pmc": "PMC4761110", "pubmed": "26896847", - "title": "Ensembl comparative genomics resources.", + "title": "Ensembl comparative genomics resources", "year": 2016 }, { "doi": "10.1093/database/bav119", "pmc": "PMC4756621", "pubmed": "26888907", - "title": "Ensembl regulation resources.", + "title": "Ensembl regulation resources", "year": 2016 }, { "doi": "10.1093/nar/gkv1157", "pmc": "PMC4702834", "pubmed": "26687719", - "title": "Ensembl 2016.", + "title": "Ensembl 2016", "year": 2015 }, { "doi": "10.1186/s13059-015-0621-5", "pmc": "PMC4407537", "pubmed": "25887522", - "title": "The ensembl regulatory build.", + "title": "The ensembl regulatory build", "year": 2015 }, - { - "doi": "doi:10.1093/nar/gku1010", - "pmc": "PMC4383879", - "pubmed": "25352552", - "title": "Ensembl 2015", - "year": null - }, { "doi": "10.1093/nar/gku1010", "pmc": "PMC4383879", "pubmed": "25352552", - "title": "Ensembl 2015.", + "title": "Ensembl 2015", "year": 2014 }, { "doi": "10.1093/bioinformatics/btu613", "pmc": "PMC4271150", "pubmed": "25236461", - "title": "The Ensembl REST API: Ensembl Data for Any Language.", + "title": "The Ensembl REST API: Ensembl Data for Any Language", "year": 2014 }, { "doi": "10.1093/bioinformatics/btt737", "pmc": "PMC3967112", "pubmed": "24363377", - "title": "WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.", + "title": "WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis", "year": 2013 }, { "doi": "10.1093/nar/gkt1196", "pmc": "PMC3964975", "pubmed": "24316576", - "title": "Ensembl 2014.", + "title": "Ensembl 2014", "year": 2013 }, { "doi": "10.1093/nar/gks1236", "pmc": "PMC3531136", "pubmed": "23203987", - "title": "Ensembl 2013.", + "title": "Ensembl 2013", "year": 2012 }, { "doi": "10.1101/gr.135350.111", "pmc": "PMC3431492", "pubmed": "22955987", - "title": "GENCODE: the reference human genome annotation for The ENCODE Project.", + "title": "GENCODE: the reference human genome annotation for The ENCODE Project", "year": 2012 }, { "doi": "10.1101/gr.137901.112", "pmc": "PMC3460200", "pubmed": "22798491", - "title": "Incorporating RNA-seq data into the zebrafish Ensembl genebuild.", + "title": "Incorporating RNA-seq data into the zebrafish Ensembl genebuild", "year": 2012 }, { "doi": "10.1093/nar/gkr991", "pmc": "PMC3245178", "pubmed": "22086963", - "title": "Ensembl 2012.", + "title": "Ensembl 2012", "year": 2011 }, { "doi": "10.1093/database/bar030", "pmc": "PMC3170168", "pubmed": "21785142", - "title": "Ensembl BioMarts: a hub for data retrieval across taxonomic space.", + "title": "Ensembl BioMarts: a hub for data retrieval across taxonomic space", "year": 2011 }, { "doi": "10.1002/0471142905.hg0611s69", "pmc": "PMC3099348", "pubmed": "21400687", - "title": "Disease and phenotype data at Ensembl.", + "title": "Disease and phenotype data at Ensembl", "year": 2011 }, { "doi": "10.1093/nar/gkq1064", "pmc": "PMC3013672", "pubmed": "21045057", - "title": "Ensembl 2011.", + "title": "Ensembl 2011", "year": 2010 }, { "doi": "10.1093/bioinformatics/btq330", "pmc": "PMC2916720", "pubmed": "20562413", - "title": "Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.", + "title": "Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor", "year": 2010 }, { "doi": "10.1186/1471-2105-11-240", "pmc": "PMC2885371", "pubmed": "20459813", - "title": "eHive: an artificial intelligence workflow system for genomic analysis.", + "title": "eHive: an artificial intelligence workflow system for genomic analysis", "year": 2010 }, { "doi": "10.1186/1471-2105-11-238", "pmc": "PMC2882931", "pubmed": "20459810", - "title": "A database and API for variation, dense genotyping and resequencing data.", + "title": "A database and API for variation, dense genotyping and resequencing data", "year": 2010 }, { "doi": "10.1186/1471-2164-11-295", "pmc": "PMC2894802", "pubmed": "20459808", - "title": "Touring Ensembl: a practical guide to genome browsing.", + "title": "Touring Ensembl: a practical guide to genome browsing", "year": 2010 }, { "doi": "10.1186/1471-2164-11-293", "pmc": "PMC2894800", "pubmed": "20459805", - "title": "Ensembl variation resources.", + "title": "Ensembl variation resources", "year": 2010 }, { "doi": "10.1093/nar/gkp972", "pmc": "PMC2808936", "pubmed": "19906699", - "title": "Ensembl's 10th year.", + "title": "Ensembl's 10th year", "year": 2009 }, { "doi": "10.1093/nar/gkn828", "pmc": "PMC2686571", "pubmed": "19033362", - "title": "Ensembl 2009.", + "title": "Ensembl 2009", "year": 2008 }, { "doi": "10.1101/gr.073585.107", "pmc": "PMC2652215", "pubmed": "19029536", - "title": "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.", + "title": "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates", "year": 2008 }, { "doi": "10.1101/gr.076521.108", "pmc": "PMC2577868", "pubmed": "18849525", - "title": "Genome-wide nucleotide-level mammalian ancestor reconstruction.", + "title": "Genome-wide nucleotide-level mammalian ancestor reconstruction", "year": 2008 }, { "doi": "10.1093/nar/gkm988", "pmc": "PMC2238821", "pubmed": "18000006", - "title": "Ensembl 2008.", + "title": "Ensembl 2008", "year": 2007 }, { "doi": "10.1093/bfgp/elm025", "pmc": null, "pubmed": "17967807", - "title": "Genome browsing with Ensembl: a practical overview.", + "title": "Genome browsing with Ensembl: a practical overview", "year": 2007 }, { "doi": "10.1093/nar/gkl996", "pmc": "PMC1761443", "pubmed": "17148474", - "title": "Ensembl 2007.", + "title": "Ensembl 2007", "year": 2006 }, { "doi": "10.1038/ng0806-853a", "pmc": "PMC2610433", "pubmed": "16874317", - "title": "TranscriptSNPView: a genome-wide catalog of mouse coding variation.", + "title": "TranscriptSNPView: a genome-wide catalog of mouse coding variation", "year": 2006 }, { "doi": "10.1093/nar/gkj133", "pmc": "PMC1347495", "pubmed": "16381931", - "title": "Ensembl 2006.", + "title": "Ensembl 2006", "year": 2006 }, { "doi": "10.1093/nar/gki138", "pmc": "PMC540092", "pubmed": "15608235", - "title": "Ensembl 2005.", + "title": "Ensembl 2005", "year": 2005 }, { "doi": "10.1016/j.tig.2004.04.002", "pmc": null, "pubmed": "15145580", - "title": "Genome information resources - developments at Ensembl.", + "title": "Genome information resources - developments at Ensembl", "year": 2004 }, { "doi": "10.1101/gr.1862204", "pmc": "PMC479129", "pubmed": "15123595", - "title": "ESTGenes: alternative splicing from ESTs in Ensembl.", + "title": "ESTGenes: alternative splicing from ESTs in Ensembl", "year": 2004 }, { "doi": "10.1101/gr.1866304", "pmc": "PMC479128", "pubmed": "15123594", - "title": "The Ensembl computing architecture.", + "title": "The Ensembl computing architecture", "year": 2004 }, { "doi": "10.1101/gr.1863004", "pmc": "PMC479125", "pubmed": "15123591", - "title": "The Ensembl Web site: mechanics of a genome browser.", + "title": "The Ensembl Web site: mechanics of a genome browser", "year": 2004 }, { "doi": "10.1101/gr.1858004", "pmc": "PMC479124", "pubmed": "15123590", - "title": "The Ensembl automatic gene annotation system.", + "title": "The Ensembl automatic gene annotation system", "year": 2004 }, { "doi": "10.1101/gr.1859804", "pmc": "PMC479123", "pubmed": "15123589", - "title": "The Ensembl analysis pipeline.", + "title": "The Ensembl analysis pipeline", "year": 2004 }, { "doi": "10.1101/gr.1857204", "pmc": "PMC479122", "pubmed": "15123588", - "title": "The Ensembl core software libraries.", + "title": "The Ensembl core software libraries", "year": 2004 }, { "doi": "10.1093/nar/gkg083", "pmc": "PMC165530", "pubmed": "12519943", - "title": "Ensembl 2002: accommodating comparative genomics.", + "title": "Ensembl 2002: accommodating comparative genomics", "year": 2003 }, { "doi": "10.1093/nar/30.1.38", "pmc": "PMC99161", "pubmed": "11752248", - "title": "The Ensembl genome database project.", + "title": "The Ensembl genome database project", "year": 2002 + }, + { + "doi": "doi:10.1093/nar/gku1010", + "pmc": null, + "pubmed": null, + "title": "Ensembl 2015", + "year": null } ], + "rdf_uri_format": "http://rdf.ebi.ac.uk/resource/ensembl/$1", "synonyms": [ "Ensembl" ], @@ -15090,26 +16796,35 @@ "part_of": "ensembl", "pattern": "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$", "preferred_prefix": "ensembl.bacteria", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ensembl.bacteria:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkz890", "pmc": "PMC6943047", "pubmed": "31598706", - "title": "Ensembl Genomes 2020-enabling non-vertebrate genomic research.", + "title": "Ensembl Genomes 2020-enabling non-vertebrate genomic research", "year": 2020 }, { "doi": "10.1093/nar/gkv1209", "pmc": "PMC4702859", "pubmed": "26578574", - "title": "Ensembl Genomes 2016: more genomes, more complexity.", + "title": "Ensembl Genomes 2016: more genomes, more complexity", "year": 2015 }, { "doi": "10.1093/nar/gkp871", "pmc": "PMC2808935", "pubmed": "19884133", - "title": "Ensembl Genomes: extending Ensembl across the taxonomic space.", + "title": "Ensembl Genomes: extending Ensembl across the taxonomic space", "year": 2009 } ], @@ -15139,19 +16854,28 @@ "part_of": "ensembl", "pattern": "^[A-Z-a-z0-9]+$", "preferred_prefix": "ensembl.fungi", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ensembl.fungi:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkz890", "pmc": "PMC6943047", "pubmed": "31598706", - "title": "Ensembl Genomes 2020-enabling non-vertebrate genomic research.", + "title": "Ensembl Genomes 2020-enabling non-vertebrate genomic research", "year": 2020 }, { "doi": "10.1093/nar/gkv1209", "pmc": "PMC4702859", "pubmed": "26578574", - "title": "Ensembl Genomes 2016: more genomes, more complexity.", + "title": "Ensembl Genomes 2016: more genomes, more complexity", "year": 2015 } ], @@ -15180,19 +16904,28 @@ "name": "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa.", "pattern": "^\\w+(\\.)?\\d+$", "preferred_prefix": "ensembl.metazoa", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ensembl.metazoa:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkz890", "pmc": "PMC6943047", "pubmed": "31598706", - "title": "Ensembl Genomes 2020-enabling non-vertebrate genomic research.", + "title": "Ensembl Genomes 2020-enabling non-vertebrate genomic research", "year": 2020 }, { "doi": "10.1093/nar/gkv1209", "pmc": "PMC4702859", "pubmed": "26578574", - "title": "Ensembl Genomes 2016: more genomes, more complexity.", + "title": "Ensembl Genomes 2016: more genomes, more complexity", "year": 2015 } ], @@ -15215,6 +16948,15 @@ "name": "Ensembl Plants", "pattern": "^\\w+(\\.\\d+)?(\\.\\d+)?$", "preferred_prefix": "ensembl.plant", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ensembl.plant:$1" + } + ], "uri_format": "https://plants.ensembl.org/id/$1" }, "ensembl.protist": { @@ -15233,11 +16975,20 @@ "name": "Ensembl Protists", "pattern": "^\\w+$", "preferred_prefix": "ensembl.protist", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ensembl.protist:$1" + } + ], "uri_format": "https://protists.ensembl.org/id/$1" }, "ensemblglossary": { "description": "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used.", - "download_owl": "http://ensembl.org/glossary/ensembl-glossary/releases/2022-08-31/ensembl-glossary.owl", + "download_owl": "http://ensembl.org/glossary/ensembl-glossary/releases/2023-01-04/ensembl-glossary.owl", "example": "0000198", "homepage": "http://ensembl.org/glossary", "keywords": [ @@ -15250,7 +17001,7 @@ "pattern": "^\\d{7}$", "preferred_prefix": "ensemblglossary", "uri_format": "http://ensembl.org/glossary/ENSGLOSSARY_$1", - "version": "2022-08-31" + "version": "2023-01-04" }, "envipath": { "contact": { @@ -15278,22 +17029,29 @@ "doi": "10.1186/s13321-021-00543-x", "pmc": "PMC8414759", "pubmed": "34479624", - "title": "Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products.", + "title": "Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products", "year": 2021 }, { "doi": "10.1039/c6em00697c", "pmc": null, "pubmed": "28229138", - "title": "Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data.", + "title": "Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data", "year": 2017 }, { "doi": "10.1093/nar/gkv1229", "pmc": "PMC4702869", "pubmed": "26582924", - "title": "enviPath--The environmental contaminant biotransformation pathway resource.", + "title": "enviPath--The environmental contaminant biotransformation pathway resource", "year": 2015 + }, + { + "doi": "10.1039/C6EM00697C", + "pmc": null, + "pubmed": null, + "title": "Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data", + "year": null } ], "twitter": "envipath", @@ -15344,6 +17102,7 @@ "ontology" ], "license": "CC0-1.0", + "logo": "https://obofoundry.org/images/envo.png", "mappings": { "aberowl": "ENVO", "agroportal": "ENVO", @@ -15365,35 +17124,36 @@ "doi": "10.1186/s13326-016-0097-6", "pmc": "PMC5035502", "pubmed": "27664130", - "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.", + "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation", "year": 2016 }, { "doi": "10.1093/database/baw005", "pmc": "PMC4761108", "pubmed": "26896844", - "title": "EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.", + "title": "EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation", "year": 2016 }, { "doi": "10.7717/peerj.1470", "pmc": "PMC4690371", "pubmed": "26713234", - "title": "Emerging semantics to link phenotype and environment.", + "title": "Emerging semantics to link phenotype and environment", "year": 2015 }, { "doi": "10.1186/2041-1480-4-43", "pmc": "PMC3904460", "pubmed": "24330602", - "title": "The environment ontology: contextualising biological and biomedical entities.", + "title": "The environment ontology: contextualising biological and biomedical entities", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ENVO_$1", "repository": "https://github.com/EnvironmentOntology/envo", "twitter": "envoTweets", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1", - "version": "2021-05-14" + "uri_format": "http://purl.obolibrary.org/obo/ENVO_$1", + "version": "2023-02-13" }, "enzo": { "contributor": { @@ -15440,6 +17200,7 @@ "plant" ], "license": "CC-BY-4.0", + "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "EO", "agroportal": "EO", @@ -15453,15 +17214,25 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "EO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/eo:$1" + } + ], "publications": [ { "doi": "10.3732/ajb.1200222", "pmc": "PMC3492881", "pubmed": "22847540", - "title": "Ontologies as integrative tools for plant science.", + "title": "Ontologies as integrative tools for plant science", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EO_$1", "repository": "https://github.com/Planteome/plant-environment-ontology", "uri_format": "http://archive.gramene.org/db/ontology/search?query=EO:$1" }, @@ -15553,14 +17324,22 @@ }, "epd": { "contact": { - "email": "ask-epd@googlegroups.com", + "email": "Philipp.Bucher@sib.swiss", "github": null, "name": "Philipp Bucher", "orcid": "0000-0002-0816-7775" }, + "contributor_extras": [ + { + "email": "sebastien.moretti@sib.swiss", + "github": "smoretti", + "name": "Sebastien Moretti", + "orcid": "0000-0003-3947-488X" + } + ], "description": "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.", "example": "TA_H3", - "homepage": "http://epd.vital-it.ch/", + "homepage": "https://epd.expasy.org/epd/", "keywords": [ "bioinformatics", "biology" @@ -15582,81 +17361,81 @@ "doi": "10.1093/nar/27.1.307", "pmc": "PMC148166", "pubmed": "9847211", - "title": "The Eukaryotic Promoter Database (EPD): recent developments.", + "title": "The Eukaryotic Promoter Database (EPD): recent developments", "year": 1999 }, { "doi": "10.1093/nar/26.1.353", "pmc": "PMC147208", "pubmed": "9399872", - "title": "The Eukaryotic Promoter Database EPD.", + "title": "The Eukaryotic Promoter Database EPD", "year": 1998 }, { "doi": "10.1093/nar/14.24.10009", "pmc": "PMC341352", "pubmed": "3808945", - "title": "Compilation and analysis of eukaryotic POL II promoter sequences.", + "title": "Compilation and analysis of eukaryotic POL II promoter sequences", "year": 1986 }, { "doi": "10.1093/nar/gkx807", "pmc": "PMC5753345", "pubmed": "28981707", - "title": "The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics.", + "title": "The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics", "year": 2018 }, { "doi": "10.1093/nar/gkw1069", "pmc": "PMC5210552", "pubmed": "27899657", - "title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.", + "title": "The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms", "year": 2016 }, { "doi": "10.1093/nar/gku1111", "pmc": "PMC4383928", "pubmed": "25378343", - "title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.", + "title": "The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools", "year": 2014 }, { "doi": "10.1093/nar/gks1233", "pmc": "PMC3531148", "pubmed": "23193273", - "title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.", + "title": "EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era", "year": 2012 }, { "doi": "10.1093/nar/gkj146", "pmc": "PMC1347508", "pubmed": "16381980", - "title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms.", + "title": "EPD in its twentieth year: towards complete promoter coverage of selected model organisms", "year": 2006 }, { "doi": "10.1093/nar/gkh122", "pmc": "PMC308856", "pubmed": "14681364", - "title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.", + "title": "The Eukaryotic Promoter Database EPD: the impact of in silico primer extension", "year": 2004 }, { "doi": "10.1093/nar/30.1.322", "pmc": "PMC99099", "pubmed": "11752326", - "title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.", + "title": "The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data", "year": 2002 }, { "doi": "10.1093/nar/28.1.302", "pmc": "PMC102462", "pubmed": "10592254", - "title": "The eukaryotic promoter database (EPD).", + "title": "The eukaryotic promoter database (EPD)", "year": 2000 } ], - "uri_format": "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1" + "uri_format": "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1" }, "epio": { "contact": { @@ -15686,6 +17465,7 @@ "name": "Epilepsy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "EPIO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/EPIO_$1", "repository": "https://github.com/SCAI-BIO/EpilepsyOntology", "uri_format": "http://purl.obolibrary.org/obo/EPIO_$1" }, @@ -15713,6 +17493,7 @@ }, "name": "Epidemiology Ontology", "preferred_prefix": "EPO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/EPO_$1", "uri_format": "http://purl.obolibrary.org/obo/EPO_$1" }, "epso": { @@ -15744,7 +17525,7 @@ "doi": "10.1136/amiajnl-2013-001696", "pmc": "PMC3912711", "pubmed": "23686934", - "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care.", + "title": "Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care", "year": 2013 } ], @@ -15779,7 +17560,7 @@ "doi": "10.1186/s13321-022-00614-7", "pmc": "PMC9400299", "pubmed": "36002868", - "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials.", + "title": "European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials", "year": 2022 } ], @@ -15822,17 +17603,25 @@ "doi": "10.1109/jcdl.2017.7991571", "pmc": "PMC5868434", "pubmed": "29599662", - "title": "Automating data citation: the eagle-i experience.", + "title": "Automating data citation: the eagle-i experience", "year": 2017 }, + { + "doi": "10.1109/JCDL.2017.7991571", + "pmc": "PMC5868434", + "pubmed": "29599662", + "title": "Automating data citation: the eagle-i experience", + "year": null + }, { "doi": "10.1093/database/bar067", "pmc": "PMC3308157", "pubmed": "22434835", - "title": "Research resources: curating the new eagle-i discovery system.", + "title": "Research resources: curating the new eagle-i discovery system", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "uri_format": "http://purl.obolibrary.org/obo/ERO_$1", "version": "2016-07-27" }, @@ -15848,6 +17637,15 @@ }, "name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow", "preferred_prefix": "eropmoscow", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/eropmoscow:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -15882,6 +17680,15 @@ }, "name": "eukaryotic Subcellular Localization database", "preferred_prefix": "esldb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/esldb:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -15938,6 +17745,9 @@ "name": "EU Clinical Trials", "pattern": "^\\d{4}\\-\\d{6}\\-\\d{2}$", "preferred_prefix": "euclinicaltrials", + "synonyms": [ + "EUCTR" + ], "uri_format": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1" }, "eugenes": { @@ -15961,12 +17771,21 @@ }, "name": "Eukaryotic Genes", "preferred_prefix": "eugenes", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/eugenes:$1" + } + ], "publications": [ { "doi": "10.1093/nar/30.1.145", "pmc": "PMC99146", "pubmed": "11752277", - "title": "euGenes: a eukaryote genome information system.", + "title": "euGenes: a eukaryote genome information system", "year": 2002 } ], @@ -16001,6 +17820,7 @@ "population genetics" ], "license": "CC-BY-4.0", + "logo": "https://raw.githubusercontent.com/EuPathDB/communitysite/master/assets/images/VEuPathDB-logo-s.png", "mappings": { "aberowl": "EUPATH", "biocontext": "EUPATH", @@ -16022,9 +17842,10 @@ "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", "repository": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", "uri_format": "http://purl.obolibrary.org/obo/EUPATH_$1", - "version": "2022-06-08" + "version": "2023-05-30" }, "eurofir": { "contributor": { @@ -16068,10 +17889,20 @@ }, "name": "eVOC (Expressed Sequence Annotation for Humans)", "preferred_prefix": "EV", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/evoc:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/EV_$1", "references": [ "https://twitter.com/Bgeedb/status/1350124337815281664" ], - "uri_format": "http://purl.obolibrary.org/obo/EV_$1" + "uri_format": "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1" }, "evm": { "contributor": { @@ -16171,15 +18002,16 @@ "doi": "10.1021/es2033857", "pmc": "PMC3314380", "pubmed": "22324457", - "title": "Providing the missing link: the exposure science ontology ExO.", + "title": "Providing the missing link: the exposure science ontology ExO", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ExO_$1", "repository": "https://github.com/CTDbase/exposure-ontology", "synonyms": [ "ExO" ], - "uri_format": "http://purl.obolibrary.org/obo/EXO_$1", + "uri_format": "http://purl.obolibrary.org/obo/ExO_$1", "version": "2022-06-29" }, "fabio": { @@ -16258,7 +18090,7 @@ "doi": "10.1242/dev.191213", "pmc": "PMC7522026", "pubmed": "32958507", - "title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research.", + "title": "FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research", "year": 2020 } ], @@ -16297,6 +18129,7 @@ "n2t": "fairsharing", "re3data": "r3d100010142" }, + "mastodon": "fairsharing@fediscience.org", "name": "FAIRsharing", "pattern": "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$", "preferred_prefix": "fairsharing", @@ -16305,14 +18138,14 @@ "doi": "10.1038/s41587-019-0080-8", "pmc": "PMC6785156", "pubmed": "30940948", - "title": "FAIRsharing as a community approach to standards, repositories and policies.", + "title": "FAIRsharing as a community approach to standards, repositories and policies", "year": 2019 }, { "doi": "10.1093/database/baw075", "pmc": "PMC4869797", "pubmed": "27189610", - "title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.", + "title": "BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences", "year": 2016 }, { @@ -16406,7 +18239,7 @@ "doi": "10.1186/s13326-016-0067-z", "pmc": "PMC4907002", "pubmed": "27296299", - "title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.", + "title": "FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation", "year": 2016 } ], @@ -16447,10 +18280,47 @@ "name": "Fungal gross anatomy", "pattern": "^\\d{7}$", "preferred_prefix": "FAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fao:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "repository": "https://github.com/obophenotype/fungal-anatomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/FAO_$1", "version": "2020-05-07" }, + "fao.asfis": { + "comment": "This resource is offered freely by FAO for download but no obvious licensing is indicated, and no caution about appropriate reuse.", + "contributor": { + "email": null, + "github": "ddooley", + "name": "Damion Dooley", + "orcid": "0000-0002-8844-9165" + }, + "description": "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)", + "example": "20560", + "github_request_issue": 872, + "homepage": "https://www.fao.org/fishery/en/collection/asfis/en", + "name": "Aquatic Sciences and Fisheries Information System", + "pattern": "^\\d+$", + "preferred_prefix": "fao.asfis", + "repository": "bioregistry", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "synonyms": [ + "asfis" + ], + "uri_format": "https://www.fao.org/fishery/en/species/$1" + }, "fbbi": { "contact": { "email": "wawong@gmail.com", @@ -16485,6 +18355,16 @@ "name": "Biological Imaging Methods Ontology", "pattern": "^\\d+$", "preferred_prefix": "FBbi", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fbbi:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FBbi_$1", "repository": "https://github.com/CRBS/Biological_Imaging_Methods_Ontology", "synonyms": [ "FBbi" @@ -16529,43 +18409,53 @@ "part_of": "flybase", "pattern": "^\\d{8}$", "preferred_prefix": "FBbt", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fbbt:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-32", "pmc": "PMC4015547", "pubmed": "24139062", - "title": "The Drosophila anatomy ontology.", + "title": "The Drosophila anatomy ontology", "year": 2013 }, { "doi": "10.1093/bioinformatics/bts113", "pmc": null, "pubmed": "22402613", - "title": "A strategy for building neuroanatomy ontologies.", + "title": "A strategy for building neuroanatomy ontologies", "year": 2012 }, { "doi": "10.1093/bioinformatics/btr677", "pmc": null, "pubmed": "22180411", - "title": "The Virtual Fly Brain browser and query interface.", + "title": "The Virtual Fly Brain browser and query interface", "year": 2011 }, { "doi": "10.1093/nar/gkj068", "pmc": "PMC1347431", "pubmed": "16381917", - "title": "FlyBase: anatomical data, images and queries.", + "title": "FlyBase: anatomical data, images and queries", "year": 2006 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FBbt_$1", "repository": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology", "synonyms": [ "FBbt", "FBbt_root" ], "uri_format": "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1", - "version": "2022-06-09" + "version": "2023-05-03" }, "fbcv": { "appears_in": [ @@ -16605,21 +18495,31 @@ "part_of": "flybase", "pattern": "^\\d{7}$", "preferred_prefix": "FBcv", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fbcv:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-30", "pmc": "PMC3816596", "pubmed": "24138933", - "title": "The Drosophila phenotype ontology.", + "title": "The Drosophila phenotype ontology", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", "repository": "https://github.com/FlyBase/flybase-controlled-vocabulary", "synonyms": [ "FBcv" ], "uri_format": "http://purl.obolibrary.org/obo/FBcv_$1", - "version": "2022-06-09" + "version": "2023-05-04" }, "fbdv": { "contact": { @@ -16656,12 +18556,22 @@ "name": "Drosophila development", "pattern": "^\\d{8}$", "preferred_prefix": "FBdv", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fbdv:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FBdv_$1", "repository": "https://github.com/FlyBase/drosophila-developmental-ontology", "synonyms": [ "FBdv" ], "uri_format": "http://purl.obolibrary.org/obo/FBdv_$1", - "version": "2022-06-08" + "version": "2023-05-03" }, "fbol": { "comment": "Website down, checked on 2021-10-07", @@ -16730,13 +18640,16 @@ "aberowl": "FB-SP", "biocontext": "FBSP", "bioportal": "FB-SP", - "obofoundry": "fbsp" + "obofoundry": "fbsp", + "ols": "fbsp" }, "name": "Fly taxonomy", "part_of": "flybase", "pattern": "^\\d{8}$", "preferred_prefix": "FBSP", - "uri_format": "http://purl.obolibrary.org/obo/FBSP_$1" + "rdf_uri_format": "http://purl.obolibrary.org/obo/FBSP_$1", + "uri_format": "http://purl.obolibrary.org/obo/FBSP_$1", + "version": "2017-11-19" }, "fbtc": { "contributor": { @@ -16752,6 +18665,9 @@ "part_of": "flybase", "pattern": "^\\d{7}$", "preferred_prefix": "fbtc", + "synonyms": [ + "FlyBase_Cell_line" + ], "uri_format": "https://flybase.org/reports/FBtc$1" }, "fcb": { @@ -16804,7 +18720,7 @@ "name": "Georgeta Bordea", "orcid": "0000-0001-9921-8234" }, - "description": "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there.", + "description": "Food-Drug interactions automatically extracted from scientific literature", "download_owl": "http://purl.obolibrary.org/obo/fideo.owl", "example": "00000021", "homepage": "https://gitub.u-bordeaux.fr/erias/fideo", @@ -16823,8 +18739,10 @@ "name": "Food Interactions with Drugs Evidence Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "FIDEO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1", "repository": "https://gitub.u-bordeaux.fr/erias/fideo", - "uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1" + "uri_format": "http://purl.obolibrary.org/obo/FIDEO_$1", + "version": "2023-02-01" }, "fishbase.species": { "contributor": { @@ -16926,6 +18844,16 @@ "part_of": "chebi", "pattern": "^\\d{7}$", "preferred_prefix": "FIX", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fix:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FIX_$1", "uri_format": "http://purl.obolibrary.org/obo/FIX_$1", "version": "2020-04-13" }, @@ -16966,20 +18894,27 @@ "doi": "10.1186/s13326-016-0107-8", "pmc": "PMC5109718", "pubmed": "27842607", - "title": "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.", + "title": "The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants", "year": 2016 }, { "doi": "10.3897/bdj.2.e1125", "pmc": "PMC4092319", "pubmed": "25057255", - "title": "Enriched biodiversity data as a resource and service.", + "title": "Enriched biodiversity data as a resource and service", "year": 2014 + }, + { + "doi": "10.3897/BDJ.2.e1125", + "pmc": "PMC4092319", + "pubmed": "25057255", + "title": "Enriched biodiversity data as a resource and service", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FLOPO_$1", "repository": "https://github.com/flora-phenotype-ontology/flopoontology", - "uri_format": "http://purl.obolibrary.org/obo/FLOPO_$1", - "version": "2019-09-09" + "uri_format": "http://purl.obolibrary.org/obo/FLOPO_$1" }, "flowrepository": { "contact": { @@ -17010,14 +18945,14 @@ "doi": "10.1002/cyto.a.22106", "pmc": null, "pubmed": "22887982", - "title": "FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications.", + "title": "FlowRepository: a resource of annotated flow cytometry datasets associated with peer-reviewed publications", "year": 2012 }, { "doi": "10.1002/0471142956.cy1018s61", "pmc": null, "pubmed": "22752950", - "title": "Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org).", + "title": "Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) compliant manuscript using the International Society for Advancement of Cytometry (ISAC) FCS file repository (FlowRepository.org)", "year": 2012 } ], @@ -17048,6 +18983,7 @@ "name": "Influenza Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "FLU", + "rdf_uri_format": "http://purl.obolibrary.org/obo/FLU_$1", "uri_format": "http://purl.obolibrary.org/obo/FLU_$1" }, "flybase": { @@ -17092,6 +19028,13 @@ "homepage": "https://www.alliancegenome.org", "name": "FlyBase through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/FB:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/flybase:$1" } ], "publications": [ @@ -17099,197 +19042,197 @@ "doi": "10.1093/nar/27.1.85", "pmc": "PMC148103", "pubmed": "9847148", - "title": "The FlyBase database of the Drosophila Genome Projects and community literature.", + "title": "The FlyBase database of the Drosophila Genome Projects and community literature", "year": 1999 }, { "doi": "10.1093/nar/26.1.85", "pmc": "PMC147222", "pubmed": "9399806", - "title": "FlyBase: a Drosophila database.", + "title": "FlyBase: a Drosophila database", "year": 1998 }, { "doi": "10.1093/nar/25.1.63", "pmc": "PMC146418", "pubmed": "9045212", - "title": "FlyBase: a Drosophila database. The FlyBase consortium.", + "title": "FlyBase: a Drosophila database. The FlyBase consortium", "year": 1997 }, { "doi": "10.1093/nar/24.1.53", "pmc": "PMC145580", "pubmed": "8594600", - "title": "FlyBase: the Drosophila database.", + "title": "FlyBase: the Drosophila database", "year": 1996 }, { "doi": "10.1093/nar/22.17.3456", "pmc": "PMC308301", "pubmed": "7937045", - "title": "FlyBase--the Drosophila database. The FlyBase Consortium.", + "title": "FlyBase--the Drosophila database. The FlyBase Consortium", "year": 1994 }, { "doi": "10.1242/dev.120.7.2077", "pmc": null, "pubmed": "7925011", - "title": "FlyBase--the Drosophila genetic database.", + "title": "FlyBase--the Drosophila genetic database", "year": 1994 }, { "doi": "10.1093/nar/gkaa1026", "pmc": "PMC7779046", "pubmed": "33219682", - "title": "FlyBase: updates to the Drosophila melanogaster knowledge base.", + "title": "FlyBase: updates to the Drosophila melanogaster knowledge base", "year": 2021 }, { "doi": "10.1093/nar/gky1003", "pmc": "PMC6323960", "pubmed": "30364959", - "title": "FlyBase 2.0: the next generation.", + "title": "FlyBase 2.0: the next generation", "year": 2019 }, { "doi": "10.1007/978-1-4939-7737-6_16", "pmc": "PMC5996772", "pubmed": "29761468", - "title": "Using FlyBase to Find Functionally Related Drosophila Genes.", + "title": "Using FlyBase to Find Functionally Related Drosophila Genes", "year": 2018 }, { "doi": "10.1002/cpbi.19", "pmc": "PMC5152691", "pubmed": "27930807", - "title": "Exploring FlyBase Data Using QuickSearch.", + "title": "Exploring FlyBase Data Using QuickSearch", "year": 2016 }, { "doi": "10.1093/nar/gkw1016", "pmc": "PMC5210523", "pubmed": "27799470", - "title": "FlyBase at 25: looking to the future.", + "title": "FlyBase at 25: looking to the future", "year": 2016 }, { "doi": "10.1242/dmm.023317", "pmc": "PMC4826978", "pubmed": "26935103", - "title": "FlyBase portals to human disease research using Drosophila models.", + "title": "FlyBase portals to human disease research using Drosophila models", "year": 2016 }, { "doi": "10.1093/nar/gkv1046", "pmc": "PMC4702782", "pubmed": "26467478", - "title": "FlyBase: establishing a Gene Group resource for Drosophila melanogaster.", + "title": "FlyBase: establishing a Gene Group resource for Drosophila melanogaster", "year": 2015 }, { "doi": "10.1534/g3.115.018929", "pmc": "PMC4528329", "pubmed": "26109357", - "title": "Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.", + "title": "Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data", "year": 2015 }, { "doi": "10.1534/g3.115.018937", "pmc": "PMC4528330", "pubmed": "26109356", - "title": "Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.", + "title": "Gene Model Annotations for Drosophila melanogaster: The Rule-Benders", "year": 2015 }, { "doi": "10.1093/nar/gku1099", "pmc": "PMC4383921", "pubmed": "25398896", - "title": "FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.", + "title": "FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations", "year": 2014 }, { "doi": "10.1093/nar/gkt1092", "pmc": "PMC3964969", "pubmed": "24234449", - "title": "FlyBase 102--advanced approaches to interrogating FlyBase.", + "title": "FlyBase 102--advanced approaches to interrogating FlyBase", "year": 2013 }, { "doi": "10.1093/database/bas024", "pmc": "PMC3342516", "pubmed": "22554788", - "title": "Directly e-mailing authors of newly published papers encourages community curation.", + "title": "Directly e-mailing authors of newly published papers encourages community curation", "year": 2012 }, { "doi": "10.1093/nar/gkr1030", "pmc": "PMC3245098", "pubmed": "22127867", - "title": "FlyBase 101--the basics of navigating FlyBase.", + "title": "FlyBase 101--the basics of navigating FlyBase", "year": 2011 }, - { - "doi": "10.1093/nar/gkn788.", - "pmc": "PMC2686450", - "pubmed": "18948289", - "title": "FlyBase: enhancing Drosophila Gene Ontology annotations.", - "year": null - }, { "doi": "10.1093/nar/gkn788", "pmc": "PMC2686450", "pubmed": "18948289", - "title": "FlyBase: enhancing Drosophila Gene Ontology annotations.", + "title": "FlyBase: enhancing Drosophila Gene Ontology annotations", "year": 2008 }, { "doi": "10.1007/978-1-59745-583-1_3", "pmc": null, "pubmed": "18641940", - "title": "FlyBase : a database for the Drosophila research community.", + "title": "FlyBase : a database for the Drosophila research community", "year": 2008 }, { "doi": "10.1093/nar/gkm930", "pmc": "PMC2238994", "pubmed": "18160408", - "title": "FlyBase: integration and improvements to query tools.", + "title": "FlyBase: integration and improvements to query tools", "year": 2007 }, { "doi": "10.1093/nar/gkl827", "pmc": "PMC1669768", "pubmed": "17099233", - "title": "FlyBase: genomes by the dozen.", + "title": "FlyBase: genomes by the dozen", "year": 2006 }, { "doi": "10.1093/nar/gkj068", "pmc": "PMC1347431", "pubmed": "16381917", - "title": "FlyBase: anatomical data, images and queries.", + "title": "FlyBase: anatomical data, images and queries", "year": 2006 }, { "doi": "10.1093/nar/gki046", "pmc": "PMC540000", "pubmed": "15608223", - "title": "FlyBase: genes and gene models.", + "title": "FlyBase: genes and gene models", "year": 2005 }, { "doi": "10.1093/nar/gkg094", "pmc": "PMC165541", "pubmed": "12519974", - "title": "The FlyBase database of the Drosophila genome projects and community literature.", + "title": "The FlyBase database of the Drosophila genome projects and community literature", "year": 2003 }, { "doi": "10.1093/nar/30.1.106", "pmc": "PMC99082", "pubmed": "11752267", - "title": "The FlyBase database of the Drosophila genome projects and community literature.", + "title": "The FlyBase database of the Drosophila genome projects and community literature", "year": 2002 + }, + { + "doi": "10.1093/nar/gkn788.", + "pmc": null, + "pubmed": null, + "title": "FlyBase: enhancing Drosophila Gene Ontology annotations.", + "year": null } ], "synonyms": [ @@ -17328,6 +19271,15 @@ }, "name": "FlyMine Chromosome Band", "preferred_prefix": "flymine.chromosome", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/flymine:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -17380,56 +19332,66 @@ "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "FMA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fma:$1" + } + ], "publications": [ { "doi": "10.1016/j.artmed.2016.04.003", "pmc": "PMC4915823", "pubmed": "27235801", - "title": "From frames to OWL2: Converting the Foundational Model of Anatomy.", + "title": "From frames to OWL2: Converting the Foundational Model of Anatomy", "year": 2016 }, { "doi": "10.1016/j.websem.2007.12.001", "pmc": "PMC2500209", "pubmed": "18688289", - "title": "Translating the Foundational Model of Anatomy into OWL.", + "title": "Translating the Foundational Model of Anatomy into OWL", "year": 2008 }, { "doi": "10.1016/j.websem.2006.05.007", "pmc": "PMC2270940", "pubmed": "18360535", - "title": "The foundational model of anatomy in OWL: Experience and perspectives.", + "title": "The foundational model of anatomy in OWL: Experience and perspectives", "year": 2006 }, { "doi": "10.1109/iembs.2004.1404513", "pmc": null, "pubmed": "17271570", - "title": "The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions.", + "title": "The foundational model of anatomy: a template for the symbolic representation of multi-scale physiological functions", "year": 2004 }, { "doi": null, "pmc": "PMC1560487", "pubmed": "16779026", - "title": "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study.", + "title": "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study", "year": 2005 }, { "doi": "10.1016/j.jbi.2003.11.007", "pmc": null, "pubmed": "14759820", - "title": "A reference ontology for biomedical informatics: the Foundational Model of Anatomy.", + "title": "A reference ontology for biomedical informatics: the Foundational Model of Anatomy", "year": 2003 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FMA_$1", "repository": "https://bitbucket.org/uwsig/fma", "synonyms": [ "FMAID", "FMA_RETIRED" ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1", + "uri_format": "http://purl.org/sig/ont/fma/fma$1", "version": "2020-04-13" }, "foaf": { @@ -17497,22 +19459,32 @@ "name": "Food-Biomarker Ontology", "pattern": "^\\d{4,6}$", "preferred_prefix": "FOBI", + "providers": [ + { + "code": "fobi.legacy", + "description": "An incorrect encoding of OBO purls", + "homepage": "http://purl.obolibrary.org/obo/fobi", + "name": "FOBI Hash", + "uri_format": "http://purl.obolibrary.org/obo/fobi.owl#FOBI:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btab626", "pmc": null, "pubmed": "34601570", - "title": "The fobitools framework: the first steps towards food enrichment analysis.", + "title": "The fobitools framework: the first steps towards food enrichment analysis", "year": 2021 }, { "doi": "10.1093/databa/baaa033", "pmc": "PMC7298227", "pubmed": "32556148", - "title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data.", + "title": "FOBI: an ontology to represent food intake data and associate it with metabolomic data", "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FOBI_$1", "repository": "https://github.com/pcastellanoescuder/FoodBiomarkerOntology", "uri_format": "http://purl.obolibrary.org/obo/FOBI_$1" }, @@ -17567,7 +19539,7 @@ "mappings": { "agroportal": "FOODEX2" }, - "name": "Food classification and description system", + "name": "Food Classification and Description System", "preferred_prefix": "foodex2", "uri_format": "http://data.food.gov.uk/codes/foodtype/id/$1" }, @@ -17632,20 +19604,21 @@ "doi": "10.1038/s41538-018-0032-6", "pmc": "PMC6550238", "pubmed": "31304272", - "title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.", + "title": "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration", "year": 2018 }, { "doi": "10.3389/fmicb.2017.01068", "pmc": "PMC5483436", "pubmed": "28694792", - "title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.", + "title": "Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance", "year": 2017 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FOODON_$1", "repository": "https://github.com/FoodOntology/foodon", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1", - "version": "2022-02-01" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1", + "version": "2023-05-03" }, "fossilworks.journal": { "contributor": { @@ -17716,7 +19689,7 @@ "ro", "uberon" ], - "description": "None", + "description": "These are the terms that are improted for FOVT to describe vertebrate traits.", "download_obo": "http://purl.obolibrary.org/obo/fovt.obo", "download_owl": "http://purl.obolibrary.org/obo/fovt.owl", "example": "0000009", @@ -17736,9 +19709,10 @@ "name": "FuTRES Ontology of Vertebrate Traits", "pattern": "^\\d{7}$", "preferred_prefix": "FOVT", + "rdf_uri_format": "http://purl.obolibrary.org/obo/FOVT_$1", "repository": "https://github.com/futres/fovt", "uri_format": "http://purl.obolibrary.org/obo/FOVT_$1", - "version": "2021-11-10" + "version": "2023-05-31" }, "fplx": { "contact": { @@ -17768,7 +19742,7 @@ "doi": "10.1186/s12859-018-2211-5", "pmc": "PMC6022344", "pubmed": "29954318", - "title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.", + "title": "FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining", "year": 2018 } ], @@ -17861,6 +19835,22 @@ "twitter": "sparontologies", "uri_format": "http://purl.org/vocab/frbr/core#$1" }, + "frbrer": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)", + "download_rdf": "http://iflastandards.info/ns/fr/frbr/frbrer.jsonld", + "example": "1001", + "homepage": "https://www.iflastandards.info/fr/frbr/frbrer", + "name": "Functional Requirements for Bibliographic Records Entity-Relationship Model", + "part_of": "frbr", + "preferred_prefix": "frbrer", + "uri_format": "http://iflastandards.info/ns/fr/frbr/frbrer/$1" + }, "fsnp": { "description": "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification.", "example": "rs17852708", @@ -17878,6 +19868,15 @@ "name": "F-SNP", "pattern": "^rs\\d+$", "preferred_prefix": "fsnp", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/fsnp:$1" + } + ], "uri_format": "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1" }, "ftt": { @@ -18015,22 +20014,29 @@ "doi": "10.1016/j.fgb.2016.04.002", "pmc": null, "pubmed": "27259951", - "title": "Database whiplash, crowdsourcing, and FungiDB.", + "title": "Database whiplash, crowdsourcing, and FungiDB", "year": 2016 }, { "doi": "10.1128/ec.00083-14", "pmc": "PMC4135733", "pubmed": "24813190", - "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus.", + "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus", "year": 2014 }, { "doi": "10.1093/nar/gkr918", "pmc": "PMC3245123", "pubmed": "22064857", - "title": "FungiDB: an integrated functional genomics database for fungi.", + "title": "FungiDB: an integrated functional genomics database for fungi", "year": 2011 + }, + { + "doi": "10.1128/EC.00083-14", + "pmc": null, + "pubmed": null, + "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus.", + "year": null } ], "twitter": "fungidb", @@ -18126,6 +20132,7 @@ "phylogenetics" ], "license": "CC-BY-4.0", + "logo": "https://github.com/pombase/website/blob/master/src/assets/FYPO_logo_tiny.png", "mappings": { "aberowl": "FYPO", "biocontext": "FYPO", @@ -18145,13 +20152,14 @@ "doi": "10.1093/bioinformatics/btt266", "pmc": "PMC3694669", "pubmed": "23658422", - "title": "FYPO: the fission yeast phenotype ontology.", + "title": "FYPO: the fission yeast phenotype ontology", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", "repository": "https://github.com/pombase/fypo", "uri_format": "http://purl.obolibrary.org/obo/FYPO_$1", - "version": "2022-07-14" + "version": "2023-06-21" }, "ga4ghdos": { "description": "Assists in resolving data across cloud resources.", @@ -18186,17 +20194,48 @@ "name": "Network of Different Plant Genomic Research Projects", "pattern": "^\\w+$", "preferred_prefix": "gabi", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gabi:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn611", "pmc": "PMC2686513", "pubmed": "18812395", - "title": "GabiPD: the GABI primary database--a plant integrative 'omics' database.", + "title": "GabiPD: the GABI primary database--a plant integrative 'omics' database", "year": 2008 } ], "uri_format": "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject" }, + "gainesville.core": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations", + "download_owl": "http://ontologies.makolab.com/gc06/gc.owl", + "example": "Aromatic", + "homepage": "http://ontologies.makolab.com/gc06/gc.html", + "keywords": [ + "ontology" + ], + "license": "CC-BY-3.0", + "name": "Gainesville Core Ontology", + "preferred_prefix": "gainesville.core", + "references": [ + "http://ontologies.makolab.com/gc/" + ], + "uri_format": "http://purl.org/gc/$1" + }, "galen": { "comment": "I really tried, but could not figure out what GALEN stands for", "contact": { @@ -18290,6 +20329,7 @@ "name": "Gazetteer", "pattern": "^\\d{8}$", "preferred_prefix": "GAZ", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GAZ_$1", "repository": "https://github.com/EnvironmentOntology/gaz", "uri_format": "http://purl.obolibrary.org/obo/GAZ_$1" }, @@ -18331,7 +20371,7 @@ "doi": "10.1371/journal.pone.0102623", "pmc": "PMC4123864", "pubmed": "25099149", - "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.", + "title": "The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet", "year": 2014 } ], @@ -18473,6 +20513,7 @@ "name": "Genomics Cohorts Knowledge Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GECKO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "repository": "https://github.com/IHCC-cohorts/GECKO", "uri_format": "http://purl.obolibrary.org/obo/GECKO_$1", "version": "2021-01-18" @@ -18493,9 +20534,15 @@ "description": "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts.", "example": "627", "homepage": "https://www.eionet.europa.eu/gemet/en/themes/", + "keywords": [ + "biodiversity", + "ecology", + "environmental science" + ], "mappings": { "agroportal": "GEMET", - "bartoc": "16" + "bartoc": "16", + "fairsharing": "FAIRsharing.9091d9" }, "name": "General Multilingual Environmental Thesaurus", "pattern": "^\\d+$", @@ -18523,19 +20570,28 @@ "name": "Genatlas", "pattern": "^\\w+$", "preferred_prefix": "genatlas", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genatlas:$1" + } + ], "publications": [ { "doi": "10.1016/s0764-4469(99)80021-3", "pmc": null, "pubmed": "9835018", - "title": "Genatlas database, genes and development defects.", + "title": "Genatlas database, genes and development defects", "year": 1998 }, { "doi": "10.1006/mgme.1999.2867", "pmc": null, "pubmed": "10444337", - "title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database.", + "title": "Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database", "year": 1999 } ], @@ -18574,103 +20630,112 @@ }, "name": "GenBank", "preferred_prefix": "genbank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genbank:$1" + } + ], "publications": [ { "doi": "10.1186/s12859-020-3537-3", "pmc": "PMC7245624", "pubmed": "32448124", - "title": "VADR: validation and annotation of virus sequence submissions to GenBank.", + "title": "VADR: validation and annotation of virus sequence submissions to GenBank", "year": 2020 }, { "doi": "10.1093/nar/gkz956", "pmc": "PMC7145611", "pubmed": "31665464", - "title": "GenBank.", + "title": "GenBank", "year": 2020 }, { "doi": "10.1093/nar/gky989", "pmc": "PMC6323954", "pubmed": "30365038", - "title": "GenBank.", + "title": "GenBank", "year": 2019 }, { "doi": "10.1093/nar/gkx1094", "pmc": "PMC5753231", "pubmed": "29140468", - "title": "GenBank.", + "title": "GenBank", "year": 2018 }, { "doi": "10.1093/nar/gkw1070", "pmc": "PMC5210553", "pubmed": "27899564", - "title": "GenBank.", + "title": "GenBank", "year": 2016 }, { "doi": "10.1093/nar/gkv1276", "pmc": "PMC4702903", "pubmed": "26590407", - "title": "GenBank.", + "title": "GenBank", "year": 2015 }, { "doi": "10.1093/nar/gku1216", "pmc": "PMC4383990", "pubmed": "25414350", - "title": "GenBank.", + "title": "GenBank", "year": 2014 }, { "doi": "10.1093/nar/gkt1030", "pmc": "PMC3965104", "pubmed": "24217914", - "title": "GenBank.", + "title": "GenBank", "year": 2013 }, { "doi": "10.1093/nar/gks1195", "pmc": "PMC3531190", "pubmed": "23193287", - "title": "GenBank.", + "title": "GenBank", "year": 2012 }, { "doi": "10.1093/nar/gkr1202", "pmc": "PMC3245039", "pubmed": "22144687", - "title": "GenBank.", + "title": "GenBank", "year": 2011 }, { "doi": "10.1093/nar/gkq1079", "pmc": "PMC3013681", "pubmed": "21071399", - "title": "GenBank.", + "title": "GenBank", "year": 2010 }, { "doi": "10.1093/nar/gkn723", "pmc": "PMC2686462", "pubmed": "18940867", - "title": "GenBank.", + "title": "GenBank", "year": 2008 }, { "doi": "10.1093/nar/gkm929", "pmc": "PMC2238942", "pubmed": "18073190", - "title": "GenBank.", + "title": "GenBank", "year": 2007 }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], @@ -18691,6 +20756,15 @@ }, "name": "Genomic Distribution of structural Superfamilies", "preferred_prefix": "gendis", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gendis:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -18727,62 +20801,78 @@ "name": "GeneCards", "pattern": "^[A-Za-z-0-9_]+(\\@)?$", "preferred_prefix": "genecards", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genecards:$1" + } + ], "publications": [ { "doi": "10.1016/s0168-9525(97)01103-7", "pmc": null, "pubmed": "9097728", - "title": "GeneCards: integrating information about genes, proteins and diseases.", + "title": "GeneCards: integrating information about genes, proteins and diseases", "year": 1997 }, { "doi": "10.1186/s12864-016-2722-2", "pmc": "PMC4928145", "pubmed": "27357693", - "title": "VarElect: the phenotype-based variation prioritizer of the GeneCards Suite.", + "title": "VarElect: the phenotype-based variation prioritizer of the GeneCards Suite", "year": 2016 }, { "doi": "10.1002/cpbi.5", "pmc": null, "pubmed": "27322403", - "title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.", + "title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses", "year": 2016 }, { "doi": "10.1093/database/baw030", "pmc": "PMC4820835", "pubmed": "27048349", - "title": "Genic insights from integrated human proteomics in GeneCards.", + "title": "Genic insights from integrated human proteomics in GeneCards", "year": 2016 }, { "doi": "10.1089/omi.2015.0168", "pmc": "PMC4799705", "pubmed": "26983021", - "title": "GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.", + "title": "GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data", "year": 2016 }, { "doi": "10.1093/database/bav006", "pmc": "PMC4343183", "pubmed": "25725062", - "title": "PathCards: multi-source consolidation of human biological pathways.", + "title": "PathCards: multi-source consolidation of human biological pathways", "year": 2015 }, { "doi": "10.1093/database/baq020", "pmc": "PMC2938269", "pubmed": "20689021", - "title": "GeneCards Version 3: the human gene integrator.", + "title": "GeneCards Version 3: the human gene integrator", "year": 2010 }, { "doi": "10.1093/bioinformatics/18.11.1542", "pmc": null, "pubmed": "12424129", - "title": "GeneCards 2002: towards a complete, object-oriented, human gene compendium.", + "title": "GeneCards 2002: towards a complete, object-oriented, human gene compendium", "year": 2002 + }, + { + "doi": "10.1016/S0168-9525(97)01103-7", + "pmc": null, + "pubmed": null, + "title": "GeneCards: integrating information about genes, proteins and diseases.", + "year": null } ], "uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1" @@ -18798,7 +20888,16 @@ "prefixcommons": "geneannot" }, "name": "GeneAnnot: Microarray Gene Annotation", - "preferred_prefix": "genecards.geneannot" + "preferred_prefix": "genecards.geneannot", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/geneannot:$1" + } + ] }, "genecards.geneloc": { "description": "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources", @@ -18812,6 +20911,15 @@ }, "name": "Gene Location", "preferred_prefix": "genecards.geneloc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/geneloc:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -18832,6 +20940,15 @@ }, "name": "Gene Normal Tissue Expression", "preferred_prefix": "genecards.genenote", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genenote:$1" + } + ], "uri_format": "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes" }, "genedb": { @@ -18859,12 +20976,21 @@ "name": "GeneDB", "pattern": "^[\\w\\d\\.-]*$", "preferred_prefix": "genedb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genedb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh007", "pmc": "PMC308742", "pubmed": "14681429", - "title": "GeneDB: a resource for prokaryotic and eukaryotic organisms.", + "title": "GeneDB: a resource for prokaryotic and eukaryotic organisms", "year": 2004 } ], @@ -18891,12 +21017,21 @@ "name": "GeneFarm", "pattern": "^\\d+$", "preferred_prefix": "genefarm", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genefarm:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gki115", "pmc": "PMC540069", "pubmed": "15608279", - "title": "GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.", + "title": "GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts", "year": 2005 } ], @@ -18938,6 +21073,7 @@ "name": "Genomic Epidemiology Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GENEPIO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GENEPIO_$1", "repository": "https://github.com/GenEpiO/genepio", "uri_format": "http://purl.obolibrary.org/obo/GENEPIO_$1", "version": "2022-02-06" @@ -18961,19 +21097,28 @@ "name": "GeneTree", "pattern": "^ENSGT\\d+$", "preferred_prefix": "genetree", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genetree:$1" + } + ], "publications": [ { "doi": "10.1093/database/bav096", "pmc": "PMC4761110", "pubmed": "26896847", - "title": "Ensembl comparative genomics resources.", + "title": "Ensembl comparative genomics resources", "year": 2016 }, { "doi": "10.1093/nar/gkj133", "pmc": "PMC1347495", "pubmed": "16381931", - "title": "Ensembl 2006.", + "title": "Ensembl 2006", "year": 2006 } ], @@ -19003,28 +21148,28 @@ "doi": "10.1093/database/baw015", "pmc": "PMC4795929", "pubmed": "26989148", - "title": "Wikidata as a semantic framework for the Gene Wiki initiative.", + "title": "Wikidata as a semantic framework for the Gene Wiki initiative", "year": 2016 }, { "doi": "10.1093/nar/gkr925", "pmc": "PMC3245148", "pubmed": "22075991", - "title": "The Gene Wiki in 2011: community intelligence applied to human gene annotation.", + "title": "The Gene Wiki in 2011: community intelligence applied to human gene annotation", "year": 2011 }, { "doi": "10.1093/nar/gkp760", "pmc": "PMC2808918", "pubmed": "19755503", - "title": "The Gene Wiki: community intelligence applied to human gene annotation.", + "title": "The Gene Wiki: community intelligence applied to human gene annotation", "year": 2009 }, { "doi": "10.1371/journal.pbio.0060175", "pmc": "PMC2443188", "pubmed": "18613750", - "title": "A gene wiki for community annotation of gene function.", + "title": "A gene wiki for community annotation of gene function", "year": 2008 } ], @@ -19062,9 +21207,10 @@ "name": "Genotype Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "GENO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GENO_$1", "repository": "https://github.com/monarch-initiative/GENO-ontology", "uri_format": "http://purl.obolibrary.org/obo/GENO_$1", - "version": "2022-03-05" + "version": "2023-02-21" }, "genpept": { "description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.", @@ -19105,12 +21251,21 @@ ], "pattern": "^GenProp\\d+$", "preferred_prefix": "genprop", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/jcvi.genprop:$1" + } + ], "uri_format": "https://www.ebi.ac.uk/interpro/genomeproperties/#$1" }, "geo": { "banana_peel": "_", "description": "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval.", - "download_owl": "http://aber-owl.net/media/ontologies/GEO/4/geo.owl", + "download_owl": "http://aber-owl.net/media/ontologies/GEO/5/geo.owl", "example": "GDS1234", "homepage": "https://www.ncbi.nlm.nih.gov/geo/", "keywords": [ @@ -19140,33 +21295,42 @@ "name": "NCBI Gene Expression Omnibus", "pattern": "^G(PL|SM|SE|DS)\\d+$", "preferred_prefix": "geo", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/geo:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gks1193", "pmc": "PMC3531084", "pubmed": "23193258", - "title": "NCBI GEO: archive for functional genomics data sets--update.", + "title": "NCBI GEO: archive for functional genomics data sets--update", "year": 2012 }, { "doi": "10.1038/nbt1206-1471", "pmc": "PMC2270403", "pubmed": "17160034", - "title": "NCBI GEO standards and services for microarray data.", + "title": "NCBI GEO standards and services for microarray data", "year": 2006 }, { "doi": "10.1093/nar/30.1.207", "pmc": "PMC99122", "pubmed": "11752295", - "title": "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.", + "title": "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository", "year": 2002 }, { "doi": "10.1038/35001676", "pmc": null, "pubmed": "10693778", - "title": "One-stop shop for microarray data.", + "title": "One-stop shop for microarray data", "year": 2000 }, { @@ -19212,6 +21376,7 @@ "namespace_in_lui": true, "pattern": "^\\d{9}$", "preferred_prefix": "GEOGEO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GEO_$1", "repository": "https://github.com/ufbmi/geographical-entity-ontology", "uri_format": "http://purl.obolibrary.org/obo/GEO_$1", "version": "2016-03-26" @@ -19286,11 +21451,10 @@ "doi": "10.1186/s12859-014-0386-y", "pmc": "PMC4279962", "pubmed": "25490885", - "title": "Finding gene regulatory network candidates using the gene expression knowledge base.", + "title": "Finding gene regulatory network candidates using the gene expression knowledge base", "year": 2014 } - ], - "version": "2019-09-18" + ] }, "gfo": { "contact": { @@ -19357,12 +21521,21 @@ "name": "GiardiaDB", "pattern": "^\\w+$", "preferred_prefix": "giardiadb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/giardiadb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn631", "pmc": "PMC2686445", "pubmed": "18824479", - "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.", + "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis", "year": 2008 } ], @@ -19506,6 +21679,15 @@ }, "name": "GlycoMapsDB", "preferred_prefix": "glycomapsdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/glycomapsdb:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -19537,26 +21719,35 @@ "name": "GlycomeDB", "pattern": "^\\w+$", "preferred_prefix": "glycomedb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/glycomedb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkq1014", "pmc": "PMC3013643", "pubmed": "21045056", - "title": "GlycomeDB--a unified database for carbohydrate structures.", + "title": "GlycomeDB--a unified database for carbohydrate structures", "year": 2010 }, { "doi": "10.1093/glycob/cwp137", "pmc": null, "pubmed": "19759275", - "title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences.", + "title": "Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences", "year": 2009 }, { "doi": "10.1186/1471-2105-9-384", "pmc": "PMC2567997", "pubmed": "18803830", - "title": "GlycomeDB - integration of open-access carbohydrate structure databases.", + "title": "GlycomeDB - integration of open-access carbohydrate structure databases", "year": 2008 } ], @@ -19633,7 +21824,7 @@ "doi": "10.1093/nar/gky994", "pmc": "PMC6323918", "pubmed": "30357361", - "title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update).", + "title": "Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)", "year": 2019 } ], @@ -19670,18 +21861,18 @@ "preferred_prefix": "glygen", "publications": [ { - "doi": "cwz080", + "doi": "10.1093/glycob/cwz080", "pmc": "PMC7335483", "pubmed": "31616925", - "title": "GlyGen: Computational and Informatics Resources for Glycoscience.", - "year": null + "title": "GlyGen: Computational and Informatics Resources for Glycoscience", + "year": 2020 }, { - "doi": "10.1093/glycob/cwz080", - "pmc": "PMC7335483", - "pubmed": "31616925", + "doi": "cwz080", + "pmc": null, + "pubmed": null, "title": "GlyGen: Computational and Informatics Resources for Glycoscience.", - "year": 2020 + "year": null } ], "twitter": "gly_gen", @@ -19710,14 +21901,14 @@ "doi": "10.1093/glycob/cwx066", "pmc": "PMC5881658", "pubmed": "28922742", - "title": "GlyTouCan: an accessible glycan structure repository.", + "title": "GlyTouCan: an accessible glycan structure repository", "year": 2017 }, { "doi": "10.1093/nar/gkv1041", "pmc": "PMC4702779", "pubmed": "26476458", - "title": "GlyTouCan 1.0--The international glycan structure repository.", + "title": "GlyTouCan 1.0--The international glycan structure repository", "year": 2015 } ], @@ -19744,18 +21935,18 @@ "preferred_prefix": "gmd", "publications": [ { - "doi": "doi:10.1007/s11306-010-0198-7", + "doi": "10.1007/s11306-010-0198-7", "pmc": "PMC2874469", "pubmed": "20526350", "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles", - "year": null + "year": 2010 }, { - "doi": "10.1007/s11306-010-0198-7", - "pmc": "PMC2874469", - "pubmed": "20526350", - "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles.", - "year": 2010 + "doi": "doi:10.1007/s11306-010-0198-7", + "pmc": null, + "pubmed": null, + "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles", + "year": null } ], "uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx" @@ -19838,6 +22029,26 @@ "https://en.wikipedia.org/wiki/Gmelin_database" ] }, + "gnd": { + "description": "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners.", + "example": "117145750", + "homepage": "https://lobid.org/", + "keywords": [ + "culture", + "knowledge and information systems", + "social science" + ], + "mappings": { + "bartoc": "430", + "fairsharing": "FAIRsharing.8337e2", + "miriam": "gnd" + }, + "name": "Gemeinsame Normdatei", + "pattern": "^[0-9X\\-]+$", + "preferred_prefix": "gnd", + "twitter": "gndnet", + "uri_format": "https://lobid.org/gnd/$1" + }, "gno": { "contact": { "email": "nje5@georgetown.edu", @@ -19894,12 +22105,13 @@ "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "repository": "https://github.com/glygen-glycan-data/GNOme", "synonyms": [ "gnome" ], "uri_format": "http://purl.obolibrary.org/obo/GNO_$1", - "version": "1.10.0" + "version": "2023-05-08" }, "gnomad": { "contact": { @@ -19930,14 +22142,14 @@ "doi": "10.1038/s41586-020-2308-7", "pmc": "PMC7334197", "pubmed": "32461654", - "title": "The mutational constraint spectrum quantified from variation in 141,456 humans.", + "title": "The mutational constraint spectrum quantified from variation in 141,456 humans", "year": 2020 }, { "doi": "10.1038/s41586-020-2287-8", "pmc": "PMC7334194", "pubmed": "32461652", - "title": "A structural variation reference for medical and population genetics.", + "title": "A structural variation reference for medical and population genetics", "year": 2020 } ], @@ -19971,12 +22183,40 @@ "doi": "10.1093/database/bat058", "pmc": "PMC3746681", "pubmed": "23959375", - "title": "GnpIS: an information system to integrate genetic and genomic data from plants and fungi.", + "title": "GnpIS: an information system to integrate genetic and genomic data from plants and fungi", "year": 2013 } ], "uri_format": "https://urgi.versailles.inra.fr/gnpis/#result/term=$1" }, + "gnps.task": { + "contact": { + "email": "mingxun.wang@cs.ucr.edu", + "github": "mwang87", + "name": "Mingxun Wang", + "orcid": "0000-0001-7647-6097" + }, + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "description": "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)", + "example": "4b848c342a4f4abc871bdf8a09a60807", + "github_request_issue": 833, + "homepage": "https://gnps.ucsd.edu/", + "name": "Global Natural Products Social Molecular Networking Task", + "pattern": "^[a-f0-9]+$", + "preferred_prefix": "gnps.task", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1" + }, "go": { "appears_in": [ "agro", @@ -20019,6 +22259,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://obofoundry.org/images/go_logo.png", "mappings": { "aberowl": "GO", "agroportal": "GO", @@ -20036,9 +22277,11 @@ "ols": "go", "ontobee": "GO", "prefixcommons": "go", + "re3data": "r3d100014165", "uniprot": "DB-0037", "wikidata": "P686" }, + "mastodon": "go@genomic.social", "name": "Gene Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", @@ -20058,6 +22301,13 @@ "name": "GO through PANTHER", "uri_format": "http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/go:$1" + }, { "code": "go_site", "description": "A non-PURL link through the GO site", @@ -20099,66 +22349,67 @@ "doi": "10.1093/nar/gkaa1113", "pmc": "PMC7779012", "pubmed": "33290552", - "title": "The Gene Ontology resource: enriching a GOld mine.", + "title": "The Gene Ontology resource: enriching a GOld mine", "year": 2021 }, { "doi": "10.1093/nar/gky1055", "pmc": "PMC6323945", "pubmed": "30395331", - "title": "The Gene Ontology Resource: 20 years and still GOing strong.", + "title": "The Gene Ontology Resource: 20 years and still GOing strong", "year": 2019 }, { "doi": "10.1093/nar/gku1179", "pmc": "PMC4383973", "pubmed": "25428369", - "title": "Gene Ontology Consortium: going forward.", + "title": "Gene Ontology Consortium: going forward", "year": 2014 }, { "doi": "10.1186/1471-2164-14-513", "pmc": "PMC3733925", "pubmed": "23895341", - "title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.", + "title": "Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology", "year": 2013 }, { "doi": "10.1093/nar/gks1050", "pmc": "PMC3531070", "pubmed": "23161678", - "title": "Gene Ontology annotations and resources.", + "title": "Gene Ontology annotations and resources", "year": 2012 }, { "doi": "10.1093/nar/gkr1028", "pmc": "PMC3245151", "pubmed": "22102568", - "title": "The Gene Ontology: enhancements for 2011.", + "title": "The Gene Ontology: enhancements for 2011", "year": 2011 }, { "doi": "10.1093/nar/gkp1018", "pmc": "PMC2808930", "pubmed": "19920128", - "title": "The Gene Ontology in 2010: extensions and refinements.", + "title": "The Gene Ontology in 2010: extensions and refinements", "year": 2009 }, { "doi": "10.1093/nar/gkh036", "pmc": "PMC308770", "pubmed": "14681407", - "title": "The Gene Ontology (GO) database and informatics resource.", + "title": "The Gene Ontology (GO) database and informatics resource", "year": 2004 }, { "doi": "10.1038/75556", "pmc": "PMC3037419", "pubmed": "10802651", - "title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.", + "title": "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium", "year": 2000 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/GO_$1", "repository": "https://github.com/geneontology/go-ontology", "synonyms": [ "gobp", @@ -20170,7 +22421,7 @@ ], "twitter": "news4go", "uri_format": "http://amigo.geneontology.org/amigo/term/GO:$1", - "version": "2022-12-04" + "version": "2023-06-11" }, "go.gpi": { "contributor": { @@ -20277,20 +22528,29 @@ "name": "Gene Ontology Annotation Database", "pattern": "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$", "preferred_prefix": "goa", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/goa:$1" + } + ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gku1113", "pmc": "PMC4383930", "pubmed": "25378336", - "title": "The GOA database: gene Ontology annotation updates for 2015.", + "title": "The GOA database: gene Ontology annotation updates for 2015", "year": 2014 }, { "doi": "10.1093/nar/gkn803", "pmc": "PMC2686469", "pubmed": "18957448", - "title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource.", + "title": "The GOA database in 2009--an integrated Gene Ontology Annotation resource", "year": 2008 } ], @@ -20313,6 +22573,7 @@ "name": "GO Chemicals", "pattern": "^\\d+$", "preferred_prefix": "GOCHE", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GOCHE_$1", "references": [ "https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638472847049400", "https://github.com/geneontology/go-ontology/issues/19535" @@ -20359,55 +22620,64 @@ "name": "Genomes Online Database", "pattern": "^[A-Z][a-z][0-9]+$", "preferred_prefix": "gold", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gold:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkaa983", "pmc": "PMC7778979", "pubmed": "33152092", - "title": "Genomes OnLine Database (GOLD) v.8: overview and updates.", + "title": "Genomes OnLine Database (GOLD) v.8: overview and updates", "year": 2021 }, { "doi": "10.1093/nar/gky977", "pmc": "PMC6323969", "pubmed": "30357420", - "title": "Genomes OnLine database (GOLD) v.7: updates and new features.", + "title": "Genomes OnLine database (GOLD) v.7: updates and new features", "year": 2019 }, { "doi": "10.1093/nar/gkp848", "pmc": "PMC2808860", "pubmed": "19914934", - "title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.", + "title": "The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata", "year": 2009 }, { "doi": "10.1093/nar/gkm884", "pmc": "PMC2238992", "pubmed": "17981842", - "title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata.", + "title": "The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata", "year": 2007 }, - { - "doi": "11125068", - "pmc": "PMC29859", - "pubmed": "11125068", - "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.", - "year": null - }, { "doi": "10.1093/nar/29.1.126", "pmc": "PMC29859", "pubmed": "11125068", - "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.", + "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide", "year": 2001 }, { "doi": "10.1093/bioinformatics/15.9.773", "pmc": null, "pubmed": "10498782", - "title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide.", + "title": "Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide", "year": 1999 + }, + { + "doi": "11125068", + "pmc": null, + "pubmed": null, + "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.", + "year": null } ], "uri_format": "https://gold.jgi.doe.gov/resolver?id=$1" @@ -20459,6 +22729,7 @@ "name": "IUPAC Gold Book Compendium of Chemical Terminology", "pattern": "^[A-Z]{1,2}\\d{5}$", "preferred_prefix": "goldbook", + "rdf_uri_format": "http://dx.doi.org/10.1351/goldbook.$1", "uri_format": "https://goldbook.iupac.org/terms/view/$1" }, "google.book": { @@ -20553,7 +22824,8 @@ "name": "Legacy OBO", "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" } - ] + ], + "uri_format": "http://purl.obolibrary.org/obo/GOREL_$1" }, "gpcrdb": { "contact": { @@ -20582,74 +22854,107 @@ "name": "G protein-coupled receptor database", "pattern": "^\\w+$", "preferred_prefix": "gpcrdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gpcrdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/26.1.275", "pmc": "PMC147194", "pubmed": "9399852", - "title": "GPCRDB: an information system for G protein-coupled receptors.", + "title": "GPCRDB: an information system for G protein-coupled receptors", "year": 1998 }, { "doi": "10.1093/nar/gkaa1080", "pmc": "PMC7778909", "pubmed": "33270898", - "title": "GPCRdb in 2021: integrating GPCR sequence, structure and function.", + "title": "GPCRdb in 2021: integrating GPCR sequence, structure and function", "year": 2021 }, { "doi": "10.1093/nar/gkx1109", "pmc": "PMC5753179", "pubmed": "29155946", - "title": "GPCRdb in 2018: adding GPCR structure models and ligands.", + "title": "GPCRdb in 2018: adding GPCR structure models and ligands", "year": 2018 }, { "doi": "10.1111/bph.13509", "pmc": "PMC4919580", "pubmed": "27155948", - "title": "GPCRdb: the G protein-coupled receptor database - an introduction.", + "title": "GPCRdb: the G protein-coupled receptor database - an introduction", "year": 2016 }, { "doi": "10.1093/nar/gkv1178", "pmc": "PMC4702843", "pubmed": "26582914", - "title": "GPCRdb: an information system for G protein-coupled receptors.", + "title": "GPCRdb: an information system for G protein-coupled receptors", "year": 2015 }, { "doi": "10.1093/nar/gkt1255", "pmc": "PMC3965068", "pubmed": "24304901", - "title": "GPCRDB: an information system for G protein-coupled receptors.", + "title": "GPCRDB: an information system for G protein-coupled receptors", "year": 2013 }, { "doi": "10.1093/nar/gkq1009", "pmc": "PMC3013641", "pubmed": "21045054", - "title": "GPCRDB: information system for G protein-coupled receptors.", + "title": "GPCRDB: information system for G protein-coupled receptors", "year": 2010 }, { "doi": "10.1093/nar/gkg103", "pmc": "PMC165550", "pubmed": "12520006", - "title": "GPCRDB information system for G protein-coupled receptors.", + "title": "GPCRDB information system for G protein-coupled receptors", "year": 2003 }, { "doi": "10.1093/nar/29.1.346", "pmc": "PMC29816", "pubmed": "11125133", - "title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.", + "title": "Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems", "year": 2001 } ], "twitter": "gpcrdb", "uri_format": "https://gpcrdb.org/protein/$1" }, + "gpcrnava": { + "description": "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.", + "example": "1150", + "homepage": "http://nava.liacs.nl/", + "keywords": [ + "pathway", + "protein" + ], + "mappings": { + "prefixcommons": "gnd" + }, + "name": "GPCR Natural Variants database", + "preferred_prefix": "gpcrnava", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gnd:$1" + } + ], + "uri_format": "http://nava.liacs.nl/cgi-bin/nava.py?id=$1" + }, "gpmdb": { "description": "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns.", "example": "GPM32310002988", @@ -20681,7 +22986,7 @@ "doi": "10.1021/pr049882h", "pmc": null, "pubmed": "15595733", - "title": "Open source system for analyzing, validating, and storing protein identification data.", + "title": "Open source system for analyzing, validating, and storing protein identification data", "year": 2004 } ], @@ -20763,6 +23068,16 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "GRO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gramene.po:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/GRO_$1", "synonyms": [ "cpga", "gro-cpga" @@ -20885,13 +23200,29 @@ "name": "16S rRNA gene database", "pattern": "^\\d+$", "preferred_prefix": "greengenes", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/greengenes:$1" + } + ], "publications": [ { "doi": "10.1128/aem.03006-05", "pmc": "PMC1489311", "pubmed": "16820507", - "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.", + "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB", "year": 2006 + }, + { + "doi": "10.1128/AEM.03006-05", + "pmc": null, + "pubmed": null, + "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.", + "year": null } ], "uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1" @@ -20928,6 +23259,15 @@ }, "name": "Germplasm Resources Information Network", "preferred_prefix": "grin", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/grin:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -20993,6 +23333,15 @@ "name": "G-Rich Sequences Database", "pattern": "^\\d+$", "preferred_prefix": "grsdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/grsdb:$1" + } + ], "uri_format": "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1" }, "gsfa": { @@ -21048,6 +23397,7 @@ "namespace_in_lui": true, "pattern": "^\\d{6}$", "preferred_prefix": "GSSO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "repository": "https://github.com/Superraptor/GSSO", "uri_format": "http://purl.obolibrary.org/obo/GSSO_$1", "version": "2.0.5" @@ -21113,15 +23463,22 @@ "doi": "10.1242/dev.063594", "pmc": "PMC3188593", "pubmed": "21652655", - "title": "The GUDMAP database--an online resource for genitourinary research.", + "title": "The GUDMAP database--an online resource for genitourinary research", "year": 2011 }, { "doi": "10.1681/asn.2007101078", "pmc": null, "pubmed": "18287559", - "title": "GUDMAP: the genitourinary developmental molecular anatomy project.", + "title": "GUDMAP: the genitourinary developmental molecular anatomy project", "year": 2008 + }, + { + "doi": "10.1681/ASN.2007101078", + "pmc": null, + "pubmed": null, + "title": "GUDMAP: the genitourinary developmental molecular anatomy project.", + "year": null } ], "twitter": "GUDMAP", @@ -21172,6 +23529,15 @@ "name": "GWAS Central Study", "pattern": "^HGVST\\d+$", "preferred_prefix": "gwascentral.study", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hgvbase:$1" + } + ], "uri_format": "https://www.gwascentral.org/study/$1" }, "gxa.expt": { @@ -21246,6 +23612,7 @@ }, "name": "Habronattus courtship", "preferred_prefix": "HABRONATTUS", + "rdf_uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1", "uri_format": "http://purl.obolibrary.org/obo/HABRONATTUS_$1" }, "hagr.genage": { @@ -21262,12 +23629,21 @@ }, "name": "The Ageing Gene Database", "preferred_prefix": "hagr.genage", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/genage:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gks1155", "pmc": "PMC3531213", "pubmed": "23193293", - "title": "Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing.", + "title": "Human Ageing Genomic Resources: integrated databases and tools for the biology and genetics of ageing", "year": 2012 } ], @@ -21294,12 +23670,21 @@ }, "name": "The Dietary Restriction Gene Database", "preferred_prefix": "hagr.gendr", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/gendr:$1" + } + ], "publications": [ { "doi": "10.1371/journal.pgen.1002834", "pmc": "PMC3415404", "pubmed": "22912585", - "title": "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes.", + "title": "Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes", "year": 2012 } ], @@ -21338,19 +23723,28 @@ "name": "High-quality Automated and Manual Annotation of microbial Proteomes", "pattern": "^MF_\\d+$", "preferred_prefix": "hamap", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hamap:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gku1002", "pmc": "PMC4383873", "pubmed": "25348399", - "title": "HAMAP in 2015: updates to the protein family classification and annotation system.", + "title": "HAMAP in 2015: updates to the protein family classification and annotation system", "year": 2014 }, { "doi": "10.1093/nar/gks1157", "pmc": "PMC3531088", "pubmed": "23193261", - "title": "HAMAP in 2013, new developments in the protein family classification and annotation system.", + "title": "HAMAP in 2013, new developments in the protein family classification and annotation system", "year": 2012 } ], @@ -21395,18 +23789,28 @@ ], "pattern": "^\\d{4}$", "preferred_prefix": "HANCESTRO", + "providers": [ + { + "code": "legacy", + "description": "Legacy URI", + "homepage": "http://www.ebi.ac.uk/ancestro", + "name": "Legacy", + "uri_format": "http://www.ebi.ac.uk/ancestro/ancestro_$1" + } + ], "publications": [ { "doi": "10.1186/s13059-018-1396-2", "pmc": "PMC5815218", "pubmed": "29448949", - "title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog.", + "title": "A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog", "year": 2018 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", "repository": "https://github.com/EBISPOT/ancestro", "uri_format": "http://purl.obolibrary.org/obo/HANCESTRO_$1", - "version": "2.6" + "version": "2023-06-20" }, "hao": { "contact": { @@ -21444,13 +23848,14 @@ "doi": "10.1371/journal.pone.0015991", "pmc": "PMC3012123", "pubmed": "21209921", - "title": "A gross anatomy ontology for hymenoptera.", + "title": "A gross anatomy ontology for hymenoptera", "year": 2010 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "repository": "https://github.com/hymao/hao", "uri_format": "http://purl.obolibrary.org/obo/HAO_$1", - "version": "2021-03-05" + "version": "2023-06-01" }, "hathitrust": { "contributor": { @@ -21502,6 +23907,15 @@ }, "name": "A Database of Human Hemoglobin Variants and Thalassemias", "preferred_prefix": "hbvar", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hbvar:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -21553,7 +23967,7 @@ }, "hcao": { "description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.", - "download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2022-12-16/hcao.owl", + "download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl", "homepage": "https://www.humancellatlas.org", "keywords": [ "ontology" @@ -21563,8 +23977,7 @@ }, "name": "Human Cell Atlas Ontology", "no_own_terms": true, - "preferred_prefix": "hcao", - "version": "2022-12-16" + "preferred_prefix": "hcao" }, "hcpcs": { "contact": { @@ -21613,8 +24026,44 @@ "name": "Hepatitis C Virus Database Project", "pattern": "^M\\d{5}$", "preferred_prefix": "hcvdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hcv:$1" + } + ], "uri_format": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1" }, + "hdl": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)", + "example": "2381/12775", + "example_extras": [ + "391/00-0000-0000-0009-3C7E-F" + ], + "homepage": "https://www.handle.net/", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "fairsharing": "FAIRsharing.0b7e54" + }, + "name": "Handle", + "pattern": "^\\d+/.+$", + "preferred_prefix": "hdl", + "synonyms": [ + "handle" + ], + "uri_format": "http://hdl.handle.net/$1" + }, "hdr": { "description": "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders.", "example": "63", @@ -21631,8 +24080,60 @@ "name": "Homeodomain Research", "pattern": "^\\d+$", "preferred_prefix": "hdr", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hdr:$1" + } + ], "uri_format": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1" }, + "hepro": { + "contact": { + "email": "paul.fabry@usherbrooke.ca", + "github": "pfabry", + "name": "Paul Fabry", + "orcid": "0000-0002-3336-2476" + }, + "contributor": { + "email": "paul.fabry@usherbrooke.ca", + "github": "pfabry", + "name": "Paul Fabry", + "orcid": "0000-0002-3336-2476" + }, + "description": "HEPRO is an ontology of informational entities and processes related to health procedures and health activities.", + "download_json": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.json", + "download_owl": "https://github.com/OpenLHS/HEPRO/raw/main/HEPRO.owl", + "example": "0000001", + "github_request_issue": 810, + "homepage": "https://openlhs.github.io/HEPRO/", + "keywords": [ + "ontology" + ], + "license": "CC-BY-4.0", + "name": "Health Procedure Ontology", + "owners": [ + { + "name": "Université de Sherbrooke", + "partnered": false, + "ror": "00kybxq39", + "wikidata": null + } + ], + "pattern": "^\\d{7}$", + "preferred_prefix": "HEPRO", + "repository": "https://github.com/OpenLHS/HEPRO", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "http://purl.obolibrary.org/obo/HEPRO_$1" + }, "hesa": { "contributor": { "email": "cthoyt@gmail.com", @@ -21703,6 +24204,13 @@ "pattern": "^\\d{1,5}$", "preferred_prefix": "hgnc", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hgnc:$1" + }, { "code": "gencc", "description": "The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organizations. The GenCC comprises organizations that currently provide online resources (e.g. ClinGen, DECIPHER, Genomics England PanelApp, OMIM, Orphanet, PanelApp Australia, TGMI’s G2P), as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge (e.g. Ambry, Illumina, Invitae, Myriad Women’s Health, Mass General Brigham Laboratory for Molecular Medicine).", @@ -21723,21 +24231,21 @@ "doi": "10.1093/nar/gkaa980", "pmc": "PMC7779007", "pubmed": "33152070", - "title": "Genenames.org: the HGNC and VGNC resources in 2021.", + "title": "Genenames.org: the HGNC and VGNC resources in 2021", "year": 2021 }, { "doi": "10.1093/nar/gky930", "pmc": "PMC6324057", "pubmed": "30304474", - "title": "Genenames.org: the HGNC and VGNC resources in 2019.", + "title": "Genenames.org: the HGNC and VGNC resources in 2019", "year": 2019 }, { "doi": "10.1159/000131404", "pmc": null, "pubmed": "295268", - "title": "International system for human gene nomenclature (1979) ISGN (1979).", + "title": "International system for human gene nomenclature (1979) ISGN (1979)", "year": 1979 } ], @@ -21858,13 +24366,13 @@ "hipsci": { "description": "Cell line databases/resources", "example": "HPSI0114i-bezi_1", - "homepage": "http://www.hipsci.org", + "homepage": "https://www.hipsci.org", "mappings": { "cellosaurus": "HipSci" }, "name": "Human Induced Pluripotent Stem Cells Initiative", "preferred_prefix": "hipsci", - "uri_format": "http://www.hipsci.org/lines/#/lines/$1" + "uri_format": "https://www.hipsci.org/lines/#/lines/$1" }, "hivreagentprogram": { "description": "Cell line collections", @@ -21938,41 +24446,50 @@ "name": "Human Metabolome Database", "pattern": "^HMDB\\d+$", "preferred_prefix": "hmdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hmdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1062", "pmc": "PMC8728138", "pubmed": "34986597", - "title": "HMDB 5.0: the Human Metabolome Database for 2022.", + "title": "HMDB 5.0: the Human Metabolome Database for 2022", "year": 2022 }, { "doi": "10.1093/nar/gkx1089", "pmc": "PMC5753273", "pubmed": "29140435", - "title": "HMDB 4.0: the human metabolome database for 2018.", + "title": "HMDB 4.0: the human metabolome database for 2018", "year": 2018 }, { "doi": "10.1093/nar/gks1065", "pmc": "PMC3531200", "pubmed": "23161693", - "title": "HMDB 3.0--The Human Metabolome Database in 2013.", + "title": "HMDB 3.0--The Human Metabolome Database in 2013", "year": 2012 }, - { - "doi": "10.1093/nar/gkn810", - "pmc": "PMC1899095", - "pubmed": "17202168", - "title": "HMDB: a knowledgebase for the human metabolome", - "year": null - }, { "doi": "10.1093/nar/gkl923", "pmc": "PMC1899095", "pubmed": "17202168", - "title": "HMDB: the Human Metabolome Database.", + "title": "HMDB: the Human Metabolome Database", "year": 2007 + }, + { + "doi": "10.1093/nar/gkn810", + "pmc": null, + "pubmed": null, + "title": "HMDB: a knowledgebase for the human metabolome", + "year": null } ], "synonyms": [ @@ -22051,6 +24568,40 @@ "preferred_prefix": "hms.lincs.dataset", "uri_format": "https://lincs.hms.harvard.edu/db/datasets/$1" }, + "hoelzel": { + "contact": { + "email": "info@hoelzel.de", + "github": null, + "name": "Carsten Linder", + "orcid": "0009-0009-3816-8777" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog.", + "example": "40592-R001-100", + "homepage": "https://www.hoelzel-biotech.com", + "keywords": [ + "antibodies", + "assays", + "biologics", + "elisa-kits", + "inhibitors", + "life sciences", + "proteins", + "vendor" + ], + "logo": "https://www.hoelzel-biotech.com/skin/frontend/ultimo/custom/images/logo.png", + "name": "Hölzel Diagnostika", + "preferred_prefix": "hoelzel", + "synonyms": [ + "hölzel" + ], + "uri_format": "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1" + }, "hog": { "contributor": { "email": "cthoyt@gmail.com", @@ -22092,20 +24643,36 @@ "name": "Database of Complete Genome Homologous Genes Families", "pattern": "^\\w+$", "preferred_prefix": "hogenom", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hogenom:$1" + } + ], "publications": [ { "doi": "10.1186/1471-2105-10-s6-s3", "pmc": "PMC2697650", "pubmed": "19534752", - "title": "Databases of homologous gene families for comparative genomics.", + "title": "Databases of homologous gene families for comparative genomics", "year": 2009 }, { "doi": "10.1101/gr.10.3.379", "pmc": "PMC311423", "pubmed": "10720578", - "title": "HOBACGEN: database system for comparative genomics in bacteria.", + "title": "HOBACGEN: database system for comparative genomics in bacteria", "year": 2000 + }, + { + "doi": "10.1186/1471-2105-10-S6-S3", + "pmc": null, + "pubmed": null, + "title": "Databases of homologous gene families for comparative genomics.", + "year": null } ], "uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1" @@ -22183,10 +24750,11 @@ "doi": "10.1016/j.tig.2009.12.012", "pmc": null, "pubmed": "20116127", - "title": "An ontology to clarify homology-related concepts.", + "title": "An ontology to clarify homology-related concepts", "year": 2010 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/HOM_$1", "repository": "https://github.com/BgeeDB/homology-ontology", "uri_format": "http://purl.obolibrary.org/obo/HOM_$1", "version": "2015-01-07" @@ -22208,12 +24776,21 @@ "name": "HOMD Sequence Metainformation", "pattern": "^SEQF\\d+$", "preferred_prefix": "homd.seq", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/homd.seq:$1" + } + ], "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", - "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.", + "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information", "year": 2010 } ], @@ -22237,12 +24814,21 @@ "name": "Human Oral Microbiome Database", "pattern": "^\\d+$", "preferred_prefix": "homd.taxon", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/homd.taxon:$1" + } + ], "publications": [ { "doi": "10.1093/database/baq013", "pmc": "PMC2911848", "pubmed": "20624719", - "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.", + "title": "The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information", "year": 2010 } ], @@ -22275,6 +24861,13 @@ "homepage": "http://homologene.bio2rdf.org/fct", "name": "Bio2RDF", "uri_format": "http://homologene.bio2rdf.org/describe/?url=http://bio2rdf.org/homologene:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/homologene:$1" } ], "publications": [ @@ -22282,7 +24875,7 @@ "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2010 } ], @@ -22299,6 +24892,35 @@ "preferred_prefix": "horizon_discovery", "uri_format": "https://horizondiscovery.com/en/search?searchterm=$1" }, + "hoso": { + "contact": { + "email": "paul.fabry@usherbrooke.ca", + "github": "pfabry", + "name": "Paul Fabry", + "orcid": "0000-0002-3336-2476" + }, + "contributor": { + "email": "paul.fabry@usherbrooke.ca", + "github": "pfabry", + "name": "Paul Fabry", + "orcid": "0000-0002-3336-2476" + }, + "description": "HOSO is an ontology of informational entities and processes related to healthcare organizations and services.", + "example": "0000001", + "github_request_issue": 813, + "homepage": "https://openlhs.github.io/HOSO/", + "license": "CC-BY-4.0", + "name": "Healthcare Organizations and Services Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "hoso", + "repository": "https://github.com/OpenLHS/HOSO", + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + } + }, "hovergen": { "contact": { "email": "duret@biomserv.univ-lyon1.fr", @@ -22325,12 +24947,21 @@ "name": "Homologous Vertebrate Genes Database", "pattern": "^HBG\\d+$", "preferred_prefix": "hovergen", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hovergen:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/bti325", "pmc": null, "pubmed": "15713731", - "title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.", + "title": "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases", "year": 2005 } ], @@ -22364,6 +24995,7 @@ "preclinical studies" ], "license": "hpo", + "logo": "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/logo/HPO-logo-black_small.png", "mappings": { "aberowl": "HP_O", "bartoc": "1937", @@ -22378,6 +25010,7 @@ "ontobee": "HP", "wikidata": "P3841" }, + "mastodon": "hpo@masto.ai", "name": "Human Phenotype Ontology", "namespace_in_lui": true, "pattern": "^\\d{7}$", @@ -22387,52 +25020,60 @@ "doi": "10.1093/nar/gky1105", "pmc": "PMC6324074", "pubmed": "30476213", - "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.", + "title": "Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources", "year": 2019 }, + { + "doi": "https://doi.org/10.1093/nar/gkw1039", + "pmc": "PMC5210535", + "pubmed": "27899602", + "title": "The Human Phenotype Ontology in 2017", + "year": null + }, { "doi": "10.1093/nar/gkw1039", "pmc": "PMC5210535", "pubmed": "27899602", - "title": "The Human Phenotype Ontology in 2017.", + "title": "The Human Phenotype Ontology in 2017", "year": 2016 }, { "doi": "10.1016/j.ajhg.2015.05.020", "pmc": "PMC4572507", "pubmed": "26119816", - "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.", + "title": "The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease", "year": 2015 }, { "doi": "10.1093/nar/gkt1026", "pmc": "PMC3965098", "pubmed": "24217912", - "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.", + "title": "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data", "year": 2013 }, { "doi": "10.1111/j.1399-0004.2010.01436.x", "pmc": null, "pubmed": "20412080", - "title": "The human phenotype ontology.", + "title": "The human phenotype ontology", "year": 2010 }, { "doi": "10.1016/j.ajhg.2008.09.017", "pmc": "PMC2668030", "pubmed": "18950739", - "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.", + "title": "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease", "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/HP_$1", "repository": "https://github.com/obophenotype/human-phenotype-ontology", "synonyms": [ "hpo" ], "twitter": "hp_ontology", "uri_format": "https://hpo.jax.org/app/browse/term/HP:$1", - "version": "2022-06-11" + "version": "2023-06-17" }, "hpa": { "contact": { @@ -22465,69 +25106,92 @@ "name": "Human Protein Atlas tissue profile information", "pattern": "^ENSG\\d{11}$", "preferred_prefix": "hpa", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hpa:$1" + } + ], "publications": [ { "doi": "10.1126/science.aan2507", "pmc": null, "pubmed": "28818916", - "title": "A pathology atlas of the human cancer transcriptome.", + "title": "A pathology atlas of the human cancer transcriptome", "year": 2017 }, - { - "doi": "eaal3321", - "pmc": null, - "pubmed": "28495876", - "title": "A subcellular map of the human proteome.", - "year": null - }, { "doi": "10.1126/science.aal3321", "pmc": null, "pubmed": "28495876", - "title": "A subcellular map of the human proteome.", + "title": "A subcellular map of the human proteome", "year": 2017 }, { "doi": "10.15252/msb.20155865", "pmc": "PMC4848759", "pubmed": "27044256", - "title": "Transcriptomics resources of human tissues and organs.", + "title": "Transcriptomics resources of human tissues and organs", "year": 2016 }, { "doi": "10.1126/science.1260419", "pmc": null, "pubmed": "25613900", - "title": "Proteomics. Tissue-based map of the human proteome.", + "title": "Proteomics. Tissue-based map of the human proteome", "year": 2015 }, { "doi": "10.1038/nbt1210-1248", "pmc": null, "pubmed": "21139605", - "title": "Towards a knowledge-based Human Protein Atlas.", + "title": "Towards a knowledge-based Human Protein Atlas", "year": 2010 }, { "doi": "10.1002/path.2440", "pmc": null, "pubmed": "18853439", - "title": "The Human Protein Atlas--a tool for pathology.", + "title": "The Human Protein Atlas--a tool for pathology", "year": 2008 }, { "doi": "10.1074/mcp.r800013-mcp200", "pmc": null, "pubmed": "18669619", - "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies.", + "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies", "year": 2008 }, { "doi": "10.1074/mcp.m500279-mcp200", "pmc": null, "pubmed": "16127175", - "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics.", + "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics", "year": 2005 + }, + { + "doi": "eaal3321", + "pmc": null, + "pubmed": null, + "title": "A subcellular map of the human proteome.", + "year": null + }, + { + "doi": "10.1074/mcp.R800013-MCP200", + "pmc": null, + "pubmed": null, + "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies.", + "year": null + }, + { + "doi": "10.1074/mcp.M500279-MCP200", + "pmc": null, + "pubmed": null, + "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics.", + "year": null } ], "twitter": "ProteinAtlas", @@ -22611,12 +25275,21 @@ "name": "Human Protein Reference Database", "pattern": "^\\d+$", "preferred_prefix": "hprd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hprd:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn892", "pmc": "PMC2686490", "pubmed": "18988627", - "title": "Human Protein Reference Database--2009 update.", + "title": "Human Protein Reference Database--2009 update", "year": 2008 } ], @@ -22647,41 +25320,20 @@ "pattern": "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$", "preferred_prefix": "hpscreg", "publications": [ - { - "doi": "s1873-5061(20)30188-4", - "pmc": null, - "pubmed": "32707486", - "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg).", - "year": null - }, { "doi": "10.1016/j.scr.2020.101887", "pmc": null, "pubmed": "32707486", - "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg).", + "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)", "year": 2020 }, - { - "doi": "s2213-6711(20)30235-6", - "pmc": "PMC7419703", - "pubmed": "32679065", - "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells.", - "year": null - }, { "doi": "10.1016/j.stemcr.2020.06.014", "pmc": "PMC7419703", "pubmed": "32679065", - "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells.", + "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells", "year": 2020 }, - { - "doi": "s1873-5061(19)30169-2", - "pmc": null, - "pubmed": "31450190", - "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg)).", - "year": null - }, { "doi": "10.1016/j.scr.2019.101539", "pmc": null, @@ -22689,26 +25341,47 @@ "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC", "year": 2019 }, - { - "doi": "s2213-6711(17)30531-3", - "pmc": "PMC5768986", - "pubmed": "29320760", - "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.", - "year": null - }, { "doi": "10.1016/j.stemcr.2017.12.002", "pmc": "PMC5768986", "pubmed": "29320760", - "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.", + "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells", "year": 2018 }, { "doi": "10.1093/nar/gkv963", "pmc": "PMC4702942", "pubmed": "26400179", - "title": "hPSCreg--the human pluripotent stem cell registry.", + "title": "hPSCreg--the human pluripotent stem cell registry", "year": 2015 + }, + { + "doi": "S2213-6711(20)30235-6", + "pmc": null, + "pubmed": null, + "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells.", + "year": null + }, + { + "doi": "S2213-6711(17)30531-3", + "pmc": null, + "pubmed": null, + "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.", + "year": null + }, + { + "doi": "S1873-5061(20)30188-4", + "pmc": null, + "pubmed": null, + "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg).", + "year": null + }, + { + "doi": "S1873-5061(19)30169-2", + "pmc": null, + "pubmed": null, + "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg)).", + "year": null } ], "uri_format": "https://hpscreg.eu/cell-line/$1" @@ -22748,11 +25421,12 @@ "name": "Human Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "HsapDv", + "rdf_uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "HsapDv" ], - "uri_format": "http://purl.obolibrary.org/obo/HSAPDV_$1", + "uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1", "version": "2020-03-10" }, "hsdb": { @@ -22806,6 +25480,16 @@ "name": "Health Surveillance Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "HSO", + "providers": [ + { + "code": "hso.legacy", + "description": "An incorrect encoding of OBO purls", + "homepage": "http://purl.obolibrary.org/obo/hso", + "name": "HSO Hash", + "uri_format": "http://purl.obolibrary.org/obo/hso.owl#HSO_$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "repository": "https://github.com/SVA-SE/HSO", "uri_format": "http://purl.obolibrary.org/obo/HSO_$1", "version": "2021-12-13" @@ -22836,6 +25520,13 @@ "homepage": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/", "name": "HSSP at CMBI", "uri_format": "ftp://ftp.cmbi.ru.nl/pub/molbio/data/hssp/$1.hssp.bz2" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hssp:$1" } ], "publications": [ @@ -22843,14 +25534,14 @@ "doi": "10.1093/nar/24.1.201", "pmc": "PMC145595", "pubmed": "8594579", - "title": "The HSSP database of protein structure-sequence alignments.", + "title": "The HSSP database of protein structure-sequence alignments", "year": 1996 }, { "doi": null, "pmc": "PMC308328", "pubmed": "7937066", - "title": "The HSSP database of protein structure-sequence alignments.", + "title": "The HSSP database of protein structure-sequence alignments", "year": 1994 } ], @@ -22882,9 +25573,9 @@ "name": "Hypertension Ontology", "pattern": "^\\d{8}$", "preferred_prefix": "HTN", + "rdf_uri_format": "http://purl.obolibrary.org/obo/HTN_$1", "repository": "https://github.com/aellenhicks/htn_owl", - "uri_format": "http://purl.obolibrary.org/obo/HTN_$1", - "version": "2019-06-10" + "uri_format": "http://purl.obolibrary.org/obo/HTN_$1" }, "huge": { "description": "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project.", @@ -22908,12 +25599,21 @@ "name": "Human Unidentified Gene-Encoded", "pattern": "^KIAA\\d{4}$", "preferred_prefix": "huge", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/huge:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh035", "pmc": "PMC308769", "pubmed": "14681467", - "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.", + "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE", "year": 2004 } ], @@ -22953,6 +25653,7 @@ "subject agnostic" ], "license": "CC-BY-4.0", + "logo": "https://avatars0.githubusercontent.com/u/13591168?v=3&s=200", "mappings": { "aberowl": "IAO", "biocontext": "IAO", @@ -22982,13 +25683,14 @@ "doi": "10.3233/978-1-61499-101-4-68", "pmc": null, "pubmed": "22874154", - "title": "An information artifact ontology perspective on data collections and associated representational artifacts.", + "title": "An information artifact ontology perspective on data collections and associated representational artifacts", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/IAO_$1", "repository": "https://github.com/information-artifact-ontology/IAO", "uri_format": "http://purl.obolibrary.org/obo/IAO_$1", - "version": "2020-12-09" + "version": "2022-11-07" }, "icd10": { "contact": { @@ -23007,7 +25709,7 @@ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", - "name": "Nico Matentzoglu", + "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, { @@ -23064,6 +25766,13 @@ "pattern": "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$", "preferred_prefix": "icd10", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/icd:$1" + }, { "code": "icd10_2008", "description": "The 2008 revision of ICD-10", @@ -23164,6 +25873,15 @@ "name": "International Classification of Diseases, 10th Revision, Clinical Modification", "pattern": "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$", "preferred_prefix": "icd10cm", + "providers": [ + { + "code": "bioportal.purl", + "description": "PURL from BioPortal", + "homepage": "http://purl.bioontology.org/ontology/ICD10CM", + "name": "BioPortal PURL", + "uri_format": "http://purl.bioontology.org/ontology/ICD10CM/$1" + } + ], "synonyms": [ "ICD10CM" ], @@ -23320,7 +26038,8 @@ ], "mappings": { "fairsharing": "FAIRsharing.d95034", - "miriam": "icdc" + "miriam": "icdc", + "re3data": "r3d100010405" }, "name": "Integrated Canine Data Commons", "pattern": "^\\d{6}$", @@ -23352,6 +26071,15 @@ "name": "International Classification of Diseases for Oncology", "pattern": "^[8-9]\\d{3}(/[0-3])?$", "preferred_prefix": "icdo", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/icdo:$1" + } + ], "synonyms": [ "ICD-O", "ICDO" @@ -23381,14 +26109,14 @@ "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", - "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", - "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], @@ -23412,14 +26140,14 @@ "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", - "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", - "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], @@ -23446,14 +26174,14 @@ "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", - "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", - "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], @@ -23482,14 +26210,14 @@ "doi": "10.1093/nar/gky1123", "pmc": "PMC6323972", "pubmed": "30407568", - "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements.", + "title": "ICEberg 2.0: an updated database of bacterial integrative and conjugative elements", "year": 2019 }, { "doi": "10.1093/nar/gkr846", "pmc": "PMC3244999", "pubmed": "22009673", - "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria.", + "title": "ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria", "year": 2011 } ], @@ -23529,10 +26257,11 @@ "doi": "10.1038/s41597-021-01112-5", "pmc": "PMC8776819", "pubmed": "35058462", - "title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements.", + "title": "ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements", "year": 2022 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "repository": "https://github.com/ontoice/ICEO", "uri_format": "http://purl.obolibrary.org/obo/ICEO_$1", "version": "2.1" @@ -23610,9 +26339,30 @@ "cellosaurus": "ICLC" }, "name": "Interlab Cell Line Collection", + "pattern": "^\\w{3}\\d+$", "preferred_prefix": "iclc", "uri_format": "http://www.iclc.it/details/det_list.php?line_id=$1" }, + "icldb": { + "contact": { + "email": "surjeet.arya@uky.edu", + "github": null, + "name": "Surjeet Kumar Arya", + "orcid": "0000-0002-2212-4771" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)", + "example": "64ba", + "homepage": "https://entomology.ca.uky.edu/aginsectcellsdatabase", + "name": "Insect Cell Line Database", + "preferred_prefix": "icldb", + "uri_format": "https://entomology.ca.uky.edu/content/$1" + }, "ico": { "appears_in": [ "scdo" @@ -23648,6 +26398,7 @@ "name": "Informed Consent Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ICO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "repository": "https://github.com/ICO-ontology/ICO", "uri_format": "http://purl.obolibrary.org/obo/ICO_$1", "version": "1.0.187" @@ -23674,7 +26425,7 @@ "doi": "10.1093/nar/gkt1010", "pmc": "PMC3965115", "pubmed": "24178034", - "title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners.", + "title": "IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners", "year": 2013 } ], @@ -23730,12 +26481,13 @@ "doi": "10.1186/s13326-021-00245-1", "pmc": "PMC8286442", "pubmed": "34275487", - "title": "The Infectious Disease Ontology in the age of COVID-19.", + "title": "The Infectious Disease Ontology in the age of COVID-19", "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/IDO_$1", "repository": "https://github.com/infectious-disease-ontology/infectious-disease-ontology", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1", + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/ido/terms?obo_id=IDO:$1", "version": "2017-11-03" }, "idocovid19": { @@ -23888,17 +26640,18 @@ "doi": "10.1186/2041-1480-4-16", "pmc": "PMC3848731", "pubmed": "24034841", - "title": "IDOMAL: the malaria ontology revisited.", + "title": "IDOMAL: the malaria ontology revisited", "year": 2013 }, { "doi": "10.1186/1475-2875-9-230", "pmc": "PMC2925367", "pubmed": "20698959", - "title": "IDOMAL: an ontology for malaria.", + "title": "IDOMAL: an ontology for malaria", "year": 2010 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", "repository": "https://github.com/VEuPathDB-ontology/IDOMAL", "twitter": "VectorBase", "uri_format": "http://purl.obolibrary.org/obo/IDOMAL_$1", @@ -23986,7 +26739,7 @@ "doi": "10.1038/nmeth.4326", "pmc": "PMC5536224", "pubmed": "28775673", - "title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform.", + "title": "The Image Data Resource: A Bioimage Data Integration and Publication Platform", "year": 2017 } ], @@ -24013,33 +26766,42 @@ "name": "Immune Epitope Database", "pattern": "^[0-9]+$", "preferred_prefix": "iedb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tied:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gku938", "pmc": "PMC4384014", "pubmed": "25300482", - "title": "The immune epitope database (IEDB) 3.0.", + "title": "The immune epitope database (IEDB) 3.0", "year": 2014 }, { "doi": "10.1111/j.1365-2567.2012.03611.x", "pmc": "PMC3461392", "pubmed": "22681406", - "title": "The immune epitope database: a historical retrospective of the first decade.", + "title": "The immune epitope database: a historical retrospective of the first decade", "year": 2012 }, { "doi": "10.1093/nar/gkp1004", "pmc": "PMC2808938", "pubmed": "19906713", - "title": "The immune epitope database 2.0.", + "title": "The immune epitope database 2.0", "year": 2009 }, { "doi": null, "pmc": null, "pubmed": "16312048", - "title": "The immune epitope database and analysis resource: from vision to blueprint.", + "title": "The immune epitope database and analysis resource: from vision to blueprint", "year": 2004 } ], @@ -24061,6 +26823,7 @@ ], "homepage": "http://www.iana.org/assignments/language-subtag-registry/language-subtag-registry", "mappings": { + "bartoc": "2022", "wikidata": "P305" }, "name": "Internet Engineering Task Force Language Tag", @@ -24089,7 +26852,17 @@ "name": "Event (INOH pathway ontology)", "pattern": "^\\d{7}$", "preferred_prefix": "IEV", - "uri_format": "http://purl.obolibrary.org/obo/IEV_$1" + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/iev:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/IEV_$1", + "uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1" }, "igrhcellid": { "description": "Cell line databases/resources", @@ -24139,14 +26912,14 @@ "doi": "10.1093/nar/gkz836", "pmc": "PMC6943028", "pubmed": "31584097", - "title": "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources.", + "title": "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources", "year": 2020 }, { "doi": "10.1038/nature15393", "pmc": "PMC4750478", "pubmed": "26432245", - "title": "A global reference for human genetic variation.", + "title": "A global reference for human genetic variation", "year": 2015 } ], @@ -24256,6 +27029,13 @@ "name": "IMEx Consortium though Intact", "uri_format": "https://imexcentral.org/icentral/imex/rec/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/imex:$1" + }, { "code": "intact.search", "description": "Search page on IntAct", @@ -24269,7 +27049,7 @@ "doi": "10.1002/pmic.200700286", "pmc": null, "pubmed": "17893861", - "title": "Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.", + "title": "Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition", "year": 2007 } ], @@ -24292,12 +27072,21 @@ "name": "Integrated Microbial Genomes Gene", "pattern": "^\\d+$", "preferred_prefix": "img.gene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/img.gene:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm846", "pmc": "PMC2238897", "pubmed": "17933782", - "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.", + "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions", "year": 2007 } ], @@ -24320,12 +27109,21 @@ "name": "Integrated Microbial Genomes Taxon", "pattern": "^\\d+$", "preferred_prefix": "img.taxon", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/img.taxon:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm846", "pmc": "PMC2238897", "pubmed": "17933782", - "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.", + "title": "The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions", "year": 2007 } ], @@ -24372,68 +27170,77 @@ ], "pattern": "^[A-Z0-9*:]+$", "preferred_prefix": "imgt.hla", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/imgthla:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkz950", "pmc": "PMC7145640", "pubmed": "31667505", - "title": "IPD-IMGT/HLA Database.", + "title": "IPD-IMGT/HLA Database", "year": 2020 }, { "doi": "10.1093/nar/gku1161", "pmc": "PMC4383959", "pubmed": "25414341", - "title": "The IPD and IMGT/HLA database: allele variant databases.", + "title": "The IPD and IMGT/HLA database: allele variant databases", "year": 2014 }, { "doi": "10.1093/nar/gkn662", "pmc": "PMC2686596", "pubmed": "18838392", - "title": "The IMGT/HLA database.", + "title": "The IMGT/HLA database", "year": 2008 }, { "doi": "10.1007/978-1-60327-118-9_3", "pmc": null, "pubmed": "18449991", - "title": "The IMGT/HLA database.", + "title": "The IMGT/HLA database", "year": 2007 }, { "doi": "10.1002/humu.20406", "pmc": null, "pubmed": "16944494", - "title": "The IMGT/HLA and IPD databases.", + "title": "The IMGT/HLA and IPD databases", "year": 2006 }, { "doi": "10.1093/nar/gkj088", "pmc": "PMC1347451", "pubmed": "16381979", - "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.", + "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences", "year": 2006 }, { "doi": "10.1093/nar/gkg070", "pmc": "PMC165517", "pubmed": "12520010", - "title": "IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.", + "title": "IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex", "year": 2003 }, { "doi": "10.1093/nar/29.1.210", "pmc": "PMC29780", "pubmed": "11125094", - "title": "IMGT/HLA Database--a sequence database for the human major histocompatibility complex.", + "title": "IMGT/HLA Database--a sequence database for the human major histocompatibility complex", "year": 2001 }, { "doi": "10.1034/j.1399-0039.2000.550314.x", "pmc": null, "pubmed": "10777106", - "title": "IMGT/HLA database--a sequence database for the human major histocompatibility complex.", + "title": "IMGT/HLA database--a sequence database for the human major histocompatibility complex", "year": 2000 } ], @@ -24467,6 +27274,13 @@ "homepage": "http://genius.embnet.dkfz-heidelberg.de/", "name": "IMGT LIGM through DKFZ (SRS)", "uri_format": "http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/srs7.1.3.1/wgetz?-id+4ktAl1fNMTA+-e+[IMGT:'$1']" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/imgt.ligm:$1" } ], "publications": [ @@ -24474,7 +27288,7 @@ "doi": "10.1093/nar/gkj088", "pmc": "PMC1347451", "pubmed": "16381979", - "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences.", + "title": "IMGT/LIGM-DB, the IMGT comprehensive database of immunoglobulin and T cell receptor nucleotide sequences", "year": 2006 } ], @@ -24493,6 +27307,15 @@ }, "name": "IMGT/PRIMER-DB", "preferred_prefix": "imgt.primerdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/imgt.primerdb:$1" + } + ], "uri_format": "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList" }, "imotdb": { @@ -24510,6 +27333,15 @@ }, "name": "Database of Spatially Interacting Motifs in Proteins", "preferred_prefix": "imotdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/imotdb:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -24543,7 +27375,17 @@ "name": "Molecule role (INOH Protein name/family name ontology)", "pattern": "^\\d{7}$", "preferred_prefix": "IMR", - "uri_format": "http://purl.obolibrary.org/obo/IMR_$1" + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/imr:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/IMR_$1", + "uri_format": "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1" }, "inaturalist.observation": { "contributor": { @@ -24671,21 +27513,28 @@ "doi": "10.1186/s13321-021-00517-z", "pmc": "PMC8147039", "pubmed": "34030732", - "title": "InChI version 1.06: now more than 99.99% reliable.", + "title": "InChI version 1.06: now more than 99.99% reliable", "year": 2021 }, + { + "doi": "https://doi.org/10.1186/s13321-015-0068-4", + "pmc": "PMC4486400", + "pubmed": "26136848", + "title": "InChI, the IUPAC International Chemical Identifier", + "year": null + }, { "doi": "10.1186/s13321-015-0068-4", "pmc": "PMC4486400", "pubmed": "26136848", - "title": "InChI, the IUPAC International Chemical Identifier.", + "title": "InChI, the IUPAC International Chemical Identifier", "year": 2015 }, { "doi": "10.1007/s10822-015-9854-3", "pmc": null, "pubmed": "26081259", - "title": "Many InChIs and quite some feat.", + "title": "Many InChIs and quite some feat", "year": 2015 } ], @@ -24740,7 +27589,7 @@ "doi": "10.1177/0192623309353423", "pmc": null, "pubmed": "20032296", - "title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract.", + "title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract", "year": 2009 } ] @@ -24785,12 +27634,21 @@ }, "name": "A Knowledge Resource for Innate Immunity Interactions and Pathways", "preferred_prefix": "innatedb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/innatedb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gks1147", "pmc": "PMC3531080", "pubmed": "23180781", - "title": "InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.", + "title": "InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation", "year": 2012 } ], @@ -24837,24 +27695,32 @@ "doi": "10.1186/s13040-016-0118-0", "pmc": "PMC5168857", "pubmed": "28031747", - "title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.", + "title": "The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature", "year": 2016 }, { "doi": "10.1186/2041-1480-6-2", "pmc": "PMC4362819", "pubmed": "25785184", - "title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.", + "title": "Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions", "year": 2015 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", - "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.", + "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology", "year": 2011 + }, + { + "doi": "10.1186/2041-1480-2-S2-S8", + "pmc": "PMC3102897", + "pubmed": "21624163", + "title": "Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/INO_$1", "repository": "https://github.com/INO-ontology/ino", "uri_format": "http://purl.obolibrary.org/obo/INO_$1", "version": "1.1.13" @@ -24862,7 +27728,7 @@ "insdc": { "description": "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.", "example": "X58356", - "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", + "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", "keywords": [ "dna" ], @@ -24876,13 +27742,6 @@ "pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$", "preferred_prefix": "insdc", "providers": [ - { - "code": "CURATOR_REVIEW", - "description": "INSDC through GenBank", - "homepage": "https://www.ncbi.nlm.nih.gov/Genbank/", - "name": "INSDC through GenBank", - "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" - }, { "code": "CURATOR_REVIEW", "description": "INSDC through DDBJ", @@ -24890,12 +27749,26 @@ "name": "INSDC through DDBJ", "uri_format": "http://getentry.ddbj.nig.ac.jp/getentry?database=ddbj&accession_number=$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/insdc:$1" + }, { "code": "ebi", "description": "INSDC through European Nucleotide Archive (ENA)", "homepage": "https://www.ebi.ac.uk/ena/", "name": "INSDC through European Nucleotide Archive (ENA)", "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" + }, + { + "code": "ncbi", + "description": "INSDC through Nucleotide database at NCBI", + "homepage": "https://www.ncbi.nlm.nih.gov/nuccore/", + "name": "INSDC through Nucleotide database at NCBI", + "uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1" } ], "publications": [ @@ -24903,28 +27776,28 @@ "doi": "10.1093/nar/18.6.1517", "pmc": "PMC330520", "pubmed": "2326192", - "title": "Recent changes in the GenBank On-line Service.", + "title": "Recent changes in the GenBank On-line Service", "year": 1990 }, { "doi": "10.1093/nar/gkl986", "pmc": "PMC1781245", "pubmed": "17202161", - "title": "GenBank.", + "title": "GenBank", "year": 2007 }, { "doi": "10.1093/nar/gkl913", "pmc": "PMC1897316", "pubmed": "17148479", - "title": "EMBL Nucleotide Sequence Database in 2006.", + "title": "EMBL Nucleotide Sequence Database in 2006", "year": 2006 }, { "doi": "10.1126/science.298.5597.1333b", "pmc": null, "pubmed": "12436968", - "title": "Nucleotide sequence database policies.", + "title": "Nucleotide sequence database policies", "year": 2002 } ], @@ -24978,9 +27851,9 @@ { "code": "ncbi", "description": "Genome assembly database NCBI", - "homepage": "https://www.ncbi.nlm.nih.gov/assembly/", + "homepage": "https://www.ncbi.nlm.nih.gov/datasets/genome/", "name": "Genome assembly database NCBI", - "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" + "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" } ], "uri_format": "https://www.ebi.ac.uk/ena/data/view/$1" @@ -25050,21 +27923,21 @@ "doi": "10.1186/s13742-015-0064-7", "pmc": "PMC4425880", "pubmed": "25960871", - "title": "Investigation into the annotation of protocol sequencing steps in the sequence read archive.", + "title": "Investigation into the annotation of protocol sequencing steps in the sequence read archive", "year": 2015 }, { "doi": "10.1093/nar/gkr854", "pmc": "PMC3245110", "pubmed": "22009675", - "title": "The Sequence Read Archive: explosive growth of sequencing data.", + "title": "The Sequence Read Archive: explosive growth of sequencing data", "year": 2011 }, { "doi": "10.1093/nar/gkm1000", "pmc": "PMC2238880", "pubmed": "18045790", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2007 } ], @@ -25106,40 +27979,49 @@ ], "pattern": "^EBI\\-[0-9]+$", "preferred_prefix": "intact", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/intact:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1115", "pmc": "PMC3965093", "pubmed": "24234451", - "title": "The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.", + "title": "The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases", "year": 2013 }, { "doi": "10.1038/nmeth.1637", "pmc": "PMC3246345", "pubmed": "21716279", - "title": "PSICQUIC and PSISCORE: accessing and scoring molecular interactions.", + "title": "PSICQUIC and PSISCORE: accessing and scoring molecular interactions", "year": 2011 }, { "doi": "10.1093/nar/gkp878", "pmc": "PMC2808934", "pubmed": "19850723", - "title": "The IntAct molecular interaction database in 2010.", + "title": "The IntAct molecular interaction database in 2010", "year": 2009 }, { "doi": "10.1186/1741-7007-5-44", "pmc": "PMC2189715", "pubmed": "17925023", - "title": "Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.", + "title": "Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions", "year": 2007 }, { "doi": "10.1093/nar/gkh052", "pmc": "PMC308786", "pubmed": "14681455", - "title": "IntAct: an open source molecular interaction database.", + "title": "IntAct: an open source molecular interaction database", "year": 2004 } ], @@ -25172,6 +28054,15 @@ }, "name": "Human Intermediate Filament Database", "preferred_prefix": "interfil", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/interfil:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -25202,7 +28093,7 @@ "doi": "10.3389/fninf.2013.00018", "pmc": "PMC3757470", "pubmed": "24009581", - "title": "NeuroLex.org: an online framework for neuroscience knowledge.", + "title": "NeuroLex.org: an online framework for neuroscience knowledge", "year": 2013 } ], @@ -25257,31 +28148,46 @@ "homepage": "http://interpro.bio2rdf.org/fct/", "name": "Bio2RDF", "uri_format": "http://interpro.bio2rdf.org/describe/?url=http://bio2rdf.org/interpro:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/interpro:$1" } ], "publications": [ + { + "doi": "10.1093/nar/gkac993", + "pmc": "PMC9825450", + "pubmed": "36350672", + "title": "InterPro in 2022", + "year": 2023 + }, { "doi": "10.1093/nar/gkaa977", "pmc": "PMC7778928", "pubmed": "33156333", - "title": "The InterPro protein families and domains database: 20 years on.", + "title": "The InterPro protein families and domains database: 20 years on", "year": 2021 }, { "doi": "10.1093/nar/gky1100", "pmc": "PMC6323941", "pubmed": "30398656", - "title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations.", + "title": "InterPro in 2019: improving coverage, classification and access to protein sequence annotations", "year": 2019 }, { "doi": "10.1093/nar/gki106", "pmc": "PMC540060", "pubmed": "15608177", - "title": "InterPro, progress and status in 2005.", + "title": "InterPro, progress and status in 2005", "year": 2005 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/IPR_$1", "repository": "https://proteinswebteam.github.io/interpro-blog/", "synonyms": [ "IP", @@ -25343,17 +28249,43 @@ }, "name": "International Protein Index", "preferred_prefix": "ipi", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ipi:$1" + } + ], "publications": [ { "doi": "10.1002/pmic.200300721", "pmc": null, "pubmed": "15221759", - "title": "The International Protein Index: an integrated database for proteomics experiments.", + "title": "The International Protein Index: an integrated database for proteomics experiments", "year": 2004 } ], "uri_format": "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default" }, + "irct": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space.", + "example": "IRCT20080904001199N7", + "homepage": "https://en.irct.ir/", + "name": "Iranian Registry of Clinical Trials", + "pattern": "^IRCT\\d+N\\d+$", + "preferred_prefix": "irct", + "references": [ + "https://en.irct.ir/trial/65035" + ] + }, "ird.segment": { "description": "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s).", "example": "CY077097", @@ -25371,12 +28303,21 @@ "name": "IRD Segment Sequence", "pattern": "^\\w+(\\_)?\\d+(\\.\\d+)?$", "preferred_prefix": "ird.segment", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ird.segment:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm905", "pmc": "PMC2238987", "pubmed": "17965094", - "title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.", + "title": "BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence", "year": 2007 } ], @@ -25402,12 +28343,21 @@ "name": "iRefWeb", "pattern": "^\\d+$", "preferred_prefix": "irefweb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/irefweb:$1" + } + ], "publications": [ { "doi": "10.1093/database/baq023", "pmc": "PMC2963317", "pubmed": "20940177", - "title": "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.", + "title": "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence", "year": 2010 } ], @@ -25429,19 +28379,28 @@ }, "name": "Database of experimentally verified IRES structures", "preferred_prefix": "iresite", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/iresite:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp981", "pmc": "PMC2808886", "pubmed": "19917642", - "title": "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites.", + "title": "IRESite--a tool for the examination of viral and cellular internal ribosome entry sites", "year": 2009 }, { "doi": "10.1093/nar/gkj081", "pmc": "PMC1347444", "pubmed": "16381829", - "title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org).", + "title": "IRESite: the database of experimentally verified IRES structures (www.iresite.org)", "year": 2006 } ], @@ -25487,6 +28446,13 @@ "pattern": "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$", "preferred_prefix": "isbn", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/isbn:$1" + }, { "code": "worldcat", "description": "ISBN database at WorldCat", @@ -25512,7 +28478,16 @@ "prefixcommons": "ised" }, "name": "Influenza Sequence and Epitope Database", - "preferred_prefix": "ised" + "preferred_prefix": "ised", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ised:$1" + } + ] }, "isfinder": { "description": "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available.", @@ -25534,12 +28509,21 @@ "name": "Insertion sequence elements database", "pattern": "^IS\\w+(\\-\\d)?$", "preferred_prefix": "isfinder", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/isfinder:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj014", "pmc": "PMC1347377", "pubmed": "16381877", - "title": "ISfinder: the reference centre for bacterial insertion sequences.", + "title": "ISfinder: the reference centre for bacterial insertion sequences", "year": 2006 } ], @@ -25576,6 +28560,45 @@ "pattern": "^\\d+$", "preferred_prefix": "iso.3166" }, + "iso15926": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)", + "download_rdf": "https://github.com/uwasystemhealth/modular_ontologies/raw/master/LIS-14.ttl", + "example": "activityBoundOf", + "homepage": "https://15926.org/home/", + "name": "ISO 15926-14", + "preferred_prefix": "iso15926", + "uri_format": "http://standards.iso.org/iso/15926/part14/$1" + }, + "isrctn": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)", + "example": "ISRCTN10175490", + "homepage": "https://www.isrctn.com/", + "name": "International Traditional Medicine Clinical Trial Registry", + "pattern": "^ISRCTN\\d+$", + "preferred_prefix": "isrctn", + "providers": [ + { + "code": "doi", + "description": "DOI resolution of ISRCTN", + "homepage": "https://doi.org/10.1186", + "name": "DOI", + "uri_format": "https://doi.org/10.1186/$1" + } + ], + "uri_format": "https://www.isrctn.com/$1" + }, "issn": { "description": "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books.", "example": "0745-4570", @@ -25633,7 +28656,24 @@ "preferred_prefix": "itis", "uri_format": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1" }, + "itmctr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)", + "example": "ITMCTR2023000002", + "homepage": "http://itmctr.ccebtcm.org.cn", + "logo": "http://itmctr.ccebtcm.org.cn/Content/images/ny_logo.png", + "name": "International Traditional Medicine Clinical Trial Registry", + "pattern": "^ITMCTR\\d+$", + "preferred_prefix": "itmctr" + }, "ito": { + "banana": "ITO", + "banana_peel": "_", "contact": { "email": "matthias.samwald@meduniwien.ac.at", "github": null, @@ -25642,8 +28682,8 @@ }, "description": "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks.", "download_owl": "http://aber-owl.net/media/ontologies/ITO/17/ito.owl", - "example": "ITO_01625", - "homepage": "https://bioportal.bioontology.org/", + "example": "01625", + "homepage": "https://openbiolink.github.io/ITOExplorer/", "keywords": [ "artificial intelligence", "ontology" @@ -25655,14 +28695,14 @@ "miriam": "ito" }, "name": "Intelligence Task Ontology", - "pattern": "^.+$", + "pattern": "^\\d+$", "preferred_prefix": "ito", "publications": [ { "doi": "10.1038/s41597-022-01435-x", "pmc": "PMC9205953", "pubmed": "35715466", - "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks.", + "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", "year": 2022 }, { @@ -25678,9 +28718,17 @@ "pubmed": null, "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", "year": 2021 + }, + { + "doi": "10.48550/arXiv.2110.01434", + "pmc": null, + "pubmed": null, + "title": "A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks", + "year": null } ], - "uri_format": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:$1" + "repository": "https://github.com/OpenBioLink/ITO", + "uri_format": "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1" }, "iuphar.family": { "description": "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits.", @@ -25698,6 +28746,15 @@ "name": "IUPHAR family", "pattern": "^\\d+$", "preferred_prefix": "iuphar.family", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/iuphar.family:$1" + } + ], "synonyms": [ "IUPHARfam" ], @@ -25743,14 +28800,14 @@ "doi": "10.1093/nar/gkab1010", "pmc": "PMC8689838", "pubmed": "34718737", - "title": "The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials.", + "title": "The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials", "year": 2022 }, { "doi": "10.1111/j.1476-5381.2012.02141.x", "pmc": "PMC3575771", "pubmed": "23003568", - "title": "GuideToPharmacology.org--an update.", + "title": "GuideToPharmacology.org--an update", "year": 2012 } ], @@ -25774,6 +28831,15 @@ }, "name": "Influenza Virus Database", "preferred_prefix": "ivdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ivdb:$1" + } + ], "uri_format": "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1" }, "jax": { @@ -25846,6 +28912,15 @@ "name": "Japan Collection of Microorganisms", "pattern": "^\\d+$", "preferred_prefix": "jcm", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/jcm:$1" + } + ], "uri_format": "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1" }, "jcrb": { @@ -25862,6 +28937,7 @@ "cellosaurus": "JCRB" }, "name": "JRBC Cell Bank", + "pattern": "^JCRB\\d+$", "preferred_prefix": "jcrb", "uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1" }, @@ -25882,8 +28958,86 @@ "name": "Japan Chemical Substance Dictionary", "pattern": "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$", "preferred_prefix": "jcsd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/jcsd:$1" + } + ], "uri_format": "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1" }, + "jgi.proposal": { + "contact": { + "email": "sewilson@lbl.gov", + "github": null, + "name": "Steven E. Wilson", + "orcid": "0000-0002-8489-208X" + }, + "contributor": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor_extras": [ + { + "email": "aclum@lbl.gov", + "github": "aclum", + "name": "Alicia Clum", + "orcid": "0000-0002-5004-3362" + } + ], + "description": "Identifiers for proposals/projects at the Joint Genome Institute", + "example": "502930", + "github_request_issue": 853, + "homepage": "https://genome.jgi.doe.gov/portal/", + "name": "Joint Genome Institute Proposals", + "pattern": "^\\d+$", + "preferred_prefix": "jgi.proposal", + "publications": [ + { + "doi": "10.1128/msystems.00804-20", + "pmc": "PMC8269246", + "pubmed": "34006627", + "title": "DOE JGI Metagenome Workflow", + "year": 2021 + } + ], + "reviewer": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "uri_format": "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1" + }, + "jrct": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)", + "example": "jRCTs041220087", + "homepage": "https://jrct.niph.go.jp", + "name": "Japan Registry of Clinical Trials", + "pattern": "^jRCT\\w?\\d+$", + "preferred_prefix": "jrct", + "providers": [ + { + "code": "", + "description": "", + "homepage": "", + "name": "", + "uri_format": "https://jrct.niph.go.jp/latest-detail/$1" + } + ], + "uri_format": "https://jrct.niph.go.jp/en-latest-detail/$1" + }, "jstor": { "description": "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration.", "example": "3075966", @@ -25930,6 +29084,13 @@ "homepage": "http://jjj.bio.vu.nl/models/", "name": "JWS Online Model Repository at Amsterdam", "uri_format": "http://jjj.bio.vu.nl/models/$1/" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/jws:$1" } ], "publications": [ @@ -25937,7 +29098,7 @@ "doi": "10.1093/bioinformatics/bth200", "pmc": null, "pubmed": "15072998", - "title": "Web-based kinetic modelling using JWS Online.", + "title": "Web-based kinetic modelling using JWS Online", "year": 2004 } ], @@ -25974,6 +29135,23 @@ "preferred_prefix": "kclb", "uri_format": "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1" }, + "kcris": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space", + "example": "KCT0008394", + "homepage": "https://cris.nih.go.kr", + "name": "Korean Clinical Research Information Service", + "pattern": "^KCT\\d+$", + "preferred_prefix": "kcris", + "references": [ + "https://cris.nih.go.kr/cris/search/detailSearchEn.do?seq=23973" + ] + }, "kegg": { "comment": "KEGG prefix has been split into several others", "deprecated": true, @@ -25982,6 +29160,7 @@ "homepage": "http://www.kegg.jp/", "mappings": { "biocontext": "KEGG", + "biolink": "KEGG", "cheminf": "000409", "go": "KEGG", "miriam": "kegg", @@ -25996,7 +29175,7 @@ "doi": "10.1093/nar/gkw1092", "pmc": "PMC5210567", "pubmed": "27899662", - "title": "KEGG: new perspectives on genomes, pathways, diseases and drugs.", + "title": "KEGG: new perspectives on genomes, pathways, diseases and drugs", "year": 2016 } ], @@ -26021,6 +29200,15 @@ "name": "KEGG BRITE", "part_of": "kegg", "preferred_prefix": "kegg.brite", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.brite:$1" + } + ], "uri_format": "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1" }, "kegg.compound": { @@ -26042,12 +29230,21 @@ "part_of": "kegg", "pattern": "^C\\d+$", "preferred_prefix": "kegg.compound", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.compound:$1" + } + ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pmc": null, "pubmed": "22700311", - "title": "Using the KEGG database resource.", + "title": "Using the KEGG database resource", "year": 2012 } ], @@ -26099,6 +29296,15 @@ "part_of": "kegg", "pattern": "^H\\d+$", "preferred_prefix": "kegg.disease", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.disease:$1" + } + ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.drug": { @@ -26120,12 +29326,21 @@ "part_of": "kegg", "pattern": "^D\\d+$", "preferred_prefix": "kegg.drug", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.drug:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", - "title": "From genomics to chemical genomics: new developments in KEGG.", + "title": "From genomics to chemical genomics: new developments in KEGG", "year": 2006 } ], @@ -26178,7 +29393,7 @@ ], "mappings": { "biocontext": "KEGG.GENES", - "biolink": "KEGG.GENE", + "biolink": "KEGG.GENES", "miriam": "kegg.genes", "n2t": "kegg.genes", "prefixcommons": "kegg.gene", @@ -26188,12 +29403,21 @@ "part_of": "kegg", "pattern": "^\\w+:[\\w\\d\\.-]*$", "preferred_prefix": "kegg.genes", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.gene:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj102", "pmc": "PMC1347464", "pubmed": "16381885", - "title": "From genomics to chemical genomics: new developments in KEGG.", + "title": "From genomics to chemical genomics: new developments in KEGG", "year": 2006 } ], @@ -26214,12 +29438,21 @@ "part_of": "kegg", "pattern": "^(T0\\d+|\\w{3,5})$", "preferred_prefix": "kegg.genome", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.genome:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", - "title": "KEGG for integration and interpretation of large-scale molecular data sets.", + "title": "KEGG for integration and interpretation of large-scale molecular data sets", "year": 2011 } ], @@ -26247,12 +29480,21 @@ "part_of": "kegg", "pattern": "^G\\d+$", "preferred_prefix": "kegg.glycan", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.glycan:$1" + } + ], "publications": [ { "doi": "10.1093/glycob/cwj010", "pmc": null, "pubmed": "16014746", - "title": "KEGG as a glycome informatics resource.", + "title": "KEGG as a glycome informatics resource", "year": 2005 } ], @@ -26287,12 +29529,21 @@ "part_of": "kegg", "pattern": "^T3\\d+$", "preferred_prefix": "kegg.metagenome", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.metagenome:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr988", "pmc": "PMC3245020", "pubmed": "22080510", - "title": "KEGG for integration and interpretation of large-scale molecular data sets.", + "title": "KEGG for integration and interpretation of large-scale molecular data sets", "year": 2011 } ], @@ -26331,6 +29582,15 @@ "part_of": "kegg", "pattern": "^K\\d+$", "preferred_prefix": "kegg.orthology", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.orthology:$1" + } + ], "uri_format": "http://www.kegg.jp/entry/$1" }, "kegg.pathway": { @@ -26354,12 +29614,21 @@ "part_of": "kegg", "pattern": "^\\w{2,4}\\d{5}$", "preferred_prefix": "kegg.pathway", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.pathway:$1" + } + ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pmc": null, "pubmed": "22700311", - "title": "Using the KEGG database resource.", + "title": "Using the KEGG database resource", "year": 2012 } ], @@ -26415,15 +29684,25 @@ "part_of": "kegg", "pattern": "^R\\d+$", "preferred_prefix": "kegg.reaction", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/kegg.reaction:$1" + } + ], "publications": [ { "doi": "10.1002/0471250953.bi0112s38", "pmc": null, "pubmed": "22700311", - "title": "Using the KEGG database resource.", + "title": "Using the KEGG database resource", "year": 2012 } ], + "rdf_uri_format": "http://www.kegg.jp/entry/$1", "synonyms": [ "KEGG_REACTION" ], @@ -26440,6 +29719,27 @@ "preferred_prefix": "kerafast", "uri_format": "https://www.kerafast.com/Search?SearchTerm="$1"" }, + "kestrelo": { + "contact": { + "email": "lindsey.anderson@pnnl.gov", + "github": "lnanderson", + "name": "Lindsey N. Anderson", + "orcid": "0000-0002-8741-7823" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains", + "example": "0000001", + "homepage": "https://gitlab.pnnl.gov/kestrel/kestrel_ontology", + "name": "KESTREL Ontology", + "pattern": "^\\d{7}$", + "preferred_prefix": "kestrelo", + "uri_format": "http://purl.obolibrary.org/obo/kestrelo_$1" + }, "knapsack": { "description": "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated.", "example": "C00000001", @@ -26530,6 +29830,7 @@ "year": 2019 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "repository": "https://github.com/OpenLHS/LABO", "uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "version": "2021-06-08" @@ -26550,6 +29851,23 @@ "preferred_prefix": "langual", "uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1" }, + "lbctr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)", + "example": "LBCTR2023015204", + "homepage": "https://lbctr.moph.gov.lb/", + "name": "Lebanon Clinical Trials Registry", + "pattern": "^LBCTR\\d+$", + "preferred_prefix": "lbctr", + "references": [ + "https://lbctr.moph.gov.lb/Trials/Details/5204" + ] + }, "lbo": { "contact": { "email": "caripark@iastate.edu", @@ -26582,6 +29900,34 @@ "repository": "https://github.com/AnimalGenome/livestock-breed-ontology", "uri_format": "http://purl.obolibrary.org/obo/LBO_$1" }, + "lcsh": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)", + "example": "nb2018006591", + "homepage": "https://id.loc.gov/authorities", + "keywords": [ + "subject agnostic" + ], + "mappings": { + "bartoc": "454", + "fairsharing": "FAIRsharing.d31795", + "wikidata": "P244" + }, + "name": "Library of Congress Subject Headings", + "pattern": "^\\w{1,2}\\d{8,10}$", + "preferred_prefix": "lcsh", + "rdf_uri_format": "http://id.loc.gov/authorities/names/$1", + "synonyms": [ + "lcnaf", + "lcnafid" + ], + "uri_format": "https://id.loc.gov/authorities/$1" + }, "leafsnap": { "description": "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide", "example": "Amelanchier laevis", @@ -26642,9 +29988,10 @@ "name": "Lepidoptera Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "LEPAO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", "repository": "https://github.com/insect-morphology/lepao", "uri_format": "http://purl.obolibrary.org/obo/LEPAO_$1", - "version": "2021-11-20" + "version": "2023-02-18" }, "lgai.cede": { "description": "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR).", @@ -26678,12 +30025,21 @@ "name": "Ligand-Gated Ion Channel database", "pattern": "^\\w+$", "preferred_prefix": "lgic", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/lgicdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/27.1.340", "pmc": "PMC148177", "pubmed": "9847222", - "title": "The Ligand Gated Ion Channel Database.", + "title": "The Ligand Gated Ion Channel Database", "year": 1999 } ], @@ -26776,6 +30132,13 @@ "homepage": "http://ligand-expo.rcsb.org/", "name": "Ligand Expo at Rutgers", "uri_format": "http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ligandexpo:$1" } ], "publications": [ @@ -26783,7 +30146,7 @@ "doi": "10.1093/bioinformatics/bth214", "pmc": null, "pubmed": "15059838", - "title": "Ligand Depot: a data warehouse for ligands bound to macromolecules.", + "title": "Ligand Depot: a data warehouse for ligands bound to macromolecules", "year": 2004 } ], @@ -26930,7 +30293,7 @@ "doi": "10.5281/zenodo.5598314", "pmc": null, "pubmed": null, - "title": "linkml/linkml-model: v1.5.0rc2", + "title": "linkml/linkml-model: v1.5.2", "year": 2023 } ], @@ -26959,12 +30322,21 @@ "name": "LipidBank", "pattern": "^\\w+\\d+$", "preferred_prefix": "lipidbank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/lipidbank:$1" + } + ], "publications": [ { "doi": null, "pmc": null, "pubmed": "12058481", - "title": "[LIPIDBANK for Web, the newly developed lipid database].", + "title": "[LIPIDBANK for Web, the newly developed lipid database]", "year": 2002 } ], @@ -26998,6 +30370,13 @@ "pattern": "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$", "preferred_prefix": "lipidmaps", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/lipidmaps:$1" + }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", @@ -27011,29 +30390,36 @@ "doi": "10.1194/jlr.r800095-jlr200", "pmc": "PMC2674711", "pubmed": "19098281", - "title": "Update of the LIPID MAPS comprehensive classification system for lipids.", + "title": "Update of the LIPID MAPS comprehensive classification system for lipids", "year": 2008 }, { "doi": "10.1093/nar/gkm324", "pmc": "PMC1933166", "pubmed": "17584797", - "title": "LIPID MAPS online tools for lipid research.", + "title": "LIPID MAPS online tools for lipid research", "year": 2007 }, { "doi": "10.1093/nar/gkl838", "pmc": "PMC1669719", "pubmed": "17098933", - "title": "LMSD: LIPID MAPS structure database.", + "title": "LMSD: LIPID MAPS structure database", "year": 2006 }, { "doi": "10.1194/jlr.e400004-jlr200", "pmc": null, "pubmed": "15722563", - "title": "A comprehensive classification system for lipids.", + "title": "A comprehensive classification system for lipids", "year": 2005 + }, + { + "doi": "10.1194/jlr.R800095-JLR200", + "pmc": null, + "pubmed": null, + "title": "Update of the LIPID MAPS comprehensive classification system for lipids.", + "year": null } ], "synonyms": [ @@ -27066,6 +30452,7 @@ }, "name": "Lipid Ontology", "preferred_prefix": "LIPRO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1", "uri_format": "http://purl.obolibrary.org/obo/LIPRO_$1" }, "lncipedia": { @@ -27091,21 +30478,21 @@ "doi": "10.1093/nar/gkv295", "pmc": "PMC4417186", "pubmed": "25829178", - "title": "An update on LNCipedia: a database for annotated human lncRNA sequences.", + "title": "An update on LNCipedia: a database for annotated human lncRNA sequences", "year": 2015 }, { "doi": "10.1093/nar/gku1060", "pmc": "PMC4383901", "pubmed": "25378313", - "title": "An update on LNCipedia: a database for annotated human lncRNA sequences.", + "title": "An update on LNCipedia: a database for annotated human lncRNA sequences", "year": 2014 }, { "doi": "10.1093/nar/gks915", "pmc": "PMC3531107", "pubmed": "23042674", - "title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures.", + "title": "LNCipedia: a database for annotated human lncRNA transcript sequences and structures", "year": 2012 } ] @@ -27129,6 +30516,7 @@ }, "name": "Loggerhead nesting", "preferred_prefix": "LOGGERHEAD", + "rdf_uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1", "uri_format": "http://purl.obolibrary.org/obo/LOGGERHEAD_$1" }, "loinc": { @@ -27170,24 +30558,25 @@ "doi": "10.1016/s1386-5056(98)00089-6", "pmc": null, "pubmed": "9749897", - "title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC).", + "title": "Combining laboratory data sets from multiple institutions using the logical observation identifier names and codes (LOINC)", "year": 1998 }, { "doi": "10.1093/jamia/ocu012", "pmc": "PMC5566197", "pubmed": "25656513", - "title": "Supporting interoperability of genetic data with LOINC.", + "title": "Supporting interoperability of genetic data with LOINC", "year": 2015 }, { "doi": "10.1016/j.jbi.2012.01.005", "pmc": "PMC3376691", "pubmed": "22285984", - "title": "Enabling international adoption of LOINC through translation.", + "title": "Enabling international adoption of LOINC through translation", "year": 2012 } ], + "rdf_uri_format": "http://loinc.org/rdf/$1", "synonyms": [ "LNC" ], @@ -27221,12 +30610,21 @@ }, "name": "The localization and quantitation atlas of the yeast proteome", "preferred_prefix": "loqate", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/loqate:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt933", "pmc": "PMC3965041", "pubmed": "24150937", - "title": "LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.", + "title": "LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast", "year": 2013 } ], @@ -27261,6 +30659,7 @@ "drugs", "metabolites" ], + "logo": "https://upload.wikimedia.org/wikipedia/commons/6/64/Lotus_initiative_logo.svg", "name": "LOTUS Initiative for Open Natural Products Research", "pattern": "^LTS\\d{7}$", "preferred_prefix": "lotus", @@ -27352,7 +30751,7 @@ "uri_format": "http://useast.ensembl.org/Homo_sapiens/LRG/Summary?lrg=$1" } ], - "uri_format": "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml" + "uri_format": "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml" }, "lspci": { "contributor": { @@ -27426,15 +30825,25 @@ "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "MA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ma:$1" + } + ], "publications": [ { "doi": "10.1186/gb-2005-6-3-r29", "pmc": "PMC1088948", "pubmed": "15774030", - "title": "The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data.", + "title": "The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data", "year": 2005 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MA_$1", "repository": "https://github.com/obophenotype/mouse-anatomy-ontology", "uri_format": "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1", "version": "2017-02-07" @@ -27459,19 +30868,28 @@ "name": "Mechanism, Annotation and Classification in Enzymes", "pattern": "^M\\d{4}$", "preferred_prefix": "macie", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/macie:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkl774", "pmc": "PMC1634735", "pubmed": "17082206", - "title": "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.", + "title": "MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms", "year": 2006 }, { "doi": "10.1093/bioinformatics/bti693", "pmc": "PMC2748267", "pubmed": "16188925", - "title": "MACiE: a database of enzyme reaction mechanisms.", + "title": "MACiE: a database of enzyme reaction mechanisms", "year": 2005 } ], @@ -27502,47 +30920,56 @@ "name": "MaizeGDB Locus", "pattern": "^\\d+$", "preferred_prefix": "maizegdb.locus", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/maizegdb:$1" + } + ], "publications": [ { "doi": "10.3389/fpls.2019.01050", "pmc": "PMC6724615", "pubmed": "31555312", - "title": "MaizeDIG: Maize Database of Images and Genomes.", + "title": "MaizeDIG: Maize Database of Images and Genomes", "year": 2019 }, { "doi": "10.1093/nar/gky1046", "pmc": "PMC6323944", "pubmed": "30407532", - "title": "MaizeGDB 2018: the maize multi-genome genetics and genomics database.", + "title": "MaizeGDB 2018: the maize multi-genome genetics and genomics database", "year": 2019 }, { "doi": "10.1007/978-1-4939-3167-5_9", "pmc": null, "pubmed": "26519406", - "title": "MaizeGDB: The Maize Genetics and Genomics Database.", + "title": "MaizeGDB: The Maize Genetics and Genomics Database", "year": 2016 }, { "doi": "10.1093/nar/gkv1007", "pmc": "PMC4702771", "pubmed": "26432828", - "title": "MaizeGDB update: new tools, data and interface for the maize model organism database.", + "title": "MaizeGDB update: new tools, data and interface for the maize model organism database", "year": 2015 }, { "doi": "10.1155/2008/496957", "pmc": "PMC2518694", "pubmed": "18769488", - "title": "MaizeGDB: The maize model organism database for basic, translational, and applied research.", + "title": "MaizeGDB: The maize model organism database for basic, translational, and applied research", "year": 2008 }, { "doi": "10.1093/nar/gkl1048", "pmc": "PMC1899092", "pubmed": "17202174", - "title": "MaizeGDB's new data types, resources and activities.", + "title": "MaizeGDB's new data types, resources and activities", "year": 2007 } ], @@ -27587,6 +31014,7 @@ "name": "Mathematical modeling ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MAMO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MAMO_$1", "repository": "http://sourceforge.net/p/mamo-ontology", "uri_format": "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1", "version": "2020-08-24" @@ -27603,6 +31031,15 @@ }, "name": "Mammalia Polymorphism Database", "preferred_prefix": "mampol", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mampol:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -27635,6 +31072,16 @@ }, "name": "Multiple alignment", "preferred_prefix": "MAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mao:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MAO_$1", "uri_format": "http://purl.obolibrary.org/obo/MAO_$1" }, "massbank": { @@ -27659,7 +31106,7 @@ "n2t": "massbank", "wikidata": "P6689" }, - "name": "MassBank accession", + "name": "MassBank", "pattern": "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$", "preferred_prefix": "massbank", "providers": [ @@ -27676,7 +31123,7 @@ "doi": "10.1002/jms.1777", "pmc": null, "pubmed": "20623627", - "title": "MassBank: a public repository for sharing mass spectral data for life sciences.", + "title": "MassBank: a public repository for sharing mass spectral data for life sciences", "year": 2010 } ], @@ -27725,35 +31172,35 @@ "doi": "10.1038/s41592-020-0955-0", "pmc": "PMC7541731", "pubmed": "32929271", - "title": "MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets.", + "title": "MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets", "year": 2020 }, { "doi": "10.1093/nar/gkz984", "pmc": "PMC7145525", "pubmed": "31686107", - "title": "The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.", + "title": "The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics", "year": 2020 }, { "doi": "10.1016/j.cels.2018.08.004", "pmc": "PMC6279426", "pubmed": "30172843", - "title": "Assembling the Community-Scale Discoverable Human Proteome.", + "title": "Assembling the Community-Scale Discoverable Human Proteome", "year": 2018 }, { "doi": "10.1093/nar/gkw936", "pmc": "PMC5210636", "pubmed": "27924013", - "title": "The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.", + "title": "The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition", "year": 2016 }, { "doi": "10.1038/nbt.3597", "pmc": "PMC5321674", "pubmed": "27504778", - "title": "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.", + "title": "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking", "year": 2016 } ], @@ -27784,6 +31231,7 @@ "name": "Minimal Anatomical Terminology", "pattern": "^\\d{7}$", "preferred_prefix": "MAT", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MAT_$1", "uri_format": "http://purl.obolibrary.org/obo/MAT_$1" }, "matrixdb": { @@ -27812,33 +31260,42 @@ }, "name": "MatrixDB", "preferred_prefix": "matrixdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/matrixdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gky1035", "pmc": "PMC6324007", "pubmed": "30371822", - "title": "MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.", + "title": "MatrixDB: integration of new data with a focus on glycosaminoglycan interactions", "year": 2019 }, { "doi": "10.1093/nar/gku1091", "pmc": "PMC4383919", "pubmed": "25378329", - "title": "MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.", + "title": "MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities", "year": 2014 }, { "doi": "10.1093/nar/gkq830", "pmc": "PMC3013758", "pubmed": "20852260", - "title": "MatrixDB, the extracellular matrix interaction database.", + "title": "MatrixDB, the extracellular matrix interaction database", "year": 2010 }, { "doi": "10.1093/bioinformatics/btp025", "pmc": "PMC2647840", "pubmed": "19147664", - "title": "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.", + "title": "MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions", "year": 2009 } ], @@ -27890,6 +31347,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png", "mappings": { "aberowl": "MAXO", "biolink": "MAXO", @@ -27901,10 +31359,11 @@ "name": "Medical Action Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MAXO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MAXO_$1", "repository": "https://github.com/monarch-initiative/MAxO", "twitter": "MonarchInit", "uri_format": "http://purl.obolibrary.org/obo/MAXO_$1", - "version": "2022-12-09" + "version": "2023-06-06" }, "mba": { "contact": { @@ -27998,6 +31457,7 @@ "name": "Microbial Conditions Ontology", "pattern": "^\\d+$", "preferred_prefix": "MCO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "repository": "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology", "uri_format": "http://purl.obolibrary.org/obo/MCO_$1", "version": "2019-05-15" @@ -28036,7 +31496,7 @@ "doi": "10.1093/database/bav121", "pmc": "PMC4750548", "pubmed": "26868052", - "title": "Portal of medical data models: information infrastructure for medical research and healthcare.", + "title": "Portal of medical data models: information infrastructure for medical research and healthcare", "year": 2016 } ], @@ -28077,17 +31537,18 @@ "doi": "10.1016/s1386-5056(00)00062-9", "pmc": null, "pubmed": "10961570", - "title": "The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM).", + "title": "The use of a medical dictionary for regulatory activities terminology (MedDRA) in prescription-event monitoring in Japan (J-PEM)", "year": 2000 }, { "doi": "10.2165/00002018-199920020-00002", "pmc": null, "pubmed": "10082069", - "title": "The medical dictionary for regulatory activities (MedDRA).", + "title": "The medical dictionary for regulatory activities (MedDRA)", "year": 1999 } ], + "rdf_uri_format": "http://purl.bioontology.org/ontology/MDRFRE/$1", "synonyms": [ "MEDRA", "MeDRA", @@ -28169,7 +31630,7 @@ "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", - "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.", + "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 } ], @@ -28204,54 +31665,63 @@ "name": "MEROPS Entry", "pattern": "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$", "preferred_prefix": "merops.entry", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/merops:$1" + } + ], "publications": [ { "doi": "10.1093/nar/27.1.325", "pmc": "PMC148173", "pubmed": "9847218", - "title": "MEROPS: the peptidase database.", + "title": "MEROPS: the peptidase database", "year": 1999 }, { "doi": "10.1042/bj2900205", "pmc": "PMC1132403", "pubmed": "8439290", - "title": "Evolutionary families of peptidases.", + "title": "Evolutionary families of peptidases", "year": 1993 }, { "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", - "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.", + "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 }, { "doi": "10.1093/nar/gkv1118", "pmc": "PMC4702814", "pubmed": "26527717", - "title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.", + "title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors", "year": 2015 }, { "doi": "10.1016/j.biochi.2015.10.003", "pmc": "PMC4756867", "pubmed": "26455268", - "title": "Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation.", + "title": "Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation", "year": 2015 }, { "doi": "10.1093/nar/gkr987", "pmc": "PMC3245014", "pubmed": "22086950", - "title": "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.", + "title": "MEROPS: the database of proteolytic enzymes, their substrates and inhibitors", "year": 2011 }, { "doi": "10.1093/nar/gkm954", "pmc": "PMC2238837", "pubmed": "17991683", - "title": "MEROPS: the peptidase database.", + "title": "MEROPS: the peptidase database", "year": 2007 } ], @@ -28281,7 +31751,7 @@ "doi": "10.1093/nar/gkx1134", "pmc": "PMC5753285", "pubmed": "29145643", - "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.", + "title": "The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database", "year": 2018 } ], @@ -28332,15 +31802,25 @@ "name": "Medical Subject Headings", "pattern": "^(C|D)\\d{6,9}$", "preferred_prefix": "mesh", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mesh:$1" + } + ], "publications": [ { "doi": null, "pmc": "PMC197951", "pubmed": "13982385", - "title": "Medical subject headings.", + "title": "Medical subject headings", "year": 1963 } ], + "rdf_uri_format": "http://id.nlm.nih.gov/mesh/$1", "synonyms": [ "MESH", "MESHA", @@ -28456,21 +31936,21 @@ "doi": "10.1093/nar/gkv1164", "pmc": "PMC4702838", "pubmed": "26527732", - "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2015 }, { "doi": "10.1093/nar/gkt1103", "pmc": "PMC3964957", "pubmed": "24225315", - "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases", "year": 2013 }, { "doi": "10.1093/nar/gkr1014", "pmc": "PMC3245006", "pubmed": "22102576", - "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.", + "title": "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", "year": 2011 } ], @@ -28679,6 +32159,15 @@ }, "name": "Metabolic Network Exchange Database", "preferred_prefix": "metnetdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/metnetdb:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -28740,9 +32229,10 @@ "name": "Mental Functioning Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MF", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MF_$1", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MF_$1", - "version": "2021-11-17" + "version": "2022-07-19" }, "mfmo": { "contact": { @@ -28785,16 +32275,17 @@ "uri_format": "http://purl.obolibrary.org/obo/mfmo.owl#MFMO_$1" } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", "repository": "https://github.com/RDruzinsky/feedontology", "uri_format": "http://purl.obolibrary.org/obo/MFMO_$1", "version": "2013-11-16" }, "mfo": { "contact": { - "email": "Thorsten.Henrich@embl-heidelberg.de", - "github": null, + "email": "henrich@embl.de", + "github": "ThorstenHen", "name": "Thorsten Henrich", - "orcid": null + "orcid": "0000-0002-1548-3290" }, "deprecated": true, "description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.", @@ -28818,6 +32309,16 @@ }, "name": "Medaka fish anatomy and development", "preferred_prefix": "MFO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mfo:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MFO_$1", "uri_format": "http://purl.obolibrary.org/obo/MFO_$1" }, "mfoem": { @@ -28854,13 +32355,14 @@ "doi": "10.1186/2041-1480-5-38", "pmc": "PMC4417517", "pubmed": "25937879", - "title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.", + "title": "Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", "repository": "https://github.com/jannahastings/emotion-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOEM_$1", - "version": "2021-11-17" + "version": "2022-07-19" }, "mfomd": { "contact": { @@ -28891,6 +32393,7 @@ "name": "Mental Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MFOMD", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "repository": "https://github.com/jannahastings/mental-functioning-ontology", "uri_format": "http://purl.obolibrary.org/obo/MFOMD_$1", "version": "2020-04-26" @@ -28918,19 +32421,28 @@ "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "mge", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/aclame:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp938", "pmc": "PMC2808911", "pubmed": "19933762", - "title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010.", + "title": "ACLAME: a CLAssification of Mobile genetic Elements, update 2010", "year": 2009 }, { "doi": "10.1093/nar/gkh084", "pmc": "PMC308818", "pubmed": "14681355", - "title": "ACLAME: a CLAssification of Mobile genetic Elements.", + "title": "ACLAME: a CLAssification of Mobile genetic Elements", "year": 2004 } ], @@ -28977,6 +32489,13 @@ "name": "MGI through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/MGI:$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mgi:$1" + }, { "code": "mgi.marker", "description": "MGI Marker", @@ -28990,70 +32509,70 @@ "doi": "10.1126/science.8091224", "pmc": null, "pubmed": "8091224", - "title": "A database for mouse development.", + "title": "A database for mouse development", "year": 1994 }, { "doi": "10.1093/nar/gky1056", "pmc": "PMC6323923", "pubmed": "30407599", - "title": "Mouse Genome Database (MGD) 2019.", + "title": "Mouse Genome Database (MGD) 2019", "year": 2019 }, { "doi": "10.1093/nar/gky922", "pmc": "PMC6324054", "pubmed": "30335138", - "title": "The mouse Gene Expression Database (GXD): 2019 update.", + "title": "The mouse Gene Expression Database (GXD): 2019 update", "year": 2019 }, { "doi": "10.1093/ilar/ilx013", "pmc": "PMC5886341", "pubmed": "28838066", - "title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.", + "title": "Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse", "year": 2017 }, { "doi": "10.1007/978-1-4939-6427-7_3", "pmc": null, "pubmed": "27933520", - "title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.", + "title": "Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research", "year": 2017 }, { "doi": "10.1093/nar/gkw1040", "pmc": "PMC5210536", "pubmed": "27899570", - "title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse.", + "title": "Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse", "year": 2016 }, { "doi": "10.1093/nar/gkt1225", "pmc": "PMC3964950", "pubmed": "24285300", - "title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse.", + "title": "The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse", "year": 2013 }, { "doi": "10.1093/nar/gks1115", "pmc": "PMC3531104", "pubmed": "23175610", - "title": "The mouse genome database: genotypes, phenotypes, and models of human disease.", + "title": "The mouse genome database: genotypes, phenotypes, and models of human disease", "year": 2012 }, { "doi": "10.1093/nar/gkr974", "pmc": "PMC3245042", "pubmed": "22075990", - "title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.", + "title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse", "year": 2011 }, { "doi": "10.1093/nar/gki113", "pmc": "PMC540067", "pubmed": "15608240", - "title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.", + "title": "The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology", "year": 2005 } ], @@ -29108,10 +32627,10 @@ "mi": { "banana": "MI", "contact": { - "email": "pporras@ebi.ac.uk", - "github": "pporrasebi", - "name": "Pablo Porras Millán", - "orcid": "0000-0002-8429-8793" + "email": "luana.licata@gmail.com", + "github": "luanalicata", + "name": "Luana Licata", + "orcid": "0000-0001-5084-9000" }, "description": "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.", "download_obo": "http://purl.obolibrary.org/obo/mi.obo", @@ -29144,20 +32663,30 @@ "namespace_in_lui": true, "pattern": "^\\d{4}$", "preferred_prefix": "MI", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/psi.mi:$1" + } + ], "publications": [ { "doi": "10.1038/nbt926", "pmc": null, "pubmed": "14755292", - "title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.", + "title": "The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MI_$1", "repository": "https://github.com/HUPO-PSI/psi-mi-CV", "synonyms": [ "PSI-MI" ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mi/terms?obo_id=MI:$1" }, "miaa": { "comment": "same as MAT", @@ -29210,13 +32739,13 @@ "doi": "10.1089/omi.2006.10.231", "pmc": "PMC3167193", "pubmed": "16901231", - "title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).", + "title": "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)", "year": 2006 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1", "repository": "https://github.com/evoinfo/miapa", - "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1", - "version": "2017-05-09" + "uri_format": "http://purl.obolibrary.org/obo/MIAPA_$1" }, "micro": { "appears_in": [ @@ -29228,6 +32757,7 @@ "name": "Carrine Blank", "orcid": "0000-0002-2100-6351" }, + "deprecated": true, "description": "An ontology of prokaryotic phenotypic and metabolic characters", "download_owl": "http://purl.obolibrary.org/obo/micro.owl", "example": "0002999", @@ -29255,10 +32785,11 @@ "doi": "10.1186/s13326-016-0060-6", "pmc": "PMC4830071", "pubmed": "27076900", - "title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.", + "title": "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions", "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "repository": "https://github.com/carrineblank/MicrO", "uri_format": "http://purl.obolibrary.org/obo/MICRO_$1", "version": "1.5.1" @@ -29286,7 +32817,7 @@ "doi": "10.1093/nar/gks1194", "pmc": "PMC3531135", "pubmed": "23193269", - "title": "MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.", + "title": "MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data", "year": 2012 } ], @@ -29309,12 +32840,21 @@ "name": "MicrosporidiaDB", "pattern": "^\\w+$", "preferred_prefix": "microsporidia", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/microsporidia:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp941", "pmc": "PMC2808945", "pubmed": "19914931", - "title": "EuPathDB: a portal to eukaryotic pathogen databases.", + "title": "EuPathDB: a portal to eukaryotic pathogen databases", "year": 2009 } ], @@ -29350,26 +32890,35 @@ "name": "MimoDB", "pattern": "^\\d+$", "preferred_prefix": "mimodb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mimodb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkv1100", "pmc": "PMC4702802", "pubmed": "26503249", - "title": "BDB: biopanning data bank.", + "title": "BDB: biopanning data bank", "year": 2015 }, { "doi": "10.1093/nar/gkr922", "pmc": "PMC3245166", "pubmed": "22053087", - "title": "MimoDB 2.0: a mimotope database and beyond.", + "title": "MimoDB 2.0: a mimotope database and beyond", "year": 2011 }, { "doi": "10.3390/molecules15118279", "pmc": "PMC6259156", "pubmed": "21079566", - "title": "MimoDB: a new repository for mimotope data derived from phage display technology.", + "title": "MimoDB: a new repository for mimotope data derived from phage display technology", "year": 2010 } ], @@ -29433,6 +32982,13 @@ "pattern": "^\\d{1,7}$", "preferred_prefix": "mint", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mint:$1" + }, { "code": "ebi", "description": "MINT subset through IntAct", @@ -29446,28 +33002,28 @@ "doi": "10.1093/nar/gkr930", "pmc": "PMC3244991", "pubmed": "22096227", - "title": "MINT, the molecular interaction database: 2012 update.", + "title": "MINT, the molecular interaction database: 2012 update", "year": 2011 }, { "doi": "10.1093/nar/gkp983", "pmc": "PMC2808973", "pubmed": "19897547", - "title": "MINT, the molecular interaction database: 2009 update.", + "title": "MINT, the molecular interaction database: 2009 update", "year": 2009 }, { "doi": "10.1093/nar/gkl950", "pmc": "PMC1751541", "pubmed": "17135203", - "title": "MINT: the Molecular INTeraction database.", + "title": "MINT: the Molecular INTeraction database", "year": 2006 }, { "doi": "10.1016/s0014-5793(01)03293-8", "pmc": null, "pubmed": "11911893", - "title": "MINT: a Molecular INTeraction database.", + "title": "MINT: a Molecular INTeraction database", "year": 2002 } ], @@ -29491,12 +33047,21 @@ "name": "MIPModDB", "pattern": "^\\w+$", "preferred_prefix": "mipmod", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mipmod:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr914", "pmc": "PMC3245135", "pubmed": "22080560", - "title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins.", + "title": "MIPModDB: a central resource for the superfamily of major intrinsic proteins", "year": 2011 } ], @@ -29542,47 +33107,56 @@ "name": "miRBase pre-miRNA", "pattern": "^MI\\d{7}$", "preferred_prefix": "mirbase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mirbase:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gky1141", "pmc": "PMC6323917", "pubmed": "30423142", - "title": "miRBase: from microRNA sequences to function.", + "title": "miRBase: from microRNA sequences to function", "year": 2019 }, { "doi": "10.1093/nar/gkt1181", "pmc": "PMC3965103", "pubmed": "24275495", - "title": "miRBase: annotating high confidence microRNAs using deep sequencing data.", + "title": "miRBase: annotating high confidence microRNAs using deep sequencing data", "year": 2013 }, { "doi": "10.1093/nar/gkq1027", "pmc": "PMC3013655", "pubmed": "21037258", - "title": "miRBase: integrating microRNA annotation and deep-sequencing data.", + "title": "miRBase: integrating microRNA annotation and deep-sequencing data", "year": 2010 }, { "doi": "10.1093/nar/gkm952", "pmc": "PMC2238936", "pubmed": "17991681", - "title": "miRBase: tools for microRNA genomics.", + "title": "miRBase: tools for microRNA genomics", "year": 2007 }, { "doi": "10.1093/nar/gkj112", "pmc": "PMC1347474", "pubmed": "16381832", - "title": "miRBase: microRNA sequences, targets and gene nomenclature.", + "title": "miRBase: microRNA sequences, targets and gene nomenclature", "year": 2006 }, { "doi": "10.1093/nar/gkh023", "pmc": "PMC308757", "pubmed": "14681370", - "title": "The microRNA Registry.", + "title": "The microRNA Registry", "year": 2004 } ], @@ -29623,6 +33197,15 @@ "name": "miRBase mature miRNA", "pattern": "^MIMAT\\d{7}$", "preferred_prefix": "mirbase.mature", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mirbase.mature:$1" + } + ], "synonyms": [ "MIRBASEM" ], @@ -29649,14 +33232,14 @@ "doi": "10.1186/s12870-015-0533-2", "pmc": "PMC4490709", "pubmed": "26141515", - "title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs.", + "title": "mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs", "year": 2015 }, { "doi": "10.1093/nar/gkr878", "pmc": "PMC3245179", "pubmed": "22013167", - "title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data.", + "title": "mirEX: a platform for comparative exploration of plant pri-miRNA expression data", "year": 2011 } ], @@ -29690,21 +33273,21 @@ "doi": "10.1093/nar/gkr1097", "pmc": "PMC3245029", "pubmed": "22140103", - "title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification.", + "title": "Identifiers.org and MIRIAM Registry: community resources to provide persistent identification", "year": 2011 }, { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", - "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.", + "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology", "year": 2007 }, { "doi": "10.1038/nbt1156", "pmc": null, "pubmed": "16333295", - "title": "Minimum information requested in the annotation of biochemical models (MIRIAM).", + "title": "Minimum information requested in the annotation of biochemical models (MIRIAM)", "year": 2005 } ], @@ -29749,12 +33332,21 @@ "part_of": "miriam", "pattern": "^001\\d{5}$", "preferred_prefix": "miriam.resource", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/miriam.resource:$1" + } + ], "publications": [ { "doi": "10.1186/1752-0509-1-58", "pmc": "PMC2259379", "pubmed": "18078503", - "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology.", + "title": "MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology", "year": 2007 } ], @@ -29785,6 +33377,7 @@ }, "name": "microRNA Ontology", "preferred_prefix": "MIRNAO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1", "uri_format": "http://purl.obolibrary.org/obo/MIRNAO_$1" }, "mirnest": { @@ -29807,19 +33400,28 @@ "name": "miRNEST", "pattern": "^MNEST\\d+$", "preferred_prefix": "mirnest", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mirnest:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1156", "pmc": "PMC3965105", "pubmed": "24243848", - "title": "miRNEST 2.0: a database of plant and animal microRNAs.", + "title": "miRNEST 2.0: a database of plant and animal microRNAs", "year": 2013 }, { "doi": "10.1093/nar/gkr1159", "pmc": "PMC3245016", "pubmed": "22135287", - "title": "miRNEST database: an integrative approach in microRNA search and annotation.", + "title": "miRNEST database: an integrative approach in microRNA search and annotation", "year": 2011 } ], @@ -29860,10 +33462,11 @@ "doi": "10.1371/journal.pntd.0000465", "pmc": "PMC2694272", "pubmed": "19547750", - "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.", + "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "repository": "https://github.com/VEuPathDB-ontology/MIRO", "uri_format": "http://purl.obolibrary.org/obo/MIRO_$1", "version": "2014-05-14" @@ -29896,7 +33499,7 @@ "doi": "10.1093/nar/gkq1107", "pmc": "PMC3013699", "pubmed": "21071411", - "title": "miRTarBase: a database curates experimentally validated microRNA-target interactions.", + "title": "miRTarBase: a database curates experimentally validated microRNA-target interactions", "year": 2010 } ], @@ -29966,7 +33569,7 @@ "doi": "10.1038/nbt.1823", "pmc": "PMC3367316", "pubmed": "21552244", - "title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.", + "title": "Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications", "year": 2011 } ], @@ -30011,12 +33614,21 @@ "name": "Molecular Modeling Database", "pattern": "^\\d{1,5}$", "preferred_prefix": "mmdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mmdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkl952", "pmc": "PMC1751549", "pubmed": "17135201", - "title": "MMDB: annotating protein sequences with Entrez's 3D-structure database.", + "title": "MMDB: annotating protein sequences with Entrez's 3D-structure database", "year": 2006 } ], @@ -30041,6 +33653,15 @@ "name": "Melanoma Molecular Map Project Biomaps", "pattern": "^\\d+$", "preferred_prefix": "mmmp.biomaps", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mmmp:$1" + } + ], "synonyms": [ "mmmp:biomaps" ], @@ -30053,7 +33674,7 @@ "name": "Jennifer Smith", "orcid": "0000-0002-6443-9376" }, - "description": "A representation of the variety of methods used to make clinical and phenotype measurements. ", + "description": "A representation of the variety of methods used to make clinical and phenotype measurements.", "download_obo": "http://purl.obolibrary.org/obo/mmo.obo", "download_owl": "http://purl.obolibrary.org/obo/mmo.owl", "example": "0000574", @@ -30083,21 +33704,22 @@ "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", - "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", + "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", - "title": "Three ontologies to define phenotype measurement data.", + "title": "Three ontologies to define phenotype measurement data", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MMO_$1", "repository": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/MMO_$1", - "version": "2019-03-27" + "version": "2.39" }, "mmp.cat": { "description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.", @@ -30176,7 +33798,7 @@ "doi": null, "pmc": null, "pubmed": "12102564", - "title": "Mutant Mouse Regional Resource Center Program: a resource for distribution of mouse models for biomedical research.", + "title": "Mutant Mouse Regional Resource Center Program: a resource for distribution of mouse models for biomedical research", "year": 2002 } ], @@ -30196,6 +33818,15 @@ }, "name": "MMsINC", "preferred_prefix": "mmsinc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mmsinc:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -30257,11 +33888,12 @@ "name": "Mouse Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "MmusDv", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MmusDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "MmusDv" ], - "uri_format": "http://purl.obolibrary.org/obo/MMUSDV_$1", + "uri_format": "http://purl.obolibrary.org/obo/MmusDv_$1", "version": "2020-03-10" }, "mo": { @@ -30300,6 +33932,7 @@ "uri_format": "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1" } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MO_$1", "uri_format": "http://purl.obolibrary.org/obo/MO_$1" }, "mobidb": { @@ -30332,35 +33965,35 @@ "doi": "10.1093/nar/gkaa1058", "pmc": "PMC7779018", "pubmed": "33237329", - "title": "MobiDB: intrinsically disordered proteins in 2021.", + "title": "MobiDB: intrinsically disordered proteins in 2021", "year": 2021 }, { "doi": "10.1093/nar/gkx1071", "pmc": "PMC5753340", "pubmed": "29136219", - "title": "MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins.", + "title": "MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins", "year": 2018 }, { "doi": "10.1093/bioinformatics/bts327", "pmc": "PMC5753340", "pubmed": "29136219", - "title": null, + "title": "MobiDB: a comprehensive database of intrinsic protein disorder annotations.", "year": null }, { "doi": "10.1093/nar/gku982", "pmc": "PMC4384034", "pubmed": "25361972", - "title": "MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins.", + "title": "MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins", "year": 2014 }, { "doi": "10.1093/bioinformatics/bts327", "pmc": null, "pubmed": "22661649", - "title": "MobiDB: a comprehensive database of intrinsic protein disorder annotations.", + "title": "MobiDB: a comprehensive database of intrinsic protein disorder annotations", "year": 2012 } ], @@ -30405,25 +34038,36 @@ "namespace_in_lui": true, "pattern": "^\\d{5}$", "preferred_prefix": "MOD", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/psi.mod:$1" + } + ], "publications": [ { "doi": "10.1038/nbt0808-864", "pmc": null, "pubmed": "18688235", - "title": "The PSI-MOD community standard for representation of protein modification data.", + "title": "The PSI-MOD community standard for representation of protein modification data", "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MOD_$1", "repository": "https://github.com/HUPO-PSI/psi-mod-CV", "synonyms": [ "PSI-MOD" ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1" + "uri_format": "http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1", + "version": "1.031.6" }, "modeldb": { "description": "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment.", "example": "45539", - "homepage": "http://senselab.med.yale.edu/ModelDB/", + "homepage": "https://modeldb.science", "keywords": [ "computational biology", "life science", @@ -30441,38 +34085,61 @@ "name": "ModelDB", "pattern": "^\\d+$", "preferred_prefix": "modeldb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/modeldb:$1" + } + ], "publications": [ { "doi": "10.1136/jamia.1996.97084512", "pmc": "PMC116323", "pubmed": "8930855", - "title": "ModelDB: an environment for running and storing computational models and their results applied to neuroscience.", + "title": "ModelDB: an environment for running and storing computational models and their results applied to neuroscience", "year": 1996 }, { "doi": "10.1007/s10827-016-0623-7", "pmc": "PMC5279891", "pubmed": "27629590", - "title": "Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience.", + "title": "Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience", "year": 2016 }, { "doi": "10.1023/b:jcns.0000023869.22017.2e", "pmc": "PMC3732827", "pubmed": "15218350", - "title": "ModelDB: A Database to Support Computational Neuroscience.", + "title": "ModelDB: A Database to Support Computational Neuroscience", "year": 2004 }, { "doi": "10.1385/ni:1:1:135", "pmc": "PMC3728921", "pubmed": "15055399", - "title": "ModelDB: making models publicly accessible to support computational neuroscience.", + "title": "ModelDB: making models publicly accessible to support computational neuroscience", "year": 2003 + }, + { + "doi": "10.1385/NI:1:1:135", + "pmc": null, + "pubmed": null, + "title": "ModelDB: making models publicly accessible to support computational neuroscience.", + "year": null + }, + { + "doi": "10.1023/B:JCNS.0000023869.22017.2e", + "pmc": null, + "pubmed": null, + "title": "ModelDB: A Database to Support Computational Neuroscience.", + "year": null } ], "twitter": "SenseLabProject", - "uri_format": "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1" + "uri_format": "https://modeldb.science/$1" }, "modeldb.concept": { "description": "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models.", @@ -30568,6 +34235,15 @@ }, "name": "Database of Macromolecular Movements", "preferred_prefix": "molmovdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/molmovdb:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -30596,6 +34272,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://raw.githubusercontent.com/monarch-initiative/mondo/master/docs/images/mondo_logo_black-stacked-small.png", "mappings": { "aberowl": "MONDO", "biocontext": "MONDO", @@ -30606,7 +34283,8 @@ "ontobee": "MONDO", "wikidata": "P5270" }, - "name": "Monarch Disease Ontology", + "mastodon": "monarch_initiative@genomic.social", + "name": "Mondo Disease Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MONDO", "publications": [ @@ -30618,10 +34296,11 @@ "year": 2022 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MONDO_$1", "repository": "https://github.com/monarch-initiative/mondo", "twitter": "MonarchInit", "uri_format": "http://purl.obolibrary.org/obo/MONDO_$1", - "version": "2022-12-01" + "version": "2023-06-01" }, "mop": { "contact": { @@ -30653,9 +34332,10 @@ "name": "Molecular Process Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MOP", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MOP_$1", "repository": "https://github.com/rsc-ontologies/rxno", "uri_format": "http://purl.obolibrary.org/obo/MOP_$1", - "version": "2022-02-01" + "version": "2022-05-11" }, "morpheus": { "description": "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n", @@ -30752,6 +34432,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "MP", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mp:$1" + }, { "code": "nextprot", "description": "The neXtProt endpoint for exploring MP", @@ -30765,31 +34452,32 @@ "doi": "10.1186/s13326-015-0009-1", "pmc": "PMC4378007", "pubmed": "25825651", - "title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens.", + "title": "Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens", "year": 2015 }, { "doi": "10.1007/s00335-012-9421-3", "pmc": "PMC3463787", "pubmed": "22961259", - "title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.", + "title": "The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data", "year": 2012 }, { "doi": "10.1002/wsbm.44", "pmc": "PMC2801442", "pubmed": "20052305", - "title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis.", + "title": "The mammalian phenotype ontology: enabling robust annotation and comparative analysis", "year": 2009 }, { "doi": "10.1186/gb-2004-6-1-r7", "pmc": "PMC549068", "pubmed": "15642099", - "title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.", + "title": "The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MP_$1", "repository": "https://github.com/mgijax/mammalian-phenotype-ontology", "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1" }, @@ -30827,15 +34515,25 @@ "name": "Mouse pathology ontology", "pattern": "^\\d+$", "preferred_prefix": "MPATH", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mpath:$1" + } + ], "publications": [ { "doi": "10.1177/0300985810374845", "pmc": "PMC3038412", "pubmed": "20587689", - "title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology.", + "title": "Pathbase and the MPATH ontology. Community resources for mouse histopathology", "year": 2010 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MPATH_$1", "repository": "https://github.com/PaulNSchofield/mpath", "synonyms": [ "MPATH" @@ -30864,6 +34562,13 @@ "pattern": "^\\d+$", "preferred_prefix": "mpid", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mpi:$1" + }, { "code": "ebi", "description": "Microbial Protein Interaction Database subset through IntAct", @@ -30877,7 +34582,7 @@ "doi": "10.1093/bioinformatics/btn285", "pmc": "PMC2638870", "pubmed": "18556668", - "title": "MPIDB: the microbial protein interaction database.", + "title": "MPIDB: the microbial protein interaction database", "year": 2008 } ], @@ -30913,6 +34618,7 @@ "name": "Minimum PDDI Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "MPIO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/MPIO_$1", "repository": "https://github.com/MPIO-Developers/MPIO", "uri_format": "http://purl.obolibrary.org/obo/MPIO_$1", "version": "2019-01-30" @@ -30951,13 +34657,14 @@ "doi": "10.1186/s13326-016-0045-5", "pmc": "PMC4709943", "pubmed": "26759709", - "title": "An ontology for major histocompatibility restriction.", + "title": "An ontology for major histocompatibility restriction", "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MRO_$1", "repository": "https://github.com/IEDB/MRO", "uri_format": "http://purl.obolibrary.org/obo/MRO_$1", - "version": "2022-06-17" + "version": "2023-06-06" }, "ms": { "banana": "MS", @@ -31000,12 +34707,14 @@ "doi": "10.1093/database/bat009", "pmc": "PMC3594986", "pubmed": "23482073", - "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.", + "title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/MS_$1", "repository": "https://github.com/HUPO-PSI/psi-ms-CV", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1" + "uri_format": "http://purl.obolibrary.org/obo/MS_$1", + "version": "4.1.127" }, "msigdb": { "contributor": { @@ -31059,6 +34768,15 @@ }, "name": "Mouse Tumor Biology Database", "preferred_prefix": "mtbd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mtbd:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -31192,6 +34910,15 @@ "name": "MycoBrowser leprae", "pattern": "^ML\\w+$", "preferred_prefix": "myco.lepra", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/myco.lepra:$1" + } + ], "uri_format": "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1" }, "myco.marinum": { @@ -31211,6 +34938,15 @@ "name": "MycoBrowser marinum", "pattern": "^MMAR\\_\\d+$", "preferred_prefix": "myco.marinum", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/myco.marinum:$1" + } + ], "uri_format": "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1" }, "myco.smeg": { @@ -31230,6 +34966,15 @@ "name": "MycoBrowser smegmatis", "pattern": "^MSMEG\\w+$", "preferred_prefix": "myco.smeg", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/myco.smeg:$1" + } + ], "uri_format": "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1" }, "myco.tuber": { @@ -31252,12 +34997,21 @@ "name": "TubercuList knowledge base", "pattern": "^Rv\\d{4}(A|B|c)?$", "preferred_prefix": "myco.tuber", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tuberculist:$1" + } + ], "publications": [ { "doi": "10.1016/j.tube.2010.09.006", "pmc": null, "pubmed": "20980200", - "title": "The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.", + "title": "The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes", "year": 2010 } ], @@ -31287,12 +35041,21 @@ "name": "Fungal Nomenclature and Species Bank", "pattern": "^\\d+$", "preferred_prefix": "mycobank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/mycobank:$1" + } + ], "publications": [ { "doi": "10.5598/imafungus.2013.04.02.16", "pmc": "PMC3905949", "pubmed": "24563843", - "title": "MycoBank gearing up for new horizons.", + "title": "MycoBank gearing up for new horizons", "year": 2013 } ], @@ -31332,7 +35095,7 @@ "doi": "10.1038/s41592-021-01184-6", "pmc": "PMC8405201", "pubmed": "34183830", - "title": "Universal Spectrum Identifier for mass spectra.", + "title": "Universal Spectrum Identifier for mass spectra", "year": 2021 } ], @@ -31375,7 +35138,7 @@ "doi": "10.1021/acs.jmedchem.6b00153", "pmc": null, "pubmed": "27028220", - "title": "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter.", + "title": "Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter", "year": 2016 }, { @@ -31391,6 +35154,20 @@ "https://twitter.com/cthoyt/status/1443929184745758723" ] }, + "nando": { + "banana": "NANDO", + "description": "Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan.", + "example": "1200031", + "homepage": "https://nanbyodata.jp/", + "mappings": { + "miriam": "nando" + }, + "name": "Nanbyo Disease Ontology", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "nando", + "uri_format": "https://nanbyodata.jp/disease/NANDO:$1" + }, "napdi": { "contact": { "email": "rdb20@pitt.edu", @@ -31419,7 +35196,7 @@ "doi": "10.1186/s13326-018-0183-z", "pmc": "PMC5944177", "pubmed": "29743102", - "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.", + "title": "Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse", "year": 2018 } ], @@ -31450,19 +35227,28 @@ "name": "Nucleic Acids Phylogenetic Profiling", "pattern": "^\\d+$", "preferred_prefix": "napp", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/napp:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr807", "pmc": "PMC3245103", "pubmed": "21984475", - "title": "NAPP: the Nucleic Acid Phylogenetic Profile Database.", + "title": "NAPP: the Nucleic Acid Phylogenetic Profile Database", "year": 2011 }, { "doi": "10.1101/gr.089714.108", "pmc": "PMC2694484", "pubmed": "19237465", - "title": "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles.", + "title": "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles", "year": 2009 } ], @@ -31511,12 +35297,21 @@ "name": "NASC code", "pattern": "^(\\w+)?\\d+$", "preferred_prefix": "nasc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nasc:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh133", "pmc": "PMC308867", "pubmed": "14681484", - "title": "NASCArrays: a repository for microarray data generated by NASC's transcriptomics service.", + "title": "NASCArrays: a repository for microarray data generated by NASC's transcriptomics service", "year": 2004 } ], @@ -31533,7 +35328,7 @@ "n2t": "nbn" }, "name": "National Bibliography Number", - "pattern": "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$", + "pattern": "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$", "preferred_prefix": "nbn", "uri_format": "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect" }, @@ -31579,20 +35374,28 @@ "doi": "10.1007/s00335-013-9481-z", "pmc": null, "pubmed": "24177753", - "title": "Analyzing gene expression data in mice with the Neuro Behavior Ontology.", + "title": "Analyzing gene expression data in mice with the Neuro Behavior Ontology", "year": 2013 }, { "doi": "10.1016/b978-0-12-388408-4.00004-6", "pmc": null, "pubmed": "23195121", - "title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.", + "title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes", "year": 2012 + }, + { + "doi": "10.1016/B978-0-12-388408-4.00004-6", + "pmc": null, + "pubmed": "23195121", + "title": "The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/NBO_$1", "repository": "https://github.com/obo-behavior/behavior-ontology", "uri_format": "http://purl.obolibrary.org/obo/NBO_$1", - "version": "2021-02-15" + "version": "2023-05-02" }, "nbrc": { "description": "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information.", @@ -31614,6 +35417,15 @@ "name": "NITE Biological Resource Center", "pattern": "^\\d+$", "preferred_prefix": "nbrc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nbrc:$1" + } + ], "uri_format": "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1" }, "ncats.bioplanet": { @@ -31644,7 +35456,7 @@ "doi": "10.3389/fphar.2019.00445", "pmc": "PMC6524730", "pubmed": "31133849", - "title": "The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics.", + "title": "The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics", "year": 2019 } ], @@ -31713,7 +35525,7 @@ "name": "Assembly", "pattern": "^[a-zA-Z0-9_\\.]+$", "preferred_prefix": "ncbi.assembly", - "uri_format": "https://www.ncbi.nlm.nih.gov/assembly/$1" + "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1" }, "ncbi.genome": { "contributor": { @@ -31809,6 +35621,13 @@ "name": "Bio2RDF", "uri_format": "http://ncbigene.bio2rdf.org/describe/?url=http://bio2rdf.org/ncbigene:$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ncbigene:$1" + }, { "code": "marrvel", "description": "Helps browse potential orthologs in model organisms for a given gene", @@ -31829,17 +35648,18 @@ "doi": "10.1093/nar/gkq1237", "pmc": "PMC3013746", "pubmed": "21115458", - "title": "Entrez Gene: gene-centered information at NCBI.", + "title": "Entrez Gene: gene-centered information at NCBI", "year": 2010 }, { "doi": "10.1093/nar/gki031", "pmc": "PMC539985", "pubmed": "15608257", - "title": "Entrez Gene: gene-centered information at NCBI.", + "title": "Entrez Gene: gene-centered information at NCBI", "year": 2005 } ], + "rdf_uri_format": "http://purl.uniprot.org/geneid/$1", "synonyms": [ "EGID", "EntrezGene", @@ -31914,6 +35734,15 @@ ], "pattern": "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$", "preferred_prefix": "NCBIProtein", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ncbi.protein:$1" + } + ], "uri_format": "https://www.ncbi.nlm.nih.gov/protein/$1" }, "ncbitaxon": { @@ -32005,6 +35834,13 @@ "name": "Bio2RDF", "uri_format": "https://bio2rdf.org/taxonomy:$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/taxonomy:$1" + }, { "code": "ebi", "description": "European Nucleotide Archive (ENA)", @@ -32025,28 +35861,30 @@ "doi": "10.1093/database/baaa062", "pmc": "PMC7408187", "pubmed": "32761142", - "title": "NCBI Taxonomy: a comprehensive update on curation, resources and tools.", + "title": "NCBI Taxonomy: a comprehensive update on curation, resources and tools", "year": 2020 }, { "doi": "10.1093/nar/gkx1094", "pmc": "PMC5753231", "pubmed": "29140468", - "title": "GenBank.", + "title": "GenBank", "year": 2018 }, { "doi": "10.1093/nar/gkr1178", "pmc": "PMC3245000", "pubmed": "22139910", - "title": "The NCBI Taxonomy database.", + "title": "The NCBI Taxonomy database", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/NCBITaxon_$1", "repository": "https://github.com/obophenotype/ncbitaxon", "synonyms": [ "NCBI Taxonomy", "NCBITaxon", + "NCBITaxonomyID", "NCBI_Taxon_ID", "NCBI_taxid", "TAX", @@ -32057,7 +35895,18 @@ "uniprot.taxonomy" ], "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1", - "version": "2022-08-18" + "version": "2023-06-20" + }, + "nci.drug": { + "description": "identifier of an entry in the NCI Drug Dictionary", + "example": "beta-carotene", + "homepage": "https://www.cancer.gov/publications/dictionaries/cancer-drug", + "mappings": { + "wikidata": "P11623" + }, + "name": "NCI Drug Dictionary ID", + "preferred_prefix": "nci.drug", + "uri_format": "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1" }, "ncim": { "description": "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical.", @@ -32135,6 +35984,13 @@ "pattern": "^C\\d+$", "preferred_prefix": "NCIT", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ncit:$1" + }, { "code": "evs", "description": "Links to a no-longer existing OWL file", @@ -32148,17 +36004,18 @@ "doi": "10.3233/ao-2008-0051", "pmc": "PMC2753293", "pubmed": "19789731", - "title": "Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.", + "title": "Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages", "year": 2008 }, { "doi": "10.3233/978-1-60750-949-3-33", "pmc": null, "pubmed": "15360769", - "title": "NCI Thesaurus: using science-based terminology to integrate cancer research results.", + "title": "NCI Thesaurus: using science-based terminology to integrate cancer research results", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/NCIT_$1", "repository": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition", "synonyms": [ "NCI", @@ -32173,7 +36030,7 @@ "ncithesaurus" ], "uri_format": "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1", - "version": "22.07d" + "version": "2022-08-19" }, "ncro": { "contact": { @@ -32208,15 +36065,15 @@ "publications": [ { "doi": "10.1186/s13326-016-0066-0", - "pmc": null, - "pubmed": null, + "pmc": "PMC4857245", + "pubmed": "27152146", "title": "The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology", - "year": null + "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/NCRO_$1", "repository": "https://github.com/OmniSearch/ncro", - "uri_format": "http://purl.obolibrary.org/obo/NCRO_$1", - "version": "2015-12-10" + "uri_format": "http://purl.obolibrary.org/obo/NCRO_$1" }, "ndc": { "description": "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily.", @@ -32308,29 +36165,36 @@ "doi": "10.1002/cpz1.258", "pmc": "PMC8544027", "pubmed": "34570431", - "title": "NDEx: Accessing Network Models and Streamlining Network Biology Workflows.", + "title": "NDEx: Accessing Network Models and Streamlining Network Biology Workflows", "year": 2021 }, { "doi": "10.1158/0008-5472.can-17-0606", "pmc": "PMC5679399", "pubmed": "29092941", - "title": "NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.", + "title": "NDEx 2.0: A Clearinghouse for Research on Cancer Pathways", "year": 2017 }, { "doi": "10.1007/978-1-4939-6783-4_13", "pmc": null, "pubmed": "28150243", - "title": "NDEx: A Community Resource for Sharing and Publishing of Biological Networks.", + "title": "NDEx: A Community Resource for Sharing and Publishing of Biological Networks", "year": 2017 }, { "doi": "10.1016/j.cels.2015.10.001", "pmc": "PMC4649937", "pubmed": "26594663", - "title": "NDEx, the Network Data Exchange.", + "title": "NDEx, the Network Data Exchange", "year": 2015 + }, + { + "doi": "10.1158/0008-5472.CAN-17-0606", + "pmc": null, + "pubmed": null, + "title": "NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.", + "year": null } ], "repository": "https://github.com/ndexbio", @@ -32372,15 +36236,25 @@ "name": "National Drug File - Reference Terminology", "pattern": "^N[0-9]{10}$", "preferred_prefix": "ndfrt", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ndfrt:$1" + } + ], "publications": [ { "doi": null, "pmc": "PMC1480331", "pubmed": "14728237", - "title": "Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications.", + "title": "Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications", "year": 2003 } ], + "rdf_uri_format": "http://purl.bioontology.org/ontology/NDFRT/$1", "synonyms": [ "NUI", "ndf-rt" @@ -32403,6 +36277,15 @@ }, "name": "Nematode & Neglected Genomics", "preferred_prefix": "nembase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nembase:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -32452,7 +36335,7 @@ "doi": "10.4056/sigs.2025347", "pmc": "PMC3235514", "pubmed": "22180824", - "title": "Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data.", + "title": "Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data", "year": 2011 }, { @@ -32470,7 +36353,7 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4802" + "orcid": "0000-0002-7509-4801" }, "description": "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex).", "example": "4", @@ -32491,12 +36374,21 @@ "part_of": "nif", "pattern": "^\\d+$", "preferred_prefix": "neurolex", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/neurolex:$1" + } + ], "publications": [ { "doi": "10.1007/s12021-008-9032-z", "pmc": "PMC2743139", "pubmed": "18975148", - "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.", + "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience", "year": 2008 } ], @@ -32526,12 +36418,21 @@ "name": "NeuroMorpho", "pattern": "^\\w+$", "preferred_prefix": "neuromorpho", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/neuromorpho:$1" + } + ], "publications": [ { "doi": "10.1038/nrn1885", "pmc": null, "pubmed": "16552417", - "title": "Mobilizing the base of neuroscience data: the case of neuronal morphologies.", + "title": "Mobilizing the base of neuroscience data: the case of neuronal morphologies", "year": 2006 } ], @@ -32586,6 +36487,15 @@ "name": "NeuronDB", "pattern": "^\\d+$", "preferred_prefix": "neurondb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/neurondb:$1" + } + ], "uri_format": "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1" }, "neurovault.collection": { @@ -32637,6 +36547,15 @@ "name": "Nematode Expression Pattern DataBase", "pattern": "^[A-Za-z0-9]+$", "preferred_prefix": "nextdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nextdb:$1" + } + ], "uri_format": "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1" }, "nextprot": { @@ -32668,57 +36587,57 @@ "doi": "10.1093/nar/gkz995", "pmc": "PMC7145669", "pubmed": "31724716", - "title": "The neXtProt knowledgebase in 2020: data, tools and usability improvements.", + "title": "The neXtProt knowledgebase in 2020: data, tools and usability improvements", "year": 2020 }, - { - "doi": "10.1093/nar/gkw1062.", - "pmc": "PMC5210547", - "pubmed": "27899619", - "title": "The neXtProt knowledgebase on human proteins: 2017 update.", - "year": null - }, { "doi": "10.1093/nar/gkw1062", "pmc": "PMC5210547", "pubmed": "27899619", - "title": "The neXtProt knowledgebase on human proteins: 2017 update.", + "title": "The neXtProt knowledgebase on human proteins: 2017 update", "year": 2016 }, - { - "doi": "10.1093/nar/gku1178.", - "pmc": "PMC4383972", - "pubmed": "25593349", - "title": "The neXtProt knowledgebase on human proteins: current status.", - "year": null - }, { "doi": "10.1093/nar/gku1178", "pmc": "PMC4383972", "pubmed": "25593349", - "title": "The neXtProt knowledgebase on human proteins: current status.", + "title": "The neXtProt knowledgebase on human proteins: current status", "year": 2015 }, - { - "doi": "10.1021/pr300830v.", - "pmc": null, - "pubmed": "23205526", - "title": "neXtProt: organizing protein knowledge in the context of human proteome projects.", - "year": null - }, { "doi": "10.1021/pr300830v", "pmc": null, "pubmed": "23205526", - "title": "neXtProt: organizing protein knowledge in the context of human proteome projects.", + "title": "neXtProt: organizing protein knowledge in the context of human proteome projects", "year": 2012 }, { "doi": "10.1093/nar/gkr1179", "pmc": "PMC3245017", "pubmed": "22139911", - "title": "neXtProt: a knowledge platform for human proteins.", + "title": "neXtProt: a knowledge platform for human proteins", "year": 2011 + }, + { + "doi": "10.1093/nar/gkw1062.", + "pmc": null, + "pubmed": null, + "title": "The neXtProt knowledgebase on human proteins: 2017 update.", + "year": null + }, + { + "doi": "10.1093/nar/gku1178.", + "pmc": null, + "pubmed": null, + "title": "The neXtProt knowledgebase on human proteins: current status.", + "year": null + }, + { + "doi": "10.1021/pr300830v.", + "pmc": null, + "pubmed": null, + "title": "neXtProt: organizing protein knowledge in the context of human proteome projects.", + "year": null } ], "synonyms": [ @@ -32746,6 +36665,97 @@ "twitter": "neXtProt_news", "uri_format": "https://www.nextprot.org/term/FA-$1" }, + "nfdi4chem.cao": { + "contact": { + "email": "williams.antony@epa.gov", + "github": null, + "name": "Antony Williams", + "orcid": "0000-0002-2668-4821" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)", + "download_owl": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl", + "example": "000064", + "homepage": "https://champ.stuchalk.domains.unf.edu", + "keywords": [ + "characterisation data heat", + "ontology", + "transport and kinetic data" + ], + "license": "CC-BY-3.0", + "mappings": { + "ols": "cao" + }, + "name": "Chemical Analysis Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "nfdi4chem.cao", + "uri_format": "http://champ-project.org/images/ontology/cao.owl#CAO_$1", + "version": "0.2" + }, + "nfdi4chem.ontocape": { + "comment": "This ontology ecosystem is near unusable", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources.", + "homepage": "https://www.avt.rwth-aachen.de/cms/AVT/Forschung/Software/~ipts/OntoCape/", + "license": "GPL-2.0", + "name": "Ontology for computer aided process engineering", + "preferred_prefix": "nfdi4chem.ontocape" + }, + "nfdi4chem.osmo": { + "comment": "locked behind a private GitLab instance", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "deprecated": true, + "description": "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)", + "homepage": "https://zenodo.org/record/5237774#.YXq72hxCRGo", + "name": "Ontology for simulation, modelling, and optimization", + "preferred_prefix": "nfdi4chem.osmo" + }, + "ngbo": { + "contact": { + "email": "dal.alghamdi92@gmail.com", + "github": "dalalghamdi", + "name": "Dalia Alghamdi", + "orcid": "0000-0002-2801-0767" + }, + "description": "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.", + "download_owl": "http://purl.obolibrary.org/obo/ngbo.owl", + "example": "6000122", + "homepage": "https://github.com/Dalalghamdi/NGBO", + "keywords": [ + "obo", + "ontology" + ], + "license": "CC-BY-4.0", + "mappings": { + "aberowl": "NGBO", + "bioportal": "NGBO", + "obofoundry": "ngbo", + "ols": "ngbo", + "ontobee": "NGBO" + }, + "name": "Next Generation Biobanking Ontology", + "preferred_prefix": "NGBO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/NGBO_$1", + "repository": "https://github.com/Dalalghamdi/NGBO", + "uri_format": "http://purl.obolibrary.org/obo/NGBO_$1", + "version": "2022-10-05" + }, "ngl": { "description": "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA.", "example": "GLDS-141", @@ -32796,17 +36806,37 @@ "name": "NIA Mouse cDNA Project", "pattern": "^\\w\\d{4}\\w\\d{2}(\\-[35])?$", "preferred_prefix": "niaest", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/niaest:$1" + } + ], "publications": [ { "doi": "10.1016/j.crvi.2003.09.008", "pmc": null, "pubmed": "14744099", - "title": "The NIA cDNA project in mouse stem cells and early embryos.", + "title": "The NIA cDNA project in mouse stem cells and early embryos", "year": 2003 } ], "uri_format": "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1" }, + "niaid.chemdb": { + "description": "ID in NIAID ChemDB", + "example": "112081", + "homepage": "http://chemdb.niaid.nih.gov", + "mappings": { + "wikidata": "P2065" + }, + "name": "NIAID ChemDB ID", + "preferred_prefix": "niaid.chemdb", + "uri_format": "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1" + }, "nif.cell": { "contact": { "email": "smtifahim@gmail.com", @@ -32831,6 +36861,7 @@ "name": "NIF Cell", "part_of": "nif", "preferred_prefix": "NIF_CELL", + "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_CELL_$1" }, "nif.dysfunction": { @@ -32853,6 +36884,7 @@ "name": "NIF Dysfunction", "part_of": "nif", "preferred_prefix": "NIF_DYSFUNCTION", + "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1" }, "nif.ext": { @@ -32909,6 +36941,7 @@ "name": "NIF Gross Anatomy", "part_of": "nif", "preferred_prefix": "NIF_GROSSANATOMY", + "rdf_uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1", "uri_format": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1" }, "nif.std": { @@ -32947,7 +36980,7 @@ "doi": "10.1007/s12021-008-9032-z", "pmc": "PMC2743139", "pubmed": "18975148", - "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.", + "title": "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience", "year": 2008 } ], @@ -32964,6 +36997,20 @@ "twitter": "SciCrunch", "uri_format": "http://uri.neuinfo.org/nif/nifstd/$1" }, + "nihhesc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)", + "example": "NIHhESC-10-0083", + "homepage": "https://grants.nih.gov/stem_cells/registry/current.htm", + "name": "NIH Human Embryonic Stem Cell Registry", + "preferred_prefix": "nihhesc", + "uri_format": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1" + }, "nihreporter.project": { "contributor": { "email": "benjamin_gyori@hms.harvard.edu", @@ -33003,6 +37050,33 @@ "NIST Chemistry WebBook" ] }, + "nkos": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004).", + "download_rdf": "https://nkos.dublincore.org/nkos.rdf", + "example": "alignedWith", + "homepage": "http://w3id.org/nkos", + "name": "Networked Knowledge Organization Systems/Services/Structures", + "preferred_prefix": "nkos", + "uri_format": "http://w3id.org/nkos/$1" + }, + "nlfff": { + "description": "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database", + "example": "345201101230312003", + "homepage": "https://nlfff.dataset.deepsolar.space/en/", + "mappings": { + "miriam": "nlfff" + }, + "name": "NLFFF Database", + "pattern": "^[0-9]+$", + "preferred_prefix": "nlfff", + "uri_format": "http://database.deepsolar.space:18080/dbs/nlfff/$1" + }, "nlm": { "contributor": { "email": "cthoyt@gmail.com", @@ -33027,7 +37101,7 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4804" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "cthoyt@gmail.com", @@ -33059,13 +37133,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4804" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4804" + "orcid": "0000-0002-7509-4801" }, "description": "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999).", "example": "145", @@ -33098,13 +37172,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4805" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4805" + "orcid": "0000-0002-7509-4801" }, "description": "NLXCELL conatins cell types with a focus on neuron types.", "example": "91005", @@ -33138,13 +37212,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4806" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4806" + "orcid": "0000-0002-7509-4801" }, "description": "NLXCHEM covers chemicals. Most classes are also in ChEBI.", "example": "90801", @@ -33178,7 +37252,7 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4804" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "cthoyt@gmail.com", @@ -33212,13 +37286,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4808" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4808" + "orcid": "0000-0002-7509-4801" }, "description": "NLXFUNC covers terms for cognitive function.", "example": "90801", @@ -33249,13 +37323,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4809" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4809" + "orcid": "0000-0002-7509-4801" }, "description": "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis.", "example": "90901", @@ -33281,13 +37355,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4810" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4810" + "orcid": "0000-0002-7509-4801" }, "description": "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system.", "example": "90806", @@ -33321,13 +37395,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4811" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4811" + "orcid": "0000-0002-7509-4801" }, "description": "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results).", "example": "0001000", @@ -33358,13 +37432,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4812" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4812" + "orcid": "0000-0002-7509-4801" }, "description": "NLXORG covers organisms.", "example": "090701", @@ -33395,13 +37469,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4813" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4813" + "orcid": "0000-0002-7509-4801" }, "description": "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO).", "example": "100810", @@ -33433,13 +37507,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4814" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4814" + "orcid": "0000-0002-7509-4801" }, "description": "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites", "example": "090924", @@ -33470,13 +37544,13 @@ "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4815" + "orcid": "0000-0002-7509-4801" }, "contributor": { "email": "tgbugs@gmail.com", "github": "tgbugs", "name": "Tom Gillespie", - "orcid": "0000-0002-7509-4815" + "orcid": "0000-0002-7509-4801" }, "description": "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO).", "example": "090803", @@ -33554,6 +37628,15 @@ }, "name": "National Microbial Pathogen Data Resource", "preferred_prefix": "nmpdr", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nmpdr:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -33595,6 +37678,16 @@ "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "NMR", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nmr:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/NMR_$1", "synonyms": [ "nmrcv" ], @@ -33627,21 +37720,21 @@ "doi": "10.1002/mrc.4263", "pmc": null, "pubmed": "25998807", - "title": "Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.", + "title": "Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories", "year": 2015 }, { "doi": "10.1016/j.phytochem.2004.08.027", "pmc": null, "pubmed": "15464159", - "title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database.", + "title": "NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database", "year": 2004 }, { "doi": "10.1021/ci0341363", "pmc": null, "pubmed": "14632418", - "title": "NMRShiftDB-constructing a free chemical information system with open-source components.", + "title": "NMRShiftDB-constructing a free chemical information system with open-source components", "year": 2003 } ], @@ -33672,6 +37765,18 @@ }, "uri_format": "https://www.fisheries.noaa.gov/species/$1" }, + "noaa.cameo": { + "description": "chemical in the database supplied by National Oceanic and Atmospheric Administration", + "example": "19757", + "homepage": "https://cameochemicals.noaa.gov", + "mappings": { + "wikidata": "P11931" + }, + "name": "CAMEO Chemicals ID", + "pattern": "^\\d*$", + "preferred_prefix": "noaa.cameo", + "uri_format": "https://cameochemicals.noaa.gov/chemical/$1" + }, "nomen": { "contact": { "email": "diapriid@gmail.com", @@ -33698,6 +37803,7 @@ "name": "A nomenclatural ontology for biological names", "pattern": "^\\d{7}$", "preferred_prefix": "NOMEN", + "rdf_uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1", "repository": "https://github.com/SpeciesFileGroup/nomen", "uri_format": "http://purl.obolibrary.org/obo/NOMEN_$1" }, @@ -33718,12 +37824,21 @@ "name": "NONCODE v3", "pattern": "^\\d+$", "preferred_prefix": "noncodev3", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/noncode:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr1175", "pmc": "PMC3245065", "pubmed": "22135294", - "title": "NONCODE v3.0: integrative annotation of long noncoding RNAs.", + "title": "NONCODE v3.0: integrative annotation of long noncoding RNAs", "year": 2011 } ], @@ -33775,19 +37890,28 @@ "name": "Nonribosomal Peptides Database", "pattern": "^NOR\\d+$", "preferred_prefix": "norine", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/norine:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkz1000", "pmc": "PMC7145658", "pubmed": "31691799", - "title": "Norine: update of the nonribosomal peptide resource.", + "title": "Norine: update of the nonribosomal peptide resource", "year": 2020 }, { "doi": "10.1093/nar/gkm792", "pmc": "PMC2238963", "pubmed": "17913739", - "title": "NORINE: a database of nonribosomal peptides.", + "title": "NORINE: a database of nonribosomal peptides", "year": 2007 } ], @@ -33855,13 +37979,27 @@ "doi": "10.1016/j.jbi.2010.03.001", "pmc": "PMC3042056", "pubmed": "20211274", - "title": "NanoParticle Ontology for cancer nanotechnology research.", + "title": "NanoParticle Ontology for cancer nanotechnology research", "year": 2010 } ], "repository": "https://github.com/sobolevnrm/npo", "uri_format": "http://purl.bioontology.org/ontology/npo#NPO_$1" }, + "nrfc": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)", + "example": "NRFC051", + "homepage": "https://mail.nbfgr.res.in/nrfc/index.php", + "name": "National Repository of Fish Cell Lines", + "pattern": "^NRFC\\d+$", + "preferred_prefix": "nrfc" + }, "nsc": { "contributor": { "email": "cthoyt@gmail.com", @@ -33951,12 +38089,21 @@ "name": "NucleaRDB", "pattern": "^\\w+\\_\\w+$", "preferred_prefix": "nucleardb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/nucleardb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr960", "pmc": "PMC3245090", "pubmed": "22064856", - "title": "NucleaRDB: information system for nuclear receptors.", + "title": "NucleaRDB: information system for nuclear receptors", "year": 2011 } ], @@ -34035,13 +38182,14 @@ "doi": "10.1186/2041-1480-5-29", "pmc": "PMC4120740", "pubmed": "25093068", - "title": "OAE: The Ontology of Adverse Events.", + "title": "OAE: The Ontology of Adverse Events", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OAE_$1", "repository": "https://github.com/OAE-ontology/OAE", "uri_format": "http://purl.obolibrary.org/obo/OAE_$1", - "version": "1.2.44" + "version": "1.2.47" }, "oarcs": { "contact": { @@ -34078,10 +38226,11 @@ "doi": "10.1093/sysbio/syw108", "pmc": null, "pubmed": "28123116", - "title": "The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.", + "title": "The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions", "year": 2017 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "repository": "https://github.com/aszool/oarcs", "uri_format": "http://purl.obolibrary.org/obo/OARCS_$1", "version": "2019-04-18" @@ -34124,17 +38273,25 @@ "pattern": "^(VT)?\\d{7}$", "preferred_prefix": "OBA", "publications": [ + { + "doi": "10.1007/s00335-023-09992-1", + "pmc": null, + "pubmed": "37076585", + "title": "The Ontology of Biological Attributes (OBA)-computational traits for the life sciences", + "year": 2023 + }, { "doi": "10.1101/2023.01.26.525742", "pmc": "PMC9900877", "pubmed": "36747660", - "title": "The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences.", + "title": "The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences", "year": 2023 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OBA_$1", "repository": "https://github.com/obophenotype/bio-attribute-ontology", "uri_format": "http://purl.obolibrary.org/obo/OBA_$1", - "version": "2022-11-26" + "version": "2023-06-07" }, "oban": { "contributor": { @@ -34168,7 +38325,7 @@ "name": "Jie Zheng", "orcid": "0000-0002-2999-0103" }, - "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ", + "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012.", "download_owl": "http://purl.obolibrary.org/obo/obcs.owl", "example": "0000121", "homepage": "https://github.com/obcs/obcs", @@ -34199,13 +38356,14 @@ "doi": "10.1186/s13326-016-0100-2", "pmc": "PMC5024438", "pubmed": "27627881", - "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.", + "title": "The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis", "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", "repository": "https://github.com/obcs/obcs", "uri_format": "http://purl.obolibrary.org/obo/OBCS_$1", - "version": "101" + "version": "2018-02-22" }, "obi": { "appears_in": [ @@ -34242,6 +38400,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png", "mappings": { "aberowl": "OBI", "biocontext": "OBI", @@ -34259,46 +38418,70 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "OBI", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/obi:$1" + } + ], "publications": [ { "doi": "10.1371/journal.pone.0154556", "pmc": "PMC4851331", "pubmed": "27128319", - "title": "The Ontology for Biomedical Investigations.", + "title": "The Ontology for Biomedical Investigations", "year": 2016 }, { "doi": "10.1093/database/bau132", "pmc": "PMC4309925", "pubmed": "25632945", - "title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.", + "title": "Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach", "year": 2015 }, { "doi": "10.1186/2041-1480-4-s1-s6", "pmc": "PMC3633001", "pubmed": "23734660", - "title": "Query enhancement through the practical application of ontology: the IEDB and OBI.", + "title": "Query enhancement through the practical application of ontology: the IEDB and OBI", "year": 2013 }, + { + "doi": "10.1186/2041-1480-4-S1-S6", + "pmc": "PMC3633001", + "pubmed": "23734660", + "title": "Query enhancement through the practical application of ontology: the IEDB and OBI", + "year": null + }, { "doi": "10.4056/sigs.1994602", "pmc": "PMC3235517", "pubmed": "22180825", - "title": "Minimum Information about a Genotyping Experiment (MIGEN).", + "title": "Minimum Information about a Genotyping Experiment (MIGEN)", "year": 2011 }, { "doi": "10.1186/2041-1480-1-s1-s7", "pmc": "PMC2903726", "pubmed": "20626927", - "title": "Modeling biomedical experimental processes with OBI.", + "title": "Modeling biomedical experimental processes with OBI", "year": 2010 + }, + { + "doi": "10.1186/2041-1480-1-S1-S7", + "pmc": "PMC2903726", + "pubmed": "20626927", + "title": "Modeling biomedical experimental processes with OBI", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OBI_$1", "repository": "https://github.com/obi-ontology/obi", "uri_format": "http://purl.obolibrary.org/obo/OBI_$1", - "version": "2022-07-11" + "version": "2023-03-10" }, "obib": { "contact": { @@ -34334,22 +38517,28 @@ "doi": "10.1186/s13326-016-0068-y", "pmc": "PMC4855778", "pubmed": "27148435", - "title": "OBIB-a novel ontology for biobanking.", + "title": "OBIB-a novel ontology for biobanking", "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", "repository": "https://github.com/biobanking/biobanking", "uri_format": "http://purl.obolibrary.org/obo/OBIB_$1", - "version": "2021-11-12" + "version": "2023-04-05" }, "obo": { "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", - "name": "Nico Matentzoglu", + "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "description": "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies.", + "example": "uberon", + "example_extras": [ + "go", + "uberon.owl" + ], "homepage": "http://www.obofoundry.org/", "keywords": [ "ontology and terminology" @@ -34365,10 +38554,15 @@ "doi": "10.1038/nbt1346", "pmc": "PMC2814061", "pubmed": "17989687", - "title": "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.", + "title": "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", "year": 2007 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/$1", + "references": [ + "https://github.com/biopragmatics/bioregistry/pull/913", + "https://github.com/biopragmatics/bioregistry/issues/910" + ], "repository": "https://github.com/OBOFoundry/OBOFoundry.github.io", "twitter": "OBOFoundry", "uri_format": "http://purl.obolibrary.org/obo/$1" @@ -34392,7 +38586,8 @@ "mappings": { "biocontext": "oboInOwl", "biolink": "oboformat", - "fairsharing": "FAIRsharing.aa0eat" + "fairsharing": "FAIRsharing.aa0eat", + "ols": "oboinowl" }, "name": "OBO in OWL", "preferred_prefix": "oboInOwl", @@ -34403,6 +38598,19 @@ ], "uri_format": "http://www.geneontology.org/formats/oboInOwl#$1" }, + "obv": { + "description": "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections.", + "example": "AC00963334", + "homepage": "https://www.obvsg.at/", + "mappings": { + "bartoc": "20430", + "miriam": "obv" + }, + "name": "Austrian Library Network", + "pattern": "^AC[0-9]{8}$", + "preferred_prefix": "obv", + "uri_format": "https://permalink.obvsg.at/$1" + }, "occ": { "description": "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law.", "example": "br/1", @@ -34417,8 +38625,8 @@ "uri_format": "https://w3id.org/oc/corpus/$1" }, "oci": { - "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings.", - "example": "1-18", + "description": "Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource.", + "example": "01027931310-01022252312", "homepage": "http://opencitations.net", "mappings": { "biocontext": "OCI", @@ -34426,7 +38634,7 @@ "n2t": "oci" }, "name": "Open Citation Identifier", - "pattern": "^[0-9]+-[0-9]+$", + "pattern": "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$", "preferred_prefix": "oci", "uri_format": "https://w3id.org/oc/oci/$1" }, @@ -34499,57 +38707,57 @@ "doi": "10.1089/neu.2019.6674", "pmc": "PMC7071068", "pubmed": "31608767", - "title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research.", + "title": "FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research", "year": 2019 }, - { - "doi": "s0014-4886(17)30137-1", - "pmc": "PMC6448396", - "pubmed": "28576567", - "title": "Developing a data sharing community for spinal cord injury research.", - "year": null - }, { "doi": "10.1016/j.expneurol.2017.05.012", "pmc": "PMC6448396", "pubmed": "28576567", - "title": "Developing a data sharing community for spinal cord injury research.", + "title": "Developing a data sharing community for spinal cord injury research", "year": 2017 }, { "doi": "10.1038/ncomms9581", "pmc": "PMC4634208", "pubmed": "26466022", - "title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury.", + "title": "Topological data analysis for discovery in preclinical spinal cord injury and traumatic brain injury", "year": 2015 }, { "doi": "10.1038/nn.3838", "pmc": "PMC4728080", "pubmed": "25349910", - "title": "Big data from small data: data-sharing in the 'long tail' of neuroscience.", + "title": "Big data from small data: data-sharing in the 'long tail' of neuroscience", "year": 2014 }, { "doi": "10.1089/neu.2014.3399", "pmc": "PMC4186058", "pubmed": "25077610", - "title": "Development of a database for translational spinal cord injury research.", + "title": "Development of a database for translational spinal cord injury research", "year": 2014 }, { "doi": "10.1371/journal.pone.0059712", "pmc": "PMC3609747", "pubmed": "23544088", - "title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats.", + "title": "Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats", "year": 2013 }, { "doi": "10.1007/s12975-011-0121-1", "pmc": "PMC3236294", "pubmed": "22207883", - "title": "Syndromics: a bioinformatics approach for neurotrauma research.", + "title": "Syndromics: a bioinformatics approach for neurotrauma research", "year": 2011 + }, + { + "doi": "S0014-4886(17)30137-1", + "pmc": null, + "pubmed": null, + "title": "Developing a data sharing community for spinal cord injury research.", + "year": null } ], "uri_format": "https://odc-sci.org/data/$1" @@ -34580,6 +38788,21 @@ "preferred_prefix": "odor", "uri_format": "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5" }, + "odrl": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model.", + "download_rdf": "https://www.w3.org/ns/odrl/2/ODRL22.rdf", + "example": "assetConcepts", + "homepage": "http://www.w3.org/ns/odrl/2", + "name": "Open Digital Rights Language Ontology", + "preferred_prefix": "odrl", + "uri_format": "http://www.w3.org/ns/odrl/2/$1" + }, "ogg": { "contact": { "email": "yongqunh@med.umich.edu", @@ -34587,7 +38810,7 @@ "name": "Yongqun Oliver He", "orcid": "0000-0001-9189-9661" }, - "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ", + "description": "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.", "download_owl": "http://purl.obolibrary.org/obo/ogg.owl", "example": "3000887619", "homepage": "https://bitbucket.org/hegroup/ogg", @@ -34610,6 +38833,7 @@ "name": "The Ontology of Genes and Genomes", "pattern": "^\\d+$", "preferred_prefix": "OGG", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "repository": "https://bitbucket.org/hegroup/ogg", "uri_format": "http://purl.obolibrary.org/obo/OGG_$1", "version": "1.0.59" @@ -34641,6 +38865,7 @@ "name": "Ontology for genetic interval", "pattern": "^\\d{7}$", "preferred_prefix": "OGI", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OGI_$1", "synonyms": [ "OGI.owl" ], @@ -34670,6 +38895,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "https://avatars2.githubusercontent.com/u/12973154?s=200&v=4", "mappings": { "aberowl": "OGMS", "bartoc": "216", @@ -34688,17 +38914,25 @@ "doi": null, "pmc": null, "pubmed": "25991121", - "title": "Biomarkers in the ontology for general medical science.", + "title": "Biomarkers in the ontology for general medical science", "year": 2015 }, { "doi": "10.1186/2041-1480-4-42", "pmc": "PMC4028878", "pubmed": "24314207", - "title": "The neurological disease ontology.", + "title": "The neurological disease ontology", "year": 2013 + }, + { + "doi": null, + "pmc": "PMC3041577", + "pubmed": "21347182", + "title": "Toward an ontological treatment of disease and diagnosis", + "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OGMS_$1", "repository": "https://github.com/OGMS/ogms", "synonyms": [ "ogms/OMRE" @@ -34742,17 +38976,18 @@ "doi": "10.1186/2041-1480-5-19", "pmc": "PMC4068904", "pubmed": "24963371", - "title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.", + "title": "The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events", "year": 2014 }, { "doi": null, "pmc": null, "pubmed": "20847592", - "title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease.", + "title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "repository": "https://github.com/linikujp/OGSF", "uri_format": "http://purl.obolibrary.org/obo/OGSF_$1", "version": "2.0" @@ -34793,13 +39028,14 @@ "doi": "10.1186/s13326-020-00222-0", "pmc": "PMC7439527", "pubmed": "32819435", - "title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology.", + "title": "Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology", "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OHD_$1", "repository": "https://github.com/oral-health-and-disease-ontologies/ohd-ontology", "uri_format": "http://purl.obolibrary.org/obo/OHD_$1", - "version": "2016-06-27" + "version": "2023-04-14" }, "ohmi": { "contact": { @@ -34830,6 +39066,7 @@ "name": "Ontology of Host-Microbiome Interactions", "pattern": "^\\d{7}$", "preferred_prefix": "OHMI", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "repository": "https://github.com/ohmi-ontology/ohmi", "uri_format": "http://purl.obolibrary.org/obo/OHMI_$1", "version": "2019-09-17" @@ -34868,13 +39105,14 @@ "doi": "10.1093/nar/gky999", "pmc": "PMC6324020", "pubmed": "30365026", - "title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens.", + "title": "Victors: a web-based knowledge base of virulence factors in human and animal pathogens", "year": 2019 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", "repository": "https://github.com/OHPI/ohpi", "uri_format": "http://purl.obolibrary.org/obo/OHPI_$1", - "version": "2019-10-02" + "version": "2019-09-30" }, "oid": { "contributor_extras": [ @@ -34956,8 +39194,9 @@ "name": "Medaka Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "OlatDv", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", - "uri_format": "http://purl.obolibrary.org/obo/OLATDV_$1", + "uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1", "version": "2020-03-10" }, "om": { @@ -34984,7 +39223,7 @@ "preferred_prefix": "om", "repository": "https://github.com/HajoRijgersberg/OM", "uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1", - "version": "2.0.38" + "version": "2.0.39" }, "oma.grp": { "description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.", @@ -35062,6 +39301,15 @@ "name": "Online Mendelian Inheritance in Animals", "pattern": "^\\d+$", "preferred_prefix": "omia", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/omia:$1" + } + ], "uri_format": "https://omia.org/OMIA$1" }, "omiabis": { @@ -35095,10 +39343,23 @@ "name": "Ontologized MIABIS", "pattern": "^\\d{7}$", "preferred_prefix": "OMIABIS", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "repository": "https://github.com/OMIABIS/omiabis-dev", "uri_format": "http://purl.obolibrary.org/obo/OMIABIS_$1", "version": "2014-05-28" }, + "omid": { + "description": "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted.", + "example": "br/0601", + "homepage": "http://opencitations.net/", + "mappings": { + "miriam": "omid" + }, + "name": "OpenCitations Meta Identifier", + "pattern": "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$", + "preferred_prefix": "omid", + "uri_format": "https://w3id.org/oc/meta/$1" + }, "omim": { "contact": { "email": "ahamosh@jhmi.edu", @@ -35141,6 +39402,13 @@ "name": "OMIM mirror at John Hopkins", "uri_format": "http://mirror.omim.org/entry/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/omim:$1" + }, { "code": "legacy", "description": "This is the actual endpoint for OMIM entries", @@ -35182,14 +39450,14 @@ "doi": "10.1093/nar/gku1205", "pmc": "PMC4383985", "pubmed": "25428349", - "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders.", + "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders", "year": 2014 }, { "doi": "10.1093/nar/gki033", "pmc": "PMC539987", "pubmed": "15608251", - "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.", + "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders", "year": 2005 } ], @@ -35292,30 +39560,31 @@ "doi": "10.1186/s13326-016-0064-2", "pmc": "PMC4863347", "pubmed": "27175225", - "title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.", + "title": "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data", "year": 2016 }, { "doi": "10.1371/journal.pone.0100855", "pmc": "PMC4099014", "pubmed": "25025130", - "title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain.", + "title": "OMIT: dynamic, semi-automated ontology development for the microRNA domain", "year": 2014 }, { "doi": "10.1007/s11095-011-0573-8", "pmc": null, "pubmed": "21879385", - "title": "OMIT: a domain-specific knowledge base for microRNA target prediction.", + "title": "OMIT: a domain-specific knowledge base for microRNA target prediction", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OMIT_$1", "repository": "https://github.com/OmniSearch/omit", "synonyms": [ "OMIT" ], - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1", - "version": "2019-06-07" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/omit/terms?short_form=OMIT_$1", + "version": "dev" }, "omo": { "appears_in": [ @@ -35345,9 +39614,10 @@ "name": "OBO Metadata Ontology", "no_own_terms": true, "preferred_prefix": "OMO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OMO_$1", "repository": "https://github.com/information-artifact-ontology/ontology-metadata", "uri_format": "http://purl.obolibrary.org/obo/OMO_$1", - "version": "2022-04-27" + "version": "2023-06-09" }, "omop": { "contributor": { @@ -35360,7 +39630,7 @@ { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", - "name": "Nico Matentzoglu", + "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" } ], @@ -35436,13 +39706,14 @@ "doi": "10.1186/s12866-014-0294-3", "pmc": "PMC4287307", "pubmed": "25433798", - "title": "An ontology for microbial phenotypes.", + "title": "An ontology for microbial phenotypes", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OMP_$1", "repository": "https://github.com/microbialphenotypes/OMP-ontology", "uri_format": "http://purl.obolibrary.org/obo/OMP_$1", - "version": "2022-08-05" + "version": "2023-06-09" }, "omrse": { "appears_in": [ @@ -35486,13 +39757,14 @@ "doi": "10.1186/s13326-016-0087-8", "pmc": "PMC4942889", "pubmed": "27406187", - "title": "The ontology of medically related social entities: recent developments.", + "title": "The ontology of medically related social entities: recent developments", "year": 2016 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", "repository": "https://github.com/ufbmi/OMRSE", "uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1", - "version": "2022-04-06" + "version": "2023-05-19" }, "oncotree": { "appears_in": [ @@ -35552,21 +39824,15 @@ "pattern": "^\\d{7}$", "preferred_prefix": "ONE", "publications": [ - { - "doi": "e1300", - "pmc": "PMC6628051", - "pubmed": "31181762", - "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.", - "year": null - }, { "doi": "10.3390/nu11061300", "pmc": "PMC6628051", "pubmed": "31181762", - "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.", + "title": "An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content", "year": 2019 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ONE_$1", "repository": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies", "uri_format": "http://purl.obolibrary.org/obo/ONE_$1" }, @@ -35617,14 +39883,46 @@ "doi": "10.1186/s12263-018-0601-y", "pmc": "PMC5928560", "pubmed": "29736190", - "title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition.", + "title": "ONS: an ontology for a standardized description of interventions and observational studies in nutrition", "year": 2018 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "repository": "https://github.com/enpadasi/Ontology-for-Nutritional-Studies", "uri_format": "http://purl.obolibrary.org/obo/ONS_$1", "version": "Release version 1.2.3" }, + "ontie": { + "contact": { + "email": "bpeters@lji.org", + "github": "bpeters42", + "name": "Bjoern Peters", + "orcid": "0000-0002-8457-6693" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.", + "download_owl": "https://raw.githubusercontent.com/IEDB/ONTIE/master/ontie.owl", + "example": "0000001", + "homepage": "https://ontology.iedb.org/", + "keywords": [ + "immunology", + "life science", + "ontology" + ], + "mappings": { + "fairsharing": "FAIRsharing.kx2md1" + }, + "name": "Ontology for Immune Epitopes", + "pattern": "^\\d{7}$", + "preferred_prefix": "ontie", + "repository": "https://github.com/IEDB/ONTIE", + "uri_format": "https://ontology.iedb.org/ontology/ONTIE_$1" + }, "ontoavida": { "contact": { "email": "fortuna@ebd.csic.es", @@ -35659,6 +39957,7 @@ "name": "Ontology for Avida digital evolution platform", "pattern": "^\\d{8}$", "preferred_prefix": "ONTOAVIDA", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ONTOAVIDA_$1", "repository": "https://gitlab.com/fortunalab/ontoavida", "uri_format": "http://purl.obolibrary.org/obo/ONTOAVIDA_$1", "version": "2022-03-15" @@ -35698,12 +39997,13 @@ "pmc": null, "pubmed": null, "title": "Ontologies for the representation of electronic medical records: The obstetric and neonatal ontology", - "year": null + "year": 2017 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", "repository": "https://github.com/ontoneo-project/Ontoneo", "uri_format": "http://purl.obolibrary.org/obo/ONTONEO_$1", - "version": "v1.6" + "version": "2021-04-29" }, "oostt": { "contact": { @@ -35712,7 +40012,7 @@ "name": "Mathias Brochhausen", "orcid": "0000-0003-1834-3856" }, - "description": "An ontology built for representating the organizational components of trauma centers and trauma systems.", + "description": "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2).", "download_owl": "http://purl.obolibrary.org/obo/oostt.owl", "example": "00000099", "homepage": "https://github.com/OOSTT/OOSTT", @@ -35734,9 +40034,10 @@ "name": "Ontology of Organizational Structures of Trauma centers and Trauma systems", "pattern": "^\\d{8}$", "preferred_prefix": "OOSTT", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", "repository": "https://github.com/OOSTT/OOSTT", "uri_format": "http://purl.obolibrary.org/obo/OOSTT_$1", - "version": "2021-01-11" + "version": "2023-03-30" }, "opb": { "banana": "OPB", @@ -35777,19 +40078,28 @@ "name": "Ontology of Physics for Biology", "pattern": "^\\d+$", "preferred_prefix": "opb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/opb:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-41", "pmc": "PMC3904761", "pubmed": "24295137", - "title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes.", + "title": "Ontology of physics for biology: representing physical dependencies as a basis for biological processes", "year": 2013 }, { "doi": "10.1371/journal.pone.0028708", "pmc": "PMC3246444", "pubmed": "22216106", - "title": "Physical properties of biological entities: an introduction to the ontology of physics for biology.", + "title": "Physical properties of biological entities: an introduction to the ontology of physics for biology", "year": 2011 } ], @@ -35863,13 +40173,14 @@ "doi": "10.1186/2041-1480-3-5", "pmc": "PMC3488002", "pubmed": "22621763", - "title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.", + "title": "The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OPL_$1", "repository": "https://github.com/OPL-ontology/OPL", "uri_format": "http://purl.obolibrary.org/obo/OPL_$1", - "version": "2021-01-28" + "version": "2023-06-23" }, "opm": { "description": "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.", @@ -35923,9 +40234,10 @@ "name": "Ontology of Precision Medicine and Investigation", "pattern": "^\\d{7}$", "preferred_prefix": "OPMI", + "rdf_uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", "repository": "https://github.com/OPMI/opmi", "uri_format": "http://purl.obolibrary.org/obo/OPMI_$1", - "version": "1.0.158" + "version": "1.0.161" }, "orcid": { "contact": { @@ -35951,6 +40263,7 @@ "n2t": "orcid", "wikidata": "P496" }, + "mastodon": "ORCID_Org@scicomm.xyz", "name": "Open Researcher and Contributor", "pattern": "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$", "preferred_prefix": "orcid", @@ -35979,6 +40292,7 @@ "year": 2020 } ], + "rdf_uri_format": "https://orcid.org/$1", "repository": "https://github.com/ORCID", "synonyms": [ "ORCID", @@ -36006,26 +40320,35 @@ "name": "Olfactory Receptor Database", "pattern": "^\\d+$", "preferred_prefix": "ordb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ordb:$1" + } + ], "publications": [ { "doi": "10.1093/database/baw132", "pmc": "PMC5045865", "pubmed": "27694208", - "title": "ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions.", + "title": "ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions", "year": 2016 }, { "doi": "10.1093/nar/30.1.354", "pmc": "PMC99065", "pubmed": "11752336", - "title": "Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences.", + "title": "Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences", "year": 2002 }, { "doi": "10.1093/nar/28.1.341", "pmc": "PMC102443", "pubmed": "10592268", - "title": "Olfactory receptor database: a sensory chemoreceptor resource.", + "title": "Olfactory receptor database: a sensory chemoreceptor resource", "year": 2000 } ], @@ -36086,6 +40409,7 @@ "name": "Ontology of RNA Sequencing", "pattern": "^\\d{7}$", "preferred_prefix": "ORNASEQ", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "repository": "https://github.com/safisher/ornaseq", "uri_format": "http://purl.obolibrary.org/obo/ORNASEQ_$1", "version": "2019-07-08" @@ -36121,6 +40445,13 @@ "homepage": "http://orphanet.bio2rdf.org/fct", "name": "Bio2RDF", "uri_format": "http://orphanet.bio2rdf.org/describe/?url=http://bio2rdf.org/orphanet:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/orphanet:$1" } ], "publications": [ @@ -36128,7 +40459,7 @@ "doi": null, "pmc": null, "pubmed": "19058507", - "title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases].", + "title": "[Orphanet and the Dutch Steering Committee Orphan Drugs. A European and Dutch databank of information on rare diseases]", "year": 2008 } ], @@ -36178,7 +40509,7 @@ "doi": null, "pmc": null, "pubmed": "22874158", - "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM.", + "title": "Rare diseases knowledge management: the contribution of proximity measurements in OntoOrpha and OMIM", "year": 2012 } ], @@ -36186,7 +40517,7 @@ "ordo" ], "uri_format": "http://www.orpha.net/ORDO/Orphanet_$1", - "version": "4.1" + "version": "4.2" }, "orth": { "contact": { @@ -36216,7 +40547,7 @@ "doi": "10.1186/s13326-016-0077-x", "pmc": "PMC4893294", "pubmed": "27259657", - "title": "The Orthology Ontology: development and applications.", + "title": "The Orthology Ontology: development and applications", "year": 2016 } ], @@ -36245,27 +40576,36 @@ "name": "OrthoDB", "pattern": "^\\w+$", "preferred_prefix": "orthodb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/orthodb:$1" + } + ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gky1053", "pmc": "PMC6323947", "pubmed": "30395283", - "title": "OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.", + "title": "OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs", "year": 2019 }, { "doi": "10.1093/nar/gku1220", "pmc": "PMC4383991", "pubmed": "25428351", - "title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.", + "title": "OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software", "year": 2014 }, { "doi": "10.1093/nar/gkq930", "pmc": "PMC3013786", "pubmed": "20972218", - "title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.", + "title": "OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011", "year": 2010 } ], @@ -36378,20 +40718,29 @@ "name": "Oryza Tag Line", "pattern": "^A[A-Z]+\\d+$", "preferred_prefix": "otl", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/otl:$1" + } + ], "publications": [ { - "doi": "17947330", + "doi": "10.1093/nar/gkm762", "pmc": "PMC2238859", "pubmed": "17947330", - "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.", - "year": null + "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library", + "year": 2007 }, { - "doi": "10.1093/nar/gkm762", - "pmc": "PMC2238859", - "pubmed": "17947330", + "doi": "17947330", + "pmc": null, + "pubmed": null, "title": "Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.", - "year": 2007 + "year": null } ], "uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1" @@ -36428,7 +40777,7 @@ "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, - "description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ", + "description": "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).", "download_owl": "http://purl.obolibrary.org/obo/ovae.owl", "example": "0000609", "homepage": "http://www.violinet.org/ovae/", @@ -36455,10 +40804,11 @@ "doi": "10.1186/2041-1480-4-40", "pmc": "PMC4177204", "pubmed": "24279920", - "title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.", + "title": "The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "repository": "https://github.com/OVAE-Ontology/ovae", "uri_format": "http://purl.obolibrary.org/obo/OVAE_$1", "version": "1.0.34" @@ -36489,11 +40839,13 @@ ], "mappings": { "biocontext": "owl", - "fairsharing": "FAIRsharing.atygwy" + "fairsharing": "FAIRsharing.atygwy", + "ols": "owl" }, "name": "Web Ontology Language", "preferred_prefix": "owl", - "uri_format": "http://www.w3.org/2002/07/owl#$1" + "uri_format": "http://www.w3.org/2002/07/owl#$1", + "version": "$Date: 2009/11/15 10:54:12 $" }, "owlstar": { "contact": { @@ -36539,6 +40891,15 @@ "name": "P3DB Protein", "pattern": "^\\d+$", "preferred_prefix": "p3db.protein", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/p3db:$1" + } + ], "uri_format": "http://www.p3db.org/protein.php?id=$1&ref=0" }, "p3db.site": { @@ -36555,6 +40916,24 @@ "preferred_prefix": "p3db.site", "uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0" }, + "pactr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)", + "example": "PACTR202304525632216", + "homepage": "https://pactr.samrc.ac.za/", + "logo": "https://pactr.samrc.ac.za/images/Banner_Split.jpg", + "name": "Pan African Clinical Trials Registry", + "pattern": "^PACTR\\d+$", + "preferred_prefix": "pactr", + "references": [ + "https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25488" + ] + }, "paleodb": { "description": "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data.", "example": "83088", @@ -36571,6 +40950,15 @@ "name": "Paleobiology Database", "pattern": "^\\d+$", "preferred_prefix": "paleodb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/paleodb:$1" + } + ], "uri_format": "http://fossilworks.org/?a=taxonInfo&taxon_no=$1" }, "pandit": { @@ -36588,6 +40976,15 @@ }, "name": "Protein and Associated NucleotideDomains with Inferred Trees", "preferred_prefix": "pandit", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pandit:$1" + } + ], "provides": "pfam", "reviewer": { "email": "cthoyt@gmail.com", @@ -36628,15 +41025,22 @@ "doi": "10.1074/mcp.ra117.000543", "pmc": "PMC5986241", "pubmed": "29487113", - "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.", + "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline", "year": 2018 }, { "doi": "10.1021/pr5006636", "pmc": "PMC4156235", "pubmed": "25102069", - "title": "Panorama: a targeted proteomics knowledge base.", + "title": "Panorama: a targeted proteomics knowledge base", "year": 2014 + }, + { + "doi": "10.1074/mcp.RA117.000543", + "pmc": null, + "pubmed": null, + "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline.", + "year": null } ], "uri_format": "https://panoramaweb.org/$1.url" @@ -36665,19 +41069,28 @@ "part_of": "panther", "pattern": "^PTHR\\d{5}(\\:SF\\d{1,3})?$", "preferred_prefix": "panther.family", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/panther:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gky1038", "pmc": "PMC6323939", "pubmed": "30407594", - "title": "PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.", + "title": "PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools", "year": 2019 }, { "doi": "10.1101/gr.772403", "pmc": "PMC403709", "pubmed": "12952881", - "title": "PANTHER: a library of protein families and subfamilies indexed by function.", + "title": "PANTHER: a library of protein families and subfamilies indexed by function", "year": 2003 } ], @@ -36748,6 +41161,7 @@ }, "name": "Plant Anatomy Ontology", "preferred_prefix": "PAO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PAO_$1", "uri_format": "http://purl.obolibrary.org/obo/PAO_$1" }, "pass2": { @@ -36770,6 +41184,15 @@ "name": "Protein Alignment organised as Structural Superfamily", "pattern": "^\\d+$", "preferred_prefix": "pass2", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pass2:$1" + } + ], "uri_format": "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1" }, "pathbank": { @@ -36827,6 +41250,15 @@ }, "name": "Pathguide", "preferred_prefix": "pathguide", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pathguide:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -36851,6 +41283,15 @@ }, "name": "PathoPlant®", "preferred_prefix": "pathoplant", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pathoplant:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -36877,12 +41318,21 @@ "name": "Pathway Commons", "pattern": "^\\d+$", "preferred_prefix": "pathwaycommons", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pathwaycommons:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkq1039", "pmc": "PMC3013659", "pubmed": "21071392", - "title": "Pathway Commons, a web resource for biological pathway data.", + "title": "Pathway Commons, a web resource for biological pathway data", "year": 2010 } ], @@ -36951,6 +41401,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "PATO", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pato:$1" + }, { "code": "purl", "description": "Legacy PURLs found in OAE", @@ -36964,27 +41421,28 @@ "doi": "10.1093/bib/bbx035", "pmc": "PMC6169674", "pubmed": "28387809", - "title": "The anatomy of phenotype ontologies: principles, properties and applications.", + "title": "The anatomy of phenotype ontologies: principles, properties and applications", "year": 2018 }, { "doi": "10.1186/gb-2010-11-1-r2", "pmc": "PMC2847714", "pubmed": "20064205", - "title": "Integrating phenotype ontologies across multiple species.", + "title": "Integrating phenotype ontologies across multiple species", "year": 2010 }, { "doi": "10.1186/gb-2004-6-1-r8", "pmc": "PMC549069", "pubmed": "15642100", - "title": "Using ontologies to describe mouse phenotypes.", + "title": "Using ontologies to describe mouse phenotypes", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PATO_$1", "repository": "https://github.com/pato-ontology/pato", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1", - "version": "2022-08-31" + "uri_format": "http://purl.obolibrary.org/obo/PATO_$1", + "version": "2023-05-18" }, "pav": { "contact": { @@ -36996,7 +41454,7 @@ "contributor": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", - "name": "Nico Matentzoglu", + "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor_extras": [ @@ -37032,7 +41490,7 @@ "doi": "10.1186/2041-1480-4-37", "pmc": "PMC4177195", "pubmed": "24267948", - "title": "PAV ontology: provenance, authoring and versioning.", + "title": "PAV ontology: provenance, authoring and versioning", "year": 2013 } ], @@ -37099,19 +41557,28 @@ "name": "Pazar Transcription Factor", "pattern": "^TF\\w+$", "preferred_prefix": "pazar", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pazar:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn783", "pmc": "PMC2686574", "pubmed": "18971253", - "title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.", + "title": "The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences", "year": 2008 }, { "doi": "10.1186/gb-2007-8-10-r207", "pmc": "PMC2246282", "pubmed": "17916232", - "title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.", + "title": "PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation", "year": 2007 } ], @@ -37191,9 +41658,10 @@ "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PCL_$1", "repository": "https://github.com/obophenotype/provisional_cell_ontology", "uri_format": "http://purl.obolibrary.org/obo/PCL_$1", - "version": "2022-10-19" + "version": "2023-02-27" }, "pco": { "appears_in": [ @@ -37245,6 +41713,7 @@ "name": "Population and Community Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PCO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PCO_$1", "repository": "https://github.com/PopulationAndCommunityOntology/pco", "uri_format": "http://purl.obolibrary.org/obo/PCO_$1", "version": "2021-05-03" @@ -37252,9 +41721,9 @@ "pd_st": { "contact": { "email": "henrich@embl.de", - "github": null, - "name": "Thorsten Heinrich", - "orcid": null + "github": "ThorstenHen", + "name": "Thorsten Henrich", + "orcid": "0000-0002-1548-3290" }, "deprecated": true, "homepage": "http://4dx.embl.de/platy", @@ -37268,6 +41737,7 @@ }, "name": "Platynereis stage ontology", "preferred_prefix": "PD_ST", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1", "uri_format": "http://purl.obolibrary.org/obo/PD_ST_$1" }, "pdb": { @@ -37313,6 +41783,13 @@ "name": "Proteopedia", "uri_format": "http://proteopedia.org/wiki/index.php/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pdbj:$1" + }, { "code": "ebi", "description": "Protein Databank through PDBsum", @@ -37347,52 +41824,53 @@ "doi": "10.1002/pro.4211", "pmc": "PMC8740847", "pubmed": "34664328", - "title": "Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.", + "title": "Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data", "year": 2021 }, { "doi": "10.1002/pro.3273", "pmc": "PMC5734392", "pubmed": "28815765", - "title": "New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).", + "title": "New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)", "year": 2017 }, { "doi": "10.1093/nar/gkw962", "pmc": "PMC5210648", "pubmed": "27789697", - "title": "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.", + "title": "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures", "year": 2016 }, { "doi": "10.1093/nar/gkr811", "pmc": "PMC3245181", "pubmed": "21976737", - "title": "Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.", + "title": "Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format", "year": 2011 }, { "doi": "10.1007/s10822-011-9460-y", "pmc": null, "pubmed": "21796434", - "title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr.", + "title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr", "year": 2011 }, { "doi": "10.1093/database/baq021", "pmc": "PMC2997606", "pubmed": "20798081", - "title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.", + "title": "PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan", "year": 2010 }, { "doi": null, "pmc": null, "pubmed": "12099029", - "title": "[Development of PDBj: Advanced database for protein structures].", + "title": "[Development of PDBj: Advanced database for protein structures]", "year": 2002 } ], + "rdf_uri_format": "https://rdf.wwpdb.org/pdb/$1", "synonyms": [ "RCSB_PDB", "pdbe", @@ -37433,12 +41911,21 @@ "name": "Chemical Component Dictionary", "pattern": "^\\w{1,3}$", "preferred_prefix": "pdb-ccd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ccd:$1" + } + ], "publications": [ { "doi": "10.1038/nsb1203-980", "pmc": null, "pubmed": "14634627", - "title": "Announcing the worldwide Protein Data Bank.", + "title": "Announcing the worldwide Protein Data Bank", "year": 2003 } ], @@ -37474,6 +41961,13 @@ "homepage": "https://www.pdbe.org/", "name": "PDB Ligand at Protein Databank in Europe (PDBe)", "uri_format": "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pdbligand:$1" } ], "synonyms": [ @@ -37504,27 +41998,36 @@ }, "name": "PDBsum; at-a-glance overview of macromolecular structures", "preferred_prefix": "pdbsum", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pdbsum:$1" + } + ], "provides": "pdb", "publications": [ { "doi": "10.1002/pro.3289", "pmc": "PMC5734310", "pubmed": "28875543", - "title": "PDBsum: Structural summaries of PDB entries.", + "title": "PDBsum: Structural summaries of PDB entries", "year": 2017 }, { "doi": "10.1093/nar/gkt940", "pmc": "PMC3965036", "pubmed": "24153109", - "title": "PDBsum additions.", + "title": "PDBsum additions", "year": 2013 }, { "doi": "10.1093/nar/gkn860", "pmc": "PMC2686501", "pubmed": "18996896", - "title": "PDBsum new things.", + "title": "PDBsum new things", "year": 2008 } ], @@ -37587,15 +42090,25 @@ "name": "The Prescription of Drugs Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PDRO", + "providers": [ + { + "code": "pdro.legacy", + "description": "An incorrect encoding of OBO purls", + "homepage": "http://purl.obolibrary.org/obo/pdro", + "name": "PDRO Hash", + "uri_format": "http://purl.obolibrary.org/obo/PDRO/PDRO.owl#PDRO_$1" + } + ], "publications": [ { "doi": "10.3390/ijerph182212025", "pmc": "PMC8619589", "pubmed": "34831777", - "title": "The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts.", + "title": "The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts", "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PDRO_$1", "repository": "https://github.com/OpenLHS/PDRO", "uri_format": "http://purl.obolibrary.org/obo/PDRO_$1", "version": "2021-06-08" @@ -37631,11 +42144,12 @@ "name": "Platynereis Developmental Stages", "pattern": "^\\d{7}$", "preferred_prefix": "PdumDv", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1", "repository": "https://github.com/obophenotype/developmental-stage-ontologies", "synonyms": [ "PdumDv" ], - "uri_format": "http://purl.obolibrary.org/obo/PDUMDV_$1", + "uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1", "version": "2020-03-10" }, "peco": { @@ -37660,6 +42174,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "PECO", "agroportal": "PECO", @@ -37678,10 +42193,11 @@ "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", - "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.", + "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PECO_$1", "repository": "https://github.com/Planteome/plant-experimental-conditions-ontology", "uri_format": "http://purl.obolibrary.org/obo/PECO_$1", "version": "2020-08-21" @@ -37706,7 +42222,7 @@ "doi": "10.1093/nar/gky1026", "pmc": "PMC6324055", "pubmed": "30364952", - "title": "Plant editosome database: a curated database of RNA editosome in plants.", + "title": "Plant editosome database: a curated database of RNA editosome in plants", "year": 2019 } ], @@ -37771,6 +42287,15 @@ }, "name": "PepBank Peptide Database", "preferred_prefix": "pepbank", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pepbank:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -37808,27 +42333,36 @@ "name": "PeptideAtlas", "pattern": "^PAp[0-9]{8}$", "preferred_prefix": "peptideatlas", - "publications": [ + "providers": [ { - "doi": "10.1038/embor.2008.56.", - "pmc": "PMC2373374", - "pubmed": "18451766", - "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.", - "year": null - }, + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/peptideatlas:$1" + } + ], + "publications": [ { "doi": "10.1038/embor.2008.56", "pmc": "PMC2373374", "pubmed": "18451766", - "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.", + "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows", "year": 2008 }, { "doi": "10.1093/nar/gkj040", "pmc": "PMC1347403", "pubmed": "16381952", - "title": "The PeptideAtlas project.", + "title": "The PeptideAtlas project", "year": 2006 + }, + { + "doi": "10.1038/embor.2008.56.", + "pmc": null, + "pubmed": null, + "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.", + "year": null } ], "uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1" @@ -37884,24 +42418,45 @@ "name": "Peroxibase", "pattern": "^\\d+$", "preferred_prefix": "peroxibase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/peroxibase:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gks1083", "pmc": "PMC3531118", "pubmed": "23180785", - "title": "PeroxiBase: a database for large-scale evolutionary analysis of peroxidases.", + "title": "PeroxiBase: a database for large-scale evolutionary analysis of peroxidases", "year": 2012 }, { "doi": "10.1093/jxb/ern317", "pmc": null, "pubmed": "19112168", - "title": "PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae.", + "title": "PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae", "year": 2008 } ], "uri_format": "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1" }, + "pesticideinfo": { + "description": "chemical in the database supplied by Pesticide Action Network North America", + "example": "PRI10", + "homepage": "https://www.pesticideinfo.org", + "mappings": { + "wikidata": "P11949" + }, + "name": "PesticideInfo chemical ID", + "pattern": "^PRI\\d*$", + "preferred_prefix": "pesticideinfo", + "uri_format": "https://www.pesticideinfo.org/chemical/$1" + }, "pesticides": { "contributor": { "email": "cthoyt@gmail.com", @@ -37925,7 +42480,7 @@ }, "description": "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.", "example": "PF11779", - "homepage": "https://pfam.xfam.org/", + "homepage": "https://www.ebi.ac.uk/interpro/", "keywords": [ "biology", "domain", @@ -37948,6 +42503,13 @@ "pattern": "^PF\\d{5}$", "preferred_prefix": "pfam", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pfam:$1" + }, { "code": "sanger", "description": "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.", @@ -37968,98 +42530,98 @@ "doi": "10.1093/nar/27.1.260", "pmc": "PMC148151", "pubmed": "9847196", - "title": "Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.", + "title": "Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins", "year": 1999 }, { "doi": "10.1093/nar/26.1.320", "pmc": "PMC147209", "pubmed": "9399864", - "title": "Pfam: multiple sequence alignments and HMM-profiles of protein domains.", + "title": "Pfam: multiple sequence alignments and HMM-profiles of protein domains", "year": 1998 }, { "doi": "10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l", "pmc": null, "pubmed": "9223186", - "title": "Pfam: a comprehensive database of protein domain families based on seed alignments.", + "title": "Pfam: a comprehensive database of protein domain families based on seed alignments", "year": 1997 }, { "doi": "10.1093/nar/gkaa913", "pmc": "PMC7779014", "pubmed": "33125078", - "title": "Pfam: The protein families database in 2021.", + "title": "Pfam: The protein families database in 2021", "year": 2021 }, { "doi": "10.1093/nar/gky995", "pmc": "PMC6324024", "pubmed": "30357350", - "title": "The Pfam protein families database in 2019.", + "title": "The Pfam protein families database in 2019", "year": 2019 }, { "doi": "10.1093/nar/gkv1344", "pmc": "PMC4702930", "pubmed": "26673716", - "title": "The Pfam protein families database: towards a more sustainable future.", + "title": "The Pfam protein families database: towards a more sustainable future", "year": 2015 }, { "doi": "10.1093/nar/gkt1223", "pmc": "PMC3965110", "pubmed": "24288371", - "title": "Pfam: the protein families database.", + "title": "Pfam: the protein families database", "year": 2013 }, { "doi": "10.1093/nar/gkr1065", "pmc": "PMC3245129", "pubmed": "22127870", - "title": "The Pfam protein families database.", + "title": "The Pfam protein families database", "year": 2011 }, { "doi": "10.1093/nar/gkp985", "pmc": "PMC2808889", "pubmed": "19920124", - "title": "The Pfam protein families database.", + "title": "The Pfam protein families database", "year": 2009 }, { "doi": "10.1093/nar/gkm960", "pmc": "PMC2238907", "pubmed": "18039703", - "title": "The Pfam protein families database.", + "title": "The Pfam protein families database", "year": 2007 }, { "doi": "10.1093/nar/gkj149", "pmc": "PMC1347511", "pubmed": "16381856", - "title": "Pfam: clans, web tools and services.", + "title": "Pfam: clans, web tools and services", "year": 2006 }, { "doi": "10.1093/nar/gkh121", "pmc": "PMC308855", "pubmed": "14681378", - "title": "The Pfam protein families database.", + "title": "The Pfam protein families database", "year": 2004 }, { "doi": "10.1093/nar/30.1.276", "pmc": "PMC99071", "pubmed": "11752314", - "title": "The Pfam protein families database.", + "title": "The Pfam protein families database", "year": 2002 }, { "doi": "10.1093/nar/28.1.263", "pmc": "PMC102420", "pubmed": "10592242", - "title": "The Pfam protein families database.", + "title": "The Pfam protein families database", "year": 2000 } ], @@ -38147,6 +42709,7 @@ }, "name": "Plant Growth and Development Stage", "preferred_prefix": "PGDSO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PGDSO_$1", "uri_format": "http://purl.obolibrary.org/obo/PGDSO_$1" }, "pgs": { @@ -38191,49 +42754,49 @@ "doi": "10.1093/nar/gku1123", "pmc": "PMC4383937", "pubmed": "25428357", - "title": "arrayMap 2014: an updated cancer genome resource.", + "title": "arrayMap 2014: an updated cancer genome resource", "year": 2014 }, { "doi": "10.1186/1471-2164-15-82", "pmc": "PMC3909908", "pubmed": "24476156", - "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.", + "title": "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens", "year": 2014 }, { "doi": "10.1093/nar/gkt1108", "pmc": "PMC3965091", "pubmed": "24225322", - "title": "Progenetix: 12 years of oncogenomic data curation.", + "title": "Progenetix: 12 years of oncogenomic data curation", "year": 2013 }, { "doi": "10.1371/journal.pone.0036944", "pmc": "PMC3356349", "pubmed": "22629346", - "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies.", + "title": "arrayMap: a reference resource for genomic copy number imbalances in human malignancies", "year": 2012 }, { "doi": "10.1186/1471-2407-7-226", "pmc": "PMC2225423", "pubmed": "18088415", - "title": "Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data.", + "title": "Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data", "year": 2007 }, { "doi": "10.2144/000112102", "pmc": null, "pubmed": "16568815", - "title": "Online database and bioinformatics toolbox to support data mining in cancer cytogenetics.", + "title": "Online database and bioinformatics toolbox to support data mining in cancer cytogenetics", "year": 2006 }, { "doi": "10.1093/bioinformatics/17.12.1228", "pmc": null, "pubmed": "11751233", - "title": "Progenetix.net: an online repository for molecular cytogenetic aberration data.", + "title": "Progenetix.net: an online repository for molecular cytogenetic aberration data", "year": 2001 } ], @@ -38309,19 +42872,28 @@ "name": "PharmGKB Disease", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.disease", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pharmgkb.disease:$1" + } + ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", - "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pmc": null, "pubmed": "11908751", - "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.", + "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], @@ -38346,19 +42918,28 @@ "name": "PharmGKB Drug", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.drug", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pharmgkb.drug:$1" + } + ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", - "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pmc": null, "pubmed": "11908751", - "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.", + "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], @@ -38387,19 +42968,28 @@ "name": "PharmGKB Gene", "pattern": "^PA\\w+$", "preferred_prefix": "pharmgkb.gene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pharmgkb.gene:$1" + } + ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", - "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1385/1-59259-957-5:179", "pmc": null, "pubmed": "16100408", - "title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base.", + "title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base", "year": 2005 } ], @@ -38425,19 +43015,28 @@ "name": "PharmGKB", "pattern": "^PA\\d+$", "preferred_prefix": "pharmgkb.pathways", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pharmgkb.pathways:$1" + } + ], "publications": [ { "doi": "10.2217/bmm.11.94", "pmc": "PMC3339046", "pubmed": "22103613", - "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource.", + "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource", "year": 2011 }, { "doi": "10.1038/sj.tpj.6500035", "pmc": null, "pubmed": "11908751", - "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.", + "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base", "year": 2001 } ], @@ -38457,13 +43056,22 @@ }, "name": "Pharmacogene Variation Consortium", "preferred_prefix": "pharmvar", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pharmvar:$1" + } + ], "provides": "hgnc.symbol", "publications": [ { "doi": "10.1002/cpt.910", "pmc": "PMC5836850", "pubmed": "29134625", - "title": "The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database.", + "title": "The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database", "year": 2017 } ], @@ -38527,22 +43135,29 @@ "doi": "10.1038/gim.2016.199", "pmc": "PMC5507752", "pubmed": "28079902", - "title": "PhenX measures for phenotyping rare genetic conditions.", + "title": "PhenX measures for phenotyping rare genetic conditions", "year": 2017 }, { "doi": "10.1093/aje/kwr193", "pmc": "PMC3141081", "pubmed": "21749974", - "title": "The PhenX Toolkit: get the most from your measures.", + "title": "The PhenX Toolkit: get the most from your measures", "year": 2011 }, { "doi": "10.1097/mol.0b013e3283377395", "pmc": "PMC8038872", "pubmed": "20154612", - "title": "PhenX: a toolkit for interdisciplinary genetics research.", + "title": "PhenX: a toolkit for interdisciplinary genetics research", "year": 2010 + }, + { + "doi": "10.1097/MOL.0b013e3283377395", + "pmc": "PMC8038872", + "pubmed": "20154612", + "title": "PhenX: a toolkit for interdisciplinary genetics research", + "year": null } ], "synonyms": [ @@ -38585,13 +43200,14 @@ "doi": "10.1093/nar/gkab1037", "pmc": "PMC8728202", "pubmed": "34788826", - "title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.", + "title": "PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions", "year": 2022 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PHIPO_$1", "repository": "https://github.com/PHI-base/phipo", "uri_format": "http://purl.obolibrary.org/obo/PHIPO_$1", - "version": "2021-07-14" + "version": "2023-06-22" }, "phosphopoint.kinase": { "description": "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information.", @@ -38699,33 +43315,42 @@ "name": "PhylomeDB", "pattern": "^\\w+$", "preferred_prefix": "phylomedb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/phylomedb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab966", "pmc": "PMC8728271", "pubmed": "34718760", - "title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.", + "title": "PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies", "year": 2022 }, { "doi": "10.1093/nar/gkt1177", "pmc": "PMC3964985", "pubmed": "24275491", - "title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.", + "title": "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome", "year": 2013 }, { "doi": "10.1093/nar/gkq1109", "pmc": "PMC3013701", "pubmed": "21075798", - "title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.", + "title": "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions", "year": 2010 }, { "doi": "10.1093/nar/gkm899", "pmc": "PMC2238872", "pubmed": "17962297", - "title": "PhylomeDB: a database for genome-wide collections of gene phylogenies.", + "title": "PhylomeDB: a database for genome-wide collections of gene phylogenies", "year": 2007 } ], @@ -38763,6 +43388,15 @@ }, "name": "Database of structurally defined protein interfaces", "preferred_prefix": "pibase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pibase:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -38809,12 +43443,21 @@ "name": "NCI Pathway Interaction Database: Pathway", "pattern": "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$", "preferred_prefix": "pid.pathway", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pid:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn653", "pmc": "PMC2686461", "pubmed": "18832364", - "title": "PID: the Pathway Interaction Database.", + "title": "PID: the Pathway Interaction Database", "year": 2008 } ], @@ -38841,6 +43484,15 @@ "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "pigqtldb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pigqtldb:$1" + } + ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "pina": { @@ -38872,21 +43524,21 @@ "doi": "10.1093/nar/gkaa1075", "pmc": "PMC7779002", "pubmed": "33231689", - "title": "PINA 3.0: mining cancer interactome.", + "title": "PINA 3.0: mining cancer interactome", "year": 2021 }, { "doi": "10.1093/nar/gkr967", "pmc": "PMC3244997", "pubmed": "22067443", - "title": "PINA v2.0: mining interactome modules.", + "title": "PINA v2.0: mining interactome modules", "year": 2011 }, { "doi": "10.1038/nmeth.1282", "pmc": null, "pubmed": "19079255", - "title": "Integrated network analysis platform for protein-protein interactions.", + "title": "Integrated network analysis platform for protein-protein interactions", "year": 2008 } ], @@ -38929,12 +43581,21 @@ "name": "PIR Superfamily Classification System", "pattern": "^PIRSF\\d{6}$", "preferred_prefix": "pirsf", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pirsf:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh097", "pmc": "PMC308831", "pubmed": "14681371", - "title": "PIRSF: family classification system at the Protein Information Resource.", + "title": "PIRSF: family classification system at the Protein Information Resource", "year": 2004 } ], @@ -38971,7 +43632,7 @@ "doi": "10.1093/nar/gkaa990", "pmc": "PMC7779054", "pubmed": "33151297", - "title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling.", + "title": "PK-DB: pharmacokinetics database for individualized and stratified computational modeling", "year": 2021 } ], @@ -39022,13 +43683,14 @@ "doi": "10.1242/dev.196097", "pmc": "PMC8353266", "pubmed": "34318308", - "title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms.", + "title": "Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms", "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", "repository": "https://github.com/obophenotype/planaria-ontology", "uri_format": "http://purl.obolibrary.org/obo/PLANA_$1", - "version": "2022-03-02" + "version": "2023-03-13" }, "planp": { "contact": { @@ -39063,6 +43725,7 @@ "name": "Planarian Phenotype Ontology", "pattern": "^\\d+$", "preferred_prefix": "PLANP", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", "repository": "https://github.com/obophenotype/planarian-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/PLANP_$1", "version": "2020-03-28" @@ -39091,26 +43754,35 @@ "name": "Plant Transcription Factor Database", "pattern": "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$", "preferred_prefix": "planttfdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/planttfdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkw982", "pmc": "PMC5210657", "pubmed": "27924042", - "title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.", + "title": "PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants", "year": 2016 }, { "doi": "10.1093/molbev/msv058", "pmc": "PMC4476157", "pubmed": "25750178", - "title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.", + "title": "An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors", "year": 2015 }, { "doi": "10.1093/nar/gkt1016", "pmc": "PMC3965000", "pubmed": "24174544", - "title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors.", + "title": "PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors", "year": 2013 } ], @@ -39138,12 +43810,21 @@ "name": "PlasmoDB", "pattern": "^\\w+$", "preferred_prefix": "plasmodb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/plasmodb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn814", "pmc": "PMC2686598", "pubmed": "18957442", - "title": "PlasmoDB: a functional genomic database for malaria parasites.", + "title": "PlasmoDB: a functional genomic database for malaria parasites", "year": 2008 } ], @@ -39172,6 +43853,7 @@ }, "name": "Plasmodium Life Cycle", "preferred_prefix": "PLO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PLO_$1", "uri_format": "http://purl.obolibrary.org/obo/PLO_$1" }, "pmap.cutdb": { @@ -39192,12 +43874,21 @@ "name": "CutDB", "pattern": "^\\d+$", "preferred_prefix": "pmap.cutdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pmap.cutdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkl813", "pmc": "PMC1669773", "pubmed": "17142225", - "title": "CutDB: a proteolytic event database.", + "title": "CutDB: a proteolytic event database", "year": 2006 } ], @@ -39221,12 +43912,21 @@ "name": "SubstrateDB", "pattern": "^\\d+$", "preferred_prefix": "pmap.substratedb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pmap.substratedb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn683", "pmc": "PMC2686432", "pubmed": "18842634", - "title": "PMAP: databases for analyzing proteolytic events and pathways.", + "title": "PMAP: databases for analyzing proteolytic events and pathways", "year": 2008 } ], @@ -39247,6 +43947,7 @@ ], "mappings": { "biocontext": "PMCID", + "biolink": "PMC", "fairsharing": "FAIRsharing.wpt5mp", "go": "PMCID", "miriam": "pmc", @@ -39258,6 +43959,13 @@ "pattern": "^PMC\\d+$", "preferred_prefix": "pmc", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pmc:$1" + }, { "code": "ncbi", "description": "PubMed Central", @@ -39271,14 +43979,14 @@ "doi": "10.1093/nar/gkr1184", "pmc": "PMC3245031", "pubmed": "22140104", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2011 }, { "doi": "10.1093/nar/gkq1172", "pmc": "PMC3013733", "pubmed": "21097890", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2010 } ], @@ -39307,12 +44015,21 @@ "name": "Protein Model Database", "pattern": "^PM\\d{7}$", "preferred_prefix": "pmdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pmdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkj105", "pmc": "PMC1347467", "pubmed": "16381873", - "title": "The PMDB Protein Model Database.", + "title": "The PMDB Protein Model Database", "year": 2006 } ], @@ -39336,13 +44053,22 @@ "name": "Protein Model Portal", "pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$", "preferred_prefix": "pmp", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pmp:$1" + } + ], "provides": "uniprot", "publications": [ { "doi": "10.1007/s10969-008-9048-5", "pmc": "PMC2704613", "pubmed": "19037750", - "title": "The Protein Model Portal.", + "title": "The Protein Model Portal", "year": 2008 } ], @@ -39381,43 +44107,50 @@ "doi": "10.1098/rsfs.2015.0103", "pmc": "PMC4759754", "pubmed": "27051515", - "title": "The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.", + "title": "The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable", "year": 2016 }, { "doi": "10.1186/1471-2105-12-22", "pmc": "PMC3033326", "pubmed": "21235804", - "title": "Revision history aware repositories of computational models of biological systems.", + "title": "Revision history aware repositories of computational models of biological systems", "year": 2011 }, { "doi": "10.1093/bioinformatics/btq723", "pmc": null, "pubmed": "21216774", - "title": "The Physiome Model Repository 2.", + "title": "The Physiome Model Repository 2", "year": 2011 }, { "doi": "10.1098/rsta.2008.0310", "pmc": "PMC3268215", "pubmed": "19380315", - "title": "CellML metadata standards, associated tools and repositories.", + "title": "CellML metadata standards, associated tools and repositories", "year": 2009 }, { "doi": "10.1093/bioinformatics/btn390", "pmc": null, "pubmed": "18658182", - "title": "The CellML Model Repository.", + "title": "The CellML Model Repository", "year": 2008 }, { "doi": "10.1109/iembs.2006.260202", "pmc": null, "pubmed": "17947072", - "title": "Toward a curated CellML model repository.", + "title": "Toward a curated CellML model repository", "year": 2006 + }, + { + "doi": "10.1109/IEMBS.2006.260202", + "pmc": null, + "pubmed": null, + "title": "Toward a curated CellML model repository.", + "year": null } ], "twitter": "physiomeproject", @@ -39464,6 +44197,7 @@ "structure" ], "license": "CC-BY-4.0", + "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "PO", "agroportal": "PO", @@ -39483,57 +44217,67 @@ "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "PO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/po:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", - "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.", + "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 }, { "doi": "10.1007/978-1-4939-3167-5_5", "pmc": null, "pubmed": "26519402", - "title": "The Plant Ontology: A Tool for Plant Genomics.", + "title": "The Plant Ontology: A Tool for Plant Genomics", "year": 2016 }, { "doi": "10.1371/journal.pbio.1002033", "pmc": "PMC4285398", "pubmed": "25562316", - "title": "Finding our way through phenotypes.", + "title": "Finding our way through phenotypes", "year": 2015 }, { "doi": "10.1093/pcp/pcs163", "pmc": "PMC3583023", "pubmed": "23220694", - "title": "The plant ontology as a tool for comparative plant anatomy and genomic analyses.", + "title": "The plant ontology as a tool for comparative plant anatomy and genomic analyses", "year": 2012 }, { "doi": "10.1002/cfg.496", "pmc": "PMC2447502", "pubmed": "18629207", - "title": "Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.", + "title": "Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages", "year": 2005 }, { "doi": "10.1002/cfg.154", "pmc": "PMC2447263", "pubmed": "18628842", - "title": "The Plant Ontology Consortium and plant ontologies.", + "title": "The Plant Ontology Consortium and plant ontologies", "year": 2002 }, { "doi": "10.1093/nar/gkm908", "pmc": "PMC2238838", "pubmed": "18194960", - "title": "The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.", + "title": "The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations", "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PO_$1", "repository": "https://github.com/Planteome/plant-ontology", "twitter": "planteome", "uri_format": "http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1", @@ -39560,14 +44304,14 @@ "doi": "10.1093/nar/gkr825", "pmc": "PMC3245087", "pubmed": "22080553", - "title": "Pocketome: an encyclopedia of small-molecule binding sites in 4D.", + "title": "Pocketome: an encyclopedia of small-molecule binding sites in 4D", "year": 2011 }, { "doi": "10.1007/978-1-60761-274-2_11", "pmc": "PMC2975493", "pubmed": "19727619", - "title": "The flexible pocketome engine for structural chemogenomics.", + "title": "The flexible pocketome engine for structural chemogenomics", "year": 2009 } ], @@ -39595,7 +44339,7 @@ "doi": "10.1093/nar/gkr847", "pmc": "PMC3245023", "pubmed": "21993301", - "title": "Polbase: a repository of biochemical, genetic and structural information about DNA polymerases.", + "title": "Polbase: a repository of biochemical, genetic and structural information about DNA polymerases", "year": 2011 } ], @@ -39624,68 +44368,77 @@ "name": "PomBase", "pattern": "^S\\w+(\\.)?\\w+(\\.)?$", "preferred_prefix": "pombase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pombase:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gky961", "pmc": "PMC6324063", "pubmed": "30321395", - "title": "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.", + "title": "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information", "year": 2019 }, { "doi": "10.1186/s12915-016-0276-z", "pmc": "PMC4918006", "pubmed": "27334346", - "title": "Model organism databases: essential resources that need the support of both funders and users.", + "title": "Model organism databases: essential resources that need the support of both funders and users", "year": 2016 }, { "doi": "10.1093/nar/gku1040", "pmc": "PMC4383888", "pubmed": "25361970", - "title": "PomBase 2015: updates to the fission yeast database.", + "title": "PomBase 2015: updates to the fission yeast database", "year": 2014 }, { "doi": "10.1186/1471-2105-15-155", "pmc": "PMC4039540", "pubmed": "24885854", - "title": "A method for increasing expressivity of Gene Ontology annotations using a compositional approach.", + "title": "A method for increasing expressivity of Gene Ontology annotations using a compositional approach", "year": 2014 }, { "doi": "10.1093/bioinformatics/btu103", "pmc": "PMC4058955", "pubmed": "24574118", - "title": "Canto: an online tool for community literature curation.", + "title": "Canto: an online tool for community literature curation", "year": 2014 }, { "doi": "10.1093/bioinformatics/btt266", "pmc": "PMC3694669", "pubmed": "23658422", - "title": "FYPO: the fission yeast phenotype ontology.", + "title": "FYPO: the fission yeast phenotype ontology", "year": 2013 }, { "doi": "10.1093/nar/gks1050", "pmc": "PMC3531070", "pubmed": "23161678", - "title": "Gene Ontology annotations and resources.", + "title": "Gene Ontology annotations and resources", "year": 2012 }, { "doi": "10.1093/nar/gkr1028", "pmc": "PMC3245151", "pubmed": "22102568", - "title": "The Gene Ontology: enhancements for 2011.", + "title": "The Gene Ontology: enhancements for 2011", "year": 2011 }, { "doi": "10.1093/nar/gkr853", "pmc": "PMC3245111", "pubmed": "22039153", - "title": "PomBase: a comprehensive online resource for fission yeast.", + "title": "PomBase: a comprehensive online resource for fission yeast", "year": 2011 } ], @@ -39735,10 +44488,11 @@ "doi": "10.1186/2041-1480-5-39", "pmc": "PMC4177528", "pubmed": "25276334", - "title": "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.", + "title": "The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PORO_$1", "repository": "https://github.com/obophenotype/porifera-ontology", "uri_format": "http://purl.obolibrary.org/obo/PORO_$1", "version": "2016-10-06" @@ -39773,14 +44527,14 @@ "doi": "10.1093/nar/gkt1027", "pmc": "PMC3965062", "pubmed": "24194597", - "title": "ppdb: plant promoter database version 3.0.", + "title": "ppdb: plant promoter database version 3.0", "year": 2013 }, { "doi": "10.1093/nar/gkm785", "pmc": "PMC2238996", "pubmed": "17947329", - "title": "ppdb: a plant promoter database.", + "title": "ppdb: a plant promoter database", "year": 2007 } ], @@ -39821,10 +44575,11 @@ "doi": "10.3389/fpls.2018.00517", "pmc": "PMC5938398", "pubmed": "29765382", - "title": "The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data.", + "title": "The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data", "year": 2018 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PPO_$1", "repository": "https://github.com/PlantPhenoOntology/PPO", "uri_format": "http://purl.obolibrary.org/obo/PPO_$1", "version": "2018-10-26" @@ -39836,16 +44591,34 @@ "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, + "contributor_extras": [ + { + "email": "egon.willighagen@gmail.com", + "github": "egonw", + "name": "Egon Willighagen", + "orcid": "0000-0001-7542-0286" + }, + { + "email": "javier.millanacosta@maastrichtuniversity.nl", + "github": "jmillanacosta", + "name": "Javier Millán Acosta", + "orcid": "0000-0002-4166-7093" + } + ], "description": "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000.", - "example": "ppr103739", - "homepage": "https://europepmc.org", + "example": "PPR103739", + "homepage": "https://europepmc.org/Preprints", "keywords": [ "bibliometrics", "preprints", "publishing" ], "name": "Europe PMC Preprints", + "pattern": "^PPR\\d+$", "preferred_prefix": "ppr", + "references": [ + "https://github.com/bridgedb/tiwid/pull/21" + ], "uri_format": "https://europepmc.org/article/ppr/$1" }, "pr": { @@ -39875,6 +44648,7 @@ "protein" ], "license": "CC-BY-4.0", + "logo": "https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png", "mappings": { "aberowl": "PR", "agroportal": "PR", @@ -39895,50 +44669,74 @@ "namespace_in_lui": true, "pattern": "^\\d+$", "preferred_prefix": "PR", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pr:$1" + }, + { + "code": "ontorat", + "description": "Misguided re-labeling of IRIs from ontorat tool", + "homepage": "http://purl.obolibrary.org/obo/vo/ontorat", + "name": "OntoRat", + "uri_format": "http://purl.obolibrary.org/obo/vo/ontorat/PR_$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkw1075", "pmc": "PMC5210558", "pubmed": "27899649", - "title": "Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.", + "title": "Protein Ontology (PRO): enhancing and scaling up the representation of protein entities", "year": 2016 }, { "doi": "10.1093/nar/gkt1173", "pmc": "PMC3964965", "pubmed": "24270789", - "title": "Protein Ontology: a controlled structured network of protein entities.", + "title": "Protein Ontology: a controlled structured network of protein entities", "year": 2013 }, { "doi": "10.1186/1471-2105-12-371", "pmc": "PMC3189193", "pubmed": "21929785", - "title": "The representation of protein complexes in the Protein Ontology (PRO).", + "title": "The representation of protein complexes in the Protein Ontology (PRO)", "year": 2011 }, { "doi": "10.1093/nar/gkq907", "pmc": "PMC3013777", "pubmed": "20935045", - "title": "The Protein Ontology: a structured representation of protein forms and complexes.", + "title": "The Protein Ontology: a structured representation of protein forms and complexes", "year": 2010 }, { "doi": "10.1186/1471-2105-8-s9-s1", "pmc": "PMC2217659", "pubmed": "18047702", - "title": "Framework for a protein ontology.", + "title": "Framework for a protein ontology", "year": 2007 + }, + { + "doi": "10.1186/1471-2105-8-S9-S1", + "pmc": "PMC2217659", + "pubmed": "18047702", + "title": "Framework for a protein ontology", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PR_$1", "repository": "https://github.com/PROconsortium/PRoteinOntology", "synonyms": [ "PR", "PRO" ], "uri_format": "https://proconsortium.org/app/entry/PR:$1", - "version": "67.0" + "version": "68.0" }, "prefixcommons": { "contributor": { @@ -39984,75 +44782,84 @@ "name": "PRIDE Controlled Vocabulary", "pattern": "^\\d{7}$", "preferred_prefix": "pride", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pride:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1038", "pmc": "PMC8728295", "pubmed": "34723319", - "title": "The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.", + "title": "The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences", "year": 2022 }, { "doi": "10.1093/nar/gky1106", "pmc": "PMC6323896", "pubmed": "30395289", - "title": "The PRIDE database and related tools and resources in 2019: improving support for quantification data.", + "title": "The PRIDE database and related tools and resources in 2019: improving support for quantification data", "year": 2019 }, { "doi": "10.1093/nar/gkv1145", "pmc": "PMC4702828", "pubmed": "26527722", - "title": "2016 update of the PRIDE database and its related tools.", + "title": "2016 update of the PRIDE database and its related tools", "year": 2015 }, { "doi": "10.1002/pmic.201400120", "pmc": null, "pubmed": "25047258", - "title": "How to submit MS proteomics data to ProteomeXchange via the PRIDE database.", + "title": "How to submit MS proteomics data to ProteomeXchange via the PRIDE database", "year": 2014 }, { "doi": "10.1038/nbt.2839", "pmc": "PMC3986813", "pubmed": "24727771", - "title": "ProteomeXchange provides globally coordinated proteomics data submission and dissemination.", + "title": "ProteomeXchange provides globally coordinated proteomics data submission and dissemination", "year": 2014 }, { "doi": "10.1093/nar/gks1262", "pmc": "PMC3531176", "pubmed": "23203882", - "title": "The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.", + "title": "The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013", "year": 2012 }, { "doi": "10.1002/0471250953.bi1308s21", "pmc": null, "pubmed": "18428683", - "title": "Using the Proteomics Identifications Database (PRIDE).", + "title": "Using the Proteomics Identifications Database (PRIDE)", "year": 2008 }, { "doi": "10.1093/nar/gkm1021", "pmc": "PMC2238846", "pubmed": "18033805", - "title": "PRIDE: new developments and new datasets.", + "title": "PRIDE: new developments and new datasets", "year": 2007 }, { "doi": "10.1093/nar/gkj138", "pmc": "PMC1347500", "pubmed": "16381953", - "title": "PRIDE: a public repository of protein and peptide identifications for the proteomics community.", + "title": "PRIDE: a public repository of protein and peptide identifications for the proteomics community", "year": 2006 }, { "doi": "10.1002/pmic.200401303", "pmc": null, "pubmed": "16041671", - "title": "PRIDE: the proteomics identifications database.", + "title": "PRIDE: the proteomics identifications database", "year": 2005 } ], @@ -40107,6 +44914,13 @@ "pattern": "^PR\\d{5}$", "preferred_prefix": "prints", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sprint:$1" + }, { "code": "prints.alt1", "description": "Alternative access", @@ -40120,28 +44934,28 @@ "doi": "10.1093/database/bas019", "pmc": "PMC3326521", "pubmed": "22508994", - "title": "The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012.", + "title": "The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012", "year": 2012 }, { "doi": "10.1093/nar/gkg030", "pmc": "PMC165477", "pubmed": "12520033", - "title": "PRINTS and its automatic supplement, prePRINTS.", + "title": "PRINTS and its automatic supplement, prePRINTS", "year": 2003 }, { "doi": "10.1093/bioinformatics/15.10.799", "pmc": null, "pubmed": "10705433", - "title": "FingerPRINTScan: intelligent searching of the PRINTS motif database.", + "title": "FingerPRINTScan: intelligent searching of the PRINTS motif database", "year": 1999 }, { "doi": "10.1093/nar/28.1.225", "pmc": "PMC102408", "pubmed": "10592232", - "title": "PRINTS-S: the database formerly known as PRINTS.", + "title": "PRINTS-S: the database formerly known as PRINTS", "year": 2000 } ], @@ -40185,7 +44999,7 @@ "orcid": "0000-0003-4614-562X" }, "description": "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities.", - "download_owl": "https://raw.githubusercontent.com/probonto/ontology/master/probonto4ols.owl", + "download_owl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/probonto.ttl", "example": "c0000005", "example_extras": [ "k0001285" @@ -40213,7 +45027,7 @@ "doi": "10.1093/bioinformatics/btw170", "pmc": "PMC5013898", "pubmed": "27153608", - "title": "ProbOnto: ontology and knowledge base of probability distributions.", + "title": "ProbOnto: ontology and knowledge base of probability distributions", "year": 2016 } ], @@ -40254,9 +45068,10 @@ "name": "Process Chemistry Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PROCO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PROCO_$1", "repository": "https://github.com/proco-ontology/PROCO", "uri_format": "http://purl.obolibrary.org/obo/PROCO_$1", - "version": "PROCO release 20220414" + "version": "2022-04-11" }, "prodom": { "description": "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.", @@ -40277,19 +45092,28 @@ "name": "ProDom", "pattern": "^PD\\d+$", "preferred_prefix": "prodom", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/prodom:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gki034", "pmc": "PMC539988", "pubmed": "15608179", - "title": "The ProDom database of protein domain families: more emphasis on 3D.", + "title": "The ProDom database of protein domain families: more emphasis on 3D", "year": 2005 }, { "doi": "10.1093/bib/3.3.246", "pmc": null, "pubmed": "12230033", - "title": "ProDom: automated clustering of homologous domains.", + "title": "ProDom: automated clustering of homologous domains", "year": 2002 } ], @@ -40336,6 +45160,16 @@ }, "name": "Proteomics data and process provenance", "preferred_prefix": "PROPREO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/propreo:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PROPREO_$1", "uri_format": "http://purl.obolibrary.org/obo/PROPREO_$1" }, "prosite": { @@ -40360,26 +45194,35 @@ "name": "PROSITE", "pattern": "^PS\\d{5}$", "preferred_prefix": "prosite", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/prosite:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btt129", "pmc": "PMC3634184", "pubmed": "23505298", - "title": "pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.", + "title": "pfsearchV3: a code acceleration and heuristic to search PROSITE profiles", "year": 2013 }, { "doi": "10.1093/nar/gks1067", "pmc": "PMC3531220", "pubmed": "23161676", - "title": "New and continuing developments at PROSITE.", + "title": "New and continuing developments at PROSITE", "year": 2012 }, { "doi": "10.1093/nar/gkj063", "pmc": "PMC1347426", "pubmed": "16381852", - "title": "The PROSITE database.", + "title": "The PROSITE database", "year": 2006 } ], @@ -40406,12 +45249,21 @@ "name": "ProtClustDB", "pattern": "^\\w+$", "preferred_prefix": "protclustdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/protclustdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkn734", "pmc": "PMC2686591", "pubmed": "18940865", - "title": "The National Center for Biotechnology Information's Protein Clusters Database.", + "title": "The National Center for Biotechnology Information's Protein Clusters Database", "year": 2008 } ], @@ -40432,6 +45284,15 @@ }, "name": "Database of protein-protein complexes", "preferred_prefix": "protcom", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/protcom:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -40487,12 +45348,21 @@ "name": "ProtoNet Cluster", "pattern": "^\\d+$", "preferred_prefix": "protonet.cluster", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/protonet.cluster:$1" + } + ], "publications": [ { "doi": "10.1110/ps.062185706", "pmc": "PMC2242553", "pubmed": "16672244", - "title": "Functional annotation prediction: all for one and one for all.", + "title": "Functional annotation prediction: all for one and one for all", "year": 2006 } ], @@ -40514,12 +45384,21 @@ "name": "ProtoNet ProteinCard", "pattern": "^\\d+$", "preferred_prefix": "protonet.proteincard", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/protonet.proteincard:$1" + } + ], "publications": [ { "doi": "10.1110/ps.062185706", "pmc": "PMC2242553", "pubmed": "16672244", - "title": "Functional annotation prediction: all for one and one for all.", + "title": "Functional annotation prediction: all for one and one for all", "year": 2006 } ], @@ -40533,7 +45412,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web.", - "download_owl": "http://www.w3.org/ns/prov-o-20130430", + "download_owl": "https://www.w3.org/ns/prov-o", "example": "Activity", "homepage": "https://www.w3.org/ns/prov", "keywords": [ @@ -40547,8 +45426,7 @@ }, "name": "PROV Namespace", "preferred_prefix": "prov", - "uri_format": "http://www.w3.org/ns/prov#$1", - "version": "2013-04-30" + "uri_format": "http://www.w3.org/ns/prov#$1" }, "pscdb": { "description": "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion.", @@ -40571,14 +45449,14 @@ "doi": "10.1093/nar/gkr966", "pmc": "PMC3245091", "pubmed": "22080505", - "title": "PSCDB: a database for protein structural change upon ligand binding.", + "title": "PSCDB: a database for protein structural change upon ligand binding", "year": 2011 }, { "doi": "10.1016/j.jmb.2011.02.058", "pmc": null, "pubmed": "21376729", - "title": "Classification and annotation of the relationship between protein structural change and ligand binding.", + "title": "Classification and annotation of the relationship between protein structural change and ligand binding", "year": 2011 } ], @@ -40597,7 +45475,7 @@ "ro", "stato" ], - "description": "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed.", + "description": "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf", "download_owl": "http://purl.obolibrary.org/obo/psdo.owl", "example": "0000055", "homepage": "https://github.com/Display-Lab/psdo", @@ -40616,9 +45494,10 @@ "name": "Performance Summary Display Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "PSDO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", "repository": "https://github.com/Display-Lab/psdo", "uri_format": "http://purl.obolibrary.org/obo/PSDO_$1", - "version": "1.0.0" + "version": "1.0.1" }, "pseudogene": { "contact": { @@ -40646,6 +45525,15 @@ }, "name": "PseudoGene", "preferred_prefix": "pseudogene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pseudogene:$1" + } + ], "synonyms": [ "pseudogene.org" ], @@ -40720,10 +45608,11 @@ "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", - "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.", + "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PSO_$1", "repository": "https://github.com/Planteome/plant-stress-ontology", "uri_format": "http://purl.obolibrary.org/obo/PSO_$1", "version": "2020-05-19" @@ -40759,15 +45648,28 @@ "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.bioassay", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pubchem.bioassay:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], + "synonyms": [ + "pubchem.aid", + "pubchem.assay" + ], "twitter": "pubchem", "uri_format": "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1" }, @@ -40844,6 +45746,13 @@ "pattern": "^\\d+$", "preferred_prefix": "pubchem.compound", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pubchem.compound:$1" + }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", @@ -40857,59 +45766,60 @@ "doi": "10.1093/nar/gkaa971", "pmc": "PMC7778930", "pubmed": "33151290", - "title": "PubChem in 2021: new data content and improved web interfaces.", + "title": "PubChem in 2021: new data content and improved web interfaces", "year": 2021 }, { "doi": "10.1093/nar/gky1033", "pmc": "PMC6324075", "pubmed": "30371825", - "title": "PubChem 2019 update: improved access to chemical data.", + "title": "PubChem 2019 update: improved access to chemical data", "year": 2019 }, { "doi": "10.1093/nar/gkw1118", "pmc": "PMC5210581", "pubmed": "27899599", - "title": "PubChem BioAssay: 2017 update.", + "title": "PubChem BioAssay: 2017 update", "year": 2016 }, { "doi": "10.1093/nar/gkt978", "pmc": "PMC3965008", "pubmed": "24198245", - "title": "PubChem BioAssay: 2014 update.", + "title": "PubChem BioAssay: 2014 update", "year": 2013 }, { "doi": "10.1093/nar/gkr1132", "pmc": "PMC3245056", "pubmed": "22140110", - "title": "PubChem's BioAssay Database.", + "title": "PubChem's BioAssay Database", "year": 2011 }, { "doi": "10.1016/j.drudis.2010.10.003", "pmc": "PMC3010383", "pubmed": "20970519", - "title": "PubChem as a public resource for drug discovery.", + "title": "PubChem as a public resource for drug discovery", "year": 2010 }, { "doi": "10.1093/nar/gkp456", "pmc": "PMC2703903", "pubmed": "19498078", - "title": "PubChem: a public information system for analyzing bioactivities of small molecules.", + "title": "PubChem: a public information system for analyzing bioactivities of small molecules", "year": 2009 }, { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], + "rdf_uri_format": "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID$1", "synonyms": [ "CID", "DSSTox_CID", @@ -40963,15 +45873,25 @@ "part_of": "pubchem", "pattern": "^\\d+$", "preferred_prefix": "pubchem.substance", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pubchem.substance:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkl1031", "pmc": "PMC1781113", "pubmed": "17170002", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], + "rdf_uri_format": "http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID$1", "synonyms": [ "DSSTox_Generic_SID" ], @@ -41042,6 +45962,13 @@ "name": "PubMed through Linkedlife data", "uri_format": "http://linkedlifedata.com/resource/pubmed/id/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pubmed:$1" + }, { "code": "epmc", "description": "Europe PMC", @@ -41090,10 +46017,11 @@ "doi": "10.1093/nar/gkj158", "pmc": "PMC1347520", "pubmed": "16381840", - "title": "Database resources of the National Center for Biotechnology Information.", + "title": "Database resources of the National Center for Biotechnology Information", "year": 2006 } ], + "rdf_uri_format": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/$1", "synonyms": [ "MEDLINE", "PMID", @@ -41161,6 +46089,7 @@ "pathway" ], "license": "CC-BY-4.0", + "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "PW", "biocontext": "PW", @@ -41179,6 +46108,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "PW", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pw:$1" + }, { "code": "miriam_obo_legacy", "description": "An old URI style for MIRIAM", @@ -41192,28 +46128,29 @@ "doi": "10.1186/s40246-014-0017-8", "pmc": "PMC4191248", "pubmed": "25265995", - "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.", + "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease", "year": 2014 }, { "doi": "10.1186/2041-1480-5-7", "pmc": "PMC3922094", "pubmed": "24499703", - "title": "The pathway ontology - updates and applications.", + "title": "The pathway ontology - updates and applications", "year": 2014 }, { "doi": "10.1093/database/bar010", "pmc": "PMC3072770", "pubmed": "21478484", - "title": "The Rat Genome Database pathway portal.", + "title": "The Rat Genome Database pathway portal", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/PW_$1", "repository": "https://github.com/rat-genome-database/PW-Pathway-Ontology", "twitter": "ratgenome", "uri_format": "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1", - "version": "2019-10-23" + "version": "7.52" }, "pwo": { "contact": { @@ -41240,6 +46177,13 @@ "name": "Publishing Workflow Ontology", "preferred_prefix": "PWO", "publications": [ + { + "doi": "https://doi.org/10.3233/SW-160230", + "pmc": null, + "pubmed": null, + "title": "The Publishing Workflow Ontology (PWO)", + "year": null + }, { "doi": "10.3233/sw-160230", "pmc": null, @@ -41338,6 +46282,15 @@ }, "name": "Quantities, Units, Dimensions, and Types Ontology", "preferred_prefix": "qudt", + "providers": [ + { + "code": "v11", + "description": "Version 1.1 provider", + "homepage": "http://qudt.org", + "name": "Version 1.1", + "uri_format": "http://qudt.org/1.1/schema/qudt#$1" + } + ], "repository": "https://github.com/qudt/qudt-public-repo", "uri_format": "http://qudt.org/schema/qudt#$1" }, @@ -41401,21 +46354,21 @@ "doi": "10.1016/j.jvir.2009.04.031", "pmc": null, "pubmed": "19560008", - "title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology.", + "title": "The IR Radlex Project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology", "year": 2009 }, { "doi": "10.1016/j.jvir.2008.10.022", "pmc": null, "pubmed": "19081735", - "title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology.", + "title": "The IR RadLex project: an interventional radiology lexicon--a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology", "year": 2008 }, { "doi": "10.2214/ajr.174.5.1741463", "pmc": null, "pubmed": "10789815", - "title": "Radiology lexicon.", + "title": "Radiology lexicon", "year": 2000 } ], @@ -41454,6 +46407,15 @@ "name": "Rice annotation Project database", "pattern": "^Os\\S+t\\d{7}-\\d{2}$", "preferred_prefix": "rapdb.transcript", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rapdb:$1" + } + ], "uri_format": "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1" }, "ratmap": { @@ -41473,6 +46435,15 @@ }, "name": "Rat Genome Database", "preferred_prefix": "ratmap", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ratmap:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -41505,8 +46476,15 @@ "doi": "10.1681/asn.2016101077", "pmc": "PMC5407737", "pubmed": "28096308", - "title": "(Re)Building a Kidney.", + "title": "(Re)Building a Kidney", "year": 2017 + }, + { + "doi": "10.1681/ASN.2016101077", + "pmc": null, + "pubmed": null, + "title": "(Re)Building a Kidney.", + "year": null } ], "repository": "https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets", @@ -41552,9 +46530,10 @@ "name": "Radiation Biology Ontology", "pattern": "^\\d{6,8}$", "preferred_prefix": "RBO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/RBO_$1", "repository": "https://github.com/Radiobiology-Informatics-Consortium/RBO", "uri_format": "http://purl.obolibrary.org/obo/RBO_$1", - "version": "2022-06-02" + "version": "2023-06-15" }, "rcb": { "contributor": { @@ -41630,7 +46609,8 @@ "aberowl": "RDFS", "biocontext": "rdfs", "bioportal": "RDFS", - "fairsharing": "FAIRsharing.v9n3gk" + "fairsharing": "FAIRsharing.v9n3gk", + "ols": "rdfs" }, "name": "RDF Schema", "preferred_prefix": "rdfs", @@ -41693,6 +46673,13 @@ "pattern": "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$", "preferred_prefix": "reactome", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/reactome:$1" + }, { "code": "pathwaycommons", "description": "Pathway diagram drawn with Cytoscape", @@ -41706,7 +46693,7 @@ "doi": "10.1093/nar/gki072", "pmc": "PMC540026", "pubmed": "15608231", - "title": "Reactome: a knowledgebase of biological pathways.", + "title": "Reactome: a knowledgebase of biological pathways", "year": 2005 } ], @@ -41767,24 +46754,48 @@ "name": "REBASE Enzyme Number", "pattern": "^\\d+$", "preferred_prefix": "rebase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rebase:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gku1046", "pmc": "PMC4383893", "pubmed": "25378308", - "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.", + "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes", "year": 2014 }, { "doi": "10.1093/nar/gkp874", "pmc": "PMC2808884", "pubmed": "19846593", - "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.", + "title": "REBASE--a database for DNA restriction and modification: enzymes, genes and genomes", "year": 2009 } ], "uri_format": "http://rebase.neb.com/rebase/enz/$1.html" }, + "rebec": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant.", + "example": "RBR-6qvdftm", + "homepage": "https://ensaiosclinicos.gov.br", + "name": "Brazilian Registry of Clinical Trials", + "pattern": "^RBR-\\w+$", + "preferred_prefix": "rebec", + "uri_format": "https://ensaiosclinicos.gov.br/rg/$1" + }, "receptome.family": { "contributor": { "email": "cthoyt@gmail.com", @@ -41803,6 +46814,15 @@ }, "name": "Human Plasma Membrane Receptome Families", "preferred_prefix": "receptome.family", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/hpmr:$1" + } + ], "uri_format": "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1" }, "redfly": { @@ -41819,6 +46839,15 @@ }, "name": "Regulatory Elements Database for Drosophila", "preferred_prefix": "redfly", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/redfly:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -41866,19 +46895,28 @@ "name": "Reference Sequence Collection", "pattern": "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$", "preferred_prefix": "refseq", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/refseq:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkv1189", "pmc": "PMC4702849", "pubmed": "26553804", - "title": "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.", + "title": "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation", "year": 2015 }, { "doi": "10.1093/nar/gkl842", "pmc": "PMC1716718", "pubmed": "17130148", - "title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.", + "title": "NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins", "year": 2006 } ], @@ -41950,6 +46988,22 @@ "preferred_prefix": "repeatsdb.structure", "uri_format": "https://repeatsdb.org/structure/$1" }, + "repec": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)", + "example": "046-19", + "homepage": "https://ensayosclinicos-repec.ins.gob.pe/en/", + "logo": "https://ensayosclinicos-repec.ins.gob.pe/images/plantilla/img_logo_principal_repec_en.png", + "name": "Peruvian Clinical Trial Registry", + "pattern": "^\\d+-\\d+$", + "preferred_prefix": "repec", + "uri_format": "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1" + }, "reproduceme": { "contact": { "email": "sheeba.samuel@uni-jena.de", @@ -41979,7 +47033,7 @@ "email": "john.garavelli@ebi.ac.uk", "github": null, "name": "John Garavelli", - "orcid": null + "orcid": "0000-0002-4131-735X" }, "deprecated": true, "description": "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.", @@ -42004,15 +47058,25 @@ "name": "Protein covalent bond", "pattern": "^AA\\d{4}$", "preferred_prefix": "RESID", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/resid:$1" + } + ], "publications": [ { "doi": "10.1002/pmic.200300764", "pmc": null, "pubmed": "15174124", - "title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base.", + "title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base", "year": 2004 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/RESID_$1", "uri_format": "https://proteininformationresource.org/cgi-bin/resid?id=$1" }, "reto": { @@ -42039,8 +47103,7 @@ }, "name": "Regulation of Transcription Ontology", "no_own_terms": true, - "preferred_prefix": "reto", - "version": "2019-09-17" + "preferred_prefix": "reto" }, "rex": { "contact": { @@ -42075,6 +47138,16 @@ "part_of": "chebi", "pattern": "^\\d{7}$", "preferred_prefix": "REX", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rex:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/REX_$1", "uri_format": "http://purl.obolibrary.org/obo/REX_$1", "version": "2017-11-19" }, @@ -42107,11 +47180,10 @@ "doi": "10.1186/s12859-014-0386-y", "pmc": "PMC4279962", "pubmed": "25490885", - "title": "Finding gene regulatory network candidates using the gene expression knowledge base.", + "title": "Finding gene regulatory network candidates using the gene expression knowledge base", "year": 2014 } - ], - "version": "2019-04-11" + ] }, "rfam": { "description": "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion.", @@ -42137,14 +47209,14 @@ "doi": "10.1093/nar/gkx1038", "pmc": "PMC5753348", "pubmed": "29112718", - "title": "Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.", + "title": "Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families", "year": 2018 }, { "doi": "10.1093/nar/gku1063", "pmc": "PMC4383904", "pubmed": "25392425", - "title": "Rfam 12.0: updates to the RNA families database.", + "title": "Rfam 12.0: updates to the RNA families database", "year": 2014 } ], @@ -42184,12 +47256,21 @@ }, "name": "Rice Genome Annotation Project", "preferred_prefix": "rgap", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rgap:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkl976", "pmc": "PMC1751532", "pubmed": "17145706", - "title": "The TIGR Rice Genome Annotation Resource: improvements and new features.", + "title": "The TIGR Rice Genome Annotation Resource: improvements and new features", "year": 2006 } ], @@ -42251,6 +47332,13 @@ "homepage": "https://www.alliancegenome.org", "name": "RGD through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/RGD:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rgd:$1" } ], "publications": [ @@ -42258,140 +47346,140 @@ "doi": "10.1093/genetics/iyac005", "pmc": "PMC8982048", "pubmed": "35380657", - "title": "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses.", + "title": "MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses", "year": 2022 }, { "doi": "10.1007/s00335-021-09932-x", "pmc": "PMC8570235", "pubmed": "34741192", - "title": "The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research.", + "title": "The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research", "year": 2021 }, { "doi": "10.1093/nar/gkz1041", "pmc": "PMC7145519", "pubmed": "31713623", - "title": "The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.", + "title": "The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform", "year": 2020 }, { "doi": "10.1007/978-1-4939-9581-3_3", "pmc": null, "pubmed": "31228152", - "title": "Rat Genome Databases, Repositories, and Tools.", + "title": "Rat Genome Databases, Repositories, and Tools", "year": 2019 }, { "doi": "10.1007/978-1-4939-9581-3_2", "pmc": null, "pubmed": "31228151", - "title": "Rat Genome Assemblies, Annotation, and Variant Repository.", + "title": "Rat Genome Assemblies, Annotation, and Variant Repository", "year": 2019 }, { "doi": "10.1007/978-1-4939-9581-3_1", "pmc": null, "pubmed": "31228150", - "title": "The Rat: A Model Used in Biomedical Research.", + "title": "The Rat: A Model Used in Biomedical Research", "year": 2019 }, { "doi": "10.1093/database/baz037", "pmc": "PMC6444380", "pubmed": "30938777", - "title": "Quantitative phenotype analysis to identify, validate and compare rat disease models.", + "title": "Quantitative phenotype analysis to identify, validate and compare rat disease models", "year": 2019 }, { "doi": "10.1093/database/baz014", "pmc": "PMC6369425", "pubmed": "30753478", - "title": "Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.", + "title": "Integrated curation and data mining for disease and phenotype models at the Rat Genome Database", "year": 2019 }, { "doi": "10.1007/978-1-4939-7737-6_8", "pmc": "PMC6487669", "pubmed": "29761460", - "title": "A Primer for the Rat Genome Database (RGD).", + "title": "A Primer for the Rat Genome Database (RGD)", "year": 2018 }, { "doi": "10.1093/ilar/ilw041", "pmc": "PMC6057551", "pubmed": "28838068", - "title": "Rat Genome and Model Resources.", + "title": "Rat Genome and Model Resources", "year": 2017 }, { "doi": "10.1242/dmm.026021", "pmc": "PMC5087824", "pubmed": "27736745", - "title": "Exploring human disease using the Rat Genome Database.", + "title": "Exploring human disease using the Rat Genome Database", "year": 2016 }, { "doi": "10.1016/j.csbj.2015.11.006", "pmc": "PMC4700298", "pubmed": "27602200", - "title": "Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.", + "title": "Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass", "year": 2015 }, { "doi": "10.1152/physiolgenomics.00046.2016", "pmc": "PMC5005459", "pubmed": "27287925", - "title": "Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.", + "title": "Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database", "year": 2016 }, { "doi": "10.1093/database/baw034", "pmc": "PMC4805243", "pubmed": "27009807", - "title": "The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.", + "title": "The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database", "year": 2016 }, { "doi": "10.1093/nar/gku1026", "pmc": "PMC4383884", "pubmed": "25355511", - "title": "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.", + "title": "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease", "year": 2014 }, { "doi": "10.1186/s40246-014-0017-8", "pmc": "PMC4191248", "pubmed": "25265995", - "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease.", + "title": "Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease", "year": 2014 }, { "doi": "10.1093/database/bat015", "pmc": "PMC3630803", "pubmed": "23603846", - "title": "PhenoMiner: quantitative phenotype curation at the rat genome database.", + "title": "PhenoMiner: quantitative phenotype curation at the rat genome database", "year": 2013 }, { "doi": "10.1371/journal.pcbi.1000582", "pmc": "PMC2775909", "pubmed": "19956751", - "title": "The rat genome database curators: who, what, where, why.", + "title": "The rat genome database curators: who, what, where, why", "year": 2009 }, { "doi": "10.1093/nar/gkl988", "pmc": "PMC1761441", "pubmed": "17151068", - "title": "The Rat Genome Database, update 2007--easing the path from disease to data and back again.", + "title": "The Rat Genome Database, update 2007--easing the path from disease to data and back again", "year": 2006 }, { "doi": null, "pmc": null, "pubmed": "10400928", - "title": "A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.", + "title": "A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat", "year": 1999 } ], @@ -42460,47 +47548,56 @@ "name": "Rhea, the Annotated Reactions Database", "pattern": "^\\d{5}$", "preferred_prefix": "rhea", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rhea:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1016", "pmc": "PMC8728268", "pubmed": "34755880", - "title": "Rhea, the reaction knowledgebase in 2022.", + "title": "Rhea, the reaction knowledgebase in 2022", "year": 2022 }, { "doi": "10.1093/bioinformatics/btz817", "pmc": "PMC7162351", "pubmed": "31688925", - "title": "Enzyme annotation in UniProtKB using Rhea.", + "title": "Enzyme annotation in UniProtKB using Rhea", "year": 2020 }, { "doi": "10.1093/nar/gky876", "pmc": "PMC6324061", "pubmed": "30272209", - "title": "Updates in Rhea: SPARQLing biochemical reaction data.", + "title": "Updates in Rhea: SPARQLing biochemical reaction data", "year": 2019 }, { "doi": "10.1093/nar/gkw990", "pmc": "PMC5210663", "pubmed": "27789701", - "title": "Updates in Rhea - an expert curated resource of biochemical reactions.", + "title": "Updates in Rhea - an expert curated resource of biochemical reactions", "year": 2016 }, { "doi": "10.1093/nar/gku961", "pmc": "PMC4384025", "pubmed": "25332395", - "title": "Updates in Rhea--a manually curated resource of biochemical reactions.", + "title": "Updates in Rhea--a manually curated resource of biochemical reactions", "year": 2014 }, { "doi": "10.1093/nar/gkr1126", "pmc": "PMC3245052", "pubmed": "22135291", - "title": "Rhea--a manually curated resource of biochemical reactions.", + "title": "Rhea--a manually curated resource of biochemical reactions", "year": 2011 } ], @@ -42535,7 +47632,7 @@ "doi": "10.1093/nar/gkac840", "pmc": "PMC9825448", "pubmed": "36177882", - "title": "Ribocentre: a database of ribozymes.", + "title": "Ribocentre: a database of ribozymes", "year": 2023 } ], @@ -42564,6 +47661,15 @@ }, "name": "Rice Metabolic Pathways", "preferred_prefix": "ricecyc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ricecyc:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -42681,6 +47787,15 @@ }, "name": "RNA SSTRAND", "preferred_prefix": "rna_sstrand", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rna_sstrand:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -42721,14 +47836,14 @@ "doi": "10.1093/nar/gky1034", "pmc": "PMC6324050", "pubmed": "30395267", - "title": "RNAcentral: a hub of information for non-coding RNA sequences.", + "title": "RNAcentral: a hub of information for non-coding RNA sequences", "year": 2019 }, { "doi": "10.1093/nar/gkw1008", "pmc": "PMC5210518", "pubmed": "27794554", - "title": "RNAcentral: a comprehensive database of non-coding RNA sequences.", + "title": "RNAcentral: a comprehensive database of non-coding RNA sequences", "year": 2016 } ], @@ -42754,12 +47869,21 @@ }, "name": "Database of RNA Junctions and Kissing loop Structures", "preferred_prefix": "rnajunction", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rnajunction:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkm842", "pmc": "PMC2238914", "pubmed": "17947325", - "title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.", + "title": "RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign", "year": 2007 } ], @@ -42841,6 +47965,15 @@ "name": "RNA Modification Database", "pattern": "^\\d{3}$", "preferred_prefix": "rnamods", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rnamods:$1" + } + ], "uri_format": "http://mods.rna.albany.edu/mods/modifications/view/$1" }, "rnao": { @@ -42876,12 +48009,21 @@ "name": "RNA ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RNAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rnao:$1" + } + ], "publications": [ { "doi": "10.1261/rna.2343206", "pmc": "PMC1421088", "pubmed": "16484377", - "title": "The RNA Ontology Consortium: an open invitation to the RNA community.", + "title": "The RNA Ontology Consortium: an open invitation to the RNA community", "year": 2006 }, { @@ -42890,8 +48032,16 @@ "pubmed": null, "title": "The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data", "year": 2011 + }, + { + "doi": "10.3233/AO-2011-0082", + "pmc": null, + "pubmed": null, + "title": "The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", "repository": "https://github.com/BGSU-RNA/rnao", "uri_format": "http://purl.obolibrary.org/obo/RNAO_$1", "version": "2019-04-15" @@ -42909,6 +48059,15 @@ }, "name": "RNA Virus Database", "preferred_prefix": "rnavdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rvd:$1" + } + ], "uri_format": "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1" }, "ro": { @@ -42960,9 +48119,12 @@ "download_obo": "http://purl.obolibrary.org/obo/ro.obo", "download_owl": "http://purl.obolibrary.org/obo/ro.owl", "example": "0002533", + "example_extras": [ + "HOM0000022" + ], "homepage": "https://oborel.github.io/", "keywords": [ - "natural science", + "life science", "obo", "ontology", "relations" @@ -42974,7 +48136,7 @@ "biocontext": "RO", "biolink": "RO", "bioportal": "OBOREL", - "fairsharing": "FAIRsharing.cp0ybc", + "fairsharing": "FAIRsharing.9w8ea0", "go": "RO", "miriam": "ro", "n2t": "ro", @@ -42986,24 +48148,34 @@ }, "name": "Relation Ontology", "namespace_in_lui": true, - "pattern": "^\\d{7}$", + "pattern": "^(HOM)?\\d{7}$", "preferred_prefix": "RO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ro:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-5-41", "pmc": "PMC4177597", "pubmed": "25276335", - "title": "Structuring research methods and data with the research object model: genomics workflows as a case study.", + "title": "Structuring research methods and data with the research object model: genomics workflows as a case study", "year": 2014 }, { "doi": "10.1186/gb-2005-6-5-r46", "pmc": "PMC1175958", "pubmed": "15892874", - "title": "Relations in biomedical ontologies.", + "title": "Relations in biomedical ontologies", "year": 2005 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/RO_$1", "repository": "https://github.com/oborel/obo-relations", "synonyms": [ "RO_proposed_relation", @@ -43011,7 +48183,7 @@ "oborel" ], "uri_format": "http://purl.obolibrary.org/obo/RO_$1", - "version": "2022-10-26" + "version": "2023-02-22" }, "roleo": { "banana": "RoleO", @@ -43040,6 +48212,15 @@ "name": "Role Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RoleO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/roleo:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -43050,22 +48231,25 @@ }, "ror": { "contact": { - "email": "info@ror.org", - "github": null, + "email": "maria.gould@ucop.edu", + "github": "mariagould", "name": "Maria Gould", "orcid": "0000-0002-2916-3423" }, "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite.", + "download_owl": "https://w3id.org/rorio/rorio.owl", "example": "03yrm5c26", "homepage": "https://ror.org", "keywords": [ - "data management" + "data management", + "ontology" ], "mappings": { "fairsharing": "FAIRsharing.1jKfji", "miriam": "ror", "n2t": "ror" }, + "mastodon": "ResearchOrgs@mastodon.social", "name": "Research Organization Registry", "pattern": "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$", "preferred_prefix": "ror", @@ -43093,17 +48277,41 @@ "name": "Rodent Unidentified Gene-Encoded Large Proteins", "pattern": "^m\\w+$", "preferred_prefix": "rouge", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rouge:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh035", "pmc": "PMC308769", "pubmed": "14681467", - "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE.", + "title": "HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE", "year": 2004 } ], "uri_format": "https://www.kazusa.or.jp/rouge/gfpage/$1" }, + "rpcec": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)", + "example": "RPCEC00000423", + "homepage": "https://rpcec.sld.cu/en/home", + "name": "Cuban Registry of Clinical Trials", + "pattern": "^RPCEC\\d+$", + "preferred_prefix": "rpcec", + "uri_format": "https://rpcec.sld.cu/en/trials/$1" + }, "rrid": { "banana": "RRID", "description": "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch.", @@ -43128,35 +48336,35 @@ "doi": "10.1038/nmeth.3995", "pmc": null, "pubmed": "27595404", - "title": "A proposal for validation of antibodies.", + "title": "A proposal for validation of antibodies", "year": 2016 }, { "doi": "10.1016/j.neuron.2016.04.030", "pmc": "PMC5854161", "pubmed": "27151636", - "title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods.", + "title": "RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods", "year": 2016 }, { "doi": "10.1002/cne.23913", "pmc": "PMC4684178", "pubmed": "26599696", - "title": "The Resource Identification Initiative: A Cultural Shift in Publishing.", + "title": "The Resource Identification Initiative: A Cultural Shift in Publishing", "year": 2016 }, { "doi": "10.12688/f1000research.6555.2", "pmc": "PMC4648211", "pubmed": "26594330", - "title": "The Resource Identification Initiative: A cultural shift in publishing.", + "title": "The Resource Identification Initiative: A cultural shift in publishing", "year": 2015 }, { "doi": "10.7717/peerj.148", "pmc": "PMC3771067", "pubmed": "24032093", - "title": "On the reproducibility of science: unique identification of research resources in the biomedical literature.", + "title": "On the reproducibility of science: unique identification of research resources in the biomedical literature", "year": 2013 } ], @@ -43180,6 +48388,7 @@ "ontology" ], "license": "CC-BY-4.0", + "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "RS", "biocontext": "RS", @@ -43193,26 +48402,36 @@ "name": "Rat Strain Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RS", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/rs:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-36", "pmc": "PMC4177145", "pubmed": "24267899", - "title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.", + "title": "Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD", "year": 2013 }, { "doi": "10.1093/database/bat015", "pmc": "PMC3630803", "pubmed": "23603846", - "title": "PhenoMiner: quantitative phenotype curation at the rat genome database.", + "title": "PhenoMiner: quantitative phenotype curation at the rat genome database", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/RS_$1", "repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology", "twitter": "ratgenome", "uri_format": "http://purl.obolibrary.org/obo/RS_$1", - "version": "2019-12-13" + "version": "6.107" }, "rtecs": { "contributor": { @@ -43288,8 +48507,9 @@ "name": "Name Reaction Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "RXNO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/RXNO_$1", "repository": "https://github.com/rsc-ontologies/rxno", - "uri_format": "http://purl.obolibrary.org/obo/RXNO_$1", + "uri_format": "http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=$1", "version": "2021-12-16" }, "rxnorm": { @@ -43339,14 +48559,14 @@ "doi": "10.1136/amiajnl-2011-000116", "pmc": "PMC3128404", "pubmed": "21515544", - "title": "Normalized names for clinical drugs: RxNorm at 6 years.", + "title": "Normalized names for clinical drugs: RxNorm at 6 years", "year": 2011 }, { "doi": null, "pmc": "PMC2655997", "pubmed": "18998891", - "title": "RxTerms - a drug interface terminology derived from RxNorm.", + "title": "RxTerms - a drug interface terminology derived from RxNorm", "year": 2008 }, { @@ -43355,6 +48575,13 @@ "pubmed": null, "title": "RxNorm: prescription for electronic drug information exchange", "year": 2005 + }, + { + "doi": "10.1109/MITP.2005.122", + "pmc": null, + "pubmed": null, + "title": "RxNorm: prescription for electronic drug information exchange", + "year": null } ], "synonyms": [ @@ -43374,6 +48601,15 @@ }, "name": "The S/MAR transaction DataBase", "preferred_prefix": "s_mart_db", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/s_mart_db:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -43411,13 +48647,22 @@ "name": "SABIO-RK EC Record", "pattern": "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$", "preferred_prefix": "sabiork.ec", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sabiork.ec:$1" + } + ], "provides": "eccode", "publications": [ { "doi": null, "pmc": null, "pubmed": "17822389", - "title": "Storing and annotating of kinetic data.", + "title": "Storing and annotating of kinetic data", "year": 2007 } ], @@ -43442,12 +48687,21 @@ "name": "SABIO Reaction Kinetics", "pattern": "^\\d+$", "preferred_prefix": "sabiork.kineticrecord", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sabiork.kinetic:$1" + } + ], "publications": [ { "doi": null, "pmc": null, "pubmed": "17822389", - "title": "Storing and annotating of kinetic data.", + "title": "Storing and annotating of kinetic data", "year": 2007 } ], @@ -43477,12 +48731,21 @@ "name": "SABIO-RK Reaction", "pattern": "^\\d+$", "preferred_prefix": "sabiork.reaction", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sabiork.reaction:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr1046", "pmc": "PMC3245076", "pubmed": "22102587", - "title": "SABIO-RK--database for biochemical reaction kinetics.", + "title": "SABIO-RK--database for biochemical reaction kinetics", "year": 2011 } ], @@ -43506,7 +48769,7 @@ "doi": "10.1002/cfg.434", "pmc": "PMC2447422", "pubmed": "18629134", - "title": "The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data.", + "title": "The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data", "year": 2004 } ] @@ -43530,6 +48793,29 @@ "preferred_prefix": "salk", "uri_format": "https://abrc.osu.edu/stocks/number/SALK_$1" }, + "salmon": { + "contact": { + "email": "brycemecum@gmail.com", + "github": "amoeba", + "name": "Bryce Mecum", + "orcid": "0000-0002-0381-3766" + }, + "description": "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms.", + "download_owl": "http://aber-owl.net/media/ontologies/SALMON/2/salmon.owl", + "example": "00000674", + "homepage": "https://github.com/DataONEorg/sem-prov-ontologies/", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "SALMON", + "bioportal": "SALMON" + }, + "name": "Salmon Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "salmon", + "uri_format": "https://purl.dataone.org/odo/SALMON_$1" + }, "sao": { "contact": { "email": "slarson@ncmir.ucsd.edu", @@ -43558,11 +48844,44 @@ "name": "Subcellular Anatomy Ontology", "pattern": "^\\d+$", "preferred_prefix": "SAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sao:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SAO_$1", "references": [ "http://www.ontobee.org/ontology/SAO" ], "uri_format": "http://uri.neuinfo.org/nif/nifstd/sao$1" }, + "sasap": { + "contact": { + "email": "brycemecum@gmail.com", + "github": "amoeba", + "name": "Bryce Mecum", + "orcid": "0000-0002-0381-3766" + }, + "description": "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities.", + "download_owl": "http://aber-owl.net/media/ontologies/SASAP/2/sasap.owl", + "example": "00000101", + "homepage": "https://github.com/DataONEorg/sem-prov-ontologies", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "SASAP", + "bioportal": "SASAP" + }, + "name": "The State of Alaska's Salmon and People Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "sasap", + "uri_format": "https://purl.dataone.org/odo/SASAP_$1" + }, "sasbdb": { "contact": { "email": "a.kikhney@embl-hamburg.de", @@ -43593,14 +48912,14 @@ "doi": "10.1002/pro.3731", "pmc": "PMC6933840", "pubmed": "31576635", - "title": "SASBDB: Towards an automatically curated and validated repository for biological scattering data.", + "title": "SASBDB: Towards an automatically curated and validated repository for biological scattering data", "year": 2019 }, { "doi": "10.1093/nar/gku1047", "pmc": "PMC4383894", "pubmed": "25352555", - "title": "SASBDB, a repository for biological small-angle scattering data.", + "title": "SASBDB, a repository for biological small-angle scattering data", "year": 2014 } ], @@ -43646,6 +48965,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "SBO", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sbo:$1" + }, { "code": "biomodels", "description": "Provider for SBO at BioModels", @@ -43659,20 +48985,21 @@ "doi": "10.1038/msb.2011.77", "pmc": "PMC3261705", "pubmed": "22027554", - "title": "Controlled vocabularies and semantics in systems biology.", + "title": "Controlled vocabularies and semantics in systems biology", "year": 2011 }, { "doi": "10.1186/1471-2202-7-s1-s11", "pmc": "PMC1775041", "pubmed": "17118155", - "title": "Model storage, exchange and integration.", + "title": "Model storage, exchange and integration", "year": 2006 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SBO_$1", "repository": "https://github.com/EBI-BioModels/SBO", "twitter": "biomodels", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/sbo/terms?obo_id=SBO:$1", + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/sbo/terms?obo_id=SBO:$1", "version": "2021-08-28" }, "scdo": { @@ -43742,24 +49069,25 @@ "doi": "10.1093/database/baac014", "pmc": "PMC9216550", "pubmed": "35363306", - "title": "The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation.", + "title": "The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation", "year": 2022 }, { "doi": "10.1089/omi.2020.0153", "pmc": "PMC7549008", "pubmed": "33021900", - "title": "The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications.", + "title": "The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications", "year": 2020 }, { "doi": "10.1093/database/baz118", "pmc": "PMC6878945", "pubmed": "31769834", - "title": "The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation.", + "title": "The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation", "year": 2019 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SCDO_$1", "repository": "https://github.com/scdodev/scdo-ontology", "uri_format": "http://purl.obolibrary.org/obo/SCDO_$1", "version": "2021-04-15" @@ -43798,7 +49126,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.", - "download_owl": "http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl", + "download_owl": "https://schema.org/version/latest/schemaorg-all-http.rdf", "example": "Person", "homepage": "https://schema.org", "keywords": [ @@ -43810,7 +49138,8 @@ "aberowl": "SCHEMAORG", "biolink": "schema", "bioportal": "SCHEMA", - "fairsharing": "FAIRsharing.hzdzq8" + "fairsharing": "FAIRsharing.hzdzq8", + "ols": "schemaorg_http" }, "name": "Schema.org", "preferred_prefix": "schema", @@ -43909,6 +49238,13 @@ "name": "SCOP at Berkeley", "uri_format": "http://scop.berkeley.edu/sunid=$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/scop:$1" + }, { "code": "mrc", "description": "SCOP at UK Medical Research council (MRC)", @@ -43922,28 +49258,28 @@ "doi": "10.1093/nar/27.1.254", "pmc": "PMC148149", "pubmed": "9847194", - "title": "SCOP: a Structural Classification of Proteins database.", + "title": "SCOP: a Structural Classification of Proteins database", "year": 1999 }, { "doi": "10.1093/nar/25.1.236", "pmc": "PMC146380", "pubmed": "9016544", - "title": "SCOP: a structural classification of proteins database.", + "title": "SCOP: a structural classification of proteins database", "year": 1997 }, { "doi": "10.1093/nar/28.1.257", "pmc": "PMC102479", "pubmed": "10592240", - "title": "SCOP: a structural classification of proteins database.", + "title": "SCOP: a structural classification of proteins database", "year": 2000 }, { "doi": "10.1107/s0907444998009172", "pmc": null, "pubmed": "10089491", - "title": "SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data.", + "title": "SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data", "year": 1998 } ], @@ -44032,12 +49368,55 @@ ], "mappings": { "biolink": "ScopusID", - "fairsharing": "FAIRsharing.0a674c" + "fairsharing": "FAIRsharing.0a674c", + "wikidata": "P1153" }, "name": "Scopus Researcher", "pattern": "^\\d+$", "preferred_prefix": "scopus", - "twitter": "Scopus" + "synonyms": [ + "scopus.author" + ], + "twitter": "Scopus", + "uri_format": "https://www.scopus.com/authid/detail.uri?authorId=$1" + }, + "scopus.affiliation": { + "description": "identifier for an organisation in author affiliations per Scopus", + "example": "60025709", + "homepage": "http://info.sciencedirect.com/scopus/scopus-in-detail/tools/affiliationidentifier", + "mappings": { + "wikidata": "P1155" + }, + "name": "Scopus affiliation ID", + "preferred_prefix": "scopus.affiliation", + "uri_format": "https://www.scopus.com/affil/profile.uri?afid=$1" + }, + "scopus.publication": { + "description": "identifier for a source/publication venue (journal, conference, etc) in Scopus", + "example": "16129", + "homepage": "https://www.scopus.com/", + "mappings": { + "wikidata": "P1156" + }, + "name": "Scopus Publication", + "pattern": "^[1-9]\\d{0,11}$", + "preferred_prefix": "scopus.publication", + "uri_format": "https://www.scopus.com/sourceid/$1" + }, + "scopus.work": { + "description": "unique academic work identifier assigned in Scopus bibliographic database", + "example": "2-s2.0-0030770923", + "homepage": "https://www.scopus.com/", + "mappings": { + "wikidata": "P1154" + }, + "name": "Scopus Work", + "pattern": "^2-s2\\.0-\\d+$", + "preferred_prefix": "scopus.work", + "synonyms": [ + "scopus.eid" + ], + "uri_format": "http://www.scopus.com/record/display.url?origin=inward&eid=$1" }, "scoro": { "contact": { @@ -44064,6 +49443,13 @@ "name": "Scholarly Contributions and Roles Ontology", "preferred_prefix": "SCoRO", "publications": [ + { + "doi": "https://doi.org/10.3233/SW-150177", + "pmc": null, + "pubmed": null, + "title": "The Document Components Ontology (DoCO)", + "year": null + }, { "doi": "10.3233/sw-150177", "pmc": null, @@ -44091,6 +49477,15 @@ }, "name": "Saccharomyces cerevisiae promoter database", "preferred_prefix": "scpd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/scpd:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -44125,7 +49520,7 @@ "doi": "10.1002/cne.23913", "pmc": "PMC4684178", "pubmed": "26599696", - "title": "The Resource Identification Initiative: A Cultural Shift in Publishing.", + "title": "The Resource Identification Initiative: A Cultural Shift in Publishing", "year": 2016 } ], @@ -44161,6 +49556,15 @@ }, "name": "Structural Database of Allergenic Proteins", "preferred_prefix": "sdap", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sdap:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -44212,7 +49616,7 @@ "doi": "10.1186/s13326-016-0097-6", "pmc": "PMC5035502", "pubmed": "27664130", - "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.", + "title": "The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation", "year": 2016 } ], @@ -44220,8 +49624,7 @@ "https://github.com/SDG-InterfaceOntology/sdgio/issues/233" ], "repository": "https://github.com/SDG-InterfaceOntology/sdgio", - "uri_format": "http://purl.unep.org/sdg/SDGIO_$1", - "version": "2018-08-10" + "uri_format": "http://purl.unep.org/sdg/SDGIO_$1" }, "sdis": { "contributor": { @@ -44344,7 +49747,7 @@ "contact": { "email": "nicolas.matentzoglu@gmail.com", "github": "matentzn", - "name": "Nico Matentzoglu", + "name": "Nicolas Matentzoglu", "orcid": "0000-0002-7356-1779" }, "contributor": { @@ -44379,6 +49782,45 @@ ], "uri_format": "https://w3id.org/semapv/vocab/$1" }, + "senso": { + "contact": { + "email": "brycemecum@gmail.com", + "github": "amoeba", + "name": "Bryce Mecum", + "orcid": "0000-0002-0381-3766" + }, + "description": "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.", + "download_owl": "http://aber-owl.net/media/ontologies/SENSO/1/senso.owl", + "download_rdf": "https://ontologies.dataone.org/SENSO.ttl", + "example": "00000003", + "homepage": "https://github.com/DataONEorg/sem-prov-ontologies", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "SENSO", + "bioportal": "SENSO" + }, + "name": "Sensitive Data Ontology", + "pattern": "^\\d+$", + "preferred_prefix": "senso", + "uri_format": "http://purl.dataone.org/odo/SENSO_$1" + }, + "seo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops.", + "download_rdf": "https://raw.githubusercontent.com/saidfathalla/SEOontology/master/SEO.ttl", + "example": "Symposium", + "homepage": "https://w3id.org/seo", + "name": "Scientific Event Ontology", + "preferred_prefix": "seo", + "uri_format": "https://w3id.org/seo#$1" + }, "sep": { "contact": { "email": "psidev-gps-dev@lists.sourceforge.net", @@ -44408,6 +49850,16 @@ "name": "Sample processing and separation techniques", "pattern": "^\\d{5,6}$", "preferred_prefix": "SEP", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sep:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SEP_$1", "uri_format": "http://purl.obolibrary.org/obo/SEP_$1" }, "sepio": { @@ -44426,6 +49878,7 @@ "ontology" ], "license": "CC-BY-3.0", + "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/SEPIO-LOGOS/sepio_logo_black-banner.png", "mappings": { "aberowl": "SEPIO", "biocontext": "SEPIO", @@ -44437,9 +49890,10 @@ "name": "Scientific Evidence and Provenance Information Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SEPIO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/SEPIO_$1", "repository": "https://github.com/monarch-initiative/SEPIO-ontology", "uri_format": "http://purl.obolibrary.org/obo/SEPIO_$1", - "version": "$Revision$" + "version": "2023-02-21" }, "sfam": { "contributor": { @@ -44504,6 +49958,13 @@ "homepage": "https://www.alliancegenome.org", "name": "SGD through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/SGD:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sgd:$1" } ], "publications": [ @@ -44511,308 +49972,308 @@ "doi": "10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g", "pmc": "PMC3037831", "pubmed": "9885151", - "title": "Expanding yeast knowledge online.", + "title": "Expanding yeast knowledge online", "year": 1998 }, { "doi": "10.1126/science.282.5396.2022", "pmc": "PMC3057080", "pubmed": "9851918", - "title": "Comparison of the complete protein sets of worm and yeast: orthology and divergence.", + "title": "Comparison of the complete protein sets of worm and yeast: orthology and divergence", "year": 1998 }, { "doi": "10.1093/nar/27.1.74", "pmc": "PMC148101", "pubmed": "9847146", - "title": "Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.", + "title": "Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure", "year": 1999 }, { "doi": "10.1093/nar/26.1.73", "pmc": "PMC147204", "pubmed": "9399804", - "title": "SGD: Saccharomyces Genome Database.", + "title": "SGD: Saccharomyces Genome Database", "year": 1998 }, { "doi": "10.1126/science.277.5330.1259", "pmc": "PMC3039837", "pubmed": "9297238", - "title": "Yeast as a model organism.", + "title": "Yeast as a model organism", "year": 1997 }, { "doi": null, "pmc": "PMC3057085", "pubmed": "9169866", - "title": "Genetic and physical maps of Saccharomyces cerevisiae.", + "title": "Genetic and physical maps of Saccharomyces cerevisiae", "year": 1997 }, { "doi": "10.1073/pnas.94.11.5506", "pmc": "PMC34160", "pubmed": "9159100", - "title": "Molecular linguistics: extracting information from gene and protein sequences.", + "title": "Molecular linguistics: extracting information from gene and protein sequences", "year": 1997 }, { "doi": null, "pmc": null, "pubmed": "7660459", - "title": "Genetic nomenclature guide. Saccharomyces cerevisiae.", + "title": "Genetic nomenclature guide. Saccharomyces cerevisiae", "year": 1995 }, { "doi": "10.1093/database/baw020", "pmc": "PMC4795930", "pubmed": "26989152", - "title": "From one to many: expanding the Saccharomyces cerevisiae reference genome panel.", + "title": "From one to many: expanding the Saccharomyces cerevisiae reference genome panel", "year": 2016 }, { "doi": "10.1101/pdb.top083840", "pmc": "PMC5673599", "pubmed": "26631132", - "title": "The Saccharomyces Genome Database: A Tool for Discovery.", + "title": "The Saccharomyces Genome Database: A Tool for Discovery", "year": 2015 }, { "doi": "10.1101/pdb.prot088922", "pmc": "PMC5673602", "pubmed": "26631126", - "title": "The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.", + "title": "The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations", "year": 2015 }, { "doi": "10.1101/pdb.prot088914", "pmc": "PMC5673600", "pubmed": "26631125", - "title": "The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.", + "title": "The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component", "year": 2015 }, { "doi": "10.1101/pdb.prot088906", "pmc": "PMC5673598", "pubmed": "26631124", - "title": "The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.", + "title": "The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining", "year": 2015 }, { "doi": "10.1101/pdb.prot088898", "pmc": "PMC5673601", "pubmed": "26631123", - "title": "The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes.", + "title": "The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes", "year": 2015 }, { "doi": "10.1093/nar/gkv1250", "pmc": "PMC4702884", "pubmed": "26578556", - "title": "The Saccharomyces Genome Database Variant Viewer.", + "title": "The Saccharomyces Genome Database Variant Viewer", "year": 2015 }, { "doi": "10.1002/dvg.22862", "pmc": "PMC4545726", "pubmed": "25997651", - "title": "Biocuration at the Saccharomyces genome database.", + "title": "Biocuration at the Saccharomyces genome database", "year": 2015 }, { "doi": "10.1371/journal.pone.0120671", "pmc": "PMC4363492", "pubmed": "25781462", - "title": "AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.", + "title": "AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae", "year": 2015 }, { "doi": "10.1093/nar/gku975", "pmc": "PMC4384031", "pubmed": "25313161", - "title": "The complex portal--an encyclopaedia of macromolecular complexes.", + "title": "The complex portal--an encyclopaedia of macromolecular complexes", "year": 2014 }, { "doi": "10.1093/database/bau075", "pmc": "PMC4105709", "pubmed": "25052702", - "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO).", + "title": "Standardized description of scientific evidence using the Evidence Ontology (ECO)", "year": 2014 }, { "doi": "10.1534/g3.113.008995", "pmc": "PMC3962479", "pubmed": "24374639", - "title": "The reference genome sequence of Saccharomyces cerevisiae: then and now.", + "title": "The reference genome sequence of Saccharomyces cerevisiae: then and now", "year": 2014 }, { "doi": "10.1093/nar/gkt1158", "pmc": "PMC3965049", "pubmed": "24265222", - "title": "Saccharomyces genome database provides new regulation data.", + "title": "Saccharomyces genome database provides new regulation data", "year": 2013 }, { "doi": "10.1093/database/bat054", "pmc": "PMC3706743", "pubmed": "23842463", - "title": "A guide to best practices for Gene Ontology (GO) manual annotation.", + "title": "A guide to best practices for Gene Ontology (GO) manual annotation", "year": 2013 }, { "doi": "10.1093/database/bat012", "pmc": "PMC3595989", "pubmed": "23487186", - "title": "The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database.", + "title": "The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database", "year": 2013 }, { "doi": "10.1093/database/bat004", "pmc": "PMC3567487", "pubmed": "23396302", - "title": "The YeastGenome app: the Saccharomyces Genome Database at your fingertips.", + "title": "The YeastGenome app: the Saccharomyces Genome Database at your fingertips", "year": 2013 }, { "doi": "10.1093/database/bas001", "pmc": "PMC3308158", "pubmed": "22434836", - "title": "CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.", + "title": "CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations", "year": 2012 }, { "doi": "10.1093/database/bar062", "pmc": "PMC3308152", "pubmed": "22434830", - "title": "YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit.", + "title": "YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit", "year": 2012 }, { "doi": "10.1093/database/bar057", "pmc": "PMC3308148", "pubmed": "22434826", - "title": "Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report.", + "title": "Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report", "year": 2012 }, { "doi": "10.1093/nar/gkr1029", "pmc": "PMC3245034", "pubmed": "22110037", - "title": "Saccharomyces Genome Database: the genomics resource of budding yeast.", + "title": "Saccharomyces Genome Database: the genomics resource of budding yeast", "year": 2011 }, { "doi": "10.1093/database/bar004", "pmc": "PMC3067894", "pubmed": "21411447", - "title": "Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.", + "title": "Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study", "year": 2011 }, { "doi": "10.1093/database/bap001", "pmc": "PMC2790299", "pubmed": "20157474", - "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database.", + "title": "New mutant phenotype data curation system in the Saccharomyces Genome Database", "year": 2009 }, { "doi": "10.1093/nar/gkp917", "pmc": "PMC2808950", "pubmed": "19906697", - "title": "Saccharomyces Genome Database provides mutant phenotype data.", + "title": "Saccharomyces Genome Database provides mutant phenotype data", "year": 2009 }, { "doi": "10.1016/j.tim.2009.04.005", "pmc": "PMC3057094", "pubmed": "19577472", - "title": "Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.", + "title": "Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns", "year": 2009 }, { "doi": "10.1093/nar/gkm909", "pmc": "PMC2238894", "pubmed": "17982175", - "title": "Gene Ontology annotations at SGD: new data sources and annotation methods.", + "title": "Gene Ontology annotations at SGD: new data sources and annotation methods", "year": 2007 }, { "doi": "10.1093/nar/gkl931", "pmc": "PMC1669759", "pubmed": "17142221", - "title": "Expanded protein information at SGD: new pages and proteome browser.", + "title": "Expanded protein information at SGD: new pages and proteome browser", "year": 2006 }, { "doi": "10.1002/yea.1400", "pmc": "PMC3040122", "pubmed": "17001629", - "title": "Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.", + "title": "Saccharomyces cerevisiae S288C genome annotation: a working hypothesis", "year": 2006 }, { "doi": "10.1093/nar/gkj117", "pmc": "PMC1347479", "pubmed": "16381907", - "title": "Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.", + "title": "Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome", "year": 2006 }, { "doi": "10.1093/nar/gki023", "pmc": "PMC539977", "pubmed": "15608219", - "title": "Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).", + "title": "Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)", "year": 2005 }, { "doi": "10.1093/bib/5.1.9", "pmc": "PMC3037832", "pubmed": "15153302", - "title": "Saccharomyces genome database: underlying principles and organisation.", + "title": "Saccharomyces genome database: underlying principles and organisation", "year": 2004 }, { "doi": "10.1093/nar/gkh033", "pmc": "PMC308767", "pubmed": "14681421", - "title": "Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.", + "title": "Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms", "year": 2004 }, { "doi": "10.1093/nar/gkg054", "pmc": "PMC165501", "pubmed": "12519985", - "title": "Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.", + "title": "Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins", "year": 2003 }, { "doi": "10.1016/s0076-6879(02)50972-1", "pmc": null, "pubmed": "12073322", - "title": "Saccharomyces Genome Database.", + "title": "Saccharomyces Genome Database", "year": 2002 }, { "doi": "10.1093/nar/30.1.69", "pmc": "PMC99086", "pubmed": "11752257", - "title": "Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).", + "title": "Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)", "year": 2002 }, { "doi": "10.1093/nar/29.1.80", "pmc": "PMC29796", "pubmed": "11125055", - "title": "Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data.", + "title": "Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data", "year": 2001 }, { "doi": "10.1093/nar/28.1.77", "pmc": "PMC102447", "pubmed": "10592186", - "title": "Integrating functional genomic information into the Saccharomyces genome database.", + "title": "Integrating functional genomic information into the Saccharomyces genome database", "year": 2000 }, { @@ -44821,6 +50282,13 @@ "pubmed": null, "title": "Using Model Organism Databases (MODs)", "year": 2009 + }, + { + "doi": "10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G", + "pmc": null, + "pubmed": null, + "title": "Expanding yeast knowledge online.", + "year": null } ], "twitter": "yeastgenome", @@ -44844,12 +50312,21 @@ "name": "Saccharomyces genome database pathways", "pattern": "^PWY\\w{2}\\-\\d{3}$", "preferred_prefix": "sgd.pathways", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sgd.pathways:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkh033", "pmc": "PMC308767", "pubmed": "14681421", - "title": "Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.", + "title": "Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms", "year": 2004 } ], @@ -44882,19 +50359,28 @@ "name": "Sol Genomics Network", "pattern": "^\\d+$", "preferred_prefix": "sgn", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sgn:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gku1195", "pmc": "PMC4383978", "pubmed": "25428362", - "title": "The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.", + "title": "The Sol Genomics Network (SGN)--from genotype to phenotype to breeding", "year": 2014 }, { "doi": "10.1093/nar/gkq866", "pmc": "PMC3013765", "pubmed": "20935049", - "title": "The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl.", + "title": "The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl", "year": 2010 } ], @@ -44977,7 +50463,7 @@ "doi": "10.1038/s41597-022-01655-1", "pmc": "PMC9464254", "pubmed": "36088355", - "title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.", + "title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series", "year": 2022 } ], @@ -45016,7 +50502,7 @@ "doi": "10.1038/s41597-022-01655-1", "pmc": "PMC9464254", "pubmed": "36088355", - "title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.", + "title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series", "year": 2022 } ], @@ -45055,7 +50541,7 @@ "doi": "10.1038/s41597-022-01655-1", "pmc": "PMC9464254", "pubmed": "36088355", - "title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.", + "title": "Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series", "year": 2022 } ], @@ -45086,6 +50572,15 @@ "part_of": "qtldb", "pattern": "^\\d+$", "preferred_prefix": "sheepqtldb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sheepqtldb:$1" + } + ], "uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1" }, "shex": { @@ -45121,6 +50616,15 @@ }, "name": "ShiBASE", "preferred_prefix": "shibase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/shibase:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -45160,6 +50664,7 @@ "name": "Social Insect Behavior Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SIBO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/SIBO_$1", "repository": "https://github.com/obophenotype/sibo", "uri_format": "http://purl.obolibrary.org/obo/SIBO_$1", "version": "2015-06-15" @@ -45232,26 +50737,35 @@ "name": "Signaling Gateway", "pattern": "^A\\d{6}$", "preferred_prefix": "signaling-gateway", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/signaling-gateway:$1" + } + ], "publications": [ { "doi": "10.1093/bioinformatics/btr190", "pmc": "PMC3106186", "pubmed": "21505029", - "title": "Signaling gateway molecule pages--a data model perspective.", + "title": "Signaling gateway molecule pages--a data model perspective", "year": 2011 }, { "doi": "10.1093/nar/gkm907", "pmc": "PMC2238911", "pubmed": "17965093", - "title": "The Molecule Pages database.", + "title": "The Molecule Pages database", "year": 2007 }, { "doi": "10.1038/nature01307", "pmc": null, "pubmed": "12478304", - "title": "The Molecule Pages database.", + "title": "The Molecule Pages database", "year": 2002 } ], @@ -45283,7 +50797,7 @@ "doi": "10.1093/nar/gkv1048", "pmc": "PMC4702784", "pubmed": "26467481", - "title": "SIGNOR: a database of causal relationships between biological entities.", + "title": "SIGNOR: a database of causal relationships between biological entities", "year": 2015 } ], @@ -45327,7 +50841,7 @@ "orcid": "0000-0003-4727-9435" }, "description": "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.", - "download_owl": "http://semanticscience.org/ontology/sio/v1.53/sio-release.owl", + "download_owl": "http://semanticscience.org/ontology/sio/v1.59/sio-release.owl", "example": "000912", "homepage": "https://github.com/micheldumontier/semanticscience", "keywords": [ @@ -45354,13 +50868,13 @@ "doi": "10.1186/2041-1480-5-14", "pmc": "PMC4015691", "pubmed": "24602174", - "title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.", + "title": "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery", "year": 2014 } ], "repository": "https://github.com/micheldumontier/semanticscience", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1", - "version": "1.53" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1", + "version": "1.59" }, "siren": { "comment": "appears in FOODON, there is no website other than the spreadsheet referenced below on langual's site", @@ -45433,14 +50947,14 @@ "doi": "10.1371/journal.pone.0128524", "pmc": "PMC4452275", "pubmed": "26030606", - "title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty.", + "title": "Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty", "year": 2015 }, { "doi": "10.1371/journal.pgen.1004494", "pmc": "PMC4117444", "pubmed": "25078778", - "title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population.", + "title": "Distribution and medical impact of loss-of-function variants in the Finnish founder population", "year": 2014 } ], @@ -45467,12 +50981,21 @@ "name": "SitEx", "pattern": "^\\d+$", "preferred_prefix": "sitex", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sitex:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr1187", "pmc": "PMC3245165", "pubmed": "22139920", - "title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes.", + "title": "SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes", "year": 2011 } ], @@ -45522,7 +51045,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web", - "download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl", + "download_owl": "http://www.w3.org/TR/skos-reference/skos.rdf", "example": "prefLabel", "homepage": "https://www.w3.org/2004/02/skos/", "keywords": [ @@ -45532,7 +51055,8 @@ "mappings": { "aberowl": "skos", "biocontext": "skos", - "fairsharing": "FAIRsharing.48e326" + "fairsharing": "FAIRsharing.48e326", + "ols": "skos" }, "name": "Simple Knowledge Organization System", "preferred_prefix": "skos", @@ -45558,6 +51082,24 @@ "preferred_prefix": "skosxl", "uri_format": "http://www.w3.org/2008/05/skos-xl#$1" }, + "slctr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)", + "example": "SLCTR/2023/010", + "homepage": "https://slctr.lk/", + "logo": "https://slctr.lk/images/logo.png", + "name": "Sri Lanka Clinical Trials Registry", + "pattern": "^SLCTR/\\d{4}/\\d+$", + "preferred_prefix": "slctr", + "references": [ + "https://slctr.lk/trials/slctr-2023-010" + ] + }, "slkbase": { "description": "Cell line databases/resources", "example": "3618", @@ -45570,6 +51112,52 @@ "preferred_prefix": "slkbase", "uri_format": "https://sumlineknowledgebase.com/?page_id=$1" }, + "slm": { + "banana": "SLM", + "contact": { + "email": "swisslipids@isb-sib.ch", + "github": null, + "name": "Alan Bridge", + "orcid": "0000-0003-2148-9135" + }, + "description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.", + "download_owl": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl", + "example": "000000341", + "homepage": "http://www.swisslipids.org/#/", + "keywords": [ + "life science", + "metabolomics", + "ontology" + ], + "mappings": { + "biocontext": "SWISSLIPID", + "fairsharing": "FAIRsharing.pxr7x2", + "miriam": "slm", + "n2t": "swisslipid", + "ols": "slm", + "re3data": "r3d100012603", + "uniprot": "DB-0197", + "wikidata": "P8691" + }, + "name": "SwissLipid", + "namespace_in_lui": true, + "pattern": "^\\d+$", + "preferred_prefix": "SLM", + "publications": [ + { + "doi": "10.1093/bioinformatics/btv285", + "pmc": "PMC4547616", + "pubmed": "25943471", + "title": "The SwissLipids knowledgebase for lipid biology", + "year": 2015 + } + ], + "synonyms": [ + "swisslipid", + "swisslipids" + ], + "uri_format": "https://www.swisslipids.org/#/entity/SLM:$1" + }, "smart": { "description": "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures.", "example": "SM00015", @@ -45592,76 +51180,92 @@ "name": "Simple Modular Architecture Research Tool", "pattern": "^SM\\d{5}$", "preferred_prefix": "smart", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/smart:$1" + } + ], "publications": [ { "doi": "10.1093/nar/27.1.229", "pmc": "PMC148142", "pubmed": "9847187", - "title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences.", + "title": "SMART: identification and annotation of domains from signalling and extracellular protein sequences", "year": 1999 }, { "doi": "10.1093/nar/gkx922", "pmc": "PMC5753352", "pubmed": "29040681", - "title": "20 years of the SMART protein domain annotation resource.", + "title": "20 years of the SMART protein domain annotation resource", "year": 2018 }, { "doi": "10.1093/nar/gku949", "pmc": "PMC4384020", "pubmed": "25300481", - "title": "SMART: recent updates, new developments and status in 2015.", + "title": "SMART: recent updates, new developments and status in 2015", "year": 2014 }, { "doi": "10.1093/nar/gkr931", "pmc": "PMC3245027", "pubmed": "22053084", - "title": "SMART 7: recent updates to the protein domain annotation resource.", + "title": "SMART 7: recent updates to the protein domain annotation resource", "year": 2011 }, { "doi": "10.1093/nar/gkn808", "pmc": "PMC2686533", "pubmed": "18978020", - "title": "SMART 6: recent updates and new developments.", + "title": "SMART 6: recent updates and new developments", "year": 2008 }, { "doi": "10.1093/nar/gkj079", "pmc": "PMC1347442", "pubmed": "16381859", - "title": "SMART 5: domains in the context of genomes and networks.", + "title": "SMART 5: domains in the context of genomes and networks", "year": 2006 }, { "doi": "10.1093/nar/gkh088", "pmc": "PMC308822", "pubmed": "14681379", - "title": "SMART 4.0: towards genomic data integration.", + "title": "SMART 4.0: towards genomic data integration", "year": 2004 }, { "doi": "10.1093/nar/30.1.242", "pmc": "PMC99073", "pubmed": "11752305", - "title": "Recent improvements to the SMART domain-based sequence annotation resource.", + "title": "Recent improvements to the SMART domain-based sequence annotation resource", "year": 2002 }, { "doi": "10.1093/nar/28.1.231", "pmc": "PMC102444", "pubmed": "10592234", - "title": "SMART: a web-based tool for the study of genetically mobile domains.", + "title": "SMART: a web-based tool for the study of genetically mobile domains", "year": 2000 }, { "doi": "10.1016/s0959-440x(99)80055-4", "pmc": null, "pubmed": "10361098", - "title": "Protein families in multicellular organisms.", + "title": "Protein families in multicellular organisms", "year": 1999 + }, + { + "doi": "10.1016/S0959-440X(99)80055-4", + "pmc": null, + "pubmed": null, + "title": "Protein families in multicellular organisms.", + "year": null } ], "uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1" @@ -45716,7 +51320,7 @@ "doi": "10.1186/1758-2946-4-24", "pmc": "PMC3551648", "pubmed": "23031664", - "title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code.", + "title": "mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATE X code", "year": 2012 }, { @@ -45767,27 +51371,36 @@ "name": "Small Molecule Pathway Database", "pattern": "^SMP\\d+$", "preferred_prefix": "smpdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/smpdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1067", "pmc": "PMC3965088", "pubmed": "24203708", - "title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database.", + "title": "SMPDB 2.0: big improvements to the Small Molecule Pathway Database", "year": 2013 }, { - "doi": "doi:10.1093/nar/gkp1002", + "doi": "10.1093/nar/gkp1002", "pmc": "PMC2808928", "pubmed": "19948758", - "title": "SMPDB: The Small Molecule Pathway Database.", - "year": null + "title": "SMPDB: The Small Molecule Pathway Database", + "year": 2009 }, { - "doi": "10.1093/nar/gkp1002", - "pmc": "PMC2808928", - "pubmed": "19948758", + "doi": "doi:10.1093/nar/gkp1002", + "pmc": null, + "pubmed": null, "title": "SMPDB: The Small Molecule Pathway Database.", - "year": 2009 + "year": null } ], "synonyms": [ @@ -45817,7 +51430,16 @@ }, "name": "Snapshot", "preferred_prefix": "snap", - "uri_format": "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1" + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/snap:$1" + } + ], + "uri_format": "http://www.ifomis.org/bfo/1.1/snap#$1" }, "snomedct": { "contact": { @@ -45826,6 +51448,14 @@ "name": "NLM Customer Service", "orcid": null }, + "contributor_extras": [ + { + "email": "nicolas.matentzoglu@gmail.com", + "github": "matentzn", + "name": "Nicolas Matentzoglu", + "orcid": "0000-0002-7356-1779" + } + ], "description": "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc.", "download_owl": "http://snomed.info/sct/900000000000207008/version/20200131", "example": "284196006", @@ -45853,15 +51483,25 @@ "name": "SNOMED CT (International Edition)", "pattern": "^(\\w+)?\\d+$", "preferred_prefix": "snomedct", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/snomedct:$1" + } + ], "publications": [ { "doi": "10.1097/00024665-200609000-00011", "pmc": null, "pubmed": "16980782", - "title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method.", + "title": "Standardized nursing language in the systematized nomenclature of medicine clinical terms: A cross-mapping validation method", "year": 2006 } ], + "rdf_uri_format": "http://snomed.info/id/$1", "synonyms": [ "SCTID", "SCTID_2010_1_31", @@ -45889,13 +51529,14 @@ "SNOMEDCT_US_2022_07_31", "SNOMEDCT_US_2022_09_01", "SNOMEDCT_US_2022_12_31", + "SNOMEDCT_US_2023_02_28", "SNOMED_CT", "SNOMED_CT_US_2018_03_01", "SNOWMEDCT", "SNOWMEDCT_US", "SNOWMEDCT_US_2018_03_01" ], - "uri_format": "http://www.snomedbrowser.com/Codes/Details/$1", + "uri_format": "http://snomed.info/id/$1", "version": "2020-01-31" }, "snornabase": { @@ -45916,6 +51557,15 @@ }, "name": "snoRNABase", "preferred_prefix": "snornabase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/snornalbmedb:$1" + } + ], "uri_format": "http://www-snorna.biotoul.fr/plus.php?id=$1" }, "snp2tfbs": { @@ -45945,6 +51595,15 @@ }, "name": "SNP500Cancer", "preferred_prefix": "snp500cancer", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/snp500cancer:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -45980,6 +51639,7 @@ "structure" ], "license": "CC-BY-4.0", + "logo": "https://obofoundry.org/images/so_logo.png", "mappings": { "aberowl": "SO", "agroportal": "SO", @@ -45998,29 +51658,39 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "SO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/so:$1" + } + ], "publications": [ { "doi": "10.1186/gb-2010-11-8-r88", "pmc": "PMC2945790", "pubmed": "20796305", - "title": "A standard variation file format for human genome sequences.", + "title": "A standard variation file format for human genome sequences", "year": 2010 }, { "doi": "10.1016/j.jbi.2010.03.002", "pmc": "PMC3052763", "pubmed": "20226267", - "title": "Evolution of the Sequence Ontology terms and relationships.", + "title": "Evolution of the Sequence Ontology terms and relationships", "year": 2010 }, { "doi": "10.1186/gb-2005-6-5-r44", "pmc": "PMC1175956", "pubmed": "15892872", - "title": "The Sequence Ontology: a tool for the unification of genome annotations.", + "title": "The Sequence Ontology: a tool for the unification of genome annotations", "year": 2005 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SO_$1", "repository": "https://github.com/The-Sequence-Ontology/SO-Ontologies", "uri_format": "http://www.sequenceontology.org/miso/current_release/term/SO:$1", "version": "2021-11-22" @@ -46048,6 +51718,7 @@ }, "name": "Suggested Ontology for Pharmacogenomics", "preferred_prefix": "SOPHARM", + "rdf_uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1", "uri_format": "http://purl.obolibrary.org/obo/SOPHARM_$1" }, "soybase": { @@ -46082,12 +51753,21 @@ "name": "SoyBase", "pattern": "^\\w+(\\-)?\\w+(\\-)?\\w+$", "preferred_prefix": "soybase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/soy:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkp798", "pmc": "PMC2808871", "pubmed": "20008513", - "title": "SoyBase, the USDA-ARS soybean genetics and genomics database.", + "title": "SoyBase, the USDA-ARS soybean genetics and genomics database", "year": 2009 } ], @@ -46127,6 +51807,15 @@ }, "name": "SpBase", "preferred_prefix": "spbase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/spbase:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -46169,6 +51858,15 @@ "name": "Spider Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SPD", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/spdo:$1" + } + ], "publications": [ { "doi": "10.3390/d11100202", @@ -46178,9 +51876,10 @@ "year": 2019 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SPD_$1", "repository": "https://github.com/obophenotype/spider-ontology", "uri_format": "http://purl.obolibrary.org/obo/SPD_$1", - "version": "2019-02-27" + "version": "1.0" }, "spdx": { "description": "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception.", @@ -46209,8 +51908,8 @@ "orcid": "0000-0002-3583-7340" }, "description": "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/).", - "download_owl": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/ontology/sphn_ontology.owl?inline=false", - "download_rdf": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/ontology/sphn_ontology.ttl?inline=false", + "download_owl": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.owl", + "download_rdf": "https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-ontology/-/raw/master/rdf_schema/sphn_rdf_schema.ttl", "example": "Allergy", "github_request_issue": 535, "homepage": "https://www.sphn.ch", @@ -46248,19 +51947,28 @@ "name": "SPIKE Map", "pattern": "^spike\\d{5}$", "preferred_prefix": "spike.map", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/spike:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkq1167", "pmc": "PMC3014840", "pubmed": "21097778", - "title": "SPIKE: a database of highly curated human signaling pathways.", + "title": "SPIKE: a database of highly curated human signaling pathways", "year": 2010 }, { "doi": "10.1186/1471-2105-9-110", "pmc": "PMC2263022", "pubmed": "18289391", - "title": "SPIKE--a database, visualization and analysis tool of cellular signaling pathways.", + "title": "SPIKE--a database, visualization and analysis tool of cellular signaling pathways", "year": 2008 } ], @@ -46296,6 +52004,15 @@ }, "name": "SpliceNest", "preferred_prefix": "splicenest", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/splicenest:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -46331,7 +52048,7 @@ "doi": "10.1038/s41597-019-0193-4", "pmc": "PMC6823428", "pubmed": "31672983", - "title": "The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways.", + "title": "The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways", "year": 2019 } ], @@ -46401,7 +52118,7 @@ "doi": "10.1093/bioinformatics/btw417", "pmc": "PMC5181557", "pubmed": "27412095", - "title": "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena.", + "title": "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena", "year": 2016 } ], @@ -46467,6 +52184,15 @@ }, "name": "Sequence-Structural Templates of Single-member Superfamilies", "preferred_prefix": "sstoss", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/sstoss:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -46497,28 +52223,28 @@ "doi": "10.1093/bioinformatics/btv595", "pmc": null, "pubmed": "26504145", - "title": "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.", + "title": "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores", "year": 2015 }, { "doi": "10.1371/journal.pone.0108888", "pmc": "PMC4184813", "pubmed": "25279564", - "title": "Protein NMR structures refined without NOE data.", + "title": "Protein NMR structures refined without NOE data", "year": 2014 }, { "doi": "10.1002/prot.24265", "pmc": null, "pubmed": "23408564", - "title": "Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach.", + "title": "Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach", "year": 2013 }, { "doi": "10.1093/nar/gkr1021", "pmc": "PMC3245188", "pubmed": "22102572", - "title": "STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures.", + "title": "STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures", "year": 2011 } ], @@ -46547,6 +52273,7 @@ "statistics" ], "license": "CC-BY-3.0", + "logo": "https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png", "mappings": { "aberowl": "STATO", "biocontext": "STATO", @@ -46559,6 +52286,7 @@ "name": "The Statistical Methods Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "STATO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/STATO_$1", "repository": "https://github.com/ISA-tools/stato", "uri_format": "http://purl.obolibrary.org/obo/STATO_$1", "version": "1.4" @@ -46583,33 +52311,42 @@ "name": "Search Tool for Interactions of Chemicals", "pattern": "^\\w{14}$", "preferred_prefix": "stitch", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/stitch:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1207", "pmc": "PMC3964996", "pubmed": "24293645", - "title": "STITCH 4: integration of protein-chemical interactions with user data.", + "title": "STITCH 4: integration of protein-chemical interactions with user data", "year": 2013 }, { "doi": "10.1093/nar/gkr1011", "pmc": "PMC3245073", "pubmed": "22075997", - "title": "STITCH 3: zooming in on protein-chemical interactions.", + "title": "STITCH 3: zooming in on protein-chemical interactions", "year": 2011 }, { "doi": "10.1093/nar/gkp937", "pmc": "PMC2808890", "pubmed": "19897548", - "title": "STITCH 2: an interaction network database for small molecules and proteins.", + "title": "STITCH 2: an interaction network database for small molecules and proteins", "year": 2009 }, { "doi": "10.1093/nar/gkm795", "pmc": "PMC2238848", "pubmed": "18084021", - "title": "STITCH: interaction networks of chemicals and proteins.", + "title": "STITCH: interaction networks of chemicals and proteins", "year": 2007 } ], @@ -46741,6 +52478,13 @@ "homepage": "http://string-db.org/", "name": "STRING Mirror at Heidelberg", "uri_format": "http://string-db.org/interactions/$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/string:$1" } ], "provides": "uniprot", @@ -46749,42 +52493,42 @@ "doi": "10.1093/nar/gky1131", "pmc": "PMC6323986", "pubmed": "30476243", - "title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.", + "title": "STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets", "year": 2019 }, { "doi": "10.1093/nar/gkw937", "pmc": "PMC5210637", "pubmed": "27924014", - "title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.", + "title": "The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible", "year": 2016 }, { "doi": "10.1093/bioinformatics/btv696", "pmc": "PMC4896368", "pubmed": "26614125", - "title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.", + "title": "SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles", "year": 2015 }, { "doi": "10.1093/nar/gku1003", "pmc": "PMC4383874", "pubmed": "25352553", - "title": "STRING v10: protein-protein interaction networks, integrated over the tree of life.", + "title": "STRING v10: protein-protein interaction networks, integrated over the tree of life", "year": 2014 }, { "doi": "10.1093/nar/gks1094", "pmc": "PMC3531103", "pubmed": "23203871", - "title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration.", + "title": "STRING v9.1: protein-protein interaction networks, with increased coverage and integration", "year": 2012 }, { "doi": "10.1093/nar/gkn760", "pmc": "PMC2686466", "pubmed": "18940858", - "title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms.", + "title": "STRING 8--a global view on proteins and their functional interactions in 630 organisms", "year": 2008 } ], @@ -46803,6 +52547,14 @@ "name": "Charles Tapley Hoyt", "orcid": "0000-0003-4423-4370" }, + "contributor_extras": [ + { + "email": "tiago.lubiana.alves@usp.br", + "github": "lubianat", + "name": "Tiago Lubiana", + "orcid": "0000-0003-2473-2313" + } + ], "description": "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types.", "example": "T039", "homepage": "https://lhncbc.nlm.nih.gov/semanticnetwork/", @@ -46814,17 +52566,27 @@ "agroportal": "STY", "biolink": "UMLSSG", "bioportal": "STY", - "ecoportal": "STY" + "ecoportal": "STY", + "wikidata": "P11955" }, "name": "UMLS Semantic Types Ontology", "pattern": "^T\\d{3}$", "preferred_prefix": "sty", + "providers": [ + { + "code": "bioportal.purl", + "description": "BioPortal PURL", + "homepage": "http://purl.bioontology.org/ontology/STY", + "name": "BioPortal PURL", + "uri_format": "http://purl.bioontology.org/ontology/STY/$1" + } + ], "synonyms": [ "UMLSSG", "umls.st", "umls.sty" ], - "uri_format": "http://purl.bioontology.org/ontology/STY/$1" + "uri_format": "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1" }, "subtilist": { "description": "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments.", @@ -46846,12 +52608,21 @@ "name": "Bacillus subtilis genome sequencing project", "pattern": "^BG\\d+$", "preferred_prefix": "subtilist", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/subtilist:$1" + } + ], "publications": [ { "doi": "10.1093/nar/30.1.62", "pmc": "PMC99059", "pubmed": "11752255", - "title": "SubtiList: the reference database for the Bacillus subtilis genome.", + "title": "SubtiList: the reference database for the Bacillus subtilis genome", "year": 2002 } ], @@ -46878,26 +52649,35 @@ "name": "SubtiWiki", "pattern": "^BSU\\d{5}$", "preferred_prefix": "subtiwiki", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/subtiwiki:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkv1006", "pmc": "PMC4702770", "pubmed": "26433225", - "title": "SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis.", + "title": "SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis", "year": 2015 }, { "doi": "10.1093/database/bap012", "pmc": "PMC2790307", "pubmed": "20157485", - "title": "A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.", + "title": "A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki", "year": 2009 }, { "doi": "10.1099/mic.0.035790-0", "pmc": null, "pubmed": "19959575", - "title": "Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis.", + "title": "Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis", "year": 2009 } ], @@ -46915,10 +52695,12 @@ "homepage": "http://sugarbind.expasy.org/", "keywords": [ "biomedical science", - "glycomics" + "glycomics", + "ontology" ], "mappings": { "biocontext": "SUGARBIND", + "bioportal": "SUGARBIND", "fairsharing": "FAIRsharing.d064y6", "miriam": "sugarbind", "n2t": "sugarbind" @@ -46931,7 +52713,7 @@ "doi": "10.1093/nar/gkv1247", "pmc": "PMC4702881", "pubmed": "26578555", - "title": "SugarBindDB, a resource of glycan-mediated host-pathogen interactions.", + "title": "SugarBindDB, a resource of glycan-mediated host-pathogen interactions", "year": 2015 }, { @@ -46965,12 +52747,21 @@ "name": "SUPERFAMILY", "pattern": "^\\w+$", "preferred_prefix": "supfam", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/superfamily:$1" + } + ], "publications": [ { "doi": "10.1006/jmbi.2001.5080", "pmc": null, "pubmed": "11697912", - "title": "Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.", + "title": "Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure", "year": 2001 } ], @@ -46984,7 +52775,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).", - "download_obo": "https://github.com/EnvironmentOntology/envo/blob/master/src/envo/sources/sweetrealm.obo", + "download_obo": "https://raw.githubusercontent.com/EnvironmentOntology/envo/master/src/envo/sources/sweetrealm.obo", "example": "ANOVA", "homepage": "https://bioportal.bioontology.org/ontologies/SWEET", "keywords": [ @@ -47040,76 +52831,42 @@ "name": "SWISS-MODEL Repository", "pattern": "^\\w+$", "preferred_prefix": "swiss-model", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/swissmodel:$1" + } + ], "provides": "uniprot", "publications": [ { "doi": "10.1093/nar/gkw1132", "pmc": "PMC5210589", "pubmed": "27899672", - "title": "The SWISS-MODEL Repository-new features and functionality.", + "title": "The SWISS-MODEL Repository-new features and functionality", "year": 2016 }, { "doi": "10.1093/nar/gku340", "pmc": "PMC4086089", "pubmed": "24782522", - "title": "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.", + "title": "SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information", "year": 2014 }, { "doi": "10.1093/nar/gkn750", "pmc": "PMC2686475", "pubmed": "18931379", - "title": "The SWISS-MODEL Repository and associated resources.", + "title": "The SWISS-MODEL Repository and associated resources", "year": 2008 } ], "twitter": "SWISS_MODEL", "uri_format": "https://swissmodel.expasy.org/repository/uniprot/$1" }, - "swisslipid": { - "banana": "SLM", - "contact": { - "email": "swisslipids@isb-sib.ch", - "github": null, - "name": "Alan Bridge", - "orcid": "0000-0003-2148-9135" - }, - "description": "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions.", - "example": "000000341", - "homepage": "http://www.swisslipids.org/#/", - "keywords": [ - "life science", - "metabolomics" - ], - "mappings": { - "biocontext": "SWISSLIPID", - "fairsharing": "FAIRsharing.pxr7x2", - "miriam": "slm", - "n2t": "swisslipid", - "re3data": "r3d100012603", - "uniprot": "DB-0197", - "wikidata": "P8691" - }, - "name": "SwissLipid", - "namespace_in_lui": true, - "pattern": "^\\d+$", - "preferred_prefix": "swisslipid", - "publications": [ - { - "doi": "10.1093/bioinformatics/btv285", - "pmc": "PMC4547616", - "pubmed": "25943471", - "title": "The SwissLipids knowledgebase for lipid biology.", - "year": 2015 - } - ], - "synonyms": [ - "slm", - "swisslipids" - ], - "uri_format": "https://www.swisslipids.org/#/entity/SLM:$1" - }, "swissregulon": { "contact": { "email": "erik.vannimwegen@unibas.ch", @@ -47137,14 +52894,14 @@ "doi": "10.1093/nar/gks1145", "pmc": "PMC3531101", "pubmed": "23180783", - "title": "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.", + "title": "SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates", "year": 2012 }, { "doi": "10.1093/nar/gkl857", "pmc": "PMC1716717", "pubmed": "17130146", - "title": "SwissRegulon: a database of genome-wide annotations of regulatory sites.", + "title": "SwissRegulon: a database of genome-wide annotations of regulatory sites", "year": 2006 } ], @@ -47158,9 +52915,9 @@ "orcid": "0000-0002-7702-4495" }, "description": "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community.", - "download_json": "https://github.com/allysonlister/swo/raw/master/release/swo.json", - "download_obo": "https://github.com/allysonlister/swo/raw/master/release/swo.obo", - "download_owl": "https://github.com/allysonlister/swo/raw/master/release/swo.owl", + "download_json": "https://raw.githubusercontent.com/allysonlister/swo/master/swo.json", + "download_obo": "https://raw.githubusercontent.com/allysonlister/swo/master/swo.obo", + "download_owl": "https://raw.githubusercontent.com/allysonlister/swo/master/swo.owl", "example": "0000144", "homepage": "https://github.com/allysonlister/swo", "keywords": [ @@ -47184,6 +52941,13 @@ "pattern": "^\\d{7}$", "preferred_prefix": "SWO", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/swo:$1" + }, { "code": "ebi", "description": "The EBI's old SWO URIs before switching over to OBO PURLs", @@ -47211,6 +52975,13 @@ "homepage": "http://www.ebi.ac.uk/swo/license", "name": "Legacy EBI SWO", "uri_format": "http://www.ebi.ac.uk/swo/license/SWO_$1" + }, + { + "code": "ebi.maturity", + "description": "The EBI's old SWO URIs before switching over to OBO PURLs", + "homepage": "http://www.ebi.ac.uk/swo/maturity", + "name": "Legacy EBI SWO", + "uri_format": "http://www.ebi.ac.uk/swo/maturity/SWO_$1" } ], "publications": [ @@ -47218,13 +52989,14 @@ "doi": "10.1186/2041-1480-5-25", "pmc": "PMC4098953", "pubmed": "25068035", - "title": "The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.", + "title": "The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SWO_$1", "repository": "https://github.com/allysonlister/swo", "uri_format": "http://purl.obolibrary.org/obo/SWO_$1", - "version": "2022-10-11" + "version": "2023-03-05" }, "swrl": { "contributor": { @@ -47278,28 +53050,38 @@ "name": "Symptom Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SYMP", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/symptom:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1063", "pmc": "PMC8728220", "pubmed": "34755882", - "title": "The Human Disease Ontology 2022 update.", + "title": "The Human Disease Ontology 2022 update", "year": 2022 }, { "doi": "10.1093/nar/gkp832", "pmc": "PMC2808878", "pubmed": "19850722", - "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database.", + "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/SYMP_$1", "repository": "https://github.com/DiseaseOntology/SymptomOntology", "synonyms": [ "SYMP" ], - "uri_format": "http://purl.obolibrary.org/obo/SYMP_$1", - "version": "2022-07-12" + "uri_format": "https://www.ebi.ac.uk/ols/ontologies/symp/terms?iri=http://purl.obolibrary.org/obo/SYMP_$1", + "version": "2022-11-30" }, "syoid": { "contributor": { @@ -47343,19 +53125,28 @@ "name": "Toxin and Toxin Target Database", "pattern": "^T3D\\d+$", "preferred_prefix": "t3db", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/t3db:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gku1004", "pmc": "PMC4383875", "pubmed": "25378312", - "title": "T3DB: the toxic exposome database.", + "title": "T3DB: the toxic exposome database", "year": 2014 }, { "doi": "10.1093/nar/gkp934", "pmc": "PMC2808899", "pubmed": "19897546", - "title": "T3DB: a comprehensively annotated database of common toxins and their targets.", + "title": "T3DB: a comprehensively annotated database of common toxins and their targets", "year": 2009 } ], @@ -47412,9 +53203,10 @@ "year": 2021 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/T4FS_$1", "repository": "https://github.com/terms4fairskills/FAIRterminology", "uri_format": "http://purl.obolibrary.org/obo/T4FS_$1", - "version": "2022-10-05" + "version": "2023-03-02" }, "tads": { "contact": { @@ -47453,10 +53245,11 @@ "doi": "10.1111/j.1365-2583.2008.00781.x", "pmc": null, "pubmed": "18237287", - "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase.", + "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase", "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TADS_$1", "repository": "https://github.com/VEuPathDB-ontology/TADS", "uri_format": "http://purl.obolibrary.org/obo/TADS_$1", "version": "2015-08-20" @@ -47479,6 +53272,7 @@ }, "name": "Terminology of Anatomy of Human Embryology", "preferred_prefix": "TAHE", + "rdf_uri_format": "http://purl.obolibrary.org/obo/TAHE_$1", "uri_format": "http://purl.obolibrary.org/obo/TAHE_$1" }, "tahh": { @@ -47499,6 +53293,7 @@ }, "name": "Terminology of Anatomy of Human Histology", "preferred_prefix": "TAHH", + "rdf_uri_format": "http://purl.obolibrary.org/obo/TAHH_$1", "uri_format": "http://purl.obolibrary.org/obo/TAHH_$1" }, "tair.gene": { @@ -47520,12 +53315,21 @@ "part_of": "tair", "pattern": "^\\d{7}$", "preferred_prefix": "tair.gene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tair.gene:$1" + } + ], "publications": [ { "doi": "10.1007/s10142-002-0077-z", "pmc": null, "pubmed": "12444417", - "title": "TAIR: a resource for integrated Arabidopsis data.", + "title": "TAIR: a resource for integrated Arabidopsis data", "year": 2002 } ], @@ -47558,6 +53362,13 @@ "pattern": "^\\d+$", "preferred_prefix": "tair.locus", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tair.locus:$1" + }, { "code": "thalemine", "description": "Data mining on aradopsis", @@ -47571,7 +53382,7 @@ "doi": "10.1007/s10142-002-0077-z", "pmc": null, "pubmed": "12444417", - "title": "TAIR: a resource for integrated Arabidopsis data.", + "title": "TAIR: a resource for integrated Arabidopsis data", "year": 2002 } ], @@ -47595,12 +53406,21 @@ "name": "TAIR Protein", "pattern": "^\\d{10}$", "preferred_prefix": "tair.protein", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tair.protein:$1" + } + ], "publications": [ { "doi": "10.1007/s10142-002-0077-z", "pmc": null, "pubmed": "12444417", - "title": "TAIR: a resource for integrated Arabidopsis data.", + "title": "TAIR: a resource for integrated Arabidopsis data", "year": 2002 } ], @@ -47631,24 +53451,36 @@ "biocontext": "TAO", "bioportal": "TAO", "obofoundry": "tao", + "ols": "tao", "prefixcommons": "tao" }, "name": "Teleost Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tao:$1" + } + ], "publications": [ { "doi": "10.1093/sysbio/syq013", "pmc": "PMC2885267", "pubmed": "20547776", - "title": "The teleost anatomy ontology: anatomical representation for the genomics age.", + "title": "The teleost anatomy ontology: anatomical representation for the genomics age", "year": 2010 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TAO_$1", "synonyms": [ "TAO_RETIRED" ], - "uri_format": "http://purl.obolibrary.org/obo/TAO_$1" + "uri_format": "http://purl.obolibrary.org/obo/TAO_$1", + "version": "2012-08-10" }, "tarbase": { "description": "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.", @@ -47672,28 +53504,28 @@ "doi": "10.1093/nar/gkx1141", "pmc": "PMC5753203", "pubmed": "29156006", - "title": "DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions.", + "title": "DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions", "year": 2018 }, { "doi": "10.1093/nar/gku1215", "pmc": "PMC4383989", "pubmed": "25416803", - "title": "DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.", + "title": "DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions", "year": 2014 }, { "doi": "10.1093/nar/gkn809", "pmc": "PMC2686456", "pubmed": "18957447", - "title": "The database of experimentally supported targets: a functional update of TarBase.", + "title": "The database of experimentally supported targets: a functional update of TarBase", "year": 2008 }, { "doi": "10.1261/rna.2239606", "pmc": "PMC1370898", "pubmed": "16373484", - "title": "TarBase: A comprehensive database of experimentally supported animal microRNA targets.", + "title": "TarBase: A comprehensive database of experimentally supported animal microRNA targets", "year": 2005 } ], @@ -47731,15 +53563,25 @@ "name": "Taxonomic rank vocabulary", "pattern": "^\\d{7}$", "preferred_prefix": "TAXRANK", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/taxrank:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-34", "pmc": "PMC4177199", "pubmed": "24267744", - "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.", + "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TAXRANK_$1", "repository": "https://github.com/phenoscape/taxrank", "uri_format": "http://purl.obolibrary.org/obo/TAXRANK_$1", "version": "2016-04-15" @@ -47772,6 +53614,15 @@ }, "name": "The Cell Cycle DB", "preferred_prefix": "tccd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tccd:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -47813,28 +53664,44 @@ "name": "Transporter Classification Database", "pattern": "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$", "preferred_prefix": "tcdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tcdb:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkaa1004", "pmc": "PMC7778945", "pubmed": "33170213", - "title": "The Transporter Classification Database (TCDB): 2021 update.", + "title": "The Transporter Classification Database (TCDB): 2021 update", "year": 2021 }, { "doi": "10.1093/nar/gkv1103", "pmc": "PMC4702804", "pubmed": "26546518", - "title": "The Transporter Classification Database (TCDB): recent advances.", + "title": "The Transporter Classification Database (TCDB): recent advances", "year": 2015 }, { "doi": "10.1093/nar/gkt1097", "pmc": "PMC3964967", "pubmed": "24225317", - "title": "The transporter classification database.", + "title": "The transporter classification database", "year": 2013 }, + { + "doi": "10.1093/nar/gkv1103", + "pmc": "PMC4702804", + "pubmed": "19022853", + "title": "The Transporter Classification Database (TCDB): recent advances", + "year": null + }, { "doi": "10.1093/nar/gkv1103", "pmc": "PMC2686586", @@ -47846,14 +53713,14 @@ "doi": "10.1093/nar/gkn862", "pmc": "PMC2686586", "pubmed": "19022853", - "title": "The Transporter Classification Database: recent advances.", + "title": "The Transporter Classification Database: recent advances", "year": 2008 }, { "doi": "10.1093/nar/gkj001", "pmc": "PMC1334385", "pubmed": "16381841", - "title": "TCDB: the Transporter Classification Database for membrane transport protein analyses and information.", + "title": "TCDB: the Transporter Classification Database for membrane transport protein analyses and information", "year": 2006 } ], @@ -47862,6 +53729,21 @@ ], "uri_format": "http://www.tcdb.org/search/result.php?tc=$1" }, + "tctr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)", + "example": "TCTR20230429001", + "homepage": "https://www.thaiclinicaltrials.org", + "name": "Thai Clinical Trials Registry", + "pattern": "^TCTR\\d+$", + "preferred_prefix": "tctr", + "uri_format": "https://www.thaiclinicaltrials.org/show/$1" + }, "te": { "contributor": { "email": "cthoyt@gmail.com", @@ -47907,7 +53789,7 @@ "doi": "10.1093/nar/gkx987", "pmc": "PMC5753292", "pubmed": "29087517", - "title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs.", + "title": "TFClass: expanding the classification of human transcription factors to their mammalian orthologs", "year": 2018 } ], @@ -47930,6 +53812,15 @@ "name": "Tetrahymena Genome Database", "pattern": "^TTHERM\\_\\d+$", "preferred_prefix": "tgd", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tgd:$1" + } + ], "uri_format": "http://ciliate.org/index.php/feature/details/$1" }, "tgma": { @@ -47966,15 +53857,25 @@ "name": "Mosquito gross anatomy ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TGMA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tgma:$1" + } + ], "publications": [ { "doi": "10.1111/j.1365-2583.2008.00781.x", "pmc": null, "pubmed": "18237287", - "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase.", + "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase", "year": 2008 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", "repository": "https://github.com/VEuPathDB-ontology/TGMA", "uri_format": "http://purl.obolibrary.org/obo/TGMA_$1", "version": "2013-06-03" @@ -48039,6 +53940,7 @@ "vendor" ], "name": "Thermo Fisher Scientific", + "pattern": "^\\w+$", "preferred_prefix": "thermofisher", "uri_format": "https://www.thermofisher.com/antibody/product/$1" }, @@ -48068,6 +53970,15 @@ "name": "TIGR protein families", "pattern": "^TIGR\\d+$", "preferred_prefix": "tigrfam", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tigrfams:$1" + } + ], "references": [ "https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt", "https://github.com/biopragmatics/bioregistry/issues/366" @@ -48076,7 +53987,7 @@ }, "time": { "contact": { - "email": "simon.cox@csiro.au", + "email": "dr.shorthair@pm.me", "github": "dr-shorthair", "name": "Simon Cox", "orcid": "0000-0002-3884-3420" @@ -48159,6 +54070,7 @@ "trait" ], "license": "CC-BY-4.0", + "logo": "http://planteome.org/sites/default/files/garland_logo.PNG", "mappings": { "aberowl": "TO", "agroportal": "TO", @@ -48173,19 +54085,41 @@ "name": "Plant Trait Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pto:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkx1152", "pmc": "PMC5753347", "pubmed": "29186578", - "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.", + "title": "The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics", "year": 2018 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TO_$1", "repository": "https://github.com/Planteome/plant-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/TO_$1", "version": "2022-04-13" }, + "togovar": { + "description": "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.", + "example": "tgv139393198", + "homepage": "https://grch38.togovar.org/", + "mappings": { + "miriam": "togovar" + }, + "name": "TogoVar", + "pattern": "^tgv[0-9]+$", + "preferred_prefix": "togovar", + "uri_format": "https://grch38.togovar.org/variant/$1" + }, "tokue": { "deprecated": true, "description": "Cell line databases/resources", @@ -48241,6 +54175,15 @@ "name": "Topology Data Bank of Transmembrane Proteins", "pattern": "^[A-Z0-9]+$", "preferred_prefix": "topdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/topdb:$1" + } + ], "uri_format": "http://topdb.enzim.hu/?m=show&id=$1" }, "topfind": { @@ -48266,21 +54209,21 @@ "doi": "10.1093/nar/gku1012", "pmc": "PMC4383881", "pubmed": "25332401", - "title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events.", + "title": "Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events", "year": 2014 }, { "doi": "10.1093/nar/gkr1025", "pmc": "PMC3244998", "pubmed": "22102574", - "title": "TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function.", + "title": "TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function", "year": 2011 }, { "doi": "10.1038/nmeth.1669", "pmc": null, "pubmed": "21822272", - "title": "TopFIND, a knowledgebase linking protein termini with function.", + "title": "TopFIND, a knowledgebase linking protein termini with function", "year": 2011 } ], @@ -48332,25 +54275,35 @@ "name": "Pathogen Transmission Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "TRANS", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/pt:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkab1063", "pmc": "PMC8728220", "pubmed": "34755882", - "title": "The Human Disease Ontology 2022 update.", + "title": "The Human Disease Ontology 2022 update", "year": 2022 }, { "doi": "10.1093/nar/gkp832", "pmc": "PMC2808878", "pubmed": "19850722", - "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database.", + "title": "GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database", "year": 2009 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", "repository": "https://github.com/DiseaseOntology/PathogenTransmissionOntology", "uri_format": "http://purl.obolibrary.org/obo/TRANS_$1", - "version": "2020-08-04" + "version": "2022-10-10" }, "transportdb": { "description": "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available.", @@ -48364,6 +54317,15 @@ }, "name": "TransportDB", "preferred_prefix": "transportdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/transportdb:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -48399,6 +54361,15 @@ }, "name": "Transcriptional Regulatory Element Database", "preferred_prefix": "tred", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tred:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -48433,12 +54404,21 @@ "name": "TreeBASE", "pattern": "^TB[1,2]?:[A-Z][a-z]?\\d+$", "preferred_prefix": "treebase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/treebase:$1" + } + ], "publications": [ { "doi": "10.1186/1471-2148-9-93", "pmc": "PMC2685121", "pubmed": "19426482", - "title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment.", + "title": "Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment", "year": 2009 } ], @@ -48464,12 +54444,21 @@ "name": "TreeFam", "pattern": "^\\w{1,2}\\d+$", "preferred_prefix": "treefam", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/treefam:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1055", "pmc": "PMC3965059", "pubmed": "24194607", - "title": "TreeFam v9: a new website, more species and orthology-on-the-fly.", + "title": "TreeFam v9: a new website, more species and orthology-on-the-fly", "year": 2013 } ], @@ -48503,7 +54492,7 @@ "doi": "10.1093/nar/gkn631", "pmc": "PMC2686445", "pubmed": "18824479", - "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.", + "title": "GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis", "year": 2008 } ], @@ -48541,7 +54530,7 @@ "doi": "10.1093/nar/gkp851", "pmc": "PMC2808979", "pubmed": "19843604", - "title": "TriTrypDB: a functional genomic resource for the Trypanosomatidae.", + "title": "TriTrypDB: a functional genomic resource for the Trypanosomatidae", "year": 2009 } ], @@ -48565,6 +54554,15 @@ "name": "tRNA Gene Database", "preferred_prefix": "trnadbce", "proprietary": true, + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/trnadbce:$1" + } + ], "reviewer": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -48636,6 +54634,15 @@ "name": "Teleost taxonomy ontology", "pattern": "^\\d+$", "preferred_prefix": "TTO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/tto:$1" + } + ], "publications": [ { "doi": "10.1038/npre.2010.4629.1", @@ -48645,9 +54652,9 @@ "year": 2010 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TTO_$1", "repository": "https://github.com/phenoscape/teleost-taxonomy-ontology", - "uri_format": "http://purl.obolibrary.org/obo/TTO_$1", - "version": "2018-03-26" + "uri_format": "http://purl.obolibrary.org/obo/TTO_$1" }, "txpo": { "contact": { @@ -48680,13 +54687,14 @@ "doi": "10.1038/s41598-020-71370-7", "pmc": "PMC7471325", "pubmed": "32883995", - "title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management.", + "title": "Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management", "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", "repository": "https://github.com/txpo-ontology/TXPO", "uri_format": "http://purl.obolibrary.org/obo/TXPO_$1", - "version": "2020-07-09" + "version": "2022-12-07" }, "uberon": { "appears_in": [ @@ -48745,6 +54753,7 @@ "taxonomy" ], "license": "CC-BY-3.0", + "logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/uberon-logos/uberon_logo_black-banner.png", "mappings": { "aberowl": "UBERON", "biocontext": "UBERON", @@ -48777,17 +54786,18 @@ "doi": "10.1186/2041-1480-5-21", "pmc": "PMC4089931", "pubmed": "25009735", - "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.", + "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon", "year": 2014 }, { "doi": "10.1186/gb-2012-13-1-r5", "pmc": "PMC3334586", "pubmed": "22293552", - "title": "Uberon, an integrative multi-species anatomy ontology.", + "title": "Uberon, an integrative multi-species anatomy ontology", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/UBERON_$1", "repository": "https://github.com/obophenotype/uberon", "synonyms": [ "UBERON", @@ -48795,8 +54805,8 @@ "Uberon" ], "twitter": "uberanat", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/uberon/terms?obo_id=UBERON:$1", - "version": "2022-09-30" + "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/uberon/terms?obo_id=UBERON:$1", + "version": "2023-05-23" }, "ubio.namebank": { "description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.", @@ -48868,7 +54878,7 @@ "doi": "10.1093/nar/gky1095", "pmc": "PMC6323953", "pubmed": "30407534", - "title": "The UCSC Genome Browser database: 2019 update.", + "title": "The UCSC Genome Browser database: 2019 update", "year": 2019 } ], @@ -48931,7 +54941,7 @@ "doi": "10.1136/jamia.1999.0060151", "pmc": "PMC61354", "pubmed": "10094068", - "title": "Units of measure in clinical information systems.", + "title": "Units of measure in clinical information systems", "year": 1999 } ], @@ -49067,6 +55077,23 @@ ], "uri_format": "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1" }, + "uminctr": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An additional Japanese clinical trial registry", + "example": "UMIN000049383", + "homepage": "https://www.umin.ac.jp/ctr/index.htm", + "name": "University hospital Medical Information Network Clinical Trial Registry", + "pattern": "^UMIN\\d+$", + "preferred_prefix": "uminctr", + "references": [ + "https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000056224" + ] + }, "umls": { "description": "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.", "example": "C2584994", @@ -49143,12 +55170,21 @@ "name": "UniGene", "pattern": "^\\d+$", "preferred_prefix": "unigene", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/unigene:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkg033", "pmc": "PMC165480", "pubmed": "12519941", - "title": "Database resources of the National Center for Biotechnology.", + "title": "Database resources of the National Center for Biotechnology", "year": 2003 } ], @@ -49204,7 +55240,7 @@ "doi": "10.1002/pmic.200300744", "pmc": null, "pubmed": "15174123", - "title": "Unimod: Protein modifications for mass spectrometry.", + "title": "Unimod: Protein modifications for mass spectrometry", "year": 2004 } ], @@ -49237,6 +55273,13 @@ "homepage": "http://www.uniprot.org/uniparc/", "name": "UniParc through UniProt", "uri_format": "https://www.uniprot.org/uniparc/$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/uniparc:$1" } ], "publications": [ @@ -49244,7 +55287,7 @@ "doi": "10.1093/nar/gkh131", "pmc": "PMC308865", "pubmed": "14681372", - "title": "UniProt: the Universal Protein knowledgebase.", + "title": "UniProt: the Universal Protein knowledgebase", "year": 2004 } ], @@ -49305,6 +55348,13 @@ "pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$", "preferred_prefix": "uniprot", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/uniprot:$1" + }, { "code": "indra", "description": "A large scale database of biomedical statements.", @@ -49353,10 +55403,11 @@ "doi": "10.1093/nar/gkj161", "pmc": "PMC1347523", "pubmed": "16381842", - "title": "The Universal Protein Resource (UniProt): an expanding universe of protein information.", + "title": "The Universal Protein Resource (UniProt): an expanding universe of protein information", "year": 2006 } ], + "rdf_uri_format": "http://purl.uniprot.org/uniprot/$1", "synonyms": [ "SwissProt", "UP", @@ -49416,7 +55467,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary.", - "download_obo": "https://www.uniprot.org/diseases/?query=*&format=obo", + "download_obo": "https://rest.uniprot.org/diseases/stream?compressed=true&format=obo&query=%28%2A%29", "example": "DI-04240", "homepage": "https://www.uniprot.org/diseases/", "keywords": [ @@ -49494,11 +55545,12 @@ "name": "UniProt journal", "pattern": "^\\d{4}$", "preferred_prefix": "uniprot.journal", + "rdf_uri_format": "http://purl.uniprot.org/journals/$1", "uri_format": "https://www.uniprot.org/journals/$1" }, "uniprot.keyword": { "description": "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries.", - "download_obo": "https://www.uniprot.org/keywords/?format=obo", + "download_obo": "https://rest.uniprot.org/keywords/stream?compressed=true&fields=id%2Cname%2Ccategory%2Cgene_ontologies&format=tsv&query=%28%2A%29", "example": "KW-1273", "homepage": "http://www.uniprot.org/keywords/", "keywords": [ @@ -49513,6 +55565,15 @@ "part_of": "uniprot", "pattern": "^KW-\\d{4}$", "preferred_prefix": "uniprot.keyword", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/uniprot.kw:$1" + } + ], "synonyms": [ "SP_KW", "UniProtKB-KW", @@ -49529,7 +55590,7 @@ "orcid": "0000-0003-4423-4370" }, "description": "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms.", - "download_obo": "https://www.uniprot.org/locations/?query=*&format=obo", + "download_obo": "https://rest.uniprot.org/locations/stream?compressed=true&format=obo&query=%28%2A%29", "example": "SL-0002", "homepage": "https://www.uniprot.org/locations/", "keywords": [ @@ -49725,6 +55786,15 @@ "name": "Database of Sequence Tagged Sites", "pattern": "^\\d+$", "preferred_prefix": "unists", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/unists:$1" + } + ], "uri_format": "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1" }, "unite": { @@ -49759,12 +55829,21 @@ "name": "Molecular database for the identification of fungi", "pattern": "^UDB\\d{6}$", "preferred_prefix": "unite", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/unite:$1" + } + ], "publications": [ { "doi": "10.1111/j.1469-8137.2009.03160.x", "pmc": null, "pubmed": "20409185", - "title": "The UNITE database for molecular identification of fungi--recent updates and future perspectives.", + "title": "The UNITE database for molecular identification of fungi--recent updates and future perspectives", "year": 2010 } ], @@ -49787,14 +55866,14 @@ "doi": "10.1021/acs.jnatprod.6b01093", "pmc": null, "pubmed": "28616931", - "title": "Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments.", + "title": "Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments", "year": 2017 }, { "doi": "10.1371/journal.pone.0062839", "pmc": "PMC3636197", "pubmed": "23638153", - "title": "Use of natural products as chemical library for drug discovery and network pharmacology.", + "title": "Use of natural products as chemical library for drug discovery and network pharmacology", "year": 2013 } ], @@ -49846,17 +55925,28 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "UO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/uo:$1" + } + ], "publications": [ { "doi": "10.1093/database/bas033", "pmc": "PMC3468815", "pubmed": "23060432", - "title": "The Units Ontology: a tool for integrating units of measurement in science.", + "title": "The Units Ontology: a tool for integrating units of measurement in science", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/UO_$1", "repository": "https://github.com/bio-ontology-research-group/unit-ontology", - "uri_format": "https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1" + "uri_format": "http://purl.obolibrary.org/obo/UO_$1", + "version": "2023-05-25" }, "upa": { "contact": { @@ -49894,15 +55984,25 @@ "name": "Unipathway", "pattern": "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$", "preferred_prefix": "UPA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/unipathway:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkr1023", "pmc": "PMC3245108", "pubmed": "22102589", - "title": "UniPathway: a resource for the exploration and annotation of metabolic pathways.", + "title": "UniPathway: a resource for the exploration and annotation of metabolic pathways", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/UPA_$1", "repository": "https://github.com/geneontology/unipathway", "synonyms": [ "UPa", @@ -49920,9 +56020,7 @@ "orcid": "0000-0001-5208-3432" }, "description": "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.", - "download_json": "https://github.com/obophenotype/upheno/blob/master/upheno.json", - "download_obo": "https://github.com/obophenotype/upheno/blob/master/upheno.obo", - "download_owl": "https://github.com/obophenotype/upheno/blob/master/upheno.owl", + "download_owl": "http://purl.obolibrary.org/obo/upheno.owl", "homepage": "https://github.com/obophenotype/upheno", "keywords": [ "evolutionary biology", @@ -49943,6 +56041,7 @@ "name": "Unified Phenotype Ontology", "no_own_terms": true, "preferred_prefix": "UPHENO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", "repository": "https://github.com/obophenotype/upheno", "uri_format": "http://purl.obolibrary.org/obo/UPHENO_$1", "version": "2017-10-31" @@ -49986,6 +56085,18 @@ ], "uri_format": "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1" }, + "utrdb": { + "description": "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. ", + "example": "5UTR_107_ENST00000517291.2", + "homepage": "https://utrdb.cloud.ba.infn.it/utrdb/index_107.html", + "mappings": { + "miriam": "utrdb" + }, + "name": "UTRdb", + "pattern": "^([3-5][A-Z])\\w+[^A-Z][0-9]$", + "preferred_prefix": "utrdb", + "uri_format": "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1" + }, "vac": { "contributor": { "email": "cthoyt@gmail.com", @@ -50034,7 +56145,7 @@ "doi": "10.1093/nar/gku1118", "pmc": "PMC4383933", "pubmed": "25392418", - "title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.", + "title": "ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank", "year": 2014 } ], @@ -50076,7 +56187,7 @@ "doi": null, "pmc": "PMC2244318", "pubmed": "12463886", - "title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF.", + "title": "A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF", "year": 2002 } ], @@ -50121,6 +56232,7 @@ "obo", "ontology" ], + "license": "CC-BY-4.0", "mappings": { "aberowl": "VARIO", "agroportal": "VARIO", @@ -50151,39 +56263,40 @@ "doi": "10.1186/s12864-018-5262-0", "pmc": "PMC6309100", "pubmed": "30591019", - "title": "Systematics for types and effects of DNA variations.", + "title": "Systematics for types and effects of DNA variations", "year": 2018 }, { "doi": "10.1002/humu.22954", "pmc": null, "pubmed": "26773573", - "title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology.", + "title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology", "year": 2016 }, { "doi": "10.1007/s00439-015-1529-6", "pmc": null, "pubmed": "25616435", - "title": "Types and effects of protein variations.", + "title": "Types and effects of protein variations", "year": 2015 }, { "doi": "10.1186/2041-1480-5-9", "pmc": "PMC3931275", "pubmed": "24533660", - "title": "Variation ontology: annotator guide.", + "title": "Variation ontology: annotator guide", "year": 2014 }, { "doi": "10.1101/gr.157495.113", "pmc": "PMC3912426", "pubmed": "24162187", - "title": "Variation Ontology for annotation of variation effects and mechanisms.", + "title": "Variation Ontology for annotation of variation effects and mechanisms", "year": 2013 } ], - "uri_format": "http://purl.obolibrary.org/obo/VARIO_$1", + "rdf_uri_format": "http://purl.obolibrary.org/obo/VariO_$1", + "uri_format": "http://purl.obolibrary.org/obo/VariO_$1", "version": "2018-11-09" }, "vbase2": { @@ -50211,12 +56324,21 @@ "name": "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse", "pattern": "^\\w+$", "preferred_prefix": "vbase2", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vbase2:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gki088", "pmc": "PMC540042", "pubmed": "15608286", - "title": "VBASE2, an integrative V gene database.", + "title": "VBASE2, an integrative V gene database", "year": 2005 } ], @@ -50252,9 +56374,10 @@ "name": "Vertebrate Breed Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VBO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/VBO_$1", "repository": "https://github.com/monarch-initiative/vertebrate-breed-ontology", "uri_format": "http://purl.obolibrary.org/obo/VBO_$1", - "version": "2022-10-31" + "version": "2023-06-02" }, "vbrc": { "description": "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.", @@ -50269,6 +56392,15 @@ "name": "Viral Bioinformatics Resource Center", "pattern": "^\\d+$", "preferred_prefix": "vbrc", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vbrc:$1" + } + ], "uri_format": "http://vbrc.org/gene_detail.asp?gene_id=$1" }, "vcell": { @@ -50310,6 +56442,13 @@ "pattern": "^\\D{4}\\d{6}(\\-\\D{2})?$", "preferred_prefix": "vectorbase", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vectorbase:$1" + }, { "code": "vectorbase.alt1", "description": "An alternate provider based on the search functionality", @@ -50330,14 +56469,14 @@ "doi": "10.1093/nar/gku1117", "pmc": "PMC4383932", "pubmed": "25510499", - "title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.", + "title": "VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases", "year": 2014 }, { "doi": "10.1093/nar/gkn857", "pmc": "PMC2686483", "pubmed": "19028744", - "title": "VectorBase: a data resource for invertebrate vector genomics.", + "title": "VectorBase: a data resource for invertebrate vector genomics", "year": 2008 } ], @@ -50371,19 +56510,28 @@ }, "name": "Vertebrate Genome Annotation Database", "preferred_prefix": "vega", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vega:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1241", "pmc": "PMC3964964", "pubmed": "24316575", - "title": "The Vertebrate Genome Annotation browser 10 years on.", + "title": "The Vertebrate Genome Annotation browser 10 years on", "year": 2013 }, { "doi": "10.1093/nar/gkm987", "pmc": "PMC2238886", "pubmed": "18003653", - "title": "The vertebrate genome annotation (Vega) database.", + "title": "The vertebrate genome annotation (Vega) database", "year": 2007 } ], @@ -50456,33 +56604,33 @@ "pattern": "^[0-9a-zA-Z]{8}$", "preferred_prefix": "vfb", "publications": [ - { - "doi": "doi:10.1186/1471-2105-13-122", - "pmc": "PMC3412715", - "pubmed": "22676296", - "title": "Web tools for large-scale 3D biological images and atlases", - "year": null - }, { "doi": "10.1186/1471-2105-13-122", "pmc": "PMC3412715", "pubmed": "22676296", - "title": "Web tools for large-scale 3D biological images and atlases.", + "title": "Web tools for large-scale 3D biological images and atlases", "year": 2012 }, { "doi": "10.1093/bioinformatics/bts113", "pmc": null, "pubmed": "22402613", - "title": "A strategy for building neuroanatomy ontologies.", + "title": "A strategy for building neuroanatomy ontologies", "year": 2012 }, { "doi": "10.1093/bioinformatics/btr677", "pmc": null, "pubmed": "22180411", - "title": "The Virtual Fly Brain browser and query interface.", + "title": "The Virtual Fly Brain browser and query interface", "year": 2011 + }, + { + "doi": "doi:10.1186/1471-2105-13-122", + "pmc": null, + "pubmed": null, + "title": "Web tools for large-scale 3D biological images and atlases", + "year": null } ], "uri_format": "http://virtualflybrain.org/reports/$1" @@ -50537,7 +56685,7 @@ "doi": "10.1093/nar/gkaa980", "pmc": "PMC7779007", "pubmed": "33152070", - "title": "Genenames.org: the HGNC and VGNC resources in 2021.", + "title": "Genenames.org: the HGNC and VGNC resources in 2021", "year": 2021 } ], @@ -50562,6 +56710,7 @@ "obo", "ontology" ], + "logo": "http://bgee.org/img/logo/bgee13_logo.png", "mappings": { "aberowl": "VHOG", "biocontext": "VHOG", @@ -50572,6 +56721,16 @@ "name": "Vertebrate Homologous Organ Group Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VHOG", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vhog:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/VHOG_$1", "synonyms": [ "VHOG_RETIRED" ], @@ -50656,6 +56815,9 @@ "deprecated": true, "description": "Defunct vaccine information source from the He Lab", "example": "4140", + "mappings": { + "wikidata": "P1925" + }, "name": "ViolinNet", "pattern": "^\\d+$", "preferred_prefix": "violinnet", @@ -50679,7 +56841,17 @@ }, "name": "VIPERdb", "preferred_prefix": "viperdb", - "uri_format": "http://viperdb.scripps.edu/info_page.php?VDB=$1" + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/viperdb:$1" + } + ], + "provides": "pdb", + "uri_format": "https://viperdb.org/Info_Page.php?VDB=$1" }, "vipr": { "contact": { @@ -50716,14 +56888,14 @@ "doi": "10.3390/v4113209", "pmc": "PMC3509690", "pubmed": "23202522", - "title": "Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community.", + "title": "Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community", "year": 2012 }, { "doi": "10.1093/nar/gkr859", "pmc": "PMC3245011", "pubmed": "22006842", - "title": "ViPR: an open bioinformatics database and analysis resource for virology research.", + "title": "ViPR: an open bioinformatics database and analysis resource for virology research", "year": 2011 }, { @@ -50774,6 +56946,13 @@ "pattern": "^\\d+$", "preferred_prefix": "viralzone", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vz:$1" + }, { "code": "viralzone.alt1", "description": "Alternate view", @@ -50787,14 +56966,14 @@ "doi": "10.1093/nar/gks1220", "pmc": "PMC3531065", "pubmed": "23193299", - "title": "ViralZone: recent updates to the virus knowledge resource.", + "title": "ViralZone: recent updates to the virus knowledge resource", "year": 2012 }, { "doi": "10.1093/nar/gkq901", "pmc": "PMC3013774", "pubmed": "20947564", - "title": "ViralZone: a knowledge resource to understand virus diversity.", + "title": "ViralZone: a knowledge resource to understand virus diversity", "year": 2010 } ], @@ -50814,7 +56993,16 @@ "prefixcommons": "virgen" }, "name": "VirGen", - "preferred_prefix": "virgen" + "preferred_prefix": "virgen", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/virgen:$1" + } + ] }, "virmirdb": { "description": "A database containing predicted viral miRNA candidate hairpins.", @@ -50829,6 +57017,15 @@ }, "name": "Vir-Mir db", "preferred_prefix": "virmirdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/virmirdb:$1" + } + ], "provides": "ncbitaxon", "reviewer": { "email": "cthoyt@gmail.com", @@ -50850,6 +57047,15 @@ }, "name": "VirOligo", "preferred_prefix": "viroligo", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/viroligo:$1" + } + ], "uri_format": "http://viroligo.okstate.edu/main.php?vid=$1" }, "virsirna": { @@ -50878,13 +57084,22 @@ }, "name": "Virus-HostDB", "preferred_prefix": "virushostdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/virushostdb:$1" + } + ], "provides": "ncbitaxon", "publications": [ { "doi": "10.3390/v8030066", "pmc": "PMC4810256", "pubmed": "26938550", - "title": "Linking Virus Genomes with Host Taxonomy.", + "title": "Linking Virus Genomes with Host Taxonomy", "year": 2016 } ], @@ -50910,6 +57125,15 @@ }, "name": "Virus' miRNA target", "preferred_prefix": "vita", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vita:$1" + } + ], "uri_format": "http://vita.mbc.nctu.edu.tw/search.php?acc=$1" }, "vmc": { @@ -50974,7 +57198,7 @@ "name": "Yongqunh He", "orcid": "0000-0001-9189-9661" }, - "description": "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.", + "description": "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.", "download_owl": "http://purl.obolibrary.org/obo/vo.owl", "example": "0000093", "homepage": "http://www.violinet.org/vaccineontology", @@ -51002,39 +57226,56 @@ "name": "Vaccine Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vo:$1" + } + ], "publications": [ { "doi": "10.2174/1381612826666201125112131", "pmc": null, "pubmed": "33238868", - "title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development.", + "title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development", "year": 2021 }, { "doi": "10.1186/2041-1480-3-17", "pmc": "PMC3639077", "pubmed": "23256535", - "title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses.", + "title": "Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses", "year": 2012 }, { "doi": "10.1186/2041-1480-2-s2-s8", "pmc": "PMC3102897", "pubmed": "21624163", - "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.", + "title": "Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology", "year": 2011 }, { "doi": "10.1186/1745-7580-6-s1-s5", "pmc": "PMC2946783", "pubmed": "20875156", - "title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.", + "title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN", "year": 2010 + }, + { + "doi": "10.1186/1745-7580-6-S1-S5", + "pmc": "PMC2946783", + "pubmed": "20875156", + "title": "Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/VO_$1", "repository": "https://github.com/vaccineontology/VO", "uri_format": "http://purl.obolibrary.org/obo/VO_$1", - "version": "1.1.198" + "version": "1.1.218" }, "void": { "contributor": { @@ -51077,14 +57318,26 @@ "biocontext": "VSAO", "bioportal": "VSAO", "obofoundry": "vsao", + "ols": "vsao", "prefixcommons": "vao" }, "name": "Vertebrate Skeletal Anatomy Ontology", "preferred_prefix": "VSAO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vao:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/VSAO_$1", "synonyms": [ "VSAO_RETIRED" ], - "uri_format": "http://purl.obolibrary.org/obo/VSAO_$1" + "uri_format": "http://purl.obolibrary.org/obo/VSAO_$1", + "version": "2012-11-06" }, "vsdb": { "contributor": { @@ -51125,7 +57378,7 @@ "doi": "10.1603/me12169", "pmc": "PMC3695545", "pubmed": "23427646", - "title": "Ontology for vector surveillance and management.", + "title": "Ontology for vector surveillance and management", "year": 2013 } ], @@ -51158,6 +57411,15 @@ "name": "Vital Sign Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "vso", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vso:$1" + } + ], "uri_format": "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1" }, "vt": { @@ -51200,15 +57462,25 @@ "name": "Vertebrate trait ontology", "pattern": "^\\d{7}$", "preferred_prefix": "VT", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/vt:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-13", "pmc": "PMC3851175", "pubmed": "23937709", - "title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species.", + "title": "The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/VT_$1", "repository": "https://github.com/AnimalGenome/vertebrate-trait-ontology", "uri_format": "http://purl.obolibrary.org/obo/VT_$1" }, @@ -51247,10 +57519,11 @@ "doi": "10.1186/2041-1480-4-34", "pmc": "PMC4177199", "pubmed": "24267744", - "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.", + "title": "The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes", "year": 2013 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/VTO_$1", "repository": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", "uri_format": "http://purl.obolibrary.org/obo/VTO_$1", "version": "2020-11-13" @@ -51322,21 +57595,31 @@ "name": "C. elegans Gross Anatomy Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "WBbt", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wbbt:$1" + } + ], "publications": [ { "doi": "10.1002/cfg.248", "pmc": "PMC2447384", "pubmed": "18629098", - "title": "Building a cell and anatomy ontology of Caenorhabditis elegans.", + "title": "Building a cell and anatomy ontology of Caenorhabditis elegans", "year": 2003 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", "repository": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", "synonyms": [ "WBbt" ], - "uri_format": "http://purl.obolibrary.org/obo/WBbt_$1", - "version": "2022-06-13" + "uri_format": "http://wormbase.org/db/ontology/anatomy?name=$1", + "version": "2023-04-07" }, "wbls": { "contact": { @@ -51374,21 +57657,31 @@ "name": "C. elegans development ontology", "pattern": "^\\d{7}$", "preferred_prefix": "WBls", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wbls:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkz920", "pmc": "PMC7145598", "pubmed": "31642470", - "title": "WormBase: a modern Model Organism Information Resource.", + "title": "WormBase: a modern Model Organism Information Resource", "year": 2020 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/WBls_$1", "repository": "https://github.com/obophenotype/c-elegans-development-ontology", "synonyms": [ "WBls" ], "uri_format": "http://www.wormbase.org/get?name=$1", - "version": "2022-06-21" + "version": "2023-05-17" }, "wbphenotype": { "contact": { @@ -51425,21 +57718,31 @@ "name": "C. elegans phenotype", "pattern": "^\\d{7}$", "preferred_prefix": "WBPhenotype", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wbphenotype:$1" + } + ], "publications": [ { "doi": "10.1186/1471-2105-12-32", "pmc": "PMC3039574", "pubmed": "21261995", - "title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.", + "title": "Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community", "year": 2011 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", "repository": "https://github.com/obophenotype/c-elegans-phenotype-ontology", "synonyms": [ "WBPhenotype" ], "uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1", - "version": "2022-06-21" + "version": "2023-05-18" }, "webelements": { "contributor": { @@ -51596,20 +57899,17 @@ } ], "description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.", - "download_owl": "http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl", "example": "WP732", "homepage": "http://www.wikipathways.org/", "keywords": [ "epidemiology", - "ontology", "pathway", "virology" ], "license": "CC0-1.0", + "logo": "https://www.wikipathways.org/assets/img/wikipathways-logo-horizontal.svg", "mappings": { - "aberowl": "WIKIPATHWAYS", "biocontext": "WIKIPATHWAYS", - "bioportal": "WIKIPATHWAYS", "edam": "3952", "fairsharing": "FAIRsharing.g7b4rj", "miriam": "wikipathways", @@ -51618,10 +57918,18 @@ "re3data": "r3d100013316", "wikidata": "P2410" }, + "mastodon": "wikipathways@fosstodon.org", "name": "WikiPathways", "pattern": "^WP\\d{1,5}(\\_r\\d+)?$", "preferred_prefix": "wikipathways", "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wikipathways:$1" + }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.\n", @@ -51635,44 +57943,88 @@ "doi": "10.1093/nar/gkaa1024", "pmc": "PMC7779061", "pubmed": "33211851", - "title": "WikiPathways: connecting communities.", + "title": "WikiPathways: connecting communities", "year": 2021 }, { "doi": "10.1093/nar/gkx1064", "pmc": "PMC5753270", "pubmed": "29136241", - "title": "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.", + "title": "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research", "year": 2018 }, { "doi": "10.1093/nar/gkv1024", "pmc": "PMC4702772", "pubmed": "26481357", - "title": "WikiPathways: capturing the full diversity of pathway knowledge.", + "title": "WikiPathways: capturing the full diversity of pathway knowledge", "year": 2015 }, { "doi": "10.1093/nar/gkr1074", "pmc": "PMC3245032", "pubmed": "22096230", - "title": "WikiPathways: building research communities on biological pathways.", + "title": "WikiPathways: building research communities on biological pathways", "year": 2011 }, { "doi": "10.1371/journal.pbio.0060184", "pmc": "PMC2475545", "pubmed": "18651794", - "title": "WikiPathways: pathway editing for the people.", + "title": "WikiPathways: pathway editing for the people", "year": 2008 } ], + "rdf_uri_format": "http://identifiers.org/wikipathways/$1", "twitter": "WikiPathways", "uri_format": "http://www.wikipathways.org/instance/$1" }, + "wikipathways.vocab": { + "contact": { + "email": "egon.willighagen@gmail.com", + "github": "egonw", + "name": "Egon Willighagen", + "orcid": "0000-0001-7542-0286" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "An ontology supporting data modeling in WikiPathways", + "download_owl": "http://aber-owl.net/media/ontologies/WIKIPATHWAYS/225/wikipathways.owl", + "example": "DataNode", + "homepage": "http://www.wikipathways.org", + "keywords": [ + "ontology" + ], + "mappings": { + "aberowl": "WIKIPATHWAYS", + "bioportal": "WIKIPATHWAYS" + }, + "mastodon": "wikipathways@fosstodon.org", + "name": "WikiPathways Ontology", + "preferred_prefix": "wikipathways.vocab", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/818" + ], + "uri_format": "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1" + }, "wikipedia.en": { + "contributor_extras": [ + { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + } + ], "description": "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay.", "example": "SM_UB-81", + "example_extras": [ + "Pharyngeal_pouch_(embryology)" + ], "homepage": "http://en.wikipedia.org/wiki/Main_Page", "mappings": { "biocontext": "WIKIPEDIA.EN", @@ -51682,7 +58034,7 @@ "prefixcommons": "wikipedia" }, "name": "Wikipedia", - "pattern": "^[A-Za-z-0-9_]+$", + "pattern": "^\\S+$", "preferred_prefix": "wikipedia.en", "providers": [ { @@ -51692,6 +58044,13 @@ "name": "Wikipedia structured content through DBpedia", "uri_format": "http://dbpedia.org/page/$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wikipedia:$1" + }, { "code": "volupedia", "description": "A mix of wikipedia and 3d", @@ -51700,6 +58059,9 @@ "uri_format": "http://en.volupedia.org/wiki/$1" } ], + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/794" + ], "synonyms": [ "wikipedia" ], @@ -51722,6 +58084,15 @@ "name": "C. elegans ORFeome cloning project", "pattern": "^\\w+(\\.\\d+)$", "preferred_prefix": "worfdb", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/worfdb:$1" + } + ], "uri_format": "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1" }, "world2dpage": { @@ -51741,12 +58112,21 @@ }, "name": "The World-2DPAGE database", "preferred_prefix": "world2dpage", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/world2dpage:$1" + } + ], "publications": [ { "doi": "10.1016/j.jprot.2008.02.005", "pmc": null, "pubmed": "18617148", - "title": "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server.", + "title": "The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server", "year": 2008 } ], @@ -51758,6 +58138,41 @@ }, "uri_format": "https://world-2dpage.expasy.org/repository/$1" }, + "worldavatar.compchem": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)", + "download_owl": "http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl", + "homepage": "https://como.ceb.cam.ac.uk/preprints/223/", + "keywords": [ + "ontology" + ], + "name": "Computational Chemistry Ontology", + "no_own_terms": true, + "preferred_prefix": "worldavatar.compchem" + }, + "worldavatar.kin": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Represents chemical kinetic reaction mechanisms.", + "download_owl": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl", + "example": "ElementNumber", + "homepage": "http://www.theworldavatar.com/ontokin/", + "keywords": [ + "ontology" + ], + "name": "Ontology for Chemical Kinetic Reaction Mechanisms", + "preferred_prefix": "worldavatar.kin", + "uri_format": "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1" + }, "wormbase": { "description": "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities.", "example": "WBGene00000001", @@ -51793,6 +58208,13 @@ "name": "WormBase through the Alliance of Genome Resources", "uri_format": "https://www.alliancegenome.org/gene/WB:$1" }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wormbase:$1" + }, { "code": "wormbase.c_elegans", "description": "Pages describing C. Elegans genes.", @@ -51806,84 +58228,84 @@ "doi": "10.1093/nar/gkz920", "pmc": "PMC7145598", "pubmed": "31642470", - "title": "WormBase: a modern Model Organism Information Resource.", + "title": "WormBase: a modern Model Organism Information Resource", "year": 2020 }, { "doi": "10.1093/nar/gkx998", "pmc": "PMC5753391", "pubmed": "29069413", - "title": "WormBase 2017: molting into a new stage.", + "title": "WormBase 2017: molting into a new stage", "year": 2018 }, { "doi": "10.1186/1471-2105-12-175", "pmc": "PMC3213741", "pubmed": "21595960", - "title": "Toward an interactive article: integrating journals and biological databases.", + "title": "Toward an interactive article: integrating journals and biological databases", "year": 2011 }, { "doi": "10.1093/nar/gkq1116", "pmc": "PMC3013707", "pubmed": "21071413", - "title": "The BioGRID Interaction Database: 2011 update.", + "title": "The BioGRID Interaction Database: 2011 update", "year": 2010 }, { "doi": "10.1186/1471-2105-11-550", "pmc": "PMC2992068", "pubmed": "21059240", - "title": "Localizing triplet periodicity in DNA and cDNA sequences.", + "title": "Localizing triplet periodicity in DNA and cDNA sequences", "year": 2010 }, { "doi": "10.1002/mrd.21130", "pmc": "PMC2830379", "pubmed": "19921742", - "title": "Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.", + "title": "Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology", "year": 2010 }, { "doi": "10.1093/nar/gkp1018", "pmc": "PMC2808930", "pubmed": "19920128", - "title": "The Gene Ontology in 2010: extensions and refinements.", + "title": "The Gene Ontology in 2010: extensions and refinements", "year": 2009 }, { "doi": "10.1093/nar/gkp952", "pmc": "PMC2808986", "pubmed": "19910365", - "title": "WormBase: a comprehensive resource for nematode research.", + "title": "WormBase: a comprehensive resource for nematode research", "year": 2009 }, { "doi": "10.1186/1471-2105-10-228", "pmc": "PMC2719631", "pubmed": "19622167", - "title": "Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation.", + "title": "Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation", "year": 2009 }, { "doi": "10.1371/journal.pcbi.1000431", "pmc": "PMC2699109", "pubmed": "19578431", - "title": "The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.", + "title": "The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species", "year": 2009 }, { "doi": "10.1186/1471-2105-9-549", "pmc": "PMC2651883", "pubmed": "19099578", - "title": "nGASP--the nematode genome annotation assessment project.", + "title": "nGASP--the nematode genome annotation assessment project", "year": 2008 }, { "doi": "10.1093/nar/29.1.82", "pmc": "PMC29781", "pubmed": "11125056", - "title": "WormBase: network access to the genome and biology of Caenorhabditis elegans.", + "title": "WormBase: network access to the genome and biology of Caenorhabditis elegans", "year": 2001 } ], @@ -51912,6 +58334,15 @@ "name": "Wormpep", "pattern": "^CE\\d{5}$", "preferred_prefix": "wormpep", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/wormpep:$1" + } + ], "uri_format": "https://www.wormbase.org/db/seq/protein?name=$1" }, "worms": { @@ -51960,6 +58391,24 @@ "twitter": "WRMarineSpecies", "uri_format": "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1" }, + "wos": { + "description": "unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)", + "example": "000177759000002", + "homepage": "https://www.webofscience.com", + "mappings": { + "wikidata": "P8372" + }, + "name": "Web of Science ID (work)", + "preferred_prefix": "wos", + "references": [ + "https://github.com/biopragmatics/bioregistry/issues/805" + ], + "synonyms": [ + "wosid", + "wosuid" + ], + "uri_format": "https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=Publons&SrcAuth=Publons_CEL&KeyUT=WOS:$1&DestLinkType=FullRecord&DestApp=WOS_CPL" + }, "wwf.ecoregion": { "comment": "ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658", "contributor": { @@ -52031,20 +58480,28 @@ "doi": "10.1186/2041-1480-4-31", "pmc": "PMC3816597", "pubmed": "24139024", - "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.", + "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase", "year": 2013 }, { "doi": "10.1186/1471-213x-8-92", "pmc": "PMC2561031", "pubmed": "18817563", - "title": "An ontology for Xenopus anatomy and development.", + "title": "An ontology for Xenopus anatomy and development", "year": 2008 + }, + { + "doi": "10.1186/1471-213X-8-92", + "pmc": "PMC2561031", + "pubmed": "18817563", + "title": "An ontology for Xenopus anatomy and development", + "year": null } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/XAO_$1", "repository": "https://github.com/xenopus-anatomy/xao", "uri_format": "http://purl.obolibrary.org/obo/XAO_$1", - "version": "2021-03-04" + "version": "2022-08-29" }, "xco": { "appears_in": [ @@ -52070,6 +58527,7 @@ "ontology" ], "license": "CC0-1.0", + "logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif", "mappings": { "aberowl": "XCO", "biocontext": "XCO", @@ -52083,26 +58541,36 @@ "name": "Experimental condition ontology", "pattern": "^\\d{7}$", "preferred_prefix": "XCO", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/xco:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-4-26", "pmc": "PMC3882879", "pubmed": "24103152", - "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.", + "title": "The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications", "year": 2013 }, { "doi": "10.3389/fgene.2012.00087", "pmc": "PMC3361058", "pubmed": "22654893", - "title": "Three ontologies to define phenotype measurement data.", + "title": "Three ontologies to define phenotype measurement data", "year": 2012 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/XCO_$1", "repository": "https://github.com/rat-genome-database/XCO-experimental-condition-ontology", "twitter": "ratgenome", "uri_format": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1", - "version": "2019-12-18" + "version": "4.46" }, "xenbase": { "contact": { @@ -52141,28 +58609,30 @@ "name": "Xenbase", "pattern": "^XB\\-\\w+\\-\\d+$", "preferred_prefix": "xenbase", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/xenbase:$1" + } + ], "publications": [ { "doi": "10.1186/s12859-022-04636-8", "pmc": "PMC8939077", "pubmed": "35317743", - "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.", + "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development", "year": 2022 }, { "doi": "10.1093/nar/gkz933", "pmc": "PMC7145613", "pubmed": "31733057", - "title": "Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.", + "title": "Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database", "year": 2020 }, - { - "doi": "doi:10.3389/fphys.2019.00154", - "pmc": "PMC6399412", - "pubmed": "30863320", - "title": "Xenbase: Facilitating the Use of Xenopus to Model Human Disease.", - "year": null - }, { "doi": "10.3389/fphys.2019.00154", "pmc": "PMC6399412", @@ -52170,61 +58640,68 @@ "title": "Xenbase: Facilitating the Use of", "year": 2019 }, - { - "doi": "doi:10.1007/978-1-4939-7737-6_10.", - "pmc": "PMC6853059", - "pubmed": "29761462", - "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.", - "year": null - }, { "doi": "10.1007/978-1-4939-7737-6_10", "pmc": "PMC6853059", "pubmed": "29761462", - "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.", + "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database", "year": 2018 }, { "doi": "10.1093/nar/gkx936", "pmc": "PMC5753396", "pubmed": "29059324", - "title": "Xenbase: a genomic, epigenomic and transcriptomic model organism database.", + "title": "Xenbase: a genomic, epigenomic and transcriptomic model organism database", "year": 2018 }, { "doi": "10.1016/j.ydbio.2016.03.030", "pmc": "PMC5045824", "pubmed": "27039265", - "title": "Xenopus genomic data and browser resources.", + "title": "Xenopus genomic data and browser resources", "year": 2016 }, { "doi": "10.1093/database/bau108", "pmc": "PMC4224262", "pubmed": "25380782", - "title": "The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.", + "title": "The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud", "year": 2014 }, { "doi": "10.1093/nar/gku956", "pmc": "PMC4384024", "pubmed": "25313157", - "title": "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.", + "title": "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes", "year": 2014 }, { "doi": "10.1186/2041-1480-4-31", "pmc": "PMC3816597", "pubmed": "24139024", - "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.", + "title": "Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase", "year": 2013 }, { "doi": "10.1093/nar/gkp953", "pmc": "PMC2808955", "pubmed": "19884130", - "title": "Xenbase: gene expression and improved integration.", + "title": "Xenbase: gene expression and improved integration", "year": 2009 + }, + { + "doi": "doi:10.3389/fphys.2019.00154", + "pmc": null, + "pubmed": null, + "title": "Xenbase: Facilitating the Use of Xenopus to Model Human Disease.", + "year": null + }, + { + "doi": "doi:10.1007/978-1-4939-7737-6_10.", + "pmc": null, + "pubmed": null, + "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.", + "year": null } ], "synonyms": [ @@ -52266,8 +58743,7 @@ "ontobee": "XL" }, "name": "Cross-linker reagents ontology", - "preferred_prefix": "xl", - "uri_format": "http://purl.obolibrary.org/obo/XL_$1" + "preferred_prefix": "xl" }, "xlmod": { "contact": { @@ -52277,7 +58753,7 @@ "orcid": "0000-0003-4978-0864" }, "description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.", - "download_obo": "https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo", + "download_obo": "http://purl.obolibrary.org/obo/xlmod.obo", "download_owl": "http://purl.obolibrary.org/obo/xlmod.owl", "example": "00050", "homepage": "http://www.psidev.info/groups/controlled-vocabularies", @@ -52296,6 +58772,7 @@ "name": "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary", "pattern": "^\\d{5}$", "preferred_prefix": "XLMOD", + "rdf_uri_format": "http://purl.obolibrary.org/obo/XLMOD_$1", "repository": "https://github.com/HUPO-PSI/xlmod-CV", "uri_format": "http://purl.obolibrary.org/obo/XLMOD_$1", "version": "2019-10-28" @@ -52381,13 +58858,14 @@ "doi": "10.1186/s12859-022-04636-8", "pmc": "PMC8939077", "pubmed": "35317743", - "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.", + "title": "The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development", "year": 2022 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/XPO_$1", "repository": "https://github.com/obophenotype/xenopus-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/XPO_$1", - "version": "2021-03-05" + "version": "2022-09-15" }, "xsd": { "contributor": { @@ -52436,6 +58914,15 @@ "name": "Yeast Deletion and the Mitochondrial Proteomics Project", "pattern": "^Y[A-Z]{2}\\d+[CW]$", "preferred_prefix": "ydpm", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ydpm:$1" + } + ], "uri_format": "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1" }, "yeastintron": { @@ -52469,33 +58956,42 @@ }, "name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking", "preferred_prefix": "yeastract", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/yeastract:$1" + } + ], "publications": [ { "doi": "10.1093/nar/gkt1015", "pmc": "PMC3965121", "pubmed": "24170807", - "title": "The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.", + "title": "The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae", "year": 2013 }, { "doi": "10.1093/nar/gkq964", "pmc": "PMC3013800", "pubmed": "20972212", - "title": "YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.", + "title": "YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface", "year": 2010 }, { "doi": "10.1093/nar/gkm976", "pmc": "PMC2238916", "pubmed": "18032429", - "title": "YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.", + "title": "YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae", "year": 2007 }, { "doi": "10.1093/nar/gkj013", "pmc": "PMC1347376", "pubmed": "16381908", - "title": "The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.", + "title": "The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae", "year": 2006 } ], @@ -52536,6 +59032,15 @@ }, "name": "Yeast Genome Order Browser", "preferred_prefix": "ygob", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/ygob:$1" + } + ], "provides": "hgnc.symbol", "reviewer": { "email": "cthoyt@gmail.com", @@ -52585,7 +59090,7 @@ "doi": "10.1093/nar/gkr916", "pmc": "PMC3245085", "pubmed": "22064855", - "title": "YMDB: the Yeast Metabolome Database.", + "title": "YMDB: the Yeast Metabolome Database", "year": 2011 } ], @@ -52611,6 +59116,7 @@ }, "name": "Yeast Phenotype Ontology", "preferred_prefix": "YPO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/YPO_$1", "uri_format": "http://purl.obolibrary.org/obo/YPO_$1" }, "yrcpdr": { @@ -52639,6 +59145,15 @@ "name": "YRC PDR", "pattern": "^\\d+$", "preferred_prefix": "yrcpdr", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/yrc:$1" + } + ], "uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1" }, "zea": { @@ -52668,6 +59183,16 @@ }, "name": "Maize gross anatomy", "preferred_prefix": "ZEA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/zea:$1" + } + ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ZEA_$1", "uri_format": "http://purl.obolibrary.org/obo/ZEA_$1" }, "zeco": { @@ -52707,6 +59232,7 @@ "name": "Zebrafish Experimental Conditions Ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ZECO", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ZECO_$1", "repository": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology", "uri_format": "http://purl.obolibrary.org/obo/ZECO_$1", "version": "2022-02-14" @@ -52790,21 +59316,31 @@ "name": "Zebrafish anatomy and development ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ZFA", + "providers": [ + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/zfa:$1" + } + ], "publications": [ { "doi": "10.1186/2041-1480-5-12", "pmc": "PMC3944782", "pubmed": "24568621", - "title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio.", + "title": "The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio", "year": 2014 } ], + "rdf_uri_format": "http://purl.obolibrary.org/obo/ZFA_$1", "repository": "https://github.com/cerivs/zebrafish-anatomical-ontology", "synonyms": [ "ZFA_RETIRED" ], "uri_format": "http://purl.obolibrary.org/obo/ZFA_$1", - "version": "2022-03-15" + "version": "2022-12-09" }, "zfin": { "contact": { @@ -52847,6 +59383,13 @@ "homepage": "https://www.alliancegenome.org", "name": "ZFIN through the Alliance of Genome Resources", "uri_format": "https://test.alliancegenome.org/gene/ZFIN:$1" + }, + { + "code": "bio2rdf", + "description": "Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.", + "homepage": "https://bio2rdf.org", + "name": "Bio2RDF", + "uri_format": "http://bio2rdf.org/zfin:$1" } ], "publications": [ @@ -52861,56 +59404,63 @@ "doi": "10.1093/nar/gks938", "pmc": null, "pubmed": "23074187", - "title": "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics.", + "title": "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics", "year": null }, { "doi": "10.1016/b978-0-12-374814-0.00017-3", "pmc": null, "pubmed": "21924170", - "title": "Data extraction, transformation, and dissemination through ZFIN.", + "title": "Data extraction, transformation, and dissemination through ZFIN", "year": null }, { "doi": "10.1093/nar/gkq1077", "pmc": null, "pubmed": "21036866", - "title": "ZFIN: enhancements and updates to the Zebrafish Model Organism Database.", + "title": "ZFIN: enhancements and updates to the Zebrafish Model Organism Database", "year": null }, { "doi": "10.1002/0471250953.bi0118s31.", "pmc": null, "pubmed": "20836073", - "title": "Exploring zebrafish genomic, functional and phenotypic data using ZFIN.", + "title": "Exploring zebrafish genomic, functional and phenotypic data using ZFIN", "year": null }, { "doi": "10.1093/nar/gkm956", "pmc": "PMC2238839", "pubmed": "17991680", - "title": "The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.", + "title": "The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes", "year": 2007 }, { "doi": "10.1093/nar/gkj086", "pmc": null, "pubmed": "16381936", - "title": "The Zebrafish Information Network: the zebrafish model organism database.", + "title": "The Zebrafish Information Network: the zebrafish model organism database", "year": null }, { "doi": "10.1093/nar/gkg027", "pmc": null, "pubmed": "12519991", - "title": "The Zebrafish Information Network (ZFIN): the zebrafish model organism database.", + "title": "The Zebrafish Information Network (ZFIN): the zebrafish model organism database", "year": null }, { "doi": "10.1016/s0168-9525(99)01741-2", "pmc": null, "pubmed": "10354586", - "title": "Zebrafish in the Net.", + "title": "Zebrafish in the Net", + "year": null + }, + { + "doi": "10.1016/B978-0-12-374814-0.00017-3", + "pmc": null, + "pubmed": null, + "title": "Data extraction, transformation, and dissemination through ZFIN.", "year": null } ], @@ -52953,6 +59503,7 @@ "name": "Zebrafish developmental stages ontology", "pattern": "^\\d{7}$", "preferred_prefix": "ZFS", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ZFS_$1", "repository": "https://github.com/cerivs/zebrafish-anatomical-ontology", "uri_format": "http://purl.obolibrary.org/obo/ZFS_$1", "version": "2020-03-10" @@ -53010,8 +59561,9 @@ "name": "Zebrafish Phenotype Ontology", "pattern": "^\\d+$", "preferred_prefix": "ZP", + "rdf_uri_format": "http://purl.obolibrary.org/obo/ZP_$1", "repository": "https://github.com/obophenotype/zebrafish-phenotype-ontology", "uri_format": "http://purl.obolibrary.org/obo/ZP_$1", - "version": "2021-12-12" + "version": "2022-12-17" } } \ No newline at end of file diff --git a/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh b/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh deleted file mode 100644 index af32171c5..000000000 --- a/paxtools-console/src/main/java/org/biopax/paxtools/examples/commands.sh +++ /dev/null @@ -1,17 +0,0 @@ -hg clone http://biopax.hg.sourceforge.net:8000/hgroot/biopax/paxtools - ---merge ---to-sif ---to-sifnx prop1,prop2,.. - converts a BioPAX file to the extended SIF format ---integrate (experimental) ---to-level3 ---psimi-to ---to-GSEA - converts level 1 or 2 or 3 to GSEA output. Searches database for participant id or uses biopax rdf id if database is NONE. Cross species check ensures participant protein is from same species as pathway (set to true or false). ---fetch - extracts a sub-model (id1,id2, etc. - new root elements) ---get-neighbors - nearest neighborhood graph query - -java -jar paxtools.jar --merge file1.owl file2.owl output.owl - -java -Xmx2048M -jar paxtools.jar --merge file1.owl file2.owl output.owl - -java -cp paxtools.jar org.biopax.paxtools.PaxtoolsMain --validate file.owl diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java index 168292159..117786c8e 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/controller/ModelUtils.java @@ -437,21 +437,32 @@ enum FeatureType UNKNOWN_FEATURE; } - // TODO annotate - public static Set getFeatureIntersection(PhysicalEntity first, FeatureType firstClass, - PhysicalEntity second, FeatureType secondClass) + /** + * Gets the entity features that both entities have in common, taking the feature type into account. + * @param physicalEntity1 first entity + * @param featureType1 first feature type (feature/not-feature/unknown) + * @param physicalEntity2 second entity + * @param featureType2 second feature type + * @return the set of entity features + */ + public static Set getFeatureIntersection(PhysicalEntity physicalEntity1, FeatureType featureType1, + PhysicalEntity physicalEntity2, FeatureType featureType2) { - Set intersection = getFeatureSetByType(first, firstClass); - intersection.removeAll(getFeatureSetByType(second, secondClass)); + Set intersection = getFeatureSetByType(physicalEntity1, featureType1); + intersection.removeAll(getFeatureSetByType(physicalEntity2, featureType2)); return intersection; } - // TODO annotate + /** + * Get entity's features by type. + * + * @param pe + * @param type + * @return + */ public static Set getFeatureSetByType(PhysicalEntity pe, FeatureType type) { - Set modifiableSet = new HashSet<>(); - switch (type) { case FEATURE: @@ -462,12 +473,15 @@ public static Set getFeatureSetByType(PhysicalEntity pe, FeatureT break; case UNKNOWN_FEATURE: { - if (pe instanceof SimplePhysicalEntity) - { - modifiableSet.addAll(((SimplePhysicalEntity) pe).getEntityReference().getEntityFeature()); - modifiableSet.removeAll(pe.getFeature()); - modifiableSet.removeAll(pe.getNotFeature()); + if (pe instanceof SimplePhysicalEntity) { + EntityReference er = ((SimplePhysicalEntity) pe).getEntityReference(); + if(er != null) { + modifiableSet.addAll(er.getEntityFeature()); + modifiableSet.removeAll(pe.getFeature()); + modifiableSet.removeAll(pe.getNotFeature()); + } } + break; } } return modifiableSet; @@ -657,7 +671,7 @@ private static void createGenericEntityRef(Model model, SimplePhysicalEntity spe break; //got one! } } else { - return; //spe already has a ER + return; //spe already has ER //TODO: shall we add members (spe.getGenericEntityReferences()) to firstEntityReference? } @@ -1126,7 +1140,6 @@ private static Set getParentPathwaysRecursively( /** * Merges equivalent interactions (currently - Conversions only). - * TODO: shall we rename to mergeEquivalentConversions instead (this is what it does)? * * Warning: experimental; - check if the result is desirable; * the result very much depends on actual pathway data quality... diff --git a/pom.xml b/pom.xml index e99163459..fbe8f292e 100644 --- a/pom.xml +++ b/pom.xml @@ -114,8 +114,8 @@ - Travis CI - https://travis-ci.org/BioPAX/Paxtools + GitHub + https://github.com/BioPAX/Paxtools/actions/workflows/maven.yml @@ -137,6 +137,7 @@ + org.apache.maven.plugins maven-source-plugin @@ -186,6 +187,9 @@ + github BioPAX/Paxtools Maven site https://biopax.github.io/Paxtools/${project.version} @@ -279,7 +283,7 @@ org.sonatype.plugins nexus-staging-maven-plugin - 1.6.8 + 1.6.13 maven-gpg-plugin @@ -324,9 +328,9 @@ maven-surefire-plugin false - -ea -ea --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED + @@ -490,7 +494,7 @@ true true - http://download.oracle.com/javase/7/docs/api/ + http://download.oracle.com/javase/17/docs/api/ public org.biopax.validator.*:net.biomodels.* diff --git a/src/site/site.xml b/src/site/site.xml index 54d5707b1..14162b1de 100644 --- a/src/site/site.xml +++ b/src/site/site.xml @@ -1,48 +1,48 @@ - - - PathwayCommons - http://pathwaycommons.github.io/cpath2/logos/pc2logo.png - http://www.pathwaycommons.org - - - - org.apache.maven.skins - maven-fluido-skin - 1.11.2 - - - - - true - true - production - - - - - - - - - - - - - - - - - - - - - - - - - - + + PathwayCommons + http://pathwaycommons.github.io/cpath2/logos/pc2logo.png + http://www.pathwaycommons.org + + + + org.apache.maven.skins + maven-fluido-skin + 1.11.2 + + + + + true + true + production + + + + + + + + + + + + + + + + + + + + + + + + + + + From 739c050a65702eb8399c7e13f6c10cc7d94563fb Mon Sep 17 00:00:00 2001 From: Igor Rodchenkov Date: Sat, 2 Sep 2023 21:41:15 -0400 Subject: [PATCH 19/20] Updated workflow maven.yml --- .github/workflows/maven.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index 5f29f81ef..8596c995a 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -22,8 +22,8 @@ jobs: - uses: actions/checkout@v3 - uses: actions/setup-java@v3 with: - java-version: 17 + java-version: 20 distribution: 'temurin' cache: maven - - name: Build with Maven (JDK-17) + - name: Build with Maven (JDK-20) run: mvn --batch-mode --update-snapshots package From 813f572479351e8d1fba29a9b5e018bd32606ec2 Mon Sep 17 00:00:00 2001 From: IgorRodchenkov Date: Sat, 2 Sep 2023 22:13:20 -0400 Subject: [PATCH 20/20] Minor, after rebased onto "master", changes --- .../paxtools/io/jsonld/JsonldBiopaxConverterTest.java | 3 ++- .../org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java | 2 +- paxtools-search/pom.xml | 0 pom.xml | 9 +++++---- 4 files changed, 8 insertions(+), 6 deletions(-) delete mode 100644 paxtools-search/pom.xml diff --git a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java index d6496fd7d..c8cfcb2fc 100644 --- a/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java +++ b/json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java @@ -19,7 +19,8 @@ public final void test() throws IOException { JsonldConverter intf = new JsonldBiopaxConverter(); // convert owl test file in resource directory to jsonld format - InputStream in = getClass().getResourceAsStream("/PC2v5test-Signaling-By-BMP-Pathway-REACT_12034.2.owl"); + InputStream in = getClass().getResourceAsStream( + "/PC2v5test-Signaling-By-BMP-Pathway-REACT_12034.2.owl"); intf.convertToJsonld(in, new FileOutputStream(jsonldTestFileName)); // convert jsonld test file back to rdf format diff --git a/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java b/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java index 9fb84def1..3411ad8cc 100644 --- a/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java +++ b/paxtools-core/src/main/java/org/biopax/paxtools/io/BioPAXIOHandlerAdapter.java @@ -34,7 +34,7 @@ public abstract class BioPAXIOHandlerAdapter implements BioPAXIOHandler protected static final String rdfs = "http://www.w3.org/2000/01/rdf-schema#"; - protected String bp; //current BioPAX Level namespace prefix value + protected String bp; //current Level BioPAX namespace prefix protected static final String xsd = "http://www.w3.org/2001/XMLSchema#"; diff --git a/paxtools-search/pom.xml b/paxtools-search/pom.xml deleted file mode 100644 index e69de29bb..000000000 diff --git a/pom.xml b/pom.xml index fbe8f292e..fc5d2ac6d 100644 --- a/pom.xml +++ b/pom.xml @@ -1,5 +1,6 @@ - + 4.0.0 pom @@ -328,7 +329,7 @@ maven-surefire-plugin false - + -ea --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED @@ -415,12 +416,12 @@ com.fasterxml.jackson.core jackson-core - 2.14.2 + 2.15.2 com.fasterxml.jackson.core jackson-databind - 2.14.2 + 2.15.2 org.projectlombok