diff --git a/src/main/java/cpath/service/metadata/Datasource.java b/src/main/java/cpath/service/metadata/Datasource.java index 27988561..7328e59b 100755 --- a/src/main/java/cpath/service/metadata/Datasource.java +++ b/src/main/java/cpath/service/metadata/Datasource.java @@ -5,6 +5,7 @@ import java.util.Set; import java.util.regex.Pattern; +import com.fasterxml.jackson.annotation.JsonIgnore; import lombok.*; import org.apache.commons.lang3.StringUtils; import org.biopax.paxtools.controller.ModelUtils; @@ -45,6 +46,7 @@ public boolean isNotPathwayData() { } } + //the order of fields here matters as the all-args Constructor will be auto-generated! private String identifier; private List name; //data provider standard names private String description; @@ -54,7 +56,7 @@ public boolean isNotPathwayData() { private METADATA_TYPE type; private String cleanerClass; private String converterClass; - private Set files; + @JsonIgnore private Set files; private String pubmedId; private String availability; private int numPathways; diff --git a/work/application.properties b/work/application.properties index acfcf340..38a43442 100644 --- a/work/application.properties +++ b/work/application.properties @@ -32,7 +32,7 @@ Feel free to tell us more about yourself and your project. cpath2.species=Homo sapiens (9606) #cpath2.sbgn-layout-enabled=false # uncomment when building a new data model (using --build option) -#cpath2.metadata-location=file:metadata.v14.json +#cpath2.metadata-location=file:metadata.json ## Spring Boot Application #configure a different port and context-path, e.g., diff --git a/work/make_generic_pe_map.bash b/work/make_generic_pe_map.bash deleted file mode 100644 index 385a991c..00000000 --- a/work/make_generic_pe_map.bash +++ /dev/null @@ -1,8 +0,0 @@ -# After the PC data build is done, -# generates generic-physical-entity-map.json (for PC app-ui webapp). -# -# Prerequisites: -# - gunzip -# - jq (https://stedolan.github.io/jq/; or install with npm: npm install hjson -g) -gunzip -c "file:downloads/physical_entities.json.gz" | jq -cS 'map(select(.generic)) | reduce .[] as $o ({}; . + {($o.uri): {name: $o.name, label:$o.label, synonyms:$o."hgnc.symbol"}})' > downloads/generic-physical-entity-map.json -echo "Generated downloads/generic-physical-entity-map.json" diff --git a/work/metadata.json b/work/metadata.json new file mode 100644 index 00000000..0155e53d --- /dev/null +++ b/work/metadata.json @@ -0,0 +1,317 @@ +{ + "description" : "Pathway Commons data sources (metadata)", + "version" : 14, + "datasources" : [ { + "identifier" : "chebi", + "name" : [ "ChEBI" ], + "description" : "ChEBI Ontology v233, 27-Apr-2024", + "dataUrl" : "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo", + "homepageUrl" : "https://www.ebi.ac.uk/chebi/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/chebi.png", + "type" : "WAREHOUSE", + "cleanerClass" : null, + "converterClass" : "cpath.converter.ChebiOboConverter", + "pubmedId" : "23180789", + "availability" : "free" + }, { + "identifier" : "uniprot_human", + "name" : [ "UniProt", "SwissProt", "UniProtKB" ], + "description" : "UniProtKB/Swiss-Prot (human), release 2024_02", + "dataUrl" : "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.dat.gz", + "homepageUrl" : "https://www.uniprot.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/uniprot.png", + "type" : "WAREHOUSE", + "cleanerClass" : null, + "converterClass" : "cpath.converter.UniprotConverter", + "pubmedId" : "24253303", + "availability" : "free" + }, { + "identifier" : "unichem_mapping", + "name" : [ "UniChem" ], + "description" : "Selected whole-source id-mapping files (to ChEBI) from UniChem, 13-May-2024", + "dataUrl" : "ftp://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/", + "homepageUrl" : "https://www.ebi.ac.uk/unichem/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/UniChem_logo2_255.png", + "type" : "MAPPING", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "23317286", + "availability" : "free" + }, { + "identifier" : "reactome", + "name" : [ "Reactome" ], + "description" : "Reactome v88 (only 'Homo_sapiens.owl') 20-Mar-2024", + "dataUrl" : "http://www.reactome.org/download/current/biopax.zip", + "homepageUrl" : "https://www.reactome.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/reactome.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.ReactomeCleaner", + "converterClass" : null, + "pubmedId" : "29145629", + "availability" : "free" + }, { + "identifier" : "pid", + "name" : [ "pid", "NCI Pathway Interaction Database: Pathway" ], + "description" : "NCI Curated Human Pathways from PID (final); 27-Jul-2015", + "dataUrl" : "https://github.com/NCIP/pathway-interaction-database/blob/master/download/NCI-Nature-Curated-final.bp3.owl.gz", + "homepageUrl" : "https://en.wikipedia.org/wiki/NCI-Nature_Pathway_Interaction_Database", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/nci_nature.png", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "18832364", + "availability" : "free" + }, { + "identifier" : "psp", + "name" : [ "PhosphoSite", "PhosphoSitePlus" ], + "description" : "PhosphoSite Kinase-substrate information; 16-Apr-2024", + "dataUrl" : "http://www.phosphosite.org/downloads/Kinase_substrates.owl.gz", + "homepageUrl" : "https://www.phosphosite.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/psp.png", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "22135298", + "availability" : "free" + }, { + "identifier" : "humancyc", + "name" : [ "HumanCyc", "HumanCyc", "BioCyc" ], + "description" : "HumanCyc 27.5; 2023; under license from SRI International, www.biocyc.org", + "dataUrl" : "https://humancyc.org/download.shtml", + "homepageUrl" : "https://humancyc.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/humancyc.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.HumanCycCleaner", + "converterClass" : null, + "pubmedId" : "15642094", + "availability" : "academic" + }, { + "identifier" : "hprd", + "name" : [ "HPRD" ], + "description" : "HPRD PSI-MI Release 9; 13-Apr-2010", + "dataUrl" : "http://www.hprd.org/download", + "homepageUrl" : "http://www.hprd.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/hprd.png", + "type" : "PSI_MI", + "cleanerClass" : "cpath.cleaner.HPRDCleaner", + "converterClass" : "cpath.converter.PsimiConverter", + "pubmedId" : "18988627", + "availability" : "academic" + }, { + "identifier" : "panther", + "name" : [ "PANTHER", "PANTHER Pathway", "PantherDB" ], + "description" : "PANTHER Pathways 3.6.7 on 01-Aug-2023 (auto-converted to human-only model)", + "dataUrl" : "http://data.pantherdb.org/ftp/pathway/3.6.7/BioPAX.tar.gz", + "homepageUrl" : "https://www.pantherdb.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/panther.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.PantherCleaner", + "converterClass" : null, + "pubmedId" : "27899595", + "availability" : "free" + }, { + "identifier" : "dip", + "name" : [ "DIP", "Database of Interacting Proteins" ], + "description" : "DIP (human - converted Hsapi20170205.mif25.gz to BioPAX), 05-Feb-2017", + "dataUrl" : "https://dip.doe-mbi.ucla.edu/dip/Download.cgi", + "homepageUrl" : "https://dip.doe-mbi.ucla.edu", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/dip_logo.png", + "type" : "PSI_MI", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiConverter", + "pubmedId" : "14681454", + "availability" : "free" + }, { + "identifier" : "biogrid", + "name" : [ "BioGRID" ], + "description" : "BioGRID Release 4.4.227 (only BIOGRID-ORGANISM-Homo_sapiens-4.4.227.psi25.xml), 25-Oct-2023", + "dataUrl" : "https://downloads.thebiogrid.org/File/BioGRID/Release-Archive/BIOGRID-4.4.227/BIOGRID-ORGANISM-4.4.227.psi25.zip", + "homepageUrl" : "https://thebiogrid.org/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/favicon_bigger.png", + "type" : "PSI_MI", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiConverter", + "pubmedId" : "16381927", + "availability" : "free" + }, { + "identifier" : "intact", + "name" : [ "IntAct" ], + "description" : "IntAct (human), except 'negative', 06-Oct-2023", + "dataUrl" : "https://ftp.ebi.ac.uk/pub/databases/intact/2023-10-06/psi25/species/human.zip", + "homepageUrl" : "https://www.ebi.ac.uk/intact/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/logo_intact_small.gif", + "type" : "PSI_MI", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiConverter", + "pubmedId" : "24234451", + "availability" : "free" + }, { + "identifier" : "intact_complex", + "name" : [ "IntAct" ], + "description" : "IntAct Complex (human), 06-Oct-2023", + "dataUrl" : "https://ftp.ebi.ac.uk/pub/databases/intact/complex/2023-10-06/psi25/Homo_sapiens.zip", + "homepageUrl" : "https://www.ebi.ac.uk/intact/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/logo_intact_small.gif", + "type" : "PSI_MI", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiToComplexesConverter", + "pubmedId" : "24234451", + "availability" : "free" + }, { + "identifier" : "bind", + "name" : [ "BIND", "BIND", "Biomolecular Interaction Network Database" ], + "description" : "BIND (human), 15-Dec-2010", + "dataUrl" : "http://download.baderlab.org/BINDTranslation/release1_0/PSIMI25_XML/taxid9606_PSIMI25.xml", + "homepageUrl" : "https://en.wikipedia.org/wiki/Biomolecular_Object_Network_Databank#Biomolecular_Interaction_Network_Database_(BIND)", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/bindinside_logo.jpg", + "type" : "PSI_MI", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiConverter", + "pubmedId" : "12519993", + "availability" : "free" + }, { + "identifier" : "corum", + "name" : [ "CORUM" ], + "description" : "CORUM 3.0 (human complexes), 03-Sep-2018", + "dataUrl" : "https://mips.helmholtz-muenchen.de/corum/download/allComplexes.xml.zip", + "homepageUrl" : "https://mips.helmholtz-muenchen.de/genre/proj/corum/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/topright.jpg", + "type" : "PSI_MI", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiToComplexesConverter", + "pubmedId" : "30357367", + "availability" : "academic" + }, { + "identifier" : "msigdb", + "name" : [ "MSigDB", "MSigDB", "Molecular Signatures Database" ], + "description" : "MSigDB v5.2 (XML), human C3 TFT motif gene sets, 09-2016; converted with http://github.com/PathwayCommons/msigdb-to-biopax", + "dataUrl" : "http://software.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/5.2/msigdb_v5.2.xml", + "homepageUrl" : "http://software.broadinstitute.org/gsea/msigdb/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/msigdb.gif", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "16199517", + "availability" : "academic" + }, { + "identifier" : "mirtarbase", + "name" : [ "miRTarBase" ], + "description" : "Human miRNA-target gene relationships from MiRTarBase; v7.0, 15-SEP-2017, converted in Apr-2018 with http://github.com/PathwayCommons/mirtarbase-to-biopax", + "dataUrl" : "http://mirtarbase.mbc.nctu.edu.tw/cache/download/7.0/hsa_MTI.xlsx", + "homepageUrl" : "http://mirtarbase.mbc.nctu.edu.tw/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/mirtarbaselogo.png", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "29126174", + "availability" : "academic" + }, { + "identifier" : "drugbank", + "name" : [ "DrugBank" ], + "description" : "DrugBank v5.1.11, 03-Jan-2024, converted to BioPAX with our http://github.com/PathwayCommons/drugbank-to-biopax", + "dataUrl" : "https://www.drugbank.ca/releases/5-1-4/downloads/all-full-database", + "homepageUrl" : "http://www.drugbank.ca/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/drugbanklogo.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.DrugbankCleaner", + "converterClass" : null, + "pubmedId" : "29126136", + "availability" : "academic" + }, { + "identifier" : "reconx", + "name" : [ "Recon X" ], + "description" : "Recon X: Reconstruction of the Human Genome; SBML model from BioModels, Recon 2 v2.02 (2013), converted to BioPAX by us using http://github.com/PathwayCommons/reconx-to-biopax library.", + "dataUrl" : "http://www.ebi.ac.uk/biomodels-main/MODEL1109130000", + "homepageUrl" : "http://humanmetabolism.org/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/reconxlogo.png", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "23455439", + "availability" : "free" + }, { + "identifier" : "ctd", + "name" : [ "CTD", "Comparative Toxicogenomics Database", "ctdbase" ], + "description" : "Curated chemical-gene interactions from Comparative Toxicogenomics Database, MDI Biological Laboratory, and NC State University; 28-Feb-2024; converted with http://github.com/PathwayCommons/ctd-to-biopax", + "dataUrl" : "http://ctdbase.org/downloads/", + "homepageUrl" : "http://ctdbase.org/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/ctdlogo.png", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "27651457", + "availability" : "academic" + }, { + "identifier" : "kegg", + "name" : [ "KEGG", "KEGG Pathway" ], + "description" : "KEGG 07/2011 (only human, hsa* files), converted to BioPAX by BioModels (http://www.ebi.ac.uk/biomodels-main/) team", + "dataUrl" : "http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/BioPAX.zip", + "homepageUrl" : "https://www.genome.jp/kegg/", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/kegg128.gif", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.KeggHsaCleaner", + "converterClass" : null, + "pubmedId" : "23433509", + "availability" : "academic" + }, { + "identifier" : "inoh", + "name" : [ "INOH", "Integrating Network Objects with Hierarchies" ], + "description" : "INOH 4.0 (signal transduction and metabolic data), 22-MAR-2011, archive", + "dataUrl" : "http://inoh.hgc.jp/download.html#PathwayData", + "homepageUrl" : "http://inoh.hgc.jp", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/inoh_logo.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.InohCleaner", + "converterClass" : null, + "pubmedId" : "22120663", + "availability" : "free" + }, { + "identifier" : "netpath", + "name" : [ "NetPath" ], + "description" : "NetPath 12/2011", + "dataUrl" : "http://www.netpath.org/download/zipped/BioPAX.zip", + "homepageUrl" : "http://www.netpath.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/netpath_logo.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.NetPathCleaner", + "converterClass" : null, + "pubmedId" : "20067622", + "availability" : "free" + }, { + "identifier" : "pathbank", + "name" : [ "Pathbank" ], + "description" : "Pathbank 2.0 BioPAX data (primary pathways, human data only), 16-Aug-2019", + "dataUrl" : "http://pathbank.org/downloads/pathbank_primary_biopax.zip", + "homepageUrl" : "http://pathbank.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/pathbank.png", + "type" : "BIOPAX", + "cleanerClass" : "cpath.cleaner.PathbankCleaner", + "converterClass" : null, + "pubmedId" : "31602464", + "availability" : "free" + }, { + "identifier" : "innatedb", + "name" : [ "InnateDB" ], + "description" : "InnateDB Curated Interactions (human) 2017-06-18 (downloaded 2023-02-10)", + "dataUrl" : "https://www.innatedb.ca/download/interactions/innatedb_all.mitab.gz", + "homepageUrl" : "https://www.innatedb.ca", + "iconUrl" : "https://www.innatedb.com/images/Innatedb-2010-large.png", + "type" : "PSI_MITAB", + "cleanerClass" : null, + "converterClass" : "cpath.converter.PsimiTabConverter", + "pubmedId" : "23180781", + "availability" : "free" + }, { + "identifier" : "biofactoid", + "name" : [ "Biofactoid" ], + "description" : "Biofactoid BioPAX data, 2024-05-13", + "dataUrl" : "https://biofactoid.org/api/document/zip/biopax?idMapping=true", + "homepageUrl" : "https://biofactoid.org", + "iconUrl" : "https://pathwaycommons.github.io/cpath2/logos/biofactoid.png", + "type" : "BIOPAX", + "cleanerClass" : null, + "converterClass" : null, + "pubmedId" : "34860157", + "availability" : "free" + } ] +} diff --git a/work/metadata.v12.json b/work/metadata.v12.json deleted file mode 100644 index 9f9dbf66..00000000 --- a/work/metadata.v12.json +++ /dev/null @@ -1,367 +0,0 @@ -{ - "description": "Pathway Commons data sources (metadata)", - "version": 12, - "datasources": [ - { - "dataUrl": "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo", - "identifier": "chebi", - "homepageUrl": "https://www.ebi.ac.uk/chebi/", - "name": [ - "ChEBI" - ], - "converterClass": "cpath.converter.ChebiOboConverter", - "description": "ChEBI Ontology v179, 29-aug-2019", - "iconUrl": "https://pathwaycommons.github.io/cpath2/logos/chebi.png", - "availability": "free", - "type": "WAREHOUSE", - "pubmedId": "23180789" - }, - { - "dataUrl": "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_human.dat.gz", - "identifier": "uniprot_human", - "homepageUrl": "https://www.uniprot.org", - "name": [ - "UniProt", - "SwissProt", - "UniProtKB" - ], - "converterClass": "cpath.converter.UniprotConverter", - "description": "UniProtKB/Swiss-Prot (human), 12-Sep-2019", - "iconUrl": "https://pathwaycommons.github.io/cpath2/logos/uniprot.png", - "availability": "free", - "type": "WAREHOUSE", - "pubmedId": "24253303" - }, - { - "dataUrl": "ftp://ftp.ebi.ac.uk/pub/databases/chembl/UniChem/data/wholeSourceMapping/", - "identifier": "unichem_mapping", - "homepageUrl": "https://www.ebi.ac.uk/unichem/", - "name": [ - "UniChem" - ], - "description": "Selected whole-source id-mapping files (to ChEBI) from UniChem (fixed with a script), 01-sep-2019", - "iconUrl": "https://pathwaycommons.github.io/cpath2/logos/UniChem_logo2_255.png", - "availability": "free", - "type": "MAPPING", - "pubmedId": "23317286" - }, - { - "dataUrl": "http://www.reactome.org/download/current/biopax.zip", - "identifier": "reactome", - "homepageUrl": "https://www.reactome.org", - "cleanerClass": "cpath.cleaner.ReactomeCleaner", - "name": [ - "Reactome" - ], - "description": "Reactome v69 (only 'Homo_sapiens.owl') 28-May-2019", - "iconUrl": "https://pathwaycommons.github.io/cpath2/logos/reactome.png", - "availability": "free", - "type": "BIOPAX", - "pubmedId": "29145629" - }, - { - "dataUrl": "https://github.com/NCIP/pathway-interaction-database/blob/master/download/NCI-Nature-Curated-final.bp3.owl.gz", - "identifier": "pid", - "homepageUrl": "https://en.wikipedia.org/wiki/NCI-Nature_Pathway_Interaction_Database", - "name": [ - "pid", - "NCI Pathway Interaction Database: Pathway" - ], - "description": "NCI Curated Human Pathways from PID (final); 27-Jul-2015", - "iconUrl": "https://pathwaycommons.github.io/cpath2/logos/nci_nature.png", - "availability": "free", - "type": "BIOPAX", - "pubmedId": "18832364" - }, - { - "dataUrl": "http://www.phosphosite.org/downloads/Kinase_substrates.owl.gz", - "identifier": "psp", - "homepageUrl": "https://www.phosphosite.org", - "name": [ - "PhosphoSite", - "PhosphoSitePlus" - ], - "description": "PhosphoSite Kinase-substrate information; 19-Aug-2019", - "iconUrl": "https://pathwaycommons.github.io/cpath2/logos/psp.png", - "availability": "free", - "type": "BIOPAX", - "pubmedId": "25514926" - }, - { - "dataUrl": 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