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 6c176941..1c6b3bab 100644
--- a/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json
+++ b/normalizer/src/main/resources/org/biopax/paxtools/normalizer/registry.json
@@ -1,5 +1,6 @@
{
"3dmet": {
+ "deprecated": true,
"description": "3DMET is a database collecting three-dimensional structures of natural metabolites.",
"example": "B00162",
"homepage": "http://www.3dmet.dna.affrc.go.jp/",
@@ -14,6 +15,7 @@
"biocontext": "3DMET",
"edam": "2635",
"fairsharing": "FAIRsharing.5ab0n7",
+ "integbio": "nbdc00351",
"miriam": "3dmet",
"n2t": "3dmet",
"prefixcommons": "3dmet",
@@ -41,7 +43,6 @@
},
{
"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
@@ -126,6 +127,14 @@
"uri_format": "https://data.4dnucleome.org/experiment-set-replicates/$1"
},
"aaindex": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"description": "Identifier of an entry from the AAindex database.",
"example": "BUNA790102",
"homepage": "http://www.genome.ad.jp/aaindex/",
@@ -134,6 +143,7 @@
],
"mappings": {
"edam": "1128",
+ "integbio": "nbdc00004",
"prefixcommons": "aaindex"
},
"name": "AAindex",
@@ -156,6 +166,9 @@
"year": 2007
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -167,7 +180,6 @@
"aao": {
"contact": {
"email": "david.c.blackburn@gmail.com",
- "github": null,
"name": "David Blackburn",
"orcid": "0000-0002-1810-9886"
},
@@ -181,6 +193,7 @@
"ontology"
],
"mappings": {
+ "agroportal": "AAO",
"biocontext": "AAO",
"fairsharing": "FAIRsharing.mxx5rp",
"obofoundry": "aao",
@@ -208,7 +221,6 @@
},
{
"doi": "10.1142/9789812772435_0035",
- "pmc": null,
"pubmed": "17992749",
"title": "An anatomical ontology for amphibians",
"year": 2007
@@ -224,11 +236,25 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"description": "Vendor for assays, cells, and antibodies",
"example": "ab275461",
"homepage": "https://www.abcam.com",
+ "mappings": {
+ "cellosaurus": "Abcam"
+ },
"name": "Abcam",
"preferred_prefix": "abcam",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "https://www.abcam.com/$1.html"
},
"abcd": {
@@ -238,6 +264,14 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"description": "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies",
"example": "AD834",
"homepage": "https://web.expasy.org/abcd/",
@@ -261,6 +295,9 @@
"year": 2020
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "https://web.expasy.org/abcd/ABCD_$1"
},
"abm": {
@@ -272,7 +309,7 @@
"orcid": "0000-0001-9439-5346"
}
],
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "T0599",
"homepage": "https://www.abmgood.com/Cell-Biology.html",
"mappings": {
@@ -285,7 +322,6 @@
"abs": {
"contact": {
"email": "enrique.blanco@crg.eu",
- "github": null,
"name": "Enrique Blanco",
"orcid": "0000-0001-6261-7370"
},
@@ -304,6 +340,7 @@
"fairsharing": "FAIRsharing.7mnebr",
"miriam": "abs",
"n2t": "abs",
+ "pathguide": "217",
"prefixcommons": "abs"
},
"name": "Annotated Regulatory Binding Sites",
@@ -336,6 +373,14 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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",
@@ -345,6 +390,9 @@
],
"name": "Activity Streams",
"preferred_prefix": "ac",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "http://www.w3.org/ns/activitystreams#$1"
},
"aceview.worm": {
@@ -425,7 +473,7 @@
"uri_format": "https://purl.dataone.org/odo/ADCAD_$1"
},
"addexbio": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "C0020004/4992",
"homepage": "https://www.addexbio.com/productshow?id=4",
"mappings": {
@@ -440,15 +488,22 @@
"example": "50943",
"homepage": "http://addgene.org/",
"keywords": [
+ "bio.tools",
+ "faseb list",
"life science",
- "plasmid"
+ "molecular biology",
+ "plasmid",
+ "repository",
+ "sequence alignment"
],
"mappings": {
"fairsharing": "FAIRsharing.8hcczk",
+ "integbio": "nbdc00356",
"miriam": "addgene",
"n2t": "addgene",
"prefixcommons": "addgene",
- "re3data": "r3d100010741"
+ "re3data": "r3d100010741",
+ "rrid": "Addgene"
},
"name": "Addgene Plasmid Repository",
"pattern": "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$",
@@ -472,14 +527,12 @@
},
{
"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
@@ -492,8 +545,7 @@
"contact": {
"email": "bert.van.nuffelen@tenforce.com",
"github": "bertvannuffelen",
- "name": "Bert Van Nuffelen",
- "orcid": null
+ "name": "Bert Van Nuffelen"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -504,7 +556,13 @@
"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",
+ "keywords": [
+ "metadata"
+ ],
"license": "CC-BY-4.0",
+ "mappings": {
+ "lov": "adms"
+ },
"name": "Asset Description Metadata Schema Vocabulary",
"preferred_prefix": "adms",
"repository": "https://github.com/SEMICeu/ADMS/",
@@ -517,6 +575,14 @@
"name": "Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"depends_on": [
"bfo"
],
@@ -525,6 +591,7 @@
"example": "0000001",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"keywords": [
+ "alzheimer's disease",
"health science",
"obo",
"ontology"
@@ -544,24 +611,32 @@
"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
}
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/ADO_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"uri_format": "http://purl.obolibrary.org/obo/ADO_$1",
- "version": "2022-06-11"
+ "version": "2023-09-20"
},
"adw": {
"contact": {
"email": "adw_geeks@umich.edu",
- "github": null,
- "name": "Animal Diversity Web technical staff",
- "orcid": null
+ "name": "Animal Diversity Web technical staff"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"deprecated": true,
"description": "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology.",
"download_owl": "http://aber-owl.net/media/ontologies/ADW/2/adw.owl",
@@ -571,10 +646,12 @@
"anatomy",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "taxonomic classification"
],
"mappings": {
"aberowl": "ADW",
+ "agroportal": "ADW",
"biocontext": "ADW",
"bioportal": "ADW",
"fairsharing": "FAIRsharing.t9fvdn",
@@ -586,6 +663,9 @@
"pattern": "^[A-Z_a-z]+$",
"preferred_prefix": "ADW",
"rdf_uri_format": "http://purl.obolibrary.org/obo/ADW_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "https://animaldiversity.org/accounts/$1"
},
"aeo": {
@@ -594,10 +674,16 @@
],
"contact": {
"email": "J.Bard@ed.ac.uk",
- "github": null,
- "name": "Jonathan Bard",
- "orcid": null
+ "name": "Jonathan Bard"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"deprecated": true,
"description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology",
"download_obo": "http://purl.obolibrary.org/obo/aeo.obo",
@@ -634,6 +720,9 @@
}
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/AEO_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"repository": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
"synonyms": [
"AEO_RETIRED"
@@ -678,17 +767,25 @@
"aero": {
"contact": {
"email": "mcourtot@gmail.com",
- "github": null,
"name": "Melanie Courtot",
"orcid": "0000-0002-9551-6370"
},
+ "contributor_extras": [
+ {
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"deprecated": true,
"description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events",
"download_owl": "http://purl.obolibrary.org/obo/aero.owl",
"example": "0000125",
"homepage": "http://purl.obolibrary.org/obo/aero",
"keywords": [
+ "adverse reaction",
"biomedical science",
+ "electronic health record",
"health science",
"medicine",
"obo",
@@ -708,6 +805,9 @@
"pattern": "^\\d{7}$",
"preferred_prefix": "AERO",
"rdf_uri_format": "http://purl.obolibrary.org/obo/AERO_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "http://purl.obolibrary.org/obo/AERO_$1"
},
"affy.probeset": {
@@ -717,7 +817,8 @@
"mappings": {
"biocontext": "AFFY.PROBESET",
"miriam": "affy.probeset",
- "n2t": "affy.probeset"
+ "n2t": "affy.probeset",
+ "togoid": "AffyProbeset"
},
"name": "Affymetrix Probeset",
"pattern": "^\\d{4,}((_[asx])?_at)$",
@@ -736,18 +837,17 @@
"afo": {
"contact": {
"email": "more.info@allotrope.org",
- "github": null,
- "name": "Allotrope Foundation",
- "orcid": null
+ "name": "Allotrope Foundation"
},
"description": "Allotrope Merged Ontology Suite",
- "download_owl": "http://purl.allotrope.org/voc/afo/merged/REC/2023/03/merged-without-qudt-and-inferred",
+ "download_owl": "http://purl.allotrope.org/voc/afo/merged/REC/2024/03/merged-without-qudt-and-inferred",
"homepage": "https://www.allotrope.org/",
"keywords": [
"agricultural engineering",
"agriculture",
"biology",
"environmental science",
+ "food",
"food chemistry",
"forest management",
"ontology",
@@ -763,9 +863,58 @@
"name": "Allotrope Merged Ontology Suite",
"no_own_terms": true,
"preferred_prefix": "afo",
- "version": "2023/03"
+ "version": "2024/03"
+ },
+ "afpo": {
+ "contact": {
+ "email": "mcmelek@msn.com",
+ "github": "Melek-C",
+ "name": "Melek Chaouch",
+ "orcid": "0000-0001-5868-4204"
+ },
+ "description": "AfPO is a tool which enables to annotate the African individuals, and brings together knowledge accumulated about existing populations with their genetic fingerprint in a standardized format.",
+ "download_json": "http://purl.obolibrary.org/obo/afpo.json",
+ "download_obo": "http://purl.obolibrary.org/obo/afpo.obo",
+ "download_owl": "http://purl.obolibrary.org/obo/afpo.owl",
+ "example": "0000440",
+ "homepage": "https://github.com/h3abionet/afpo",
+ "keywords": [
+ "obo",
+ "ontology"
+ ],
+ "license": "CC-BY-4.0",
+ "mappings": {
+ "obofoundry": "afpo"
+ },
+ "name": "African Population Ontology",
+ "preferred_prefix": "AfPO",
+ "rdf_uri_format": "http://purl.obolibrary.org/obo/AfPO_$1",
+ "repository": "https://github.com/h3abionet/afpo",
+ "uri_format": "http://purl.obolibrary.org/obo/AfPO_$1"
+ },
+ "aftol.category": {
+ "contact": {
+ "email": "davem@umn.edu",
+ "name": "David J. McLaughlin"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Categories in the AFTOL database",
+ "example": "229",
+ "homepage": "https://aftol.umn.edu",
+ "name": "Assembling the Fungal Tree of Life - Category",
+ "preferred_prefix": "aftol.category",
+ "uri_format": "https://aftol.umn.edu/glossary?category=$1"
},
"aftol.taxonomy": {
+ "contact": {
+ "email": "davem@umn.edu",
+ "name": "David J. McLaughlin"
+ },
"contributor_extras": [
{
"email": "laylamichan@ciencias.unam.mx",
@@ -820,6 +969,12 @@
"github": "cmungall",
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
+ },
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
}
],
"description": "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century.",
@@ -844,6 +999,9 @@
"year": 2020
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"synonyms": [
"AGR",
"AGRICOLA_ID"
@@ -858,7 +1016,6 @@
"orcid": "0000-0002-6601-2165"
},
"contributor": {
- "email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
@@ -891,6 +1048,14 @@
"name": "Marie-Angélique Laporte",
"orcid": "0000-0002-8461-9745"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"depends_on": [
"bfo",
"envo",
@@ -915,6 +1080,7 @@
"keywords": [
"agriculture",
"agronomy",
+ "cropping systems",
"farming systems research",
"obo",
"ontology",
@@ -935,6 +1101,9 @@
"pattern": "^\\d{8}$",
"preferred_prefix": "AGRO",
"rdf_uri_format": "http://purl.obolibrary.org/obo/AGRO_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"repository": "https://github.com/AgriculturalSemantics/agro",
"uri_format": "http://purl.obolibrary.org/obo/AGRO_$1",
"version": "2022-11-02"
@@ -943,9 +1112,7 @@
"banana": "c_",
"contact": {
"email": "agrovoc@fao.org",
- "github": null,
- "name": "AGROVOC Team",
- "orcid": null
+ "name": "AGROVOC Team"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -962,8 +1129,10 @@
"data management",
"environmental science",
"fisheries science",
+ "food",
"forest management",
- "nutritional science"
+ "nutritional science",
+ "thesaurus"
],
"mappings": {
"agroportal": "AGROVOC",
@@ -976,38 +1145,18 @@
"pattern": "^[a-z0-9]+$",
"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,
- "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
}
@@ -1021,7 +1170,39 @@
"twitter": "FAOAIMS",
"uri_format": "http://aims.fao.org/aos/agrovoc/c_$1"
},
+ "agsc": {
+ "description": "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]",
+ "example": "100E",
+ "homepage": "https://ambystoma.uky.edu/genetic-stock-center/",
+ "keywords": [
+ "adult",
+ "ambystoma",
+ "embryo",
+ "k-12 teacher",
+ "larvae",
+ "salamander"
+ ],
+ "mappings": {
+ "rrid": "AGSC"
+ },
+ "name": "Ambystoma Genetic Stock Center",
+ "preferred_prefix": "agsc",
+ "publications": [
+ {
+ "pubmed": "16359543"
+ }
+ ],
+ "uri_format": "https://scicrunch.org/resolver/RRID:AGSC_$1"
+ },
"agsd": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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",
@@ -1046,6 +1227,9 @@
"uri_format": "http://bio2rdf.org/agsd:$1"
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -1076,7 +1260,12 @@
"homepage": "https://github.com/berkeleybop/artificial-intelligence-ontology",
"keywords": [
"artificial intelligence",
- "bioinformatics",
+ "computational biology",
+ "hidden markov model",
+ "knowledge representation",
+ "machine learning",
+ "natural language processing",
+ "network model",
"ontology"
],
"mappings": {
@@ -1086,6 +1275,13 @@
},
"name": "The Artificial Intelligence Ontology",
"preferred_prefix": "aio",
+ "publications": [
+ {
+ "doi": "10.48550/arxiv.2404.03044",
+ "title": "The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies",
+ "year": 2024
+ }
+ ],
"repository": "https://github.com/berkeleybop",
"reviewer": {
"email": "benjamin_gyori@hms.harvard.edu",
@@ -1106,6 +1302,14 @@
"name": "Jennifer C. Girón",
"orcid": "0000-0002-0851-6883"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"depends_on": [
"bfo",
"bspo",
@@ -1136,12 +1340,23 @@
"pattern": "^\\d{7}$",
"preferred_prefix": "AISM",
"rdf_uri_format": "http://purl.obolibrary.org/obo/AISM_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"repository": "https://github.com/insect-morphology/aism",
"uri_format": "http://purl.obolibrary.org/obo/AISM_$1",
- "version": "2023-04-14"
+ "version": "2024-03-16"
},
"alfred": {
"comment": "This resource doesn't exist on the web anymore",
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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",
@@ -1173,6 +1388,9 @@
"year": 2003
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -1182,6 +1400,14 @@
"uri_format": "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"
},
"allergome": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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/",
@@ -1195,6 +1421,7 @@
"mappings": {
"biocontext": "ALLERGOME",
"fairsharing": "FAIRsharing.w6cxgb",
+ "integbio": "nbdc01708",
"miriam": "allergome",
"n2t": "allergome",
"prefixcommons": "allergome",
@@ -1215,26 +1442,25 @@
"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
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"
},
"alzforum.mutation": {
@@ -1244,6 +1470,14 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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",
@@ -1254,6 +1488,9 @@
],
"name": "Alzforum Mutations",
"preferred_prefix": "alzforum.mutation",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"synonyms": [
"Alzforum_mut"
],
@@ -1283,7 +1520,6 @@
"publications": [
{
"doi": "10.1038/ng1934",
- "pmc": null,
"pubmed": "17192785",
"title": "Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database",
"year": 2007
@@ -1298,6 +1534,14 @@
"uri_format": "http://www.alzgene.org/geneoverview.asp?geneid=$1"
},
"amoebadb": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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/",
@@ -1309,6 +1553,7 @@
"mappings": {
"biocontext": "AMOEBADB",
"fairsharing": "FAIRsharing.swbypy",
+ "integbio": "nbdc01207",
"miriam": "amoebadb",
"n2t": "amoebadb",
"prefixcommons": "amoebadb",
@@ -1335,6 +1580,9 @@
"year": 2009
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"twitter": "eupathdb",
"uri_format": "https://amoebadb.org/amoeba/app/record/gene/$1"
},
@@ -1345,6 +1593,14 @@
"name": "Hector Escriva",
"orcid": "0000-0001-7577-5028"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"depends_on": [
"uberon"
],
@@ -1369,22 +1625,42 @@
"pattern": "^\\d+$",
"preferred_prefix": "AMPHX",
"rdf_uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"repository": "https://github.com/EBISPOT/amphx_ontology",
"uri_format": "http://purl.obolibrary.org/obo/AMPHX_$1",
"version": "2020-12-18"
},
"antibodyregistry": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"description": "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.",
"example": "493771",
"homepage": "http://antibodyregistry.org/",
+ "keywords": [
+ "antibody",
+ "reagent",
+ "unique identifiers"
+ ],
"mappings": {
"biocontext": "ANTIBODYREGISTRY",
"miriam": "antibodyregistry",
- "n2t": "antibodyregistry"
+ "n2t": "antibodyregistry",
+ "rrid": "AB"
},
"name": "Antibody Registry",
"pattern": "^\\d{6}$",
"preferred_prefix": "antibodyregistry",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "http://antibodyregistry.org/AB_$1"
},
"antweb": {
@@ -1399,6 +1675,7 @@
"mappings": {
"biocontext": "ANTWEB",
"fairsharing": "FAIRsharing.yk38tw",
+ "integbio": "nbdc01710",
"miriam": "antweb",
"n2t": "antweb",
"ncbi": "AntWeb",
@@ -1420,7 +1697,6 @@
"publications": [
{
"doi": "10.1038/424242b",
- "pmc": null,
"pubmed": "12867945",
"title": "Ants join online colony to boost conservation efforts",
"year": 2003
@@ -1435,6 +1711,14 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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",
@@ -1450,12 +1734,23 @@
"uri_format": "https://anzctr.org.au/ACTRN$1.aspx"
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"synonyms": [
"ACTRN"
],
"uri_format": "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1"
},
"aop": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"description": "International repository of Adverse Outcome Pathways.",
"example": "98",
"homepage": "https://aopwiki.org/",
@@ -1467,6 +1762,9 @@
"name": "AOPWiki",
"pattern": "^\\d+$",
"preferred_prefix": "aop",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "https://aopwiki.org/aops/$1"
},
"aop.events": {
@@ -1514,15 +1812,23 @@
"apaonto": {
"contact": {
"email": "awalker@apa.org",
- "github": null,
"name": "Alvin Walker",
"orcid": "0000-0003-1082-8760"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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": [
+ "behavior",
"ontology",
"psychology"
],
@@ -1534,11 +1840,17 @@
"name": "Psychology Ontology",
"preferred_prefix": "apaonto",
"references": [
- "https://github.com/biopragmatics/bioregistry/issues/528"
+ "https://github.com/biopragmatics/bioregistry/issues/528",
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
],
"uri_format": "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"
},
"apd": {
+ "contact": {
+ "email": "gwang@unmc.edu",
+ "name": "Guangshun Wang",
+ "orcid": "0000-0002-4841-7927"
+ },
"description": "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides.",
"example": "01001",
"homepage": "http://aps.unmc.edu/AP/",
@@ -1628,6 +1940,14 @@
"uri_format": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"
},
"apid.interactions": {
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"description": "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.",
"example": "P01116",
"homepage": "http://cicblade.dep.usal.es:8080/APID/",
@@ -1640,6 +1960,9 @@
"pattern": "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$",
"preferred_prefix": "apid.interactions",
"provides": "uniprot",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"uri_format": "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"
},
"apo": {
@@ -1649,6 +1972,14 @@
"name": "Stacia R Engel",
"orcid": "0000-0001-5472-917X"
},
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "sumirp",
+ "name": "Sumir H Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
"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",
@@ -1656,9 +1987,14 @@
"homepage": "http://www.yeastgenome.org/",
"keywords": [
"cell biology",
+ "life cycle stage",
"life science",
+ "morphology",
+ "mutation",
"obo",
- "ontology"
+ "ontology",
+ "phenotype",
+ "study design"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -1683,17 +2019,20 @@
}
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/APO_$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1098"
+ ],
"repository": "https://github.com/obophenotype/ascomycete-phenotype-ontology",
"twitter": "yeastgenome",
- "uri_format": "https://www.yeastgenome.org/observable/APO:$1",
- "version": "2023-04-27"
+ "uri_format": "http://purl.obolibrary.org/obo/APO_$1",
+ "version": "2024-04-26"
},
"apollosv": {
"appears_in": [
"scdo"
],
"contact": {
- "email": "hoganwr@ufl.edu",
+ "email": "hoganwr@gmail.com",
"github": "hoganwr",
"name": "William Hogan",
"orcid": "0000-0002-9881-1017"
@@ -1706,8 +2045,10 @@
"biomedical science",
"ecology",
"epidemiology",
+ "infection",
"obo",
"ontology",
+ "pathogen",
"population genetics"
],
"license": "CC-BY-4.0",
@@ -1740,7 +2081,6 @@
"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",
@@ -1750,7 +2090,7 @@
"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": "2023-06-02"
+ "version": "2024-04-19"
},
"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.",
@@ -1765,6 +2105,7 @@
"biocontext": "ARACHNOSERVER",
"edam": "2578",
"fairsharing": "FAIRsharing.c54ywe",
+ "integbio": "nbdc01221",
"miriam": "arachnoserver",
"n2t": "arachnoserver",
"prefixcommons": "arachnoserver",
@@ -1786,7 +2127,6 @@
"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
@@ -1806,8 +2146,10 @@
"example": "AT5G05330",
"homepage": "https://www.araport.org/",
"mappings": {
+ "integbio": "nbdc02433",
"miriam": "tair.name",
"ncbi": "Araport",
+ "pathguide": "768",
"uniprot": "DB-0221"
},
"name": "Arabidopsis Information Portal",
@@ -1827,7 +2169,6 @@
"archdb": {
"contact": {
"email": "narcis.fernandez@gmail.com",
- "github": null,
"name": "Narcis Fernandez-Fuentes",
"orcid": "0000-0002-6421-1080"
},
@@ -1841,6 +2182,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.tp9z4q",
+ "integbio": "nbdc01795",
"prefixcommons": "archdb"
},
"name": "ArchDB",
@@ -1918,9 +2260,12 @@
"example": "/53355/cl010066723",
"homepage": "https://arks.org",
"keywords": [
+ "centrally registered identifier",
"data management",
+ "data retrieval",
"subject agnostic"
],
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaThDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--c69281eac0647c6b7a664f0932bee0d5fd27781d/gold_boat_arka.png?disposition=inline",
"mappings": {
"biocontext": "ARK",
"fairsharing": "FAIRsharing.f928f1",
@@ -1996,6 +2341,7 @@
"biocontext": "ARRAYEXPRESS",
"cellosaurus": "ArrayExpress",
"fairsharing": "FAIRsharing.6k0kwd",
+ "integbio": "nbdc00009",
"miriam": "arrayexpress",
"n2t": "arrayexpress",
"prefixcommons": "arrayexpress",
@@ -2124,9 +2470,12 @@
"example": "0807.4956v1",
"homepage": "https://arxiv.org/",
"keywords": [
- "bibliography"
+ "bibliography",
+ "preprints",
+ "publishing"
],
"mappings": {
+ "bartoc": "20434",
"biocontext": "ARXIV",
"miriam": "arxiv",
"n2t": "arxiv",
@@ -2232,8 +2581,6 @@
"publications": [
{
"doi": "10.5334/jors.bv",
- "pmc": null,
- "pubmed": null,
"title": "Looking before Leaping: Creating a Software Registry",
"year": 2015
}
@@ -2362,7 +2709,6 @@
"publications": [
{
"doi": "10.1016/j.ygeno.2008.11.003",
- "pmc": null,
"pubmed": "19059335",
"title": "ASTD: The Alternative Splicing and Transcript Diversity database",
"year": 2008
@@ -2379,18 +2725,20 @@
"atc": {
"contact": {
"email": "whocc@fhi.no",
- "github": null,
- "name": "WHO Collaborating Centre for Drug Statistics Methodology",
- "orcid": null
+ "name": "WHO Collaborating Centre for Drug Statistics Methodology"
},
"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": [
+ "anatomical therapeutic chemical code",
+ "approved drug",
"biomedical science",
"chemical",
"chemical biology",
+ "drug",
"ontology",
+ "pharmacological family classification",
"pharmacology"
],
"mappings": {
@@ -2404,6 +2752,7 @@
"miriam": "atc",
"n2t": "atc",
"prefixcommons": "atc",
+ "togoid": "Atc",
"wikidata": "P267"
},
"name": "Anatomical Therapeutic Chemical Classification System",
@@ -2420,15 +2769,12 @@
],
"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
@@ -2504,7 +2850,6 @@
"ato": {
"contact": {
"email": "david.c.blackburn@gmail.com",
- "github": null,
"name": "David Blackburn",
"orcid": "0000-0002-1810-9886"
},
@@ -2516,6 +2861,7 @@
"keywords": [
"obo",
"ontology",
+ "taxonomic classification",
"taxonomy"
],
"mappings": {
@@ -2534,7 +2880,6 @@
"atol": {
"contact": {
"email": "pylebail@rennes.inra.fr",
- "github": null,
"name": "Pierre-Yves LeBail",
"orcid": "0000-0002-8310-5195"
},
@@ -2546,7 +2891,9 @@
"agriculture",
"animal husbandry",
"life science",
- "ontology"
+ "livestock",
+ "ontology",
+ "phenotype"
],
"mappings": {
"aberowl": "ATOL",
@@ -2575,6 +2922,18 @@
"preferred_prefix": "autdb",
"uri_format": "http://autism.mindspec.org/GeneDetail/$1"
},
+ "authorea.author": {
+ "description": "identifier for an author on the Authorea writing service",
+ "example": "229233",
+ "homepage": "https://www.authorea.com",
+ "mappings": {
+ "wikidata": "P5039"
+ },
+ "name": "Authorea author ID",
+ "pattern": "^[1-9]\\d*$",
+ "preferred_prefix": "authorea.author",
+ "uri_format": "https://www.authorea.com/users/$1"
+ },
"babelon": {
"contact": {
"email": "nicolas.matentzoglu@gmail.com",
@@ -2608,7 +2967,6 @@
"bacdive": {
"contact": {
"email": "contact@bacdive.de",
- "github": null,
"name": "Lorenz Reimer",
"orcid": "0000-0002-7805-0660"
},
@@ -2640,7 +2998,6 @@
},
{
"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
@@ -2757,19 +3114,25 @@
"bao": {
"contact": {
"email": "sschurer@med.miami.edu",
- "github": null,
- "name": "Stephan Schurer",
- "orcid": null
+ "name": "Stephan Schurer"
},
"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": [
+ "assay",
"biochemistry",
+ "biological process",
"biomedical science",
+ "cell",
+ "chemical entity",
"life science",
- "ontology"
+ "molecular entity",
+ "ontology",
+ "protein",
+ "reagent",
+ "target"
],
"mappings": {
"aberowl": "BAO",
@@ -2792,13 +3155,6 @@
"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",
@@ -2815,18 +3171,17 @@
},
{
"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",
+ "repository": "https://github.com/BioAssayOntology/BAO",
"synonyms": [
"BAO"
],
- "uri_format": "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1",
- "version": "2.8.4"
+ "uri_format": "http://www.bioassayontology.org/bao#BAO_$1",
+ "version": "2.8.11"
},
"bartoc": {
"contact": {
@@ -2867,13 +3222,12 @@
{
"name": "Verbundzentrale des GBV",
"partnered": false,
- "ror": "048vdhs48",
- "wikidata": null
+ "ror": "048vdhs48"
}
],
"pattern": "^[1-9][0-9]*$",
"preferred_prefix": "bartoc",
- "rdf_uri_format": "https://bartoc.org/en/node/$1",
+ "rdf_uri_format": "http://bartoc.org/en/node/$1",
"references": [
"https://github.com/biopragmatics/bioregistry/issues/783"
],
@@ -2904,6 +3258,47 @@
"preferred_prefix": "bbtp",
"uri_format": "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"
},
+ "bcbc": {
+ "description": "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]",
+ "example": "4623",
+ "homepage": "http://www.betacell.org/",
+ "keywords": [
+ "adenovirus",
+ "antibody",
+ "basic research",
+ "basic science",
+ "beta cell",
+ "cell line",
+ "cell regeneration",
+ "cell replacement",
+ "cell reprogramming",
+ "data set",
+ "data sharing",
+ "embryonic stem cell",
+ "embryonic stem cell line",
+ "functional genomics",
+ "gene",
+ "gene expression",
+ "genomics",
+ "mouse",
+ "mouse embryonic stem cell line",
+ "mouse strain",
+ "pancreas",
+ "pancreatic development",
+ "pancreatic islet",
+ "pancreatic islet development",
+ "pancreatic islet function",
+ "protocol"
+ ],
+ "mappings": {
+ "integbio": "nbdc00375",
+ "rrid": "BCBC"
+ },
+ "name": "Beta Cell Biology Consortium",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "bcbc",
+ "uri_format": "https://scicrunch.org/resolver/RRID:BCBC_$1"
+ },
"bcgo": {
"contact": {
"email": "jiezheng@pennmedicine.upenn.edu",
@@ -2941,7 +3336,6 @@
"bcio": {
"contact": {
"email": "srodriguez142857@gmail.com",
- "github": null,
"name": "Sergio José Rodríguez Méndez",
"orcid": "0000-0001-7203-8399"
},
@@ -2961,7 +3355,7 @@
"pattern": "^\\d{6}$",
"preferred_prefix": "bcio",
"uri_format": "https://w3id.org/BCI-ontology#$1",
- "version": "2022-08-24"
+ "version": "2024-03-12"
},
"bco": {
"appears_in": [
@@ -2979,10 +3373,14 @@
"homepage": "https://github.com/BiodiversityOntologies/bco",
"keywords": [
"biodiversity",
+ "biological sample",
+ "biological sample annotation",
"ecology",
+ "environmental material",
"metagenomics",
"obo",
"ontology",
+ "taxonomic classification",
"taxonomy"
],
"license": "CC0-1.0",
@@ -3021,7 +3419,7 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "60316",
"homepage": "https://catalog.bcrc.firdi.org.tw",
"keywords": [
@@ -3036,7 +3434,7 @@
"uri_format": "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"
},
"bcrj": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "0278",
"homepage": "https://bcrj.org.br/pesquisa/",
"mappings": {
@@ -3117,9 +3515,35 @@
"description": "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research.",
"example": "33607",
"homepage": "https://bdsc.indiana.edu/about/mission.html",
+ "keywords": [
+ "database",
+ "deficiency",
+ "deletion",
+ "disease model",
+ "duplication",
+ "faseb list",
+ "fly",
+ "gene",
+ "genetic",
+ "genetic analysis",
+ "genetic construct",
+ "germline",
+ "human disease model",
+ "insertion",
+ "invertebrate",
+ "mutation",
+ "protein trap",
+ "scientist",
+ "sequenced strain",
+ "somatic",
+ "stock",
+ "transposon",
+ "transposon insertion"
+ ],
"mappings": {
"miriam": "bdsc",
- "n2t": "bdsc"
+ "n2t": "bdsc",
+ "rrid": "BDSC"
},
"name": "Bloomington Drosophila Stock Center",
"pattern": "^\\d+$",
@@ -3138,6 +3562,7 @@
"mappings": {
"biocontext": "BEETLEBASE",
"fairsharing": "FAIRsharing.h5f091",
+ "integbio": "nbdc01820",
"miriam": "beetlebase",
"n2t": "beetlebase",
"ncbi": "BEETLEBASE",
@@ -3187,8 +3612,6 @@
"publications": [
{
"doi": "10.1135/cccc20081261",
- "pmc": null,
- "pubmed": null,
"title": "Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples",
"year": 2008
}
@@ -3202,7 +3625,7 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "MRA-253",
"homepage": "https://www.beiresources.org",
"keywords": [
@@ -3222,7 +3645,6 @@
"comment": "INDRA uses bel as a catch-all for scomp/sfam",
"contact": {
"email": "support@bel.bio",
- "github": null,
"name": "William Hayes",
"orcid": "0000-0003-0728-781X"
},
@@ -3264,6 +3686,7 @@
"pco",
"psdo",
"rbo",
+ "uberon",
"xpo",
"zp"
],
@@ -3279,6 +3702,7 @@
"example": "0000001",
"homepage": "http://ifomis.org/bfo/",
"keywords": [
+ "data retrieval",
"obo",
"ontology",
"subject agnostic"
@@ -3305,6 +3729,14 @@
"version": "2019-08-26"
},
"bgee.family": {
+ "contributor_extras": [
+ {
+ "github": "smoretti",
+ "name": "Sébastien Moretti",
+ "orcid": "0000-0003-3947-488X"
+ }
+ ],
+ "deprecated": true,
"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 expression across species.",
"example": "ENSFM00500000270089",
"homepage": "http://bgee.unil.ch/bgee/bgee",
@@ -3316,6 +3748,9 @@
"name": "Bgee family",
"pattern": "^(ENSFM|ENSGTV:)\\d+$",
"preferred_prefix": "bgee.family",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/889"
+ ],
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"
},
"bgee.gene": {
@@ -3363,6 +3798,14 @@
"uri_format": "https://www.bgee.org/gene/$1"
},
"bgee.organ": {
+ "contributor_extras": [
+ {
+ "github": "smoretti",
+ "name": "Sébastien Moretti",
+ "orcid": "0000-0003-3947-488X"
+ }
+ ],
+ "deprecated": true,
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures.",
"example": "EHDAA:2185",
"homepage": "http://bgee.unil.ch/bgee/bgee",
@@ -3374,9 +3817,20 @@
"name": "Bgee organ",
"pattern": "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$",
"preferred_prefix": "bgee.organ",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/889"
+ ],
"uri_format": "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"
},
"bgee.stage": {
+ "contributor_extras": [
+ {
+ "github": "smoretti",
+ "name": "Sébastien Moretti",
+ "orcid": "0000-0003-3947-488X"
+ }
+ ],
+ "deprecated": true,
"description": "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages.",
"example": "HsapDO:0000004",
"homepage": "http://bgee.unil.ch/bgee/bgee",
@@ -3388,14 +3842,16 @@
"name": "Bgee stage",
"pattern": "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$",
"preferred_prefix": "bgee.stage",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/889"
+ ],
"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
+ "name": "Frédérick Giasson"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -3407,8 +3863,13 @@
"example": "authorList",
"homepage": "https://bibliontology.com/",
"keywords": [
- "bibliometrics"
+ "bibliometrics",
+ "catalogs"
],
+ "mappings": {
+ "lov": "bibo",
+ "zazuko": "bibo"
+ },
"name": "The Bibliographic Ontology",
"preferred_prefix": "bibo",
"uri_format": "http://purl.org/ontology/bibo/$1"
@@ -3430,6 +3891,10 @@
"example": "CategorialBibliometricData",
"homepage": "http://www.sparontologies.net/ontologies/bido",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
"subject agnostic"
],
"mappings": {
@@ -3560,6 +4025,7 @@
"mappings": {
"biocontext": "BIND",
"edam": "1129",
+ "pathguide": "1",
"prefixcommons": "bind"
},
"name": "BIND accession number",
@@ -3583,7 +4049,6 @@
},
{
"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
@@ -3594,7 +4059,6 @@
"bindingdb": {
"contact": {
"email": "mgilson@health.ucsd.edu",
- "github": null,
"name": "Michael K. Gilson",
"orcid": "0000-0002-3375-1738"
},
@@ -3615,6 +4079,7 @@
"fairsharing": "FAIRsharing.3b36hk",
"miriam": "bindingdb",
"n2t": "bindingdb",
+ "pathguide": "50",
"prefixcommons": "bindingdb",
"re3data": "r3d100012074",
"uniprot": "DB-0127"
@@ -3699,6 +4164,34 @@
],
"uri_format": "https://www.biocatalogue.org/services/$1"
},
+ "biocompute": {
+ "contact": {
+ "email": "mazumder@gwu.edu",
+ "name": "Raja Mazumder",
+ "orcid": "0000-0001-8823-9945"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "BioCompute is shorthand for the IEEE 2791-2020 standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to facilitate communication. This pipeline documentation approach has been adopted by a few FDA centers. The goal is to ease the communication burdens between research centers, organizations, and industries. This web portal allows users to build a BioCompute Objects through the interface in a human and machine readable format.",
+ "example": "000001",
+ "homepage": "https://biocomputeobject.org",
+ "name": "Biocompute Object",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "biocompute",
+ "publications": [
+ {
+ "pubmed": "27974626",
+ "title": "BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations",
+ "year": 2017
+ }
+ ],
+ "repository": "https://github.com/biocompute-objects/BCO_Specification",
+ "uri_format": "https://biocomputeobject.org/BCO_$1"
+ },
"biocyc": {
"description": "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms.",
"example": "ECOLI:CYT-D-UBIOX-CPLX",
@@ -3712,8 +4205,10 @@
"biocontext": "BIOCYC",
"edam": "2104",
"go": "BioCyc",
+ "integbio": "nbdc00252",
"miriam": "biocyc",
"n2t": "biocyc",
+ "pathguide": "8",
"prefixcommons": "biocyc",
"uniprot": "DB-0005"
},
@@ -3730,6 +4225,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/bib/bbx085",
+ "pubmed": "29447345"
+ },
{
"doi": "10.1093/nar/gkv1164",
"pmc": "PMC4702838",
@@ -3794,7 +4293,6 @@
"biogrid": {
"contact": {
"email": "md.tyers@umontreal.ca",
- "github": null,
"name": "Mike Tyers",
"orcid": "0000-0002-9713-9994"
},
@@ -3818,6 +4316,7 @@
"fairsharing": "FAIRsharing.9d5f5r",
"miriam": "biogrid",
"n2t": "biogrid",
+ "pathguide": "7",
"prefixcommons": "biogrid",
"re3data": "r3d100010350",
"uniprot": "DB-0184"
@@ -3878,7 +4377,6 @@
"biogrid.interaction": {
"contact": {
"email": "md.tyers@umontreal.ca",
- "github": null,
"name": "Mike Tyers",
"orcid": "0000-0002-9713-9994"
},
@@ -3943,7 +4441,7 @@
"orcid": "0000-0002-6601-2165"
},
"description": "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.",
- "download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/52/biolink.owl",
+ "download_owl": "http://aber-owl.net/media/ontologies/BIOLINK/60/biolink.owl",
"example": "Gene",
"homepage": "https://biolink.github.io/biolink-model/",
"keywords": [
@@ -4078,8 +4576,11 @@
"example": "0000057",
"homepage": "https://github.com/SED-ML/KiSAO",
"keywords": [
+ "algorithm",
"bioinformatics",
"computer science",
+ "kinetic model",
+ "modeling and simulation",
"obo",
"ontology"
],
@@ -4131,7 +4632,7 @@
"biomodels.kisao",
"kisao"
],
- "uri_format": "https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_$1",
+ "uri_format": "http://purl.obolibrary.org/obo/KISAO_$1",
"version": "2.30"
},
"biomodels.teddy": {
@@ -4139,15 +4640,14 @@
"banana_peel": "_",
"contact": {
"email": "biomodels-net-support@lists.sf.net",
- "github": null,
- "name": "BioModels.net team",
- "orcid": null
+ "name": "BioModels.net team"
},
"description": "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.",
"download_owl": "http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl",
"example": "0000066",
"homepage": "http://teddyontology.sourceforge.net/",
"keywords": [
+ "modeling and simulation",
"neurophysiology",
"ontology",
"synthetic biology",
@@ -4264,7 +4764,6 @@
"bioportal": {
"contact": {
"email": "support@bioontology.org",
- "github": null,
"name": "John Graybeal",
"orcid": "0000-0001-6875-5360"
},
@@ -4284,6 +4783,7 @@
"mappings": {
"biocontext": "BIOPORTAL",
"fairsharing": "FAIRsharing.4m97ah",
+ "integbio": "nbdc02144",
"miriam": "bioportal",
"n2t": "bioportal",
"prefixcommons": "bioportal",
@@ -4324,8 +4824,7 @@
"bioproject": {
"description": "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories.",
"example": "PRJDB3",
- "has_canonical": "ena.embl",
- "homepage": "http://trace.ddbj.nig.ac.jp/bioproject/",
+ "homepage": "https://www.ncbi.nlm.nih.gov/bioproject",
"keywords": [
"life science"
],
@@ -4334,25 +4833,19 @@
"fairsharing": "FAIRsharing.aqhv1y",
"miriam": "bioproject",
"n2t": "bioproject",
- "re3data": "r3d100013330"
+ "re3data": "r3d100013330",
+ "togoid": "Bioproject"
},
"name": "BioProject",
"pattern": "^PRJ[DEN][A-Z]\\d+$",
"preferred_prefix": "bioproject",
"providers": [
{
- "code": "ebi",
- "description": "BioProject at European Nucleotide Archive (ENA)",
- "homepage": "https://www.ebi.ac.uk/ena/",
- "name": "BioProject at European Nucleotide Archive (ENA)",
- "uri_format": "https://www.ebi.ac.uk/ena/browser/view/$1"
- },
- {
- "code": "ncbi",
- "description": "BioProject at NCBI",
- "homepage": "https://www.ncbi.nlm.nih.gov/bioproject",
- "name": "BioProject at NCBI",
- "uri_format": "https://www.ncbi.nlm.nih.gov/bioproject?term=$1"
+ "code": "CURATOR_REVIEW",
+ "description": "BioProject at DNA Data Bank of Japan",
+ "homepage": "http://trace.ddbj.nig.ac.jp/bioproject/",
+ "name": "BioProject at DNA Data Bank of Japan",
+ "uri_format": "http://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=$1"
}
],
"publications": [
@@ -4400,8 +4893,6 @@
"publications": [
{
"doi": "10.1101/2022.07.08.499378",
- "pmc": null,
- "pubmed": null,
"title": "Unifying the Identification of Biomedical Entities with the Bioregistry",
"year": 2022
}
@@ -4527,7 +5018,14 @@
"example": "SAMEA2397676",
"homepage": "https://www.ebi.ac.uk/biosamples/",
"keywords": [
- "biology"
+ "biology",
+ "biomaterial",
+ "cell",
+ "cell line",
+ "dna",
+ "gold standard",
+ "rna",
+ "stem cell"
],
"mappings": {
"biocontext": "BIOSAMPLE",
@@ -4535,7 +5033,9 @@
"fairsharing": "FAIRsharing.qr6pqk",
"miriam": "biosample",
"n2t": "biosample",
- "re3data": "r3d100012828"
+ "re3data": "r3d100012828",
+ "rrid": "SAMN",
+ "togoid": "Biosample"
},
"name": "BioSample",
"pattern": "^SAM[NED](\\w)?\\d+$",
@@ -4608,7 +5108,6 @@
"biosimulators": {
"contact": {
"email": "karr@mssm.edu",
- "github": null,
"name": "Jonathan Karr",
"orcid": "0000-0002-2605-5080"
},
@@ -4640,6 +5139,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.mtjvme",
+ "integbio": "nbdc02279",
"miriam": "biostudies",
"n2t": "biostudies",
"re3data": "r3d100012627"
@@ -4678,6 +5178,7 @@
"mappings": {
"biocontext": "BIOSYSTEMS",
"fairsharing": "FAIRsharing.w2eeqr",
+ "integbio": "nbdc00379",
"miriam": "biosystems",
"n2t": "biosystems",
"prefixcommons": "biosystems",
@@ -4766,9 +5267,7 @@
"comment": "Part of the NeuroLex namespace now",
"contact": {
"email": "wbug@ncmir.ucsd.edu",
- "github": null,
- "name": "William Bug",
- "orcid": null
+ "name": "William Bug"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -4783,7 +5282,9 @@
"keywords": [
"anatomy",
"biomedical science",
- "ontology"
+ "disease",
+ "ontology",
+ "study design"
],
"mappings": {
"aberowl": "BIRNLEX",
@@ -4812,10 +5313,16 @@
"example": "BibliographicRecord",
"homepage": "http://www.sparontologies.net/ontologies/biro",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
+ "spar",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.99da5f"
+ "fairsharing": "FAIRsharing.99da5f",
+ "lov": "biro"
},
"name": "Bibliographic Reference Ontology",
"preferred_prefix": "BiRO",
@@ -4916,6 +5423,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.p06nme",
+ "integbio": "nbdc00380",
"miriam": "bmrb",
"re3data": "r3d100010191",
"uniprot": "DB-0256"
@@ -5002,9 +5510,7 @@
"bootstrep": {
"contact": {
"email": "vlee@ebi.ac.uk",
- "github": null,
- "name": "Vivian Lee",
- "orcid": null
+ "name": "Vivian Lee"
},
"deprecated": true,
"homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html",
@@ -5042,6 +5548,11 @@
"uri_format": "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"
},
"brenda": {
+ "contact": {
+ "email": "D.Schomburg@tu-braunschweig.de",
+ "name": "Dietmar Schomburg",
+ "orcid": "0000-0002-3354-822X"
+ },
"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/",
@@ -5055,6 +5566,7 @@
"go": "BRENDA",
"miriam": "brenda",
"n2t": "brenda",
+ "pathguide": "51",
"prefixcommons": "brenda",
"re3data": "r3d100010616"
},
@@ -5074,7 +5586,6 @@
"publications": [
{
"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
@@ -5123,14 +5634,12 @@
},
{
"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
@@ -5144,24 +5653,15 @@
},
{
"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
+ "title": "The BRENDA enzyme information system-From a database to an expert system."
},
{
"doi": "10.1016/S1096-7176(03)00008-9",
- "pmc": null,
- "pubmed": null,
- "title": "Review of the BRENDA Database.",
- "year": null
+ "title": "Review of the BRENDA Database."
},
{
"doi": "10.1016/S0968-0004(01)02027-8",
- "pmc": null,
- "pubmed": null,
- "title": "BRENDA: a resource for enzyme data and metabolic information.",
- "year": null
+ "title": "BRENDA: a resource for enzyme data and metabolic information."
}
],
"uri_format": "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"
@@ -5263,6 +5763,7 @@
"colao",
"fovt",
"lepao",
+ "uberon",
"zp"
],
"contact": {
@@ -5325,10 +5826,14 @@
"example": "0000590",
"homepage": "http://www.brenda-enzymes.org",
"keywords": [
+ "cell",
+ "enzyme",
"enzymology",
"life science",
"obo",
"ontology",
+ "organ",
+ "reaction data",
"tissue"
],
"license": "CC-BY-4.0",
@@ -5409,7 +5914,7 @@
"synonyms": [
"BTO"
],
- "uri_format": "https://www.brenda-enzymes.org/ontology.php?ontology_id=3&id_go=$1",
+ "uri_format": "http://purl.obolibrary.org/obo/BTO_$1",
"version": "2021-10-26"
},
"bugbase.expt": {
@@ -5473,7 +5978,6 @@
"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",
"year": 1997
@@ -5487,14 +5991,12 @@
},
{
"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",
"year": 2009
},
{
"doi": "10.1093/bioinformatics/btn462",
- "pmc": null,
"pubmed": "18772155",
"title": "Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature",
"year": 2008
@@ -5519,10 +6021,16 @@
"example": "InTextReferencePointer",
"homepage": "http://www.sparontologies.net/ontologies/c4o",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
+ "spar",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.beb855"
+ "fairsharing": "FAIRsharing.beb855",
+ "lov": "c4o"
},
"name": "Citation Counting and Context Characterisation Ontology",
"preferred_prefix": "C4O",
@@ -5533,7 +6041,6 @@
"cabri": {
"contact": {
"email": "paolo.romano@hsanmartino.it",
- "github": null,
"name": "Paolo Romano",
"orcid": "0000-0003-4694-3883"
},
@@ -5578,7 +6085,6 @@
},
{
"doi": "10.2165/00822942-200594030-00002",
- "pmc": null,
"pubmed": "16231959",
"title": "The role of informatics in the coordinated management of biological resources collections",
"year": 2005
@@ -5646,7 +6152,6 @@
"cameo": {
"contact": {
"email": "torsten.schwede@unibas.ch",
- "github": null,
"name": "Torsten Schwede",
"orcid": "0000-0003-2715-335X"
},
@@ -5676,6 +6181,57 @@
],
"uri_format": "https://www.cameo3d.org/sp/targets/target/$1"
},
+ "cao": {
+ "contact": {
+ "email": "williams.antony@epa.gov",
+ "name": "Antony Williams",
+ "orcid": "0000-0002-2668-4821"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)",
+ "download_owl": "https://champ.stuchalk.domains.unf.edu/images/ontology/cao.owl",
+ "example": "000064",
+ "homepage": "https://champ.stuchalk.domains.unf.edu",
+ "keywords": [
+ "amino acid sequence",
+ "annotation",
+ "characterisation data heat",
+ "gene",
+ "genetics",
+ "life science",
+ "ontology",
+ "orthologous",
+ "phylogenetics",
+ "protein",
+ "transcript",
+ "transport and kinetic data"
+ ],
+ "license": "CC-BY-3.0",
+ "mappings": {
+ "aberowl": "CAO",
+ "bioportal": "CAO",
+ "fairsharing": "FAIRsharing.wp0134",
+ "ols": "cao"
+ },
+ "name": "Chemical Analysis Ontology",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "cao",
+ "publications": [
+ {
+ "doi": "10.1126/science.278.5338.631",
+ "pubmed": "9381173",
+ "title": "A genomic perspective on protein families",
+ "year": 1997
+ }
+ ],
+ "uri_format": "http://champ-project.org/images/ontology/cao.owl#CAO_$1",
+ "version": "0.2"
+ },
"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",
@@ -5695,6 +6251,7 @@
"aism",
"colao",
"ehdaa2",
+ "gallont",
"lepao",
"pco"
],
@@ -5712,6 +6269,8 @@
"homepage": "https://github.com/obophenotype/caro/",
"keywords": [
"anatomy",
+ "annotation",
+ "interoperability",
"life science",
"obo",
"ontology"
@@ -5742,8 +6301,6 @@
"publications": [
{
"doi": "10.1007/978-1-84628-885-2_16",
- "pmc": null,
- "pubmed": null,
"title": "CARO – The Common Anatomy Reference Ontology",
"year": 2008
}
@@ -5759,6 +6316,7 @@
"homepage": "https://commonchemistry.cas.org/",
"keywords": [
"chemical",
+ "chemical entity",
"cheminformatics",
"structure"
],
@@ -5879,7 +6437,6 @@
"publications": [
{
"doi": "10.1016/s0969-2126(97)00260-8",
- "pmc": null,
"pubmed": "9309224",
"title": "CATH--a hierarchic classification of protein domain structures",
"year": 1997
@@ -5934,8 +6491,6 @@
"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
@@ -6036,6 +6591,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkab1045",
+ "pubmed": "34850161"
+ },
{
"doi": "10.1093/nar/gkt1178",
"pmc": "PMC3965031",
@@ -6112,16 +6671,39 @@
},
{
"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
+ "title": "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data."
}
],
"repository": "https://github.com/cBioPortal/cbioportal",
"twitter": "cbioportal",
"uri_format": "https://www.cbioportal.org/study/summary?id=$1"
},
+ "cc": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": " The Creative Commons Rights Expression Language (ccREL) lets you describe copyright licenses in RDF. For more information on describing licenses in RDF and attaching those descriptions to digital works, see [ccREL](https://wiki.creativecommons.org/CC_REL) in the [Creative Commons wiki](https://wiki.creativecommons.org/).",
+ "download_rdf": "https://creativecommons.org/schema.rdf",
+ "example": "Work",
+ "homepage": "https://creativecommons.org/ns",
+ "keywords": [
+ "metadata"
+ ],
+ "license": "CC0-1.0",
+ "mappings": {
+ "aberowl": "CC",
+ "lov": "cc",
+ "zazuko": "cc"
+ },
+ "name": "Creative Commons Rights Expression Language",
+ "pattern": "^\\w+$",
+ "preferred_prefix": "cc",
+ "twitter": "cc_opensource",
+ "uri_format": "https://creativecommons.org/ns#$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",
@@ -6146,9 +6728,11 @@
"mappings": {
"biocontext": "CCDS",
"fairsharing": "FAIRsharing.46s4nt",
+ "integbio": "nbdc00023",
"miriam": "ccds",
"n2t": "ccds",
"prefixcommons": "ccds",
+ "togoid": "Ccds",
"uniprot": "DB-0187"
},
"name": "Consensus CDS",
@@ -6164,6 +6748,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkx1031",
+ "pubmed": "29126148"
+ },
{
"doi": "10.1101/gr.080531.108",
"pmc": "PMC2704439",
@@ -6188,7 +6776,7 @@
"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",
+ "download_owl": "http://purl.org/ccf/releases/2.3.0/ccf.owl",
"example": "extraction_set",
"github_request_issue": 879,
"homepage": "https://bioportal.bioontology.org/ontologies/CCF",
@@ -6214,7 +6802,7 @@
"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"
+ "version": "2.3.0"
},
"ccle": {
"contributor": {
@@ -6226,6 +6814,7 @@
"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",
+ "license": "ODbL-1.0",
"mappings": {
"cellosaurus": "CCLE"
},
@@ -6250,16 +6839,19 @@
"example": "0000003",
"homepage": "http://www.semantic-systems-biology.org/apo",
"keywords": [
+ "cell",
"cell cycle",
"functional genomics",
"genomics",
"life science",
+ "molecular function",
"obo",
"ontology",
"proteomics"
],
"mappings": {
"aberowl": "CCO",
+ "bartoc": "20461",
"biocontext": "CCO",
"bioportal": "CCO",
"fairsharing": "FAIRsharing.xhwrnr",
@@ -6316,13 +6908,14 @@
"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.",
+ "description": "a formalization of concepts and relations relevant to evolutionary comparative analysis",
"download_owl": "http://purl.obolibrary.org/obo/cdao.owl",
"example": "0000072",
"homepage": "https://github.com/evoinfo/cdao",
"keywords": [
"bioinformatics",
"biomedical science",
+ "evolution",
"evolutionary biology",
"life science",
"molecular biology",
@@ -6357,7 +6950,7 @@
"rdf_uri_format": "http://purl.obolibrary.org/obo/CDAO_$1",
"repository": "https://github.com/evoinfo/cdao",
"uri_format": "http://purl.obolibrary.org/obo/CDAO_$1",
- "version": "2022-11-30"
+ "version": "2024-01-25"
},
"cdd": {
"description": "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.",
@@ -6374,6 +6967,7 @@
"edam": "2666",
"fairsharing": "FAIRsharing.ea287c",
"go": "CDD",
+ "integbio": "nbdc00401",
"miriam": "cdd",
"n2t": "cdd",
"ncbi": "CDD",
@@ -6394,6 +6988,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkac1096",
+ "pubmed": "36477806"
+ },
{
"doi": "10.1093/nar/gku1221",
"pmc": "PMC4383992",
@@ -6413,7 +7011,7 @@
},
"cdno": {
"contact": {
- "email": "l.andres.hernandez.18@student.scu.edu.au",
+ "email": "landreshdz@gmail.com",
"github": "LilyAndres",
"name": "Liliana Andres Hernandez",
"orcid": "0000-0002-7696-731X"
@@ -6447,18 +7045,20 @@
"pattern": "^\\d{7}$",
"preferred_prefix": "CDNO",
"publications": [
+ {
+ "doi": "10.3389/fnut.2022.928837",
+ "title": "Establishing a Common Nutritional Vocabulary - From Food Production to Diet"
+ },
{
"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
}
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/CDNO_$1",
- "repository": "https://github.com/Southern-Cross-Plant-Science/cdno",
+ "repository": "https://github.com/CompositionalDietaryNutritionOntology/cdno",
"uri_format": "http://purl.obolibrary.org/obo/CDNO_$1",
- "version": "2022-12-23"
+ "version": "2024-03-29"
},
"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).",
@@ -6500,7 +7100,7 @@
"preferred_prefix": "cdt"
},
"cell_biolabs": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "AKR-270",
"homepage": "https://www.cellbiolabs.com",
"mappings": {
@@ -6601,20 +7201,28 @@
"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://github.com/calipho-sib/cellosaurus/raw/master/cellosaurus.obo",
+ "download_obo": "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo",
"example": "0440",
"homepage": "https://cellosaurus.org",
"keywords": [
+ "cell lines",
+ "controlled vocabularies",
"life science",
- "ontology"
+ "ontologies",
+ "ontology",
+ "thesaurus"
],
+ "license": "CC-BY-4.0",
"mappings": {
"biocontext": "CELLOSAURUS",
"cellosaurus": "Cellosaurus",
"fairsharing": "FAIRsharing.hkk309",
+ "integbio": "nbdc02180",
"miriam": "cellosaurus",
"n2t": "cellosaurus",
"re3data": "r3d100013293",
+ "rrid": "CVCL",
+ "togoid": "Cellosaurus",
"wikidata": "P3289"
},
"mastodon": "cellosaurus@fediscience.org",
@@ -6640,7 +7248,6 @@
"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
@@ -6682,14 +7289,14 @@
"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/",
+ "homepage": "https://www.cellrepo.com/",
"mappings": {
"miriam": "cellrepo"
},
"name": "Cell Version Control Repository",
"pattern": "^[0-9]+$",
"preferred_prefix": "cellrepo",
- "uri_format": "https://cellrepo.ico2s.org/repositories/$1"
+ "uri_format": "https://www.cellrepo.com/repositories/$1"
},
"cemo": {
"contact": {
@@ -6751,6 +7358,7 @@
"keywords": [
"anatomy",
"fisheries science",
+ "life cycle",
"obo",
"ontology",
"zoology"
@@ -6787,6 +7395,7 @@
"biocontext": "CGD",
"fairsharing": "FAIRsharing.j7j53",
"go": "CGD",
+ "integbio": "nbdc00391",
"miriam": "cgd",
"n2t": "cgd",
"ncbi": "CGD",
@@ -6918,17 +7527,13 @@
"publications": [
{
"doi": "10.1016/s0076-6879(06)21001-2",
- "pmc": null,
"pubmed": "17352909",
"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
+ "title": "Strain collections and genetic nomenclature."
}
],
"uri_format": "http://cgsc.biology.yale.edu/Site.php?ID=$1"
@@ -6977,14 +7582,19 @@
"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",
+ "example": "138488",
"homepage": "http://www.ebi.ac.uk/chebi",
"keywords": [
"biochemistry",
"chemical",
"chemistry",
+ "molecular entity",
+ "molecular structure",
+ "natural product",
"obo",
- "ontology"
+ "ontology",
+ "small molecule",
+ "taxonomic classification"
],
"license": "CC-BY-4.0",
"logo": "https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png",
@@ -6998,6 +7608,7 @@
"edam": "1174",
"fairsharing": "FAIRsharing.62qk8w",
"go": "CHEBI",
+ "integbio": "nbdc00027",
"miriam": "chebi",
"n2t": "chebi",
"obofoundry": "chebi",
@@ -7005,6 +7616,7 @@
"ontobee": "CHEBI",
"prefixcommons": "chebi",
"re3data": "r3d100012626",
+ "togoid": "Chebi",
"wikidata": "P683"
},
"name": "Chemical Entities of Biological Interest",
@@ -7022,6 +7634,7 @@
{
"code": "chebi-img",
"description": "Image server from chebi",
+ "first_party": true,
"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"
@@ -7051,7 +7664,6 @@
},
{
"doi": "10.1002/0471250953.bi1409s26",
- "pmc": null,
"pubmed": "19496059",
"title": "ChEBI: an open bioinformatics and cheminformatics resource",
"year": 2009
@@ -7072,8 +7684,8 @@
"ChEBI"
],
"twitter": "chebit",
- "uri_format": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1",
- "version": "222"
+ "uri_format": "http://purl.obolibrary.org/obo/CHEBI_$1",
+ "version": "233"
},
"chembank": {
"comment": "This resource doesn't exist on the web anymore",
@@ -7135,10 +7747,11 @@
"medicinal chemistry",
"molecules"
],
- "license": "CC-BY-4.0",
+ "license": "CC-BY-SA-3.0",
"mappings": {
"cheminf": "000412",
"fairsharing": "FAIRsharing.m3jtpg",
+ "integbio": "nbdc02555",
"miriam": "chembl",
"prefixcommons": "chembl",
"re3data": "r3d100010539",
@@ -7215,6 +7828,7 @@
"bioactivities",
"cell lines"
],
+ "license": "CC-BY-SA-3.0",
"mappings": {
"cellosaurus": "ChEMBL-Cells"
},
@@ -7237,12 +7851,13 @@
"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",
+ "license": "CC-BY-SA-3.0",
"mappings": {
"biocontext": "CHEMBL.COMPOUND",
"edam": "2646",
"miriam": "chembl.compound",
"n2t": "chembl.compound",
+ "togoid": "ChemblCompound",
"wikidata": "P592"
},
"name": "ChEMBL",
@@ -7278,12 +7893,13 @@
"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",
+ "license": "CC-BY-SA-3.0",
"mappings": {
"biocontext": "CHEMBL.TARGET",
"cellosaurus": "ChEMBL-Targets",
"miriam": "chembl.target",
- "n2t": "chembl.target"
+ "n2t": "chembl.target",
+ "togoid": "ChemblTarget"
},
"name": "ChEMBL target",
"part_of": "chembl",
@@ -7344,14 +7960,12 @@
"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
@@ -7373,6 +7987,7 @@
"biocontext": "CHEMIDPLUS",
"edam": "2658",
"fairsharing": "FAIRsharing.5949vn",
+ "integbio": "nbdc01837",
"miriam": "chemidplus",
"n2t": "chemidplus",
"prefixcommons": "chemidplus"
@@ -7392,17 +8007,13 @@
"publications": [
{
"doi": "10.1300/j115v21n01_04",
- "pmc": null,
"pubmed": "11989279",
"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
+ "title": "ChemIDplus-super source for chemical and drug information."
}
],
"synonyms": [
@@ -7414,13 +8025,14 @@
"appears_in": [
"proco"
],
+ "banana": "CHEMINF",
"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.",
+ "description": "The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.",
"download_owl": "https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl",
"example": "000410",
"homepage": "https://github.com/semanticchemistry/semanticchemistry",
@@ -7428,6 +8040,8 @@
"biochemistry",
"chemistry",
"life science",
+ "molecular entity",
+ "molecular structure",
"obo",
"ontology"
],
@@ -7437,11 +8051,13 @@
"biocontext": "CHEMINF",
"bioportal": "CHEMINF",
"fairsharing": "FAIRsharing.sjhvyy",
+ "miriam": "cheminf",
"obofoundry": "cheminf",
"ols": "cheminf",
"ontobee": "CHEMINF"
},
"name": "Chemical Information Ontology",
+ "namespace_in_lui": true,
"pattern": "^\\d{6}$",
"preferred_prefix": "CHEMINF",
"providers": [
@@ -7464,8 +8080,8 @@
],
"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"
+ "uri_format": "http://purl.obolibrary.org/obo/CHEMINF_$1",
+ "version": "2.1.0"
},
"chemrof": {
"contact": {
@@ -7481,7 +8097,7 @@
"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",
+ "download_owl": "http://aber-owl.net/media/ontologies/CHEMROF/4/chemrof.owl",
"example": "FullySpecifiedAtom",
"homepage": "https://chemkg.github.io/chemrof/",
"keywords": [
@@ -7498,7 +8114,6 @@
"chemspider": {
"contact": {
"email": "pencehe@oneonta.edu",
- "github": null,
"name": "Harry E. Pence",
"orcid": "0000-0002-0412-9018"
},
@@ -7516,6 +8131,7 @@
"cheminf": "000405",
"edam": "1173",
"fairsharing": "FAIRsharing.96f3gm",
+ "integbio": "nbdc01863",
"miriam": "chemspider",
"n2t": "chemspider",
"prefixcommons": "chemspider",
@@ -7537,8 +8153,6 @@
"publications": [
{
"doi": "10.1021/ed100697w",
- "pmc": null,
- "pubmed": null,
"title": "ChemSpider: An Online Chemical Information Resource",
"year": 2010
}
@@ -7636,8 +8250,6 @@
"publications": [
{
"doi": "10.26434/chemrxiv.12591221",
- "pmc": null,
- "pubmed": null,
"title": "Extension of Roles in the ChEBI Ontology",
"year": 2020
}
@@ -7664,13 +8276,18 @@
"example": "0002902",
"homepage": "https://github.com/rsc-ontologies/rsc-cmo",
"keywords": [
+ "assay",
"chemistry",
+ "chromatography",
+ "electron microscopy",
+ "mass spectrometry assay",
"obo",
"ontology"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "CHMO",
+ "bartoc": "20509",
"biocontext": "CHMO",
"bioportal": "CHMO",
"fairsharing": "FAIRsharing.9j4wh2",
@@ -7699,9 +8316,14 @@
"homepage": "https://github.com/cido-ontology/cido",
"keywords": [
"bioinformatics",
+ "covid-19",
+ "disease",
+ "drug",
"drug discovery",
+ "drug interaction",
"drug repositioning",
"epidemiology",
+ "infection",
"obo",
"ontology",
"virology"
@@ -7737,7 +8359,7 @@
"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"
+ "version": "2024-02-16"
},
"cio": {
"contact": {
@@ -7752,6 +8374,7 @@
"example": "0000040",
"homepage": "https://github.com/BgeeDB/confidence-information-ontology",
"keywords": [
+ "annotation",
"biology",
"obo",
"ontology"
@@ -7786,7 +8409,6 @@
"citexplore": {
"contact": {
"email": "maria.taboada@usc.es",
- "github": null,
"name": "Maria Taboada",
"orcid": "0000-0002-2353-596X"
},
@@ -7801,7 +8423,11 @@
"homepage": "https://www.ebi.ac.uk/citexplore/",
"keywords": [
"biomedical science",
+ "brain",
+ "disease",
"genetics",
+ "lipid",
+ "phenotype",
"preclinical studies"
],
"mappings": {
@@ -7822,17 +8448,9 @@
"publications": [
{
"doi": "10.1097/mol.0b013e328362df13",
- "pmc": null,
"pubmed": "23759795",
"title": "Cerebrotendinous xanthomatosis",
"year": 2013
- },
- {
- "doi": "10.1097/MOL.0b013e328362df13",
- "pmc": null,
- "pubmed": "23759795",
- "title": "Cerebrotendinous xanthomatosis",
- "year": null
}
],
"references": [
@@ -7860,18 +8478,20 @@
"example": "sharesAuthorInstitutionWith",
"homepage": "http://www.sparontologies.net/ontologies/cito",
"keywords": [
- "knowledge and information systems"
+ "citation",
+ "data model",
+ "knowledge and information systems",
+ "spar"
],
"mappings": {
- "fairsharing": "FAIRsharing.b220d4"
+ "fairsharing": "FAIRsharing.b220d4",
+ "lov": "cito"
},
"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
}
@@ -7881,9 +8501,16 @@
"uri_format": "http://purl.org/spar/cito/$1"
},
"civic.aid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC.",
"example": "3",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.aid"
},
@@ -7891,12 +8518,22 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.aid",
+ "synonyms": [
+ "civic.assertion"
+ ],
"uri_format": "https://civicdb.org/links/assertions/$1"
},
"civic.did": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement.",
"example": "46",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.did"
},
@@ -7904,12 +8541,22 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.did",
+ "synonyms": [
+ "civic.disease"
+ ],
"uri_format": "https://civicdb.org/links/diseases/$1"
},
"civic.eid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract).",
"example": "1199",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.eid"
},
@@ -7917,12 +8564,22 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.eid",
+ "synonyms": [
+ "civic.evidence"
+ ],
"uri_format": "https://civicdb.org/links/evidence/$1"
},
"civic.gid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis",
"example": "272",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.gid",
"wikidata": "P11277"
@@ -7931,24 +8588,44 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.gid",
+ "synonyms": [
+ "civic.gene"
+ ],
"uri_format": "https://civicdb.org/links/gene/$1"
},
"civic.mpid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC.",
"example": "559",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.mpid"
},
"name": "CIViC Molecular Profile",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.mpid",
+ "synonyms": [
+ "civic.molecularprofile"
+ ],
"uri_format": "https://civicdb.org/links/molecular_profile/$1"
},
"civic.sid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source.",
"example": "62",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.sid"
},
@@ -7956,12 +8633,22 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.sid",
+ "synonyms": [
+ "civic.source"
+ ],
"uri_format": "https://civicdb.org/links/sources/$1"
},
"civic.tid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant.",
"example": "14",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.tid"
},
@@ -7969,24 +8656,44 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.tid",
+ "synonyms": [
+ "civic.therapy"
+ ],
"uri_format": "https://civicdb.org/links/drugs/$1"
},
"civic.vgid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance",
"example": "16",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.vgid"
},
"name": "CIViC Variant Group",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.vgid",
+ "synonyms": [
+ "civic.variantgroup"
+ ],
"uri_format": "https://civicdb.org/links/variant_group/$1"
},
"civic.vid": {
+ "contact": {
+ "email": "mgriffit@wustl.edu",
+ "github": "malachig",
+ "name": "Malachi Griffith",
+ "orcid": "0000-0002-6388-446X"
+ },
"description": "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making.",
"example": "12",
"homepage": "https://civicdb.org/",
+ "license": "CC0-1.0",
"mappings": {
"miriam": "civic.vid",
"wikidata": "P3329"
@@ -7995,6 +8702,9 @@
"part_of": "civic",
"pattern": "^[0-9]+$",
"preferred_prefix": "civic.vid",
+ "synonyms": [
+ "civic.variant"
+ ],
"uri_format": "https://civicdb.org/links/variant/$1"
},
"cl": {
@@ -8015,6 +8725,13 @@
"name": "Alexander Diehl",
"orcid": "0000-0001-9990-8331"
},
+ "contributor_extras": [
+ {
+ "github": "anitacaron",
+ "name": "Anita Caron",
+ "orcid": "0000-0002-6523-4866"
+ }
+ ],
"depends_on": [
"chebi",
"go",
@@ -8031,9 +8748,11 @@
"homepage": "https://obophenotype.github.io/cell-ontology/",
"keywords": [
"anatomy",
+ "annotation",
"cell",
"cell biology",
"life science",
+ "morphology",
"obo",
"ontology"
],
@@ -8067,6 +8786,13 @@
"name": "Bio2RDF",
"uri_format": "http://bio2rdf.org/cl:$1"
},
+ {
+ "code": "cellguide",
+ "description": "CellGuide is a comprehensive resource for knowledge about cell types.",
+ "homepage": "https://cellxgene.cziscience.com/cellguide",
+ "name": "Cell Guide",
+ "uri_format": "https://cellxgene.cziscience.com/cellguide/CL_$1"
+ },
{
"code": "cellxgene",
"description": "Explore single cell data through the CZ CELLxGENE portal",
@@ -8094,8 +8820,8 @@
"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?iri=http://purl.obolibrary.org/obo/$1",
- "version": "2023-06-22"
+ "uri_format": "http://purl.obolibrary.org/obo/CL_$1",
+ "version": "2024-04-05"
},
"clao": {
"contact": {
@@ -8192,7 +8918,6 @@
},
"contributor_extras": [
{
- "email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
@@ -8278,9 +9003,11 @@
"cellosaurus": "ClinVar",
"fairsharing": "FAIRsharing.wx5r6f",
"hl7": "2.16.840.1.113883.6.319",
+ "integbio": "nbdc01514",
"miriam": "clinvar",
"n2t": "clinvar",
"re3data": "r3d100013331",
+ "togoid": "Clinvar",
"wikidata": "P1929"
},
"name": "ClinVar Variation",
@@ -8347,10 +9074,10 @@
"mco"
],
"contact": {
- "email": "siiraa@umich.edu",
- "github": "siiraa",
- "name": "Sirarat Sarntivijai",
- "orcid": "0000-0002-2548-641X"
+ "email": "zhengj2007@gmail.com",
+ "github": "zhengj2007",
+ "name": "Jie Zheng",
+ "orcid": "0000-0002-2999-0103"
},
"depends_on": [
"cl",
@@ -8361,10 +9088,13 @@
"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",
+ "homepage": "https://github.com/CLO-Ontology/CLO",
"keywords": [
+ "cell",
"cell biology",
+ "cell line",
"life science",
+ "morphology",
"obo",
"ontology"
],
@@ -8422,19 +9152,19 @@
"synonyms": [
"CLO"
],
- "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/clo/terms?short_form=CLO_$1",
+ "uri_format": "http://purl.obolibrary.org/obo/CLO_$1",
"version": "2.1.178"
},
"cls": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "300108/p3934_A-172",
- "homepage": "https://cls.shop/",
+ "homepage": "https://www.cytion.com/",
"mappings": {
"cellosaurus": "CLS"
},
"name": "Cell Lines Service",
"preferred_prefix": "cls",
- "uri_format": "https://cls.shop/$1"
+ "uri_format": "https://www.cytion.com/$1"
},
"clyh": {
"contact": {
@@ -8498,7 +9228,6 @@
"cmf": {
"contact": {
"email": "engelsta@ohsu.edu",
- "github": null,
"name": "Mark Engelstad",
"orcid": "0000-0001-5889-4463"
},
@@ -8537,9 +9266,13 @@
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"keywords": [
"biomedical science",
+ "disease",
+ "electronic health record",
"life science",
+ "model organism",
"obo",
"ontology",
+ "phenotype",
"preclinical studies"
],
"license": "CC0-1.0",
@@ -8576,12 +9309,11 @@
"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"
+ "version": "2.209"
},
"cmpo": {
"contact": {
"email": "jupp@ebi.ac.uk",
- "github": null,
"name": "Simon Jupp",
"orcid": "0000-0002-0643-3144"
},
@@ -8590,8 +9322,12 @@
"example": "0000435",
"homepage": "http://www.ebi.ac.uk/cmpo",
"keywords": [
+ "cell",
"cell biology",
- "ontology"
+ "cellular component",
+ "microscopy",
+ "ontology",
+ "phenotype"
],
"mappings": {
"aberowl": "CMPO",
@@ -8638,19 +9374,19 @@
"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",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8669,18 +9405,17 @@
"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",
+ "food",
"life science",
- "ontology"
+ "phenotype"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8708,19 +9443,18 @@
"co_322": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8739,18 +9473,16 @@
"co_323": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Ramesh Verna",
- "orcid": null
+ "name": "Ramesh Verna"
},
"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"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8769,18 +9501,16 @@
"co_324": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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"
+ "food",
+ "phenotype"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8799,18 +9529,18 @@
"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",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8827,15 +9557,16 @@
"version": "2019-10-09"
},
"co_326": {
+ "contact": {
+ "email": "helpdesk@cropontology-curationtool.org",
+ "name": "Stephanie Bocs Sidibe"
+ },
"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": {
+ "agroportal": "CO_326",
"cropoct": "CO_326",
"ols": "co_326"
},
@@ -8848,18 +9579,16 @@
"co_327": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8877,19 +9606,17 @@
"co_330": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8908,19 +9635,17 @@
"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"
+ "food",
+ "life science"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8938,20 +9663,19 @@
"co_333": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017.",
- "download_owl": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology/owl",
"example": "3000045",
"homepage": "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology",
"keywords": [
"agriculture",
"botany",
+ "food",
"life science",
- "ontology",
- "plant breeding"
+ "phenotype",
+ "plant breeding",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -8969,19 +9693,18 @@
"co_334": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016",
- "download_owl": "https://cropontology.org/ontology/CO_334/Cassava/owl",
"example": "0000070",
"homepage": "https://cropontology.org/ontology/CO_334/Cassava",
"keywords": [
"agriculture",
"botany",
+ "food",
"nutritional science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9000,18 +9723,15 @@
"co_335": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "CIAT Common bean trait dictionary - version August 2014",
- "download_owl": "http://www.cropontology.org/ontology/CO_335/Common%20Bean/owl",
"example": "0000189",
"homepage": "http://www.cropontology.org/ontology/CO_335/Common%20Bean",
"keywords": [
"agriculture",
"botany",
- "ontology"
+ "food"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9029,18 +9749,18 @@
"co_336": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Soybean Trait Dictionary in template v5 - IITA - July 2015",
- "download_owl": "https://cropontology.org/ontology/CO_336/Soybean/owl",
"example": "0000339",
"homepage": "https://cropontology.org/ontology/CO_336/Soybean",
"keywords": [
"agriculture",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9058,19 +9778,19 @@
"co_337": {
"contact": {
"email": "tm.shah@cgiar.org",
- "github": null,
"name": "Trushar Shah",
"orcid": "0000-0002-0091-7981"
},
"description": "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015",
- "download_owl": "https://cropontology.org/ontology/CO_337/Groundnut/owl",
"example": "0000054",
"homepage": "https://cropontology.org/ontology/CO_337/Groundnut",
"keywords": [
"agriculture",
"botany",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9089,18 +9809,18 @@
"co_338": {
"contact": {
"email": "tm.shah@cgiar.org",
- "github": null,
"name": "Trushar Shah",
"orcid": "0000-0002-0091-7981"
},
"description": "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015",
- "download_owl": "https://cropontology.org/ontology/CO_338/Chickpea/owl",
"example": "0000138",
"homepage": "https://cropontology.org/ontology/CO_338/Chickpea",
"keywords": [
"agriculture",
"botany",
- "ontology"
+ "food",
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9119,19 +9839,18 @@
"co_339": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "Lentil Trait Dictionary in template v5 - ICARDA - July 2015",
- "download_owl": "https://cropontology.org/ontology/CO_339/Lentil/owl",
"example": "0000032",
"homepage": "https://cropontology.org/ontology/CO_339/Lentil",
"keywords": [
"agriculture",
"botany",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9150,18 +9869,17 @@
"co_340": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "Cowpea Trait Dictionary in template v5 - IITA - August 2015",
- "download_owl": "https://cropontology.org/ontology/CO_340/Cowpea/owl",
"example": "0000639",
"homepage": "https://cropontology.org/ontology/CO_340/Cowpea",
"keywords": [
"agriculture",
"botany",
- "ontology"
+ "food",
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9189,19 +9907,19 @@
"co_341": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
"name": "Elizabeth Arnaud",
"orcid": "0000-0002-6020-5919"
},
"description": "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015",
- "download_owl": "https://cropontology.org/ontology/CO_341/Pigeonpea/owl",
"example": "0000140",
"homepage": "https://cropontology.org/ontology/CO_341/Pigeonpea",
"keywords": [
"agriculture",
"botany",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9220,19 +9938,18 @@
"co_343": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "version 2019 - pvs",
- "download_owl": "https://cropontology.org/ontology/CO_343/Yam/owl",
"example": "0100010",
"homepage": "https://cropontology.org/ontology/CO_343/Yam",
"keywords": [
"agriculture",
"botany",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9251,19 +9968,17 @@
"co_345": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "Brachiaria (forages) ontology TD v5 - Version Oct 2016",
- "download_owl": "https://cropontology.org/ontology/CO_345/Brachiaria/owl",
"example": "0000127",
"homepage": "https://cropontology.org/ontology/CO_345/Brachiaria",
"keywords": [
"agriculture",
"botany",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9282,18 +9997,17 @@
"co_346": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "oct 2016",
- "download_owl": "https://cropontology.org/ontology/CO_346/Mungbean/owl",
"example": "0000199",
"homepage": "https://cropontology.org/ontology/CO_346/Mungbean",
"keywords": [
"agriculture",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9312,19 +10026,18 @@
"co_347": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "March 2017 version ",
- "download_owl": "http://www.cropontology.org/ontology/CO_347/Castor%20bean/owl",
"example": "0000108",
"homepage": "http://www.cropontology.org/ontology/CO_347/Castor%20bean",
"keywords": [
"agriculture",
"botany",
+ "food",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9342,19 +10055,17 @@
"co_348": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "helpdesk cropontology",
- "orcid": null
+ "name": "helpdesk cropontology"
},
"description": "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France).",
- "download_owl": "https://cropontology.org/ontology/CO_348/Brassica/owl",
"example": "1100107",
"homepage": "https://cropontology.org/ontology/CO_348/Brassica",
"keywords": [
"agriculture",
"botany",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9373,19 +10084,18 @@
"co_350": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
"name": "Jean-Luc Jannink",
"orcid": "0000-0003-4849-628X"
},
"description": "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo",
- "download_owl": "https://cropontology.org/ontology/CO_350/Oat/owl",
"example": "0000215",
"homepage": "https://cropontology.org/ontology/CO_350/Oat",
"keywords": [
"agriculture",
"botany",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9404,19 +10114,17 @@
"co_356": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"description": "Grape Ontology including OIV and bioversity descriptors. INRA July 2017",
- "download_owl": "https://cropontology.org/ontology/CO_356/Vitis/owl",
"example": "4000027",
"homepage": "https://cropontology.org/ontology/CO_356/Vitis",
"keywords": [
"agriculture",
"botany",
"life science",
- "ontology"
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9435,18 +10143,16 @@
"co_357": {
"contact": {
"email": "celia.michotey@inrae.fr",
- "github": null,
"name": "Célia Michotey",
"orcid": "0000-0003-1877-1703"
},
"description": "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). 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"
+ "phenotype"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9464,17 +10170,11 @@
"co_358": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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",
@@ -9491,17 +10191,11 @@
"co_359": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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",
@@ -9517,18 +10211,17 @@
"co_360": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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"
+ "marine environment",
+ "phenotype",
+ "plant phenotypes and traits"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -9546,17 +10239,11 @@
"co_365": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "ICARDA Ethiopia",
- "orcid": null
+ "name": "ICARDA Ethiopia"
},
"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",
@@ -9573,17 +10260,11 @@
"co_366": {
"contact": {
"email": "helpdesk@cropontology-curationtool.org",
- "github": null,
- "name": "Crop Ontology Helpdesk",
- "orcid": null
+ "name": "Crop Ontology Helpdesk"
},
"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",
@@ -9597,14 +10278,19 @@
"uri_format": "https://cropontology.org/rdf/CO_366:$1"
},
"co_367": {
- "description": "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021",
+ "contact": {
+ "email": "helpdesk@cropontology-curationtool.org",
+ "name": "Crop Ontology Helpdesk"
+ },
+ "description": "Quinoa Ontology database of the Crop Ontology (CO_367) of the Generation Challenge Program (GCP) describe traits variables of Quinoa Germinate Database http://germinate.quinoadb.org. Quinoa Phenotyping Consortium Creation Date 23.05.2021",
"example": "0000004",
- "homepage": "https://cropontology.org/term/CO_367:ROOT",
+ "homepage": "http://cropontology.org/term/CO_367:ROOT",
"license": "CC-BY-4.0",
"mappings": {
+ "agroportal": "CO_367",
"cropoct": "CO_367"
},
- "name": "Quinoa Ontology ontology",
+ "name": "Quinoa Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "CO_367",
"repository": "https://github.com/bioversity/Crop-Ontology",
@@ -9613,13 +10299,12 @@
"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",
+ "homepage": "http://cropontology.org/term/CO_370:ROOT",
"license": "CC-BY-4.0",
"mappings": {
"agroportal": "CO_370",
@@ -9660,7 +10345,7 @@
"rdf_uri_format": "http://purl.obolibrary.org/obo/COB_$1",
"repository": "https://github.com/OBOFoundry/COB",
"uri_format": "http://purl.obolibrary.org/obo/COB_$1",
- "version": "2023-05-12"
+ "version": "2023-11-16"
},
"coconut": {
"comment": "@mSorok is the dev of the resource, hope I got it right!",
@@ -9715,7 +10400,6 @@
"cog": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
- "github": null,
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
@@ -9737,7 +10421,9 @@
"biolink": "COG",
"fairsharing": "FAIRsharing.djsbw2",
"go": "COG_Cluster",
- "prefixcommons": "cog"
+ "miriam": "cog",
+ "prefixcommons": "cog",
+ "togoid": "Cog"
},
"name": "Cluster of orthologous genes",
"pattern": "^COG\\d+$",
@@ -9754,7 +10440,6 @@
"publications": [
{
"doi": "10.1126/science.278.5338.631",
- "pmc": null,
"pubmed": "9381173",
"title": "A genomic perspective on protein families",
"year": 1997
@@ -9775,7 +10460,6 @@
"cog.category": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
- "github": null,
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
@@ -9799,7 +10483,6 @@
"cog.pathway": {
"contact": {
"email": "cogs@ncbi.nlm.nih.gov",
- "github": null,
"name": "Michael Y Galperin",
"orcid": "0000-0002-2265-5572"
},
@@ -9927,7 +10610,7 @@
"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": "2023-04-08"
+ "version": "2024-02-14"
},
"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.",
@@ -10040,9 +10723,16 @@
"uri_format": "http://www.ontologyrepository.com/CommonCoreOntologies/$1"
},
"complexportal": {
+ "contact": {
+ "email": "bmeldal@ebi.ac.uk",
+ "github": "bmeldal-eg",
+ "name": "Birgit Meldal",
+ "orcid": "0000-0003-4062-6158"
+ },
"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",
+ "license": "CC0-1.0",
"mappings": {
"biocontext": "COMPLEXPORTAL",
"biolink": "ComplexPortal",
@@ -10190,7 +10880,6 @@
"conoserver": {
"contact": {
"email": "d.craik@imb.uq.edu.au",
- "github": null,
"name": "David Craik",
"orcid": "0000-0003-0007-6796"
},
@@ -10223,28 +10912,24 @@
},
{
"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
@@ -10330,7 +11015,6 @@
"corrdb": {
"contact": {
"email": "zhu@iastate.edu",
- "github": null,
"name": "Zhiliang Hu",
"orcid": "0000-0002-6704-7538"
},
@@ -10356,7 +11040,6 @@
"corum": {
"contact": {
"email": "andreas.ruepp@helmholtz-muenchen.de",
- "github": null,
"name": "Andreas Ruepp",
"orcid": "0000-0003-1705-3515"
},
@@ -10374,6 +11057,7 @@
"go": "CORUM",
"miriam": "corum",
"n2t": "corum",
+ "pathguide": "322",
"prefixcommons": "corum",
"uniprot": "DB-0224"
},
@@ -10472,7 +11156,6 @@
"covid19": {
"contact": {
"email": "dylan.mcgagh@magd.ox.ac.uk",
- "github": null,
"name": "Dylan McGagh",
"orcid": "0000-0002-6772-2775"
},
@@ -10560,19 +11243,15 @@
"cpt": {
"contact": {
"email": "Intellectual.PropertyServices@ama-assn.org",
- "github": null,
- "name": "American Medical Association",
- "orcid": null
+ "name": "American Medical Association"
},
"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"
@@ -10600,14 +11279,12 @@
"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
@@ -10628,10 +11305,40 @@
],
"uri_format": "https://www.aapc.com/codes/cpt-codes/$1"
},
+ "cran": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Repository of packages for the R programming language",
+ "example": "ggplot2",
+ "homepage": "https://cran.r-project.org/",
+ "mappings": {
+ "wikidata": "P5565"
+ },
+ "name": "The Comprehensive R Archive Network",
+ "preferred_prefix": "cran",
+ "uri_format": "https://cran.r-project.org/web/packages/$1"
+ },
+ "crates": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "A repository of software packages written in Rust.",
+ "example": "curies",
+ "homepage": "https://crates.io",
+ "name": "Crates.io",
+ "preferred_prefix": "crates",
+ "uri_format": "https://crates.io/crates/$1"
+ },
"credit": {
"contact": {
"email": "info@casrai.org",
- "github": null,
"name": "Liz Allen",
"orcid": "0000-0002-9298-3168"
},
@@ -10645,9 +11352,14 @@
"example": "Software",
"homepage": "https://casrai.org/credit/",
"keywords": [
+ "citation",
+ "classification",
"data quality",
+ "publication",
+ "resource metadata",
"subject agnostic"
],
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--af4f02374db4f42007e6674ea2055ccaa36aa830/credit-icon-499x500-1.png?disposition=inline",
"mappings": {
"fairsharing": "FAIRsharing.fe4816"
},
@@ -10656,36 +11368,28 @@
"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
+ "year": 2022
},
{
"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
}
@@ -10695,7 +11399,6 @@
"crisprdb": {
"contact": {
"email": "Christine.Pourcel@u-psud.fr",
- "github": null,
"name": "Christine Pourcel",
"orcid": "0000-0002-8951-466X"
},
@@ -10708,6 +11411,7 @@
"mappings": {
"biocontext": "CRISPRDB",
"fairsharing": "FAIRsharing.7sfedh",
+ "integbio": "nbdc02213",
"miriam": "crisprdb",
"n2t": "crisprdb"
},
@@ -10787,7 +11491,6 @@
"cryoem": {
"contact": {
"email": "isanchez@cnb.csic.es",
- "github": null,
"name": "Carlos Oscar S. Sorzano",
"orcid": "0000-0002-9473-283X"
},
@@ -10796,6 +11499,7 @@
"example": "0000052",
"homepage": "http://scipion.i2pc.es/ontology/cryoem",
"keywords": [
+ "electron microscopy",
"ontology",
"structural biology"
],
@@ -10814,7 +11518,6 @@
"cryptodb": {
"contact": {
"email": "jkissing@uga.edu",
- "github": null,
"name": "Jessica Kissinger",
"orcid": "0000-0003-4446-6200"
},
@@ -10830,6 +11533,7 @@
"mappings": {
"biocontext": "CRYPTODB",
"fairsharing": "FAIRsharing.t3nprm",
+ "integbio": "nbdc01780",
"miriam": "cryptodb",
"n2t": "cryptodb",
"prefixcommons": "cryptodb",
@@ -10850,7 +11554,6 @@
"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
@@ -10869,7 +11572,6 @@
"csa": {
"contact": {
"email": "nickf@ebi.ac.uk",
- "github": null,
"name": "Nicholas Furnham",
"orcid": "0000-0002-7532-1269"
},
@@ -10921,7 +11623,6 @@
"csd": {
"contact": {
"email": "support@ccdc.cam.ac.uk",
- "github": null,
"name": "Support Email",
"orcid": "0000-0002-6062-7492"
},
@@ -10952,24 +11653,17 @@
},
{
"doi": "10.1107/s0108768102003890",
- "pmc": null,
"pubmed": "12037359",
"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
+ "title": "The Cambridge Structural Database."
},
{
"doi": "10.1107/S0108768102003890",
- "pmc": null,
- "pubmed": null,
- "title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising",
- "year": null
+ "title": "The Cambridge Structural Database: a quarter of a million crystal structures and rising"
}
],
"twitter": "ccdc_cambridge",
@@ -10978,9 +11672,7 @@
"csp": {
"contact": {
"email": "af8d@nih.gov",
- "github": null,
- "name": "Anita Ghebeles",
- "orcid": null
+ "name": "Anita Ghebeles"
},
"deprecated": true,
"description": "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains.",
@@ -10991,6 +11683,8 @@
"biology",
"biomedical science",
"chemical biology",
+ "disease",
+ "food",
"medicine",
"ontology",
"social science"
@@ -10999,14 +11693,13 @@
"aberowl": "CRISP",
"bioportal": "CRISP",
"fairsharing": "FAIRsharing.1evfpc",
- "hl7": "2.16.840.1.113883.6.120"
+ "hl7": "2.16.840.1.113883.6.120",
+ "pathguide": "192"
},
"name": "Computer Retrieval of Information on Science Projects Thesaurus",
"preferred_prefix": "csp",
"publications": [
{
- "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",
"year": 1996
@@ -11033,7 +11726,8 @@
"fairsharing": "FAIRsharing.n8pxvx",
"hl7": "2.16.840.1.113883.6.62",
"miriam": "cst",
- "n2t": "cst"
+ "n2t": "cst",
+ "pathguide": "193"
},
"name": "Cell Signaling Technology Pathways",
"pattern": "^[A-Za-z0-9_-]+$",
@@ -11085,9 +11779,7 @@
],
"contact": {
"email": "ncictcaehelp@mail.nih.gov",
- "github": null,
- "name": "CTCAE Help",
- "orcid": null
+ "name": "CTCAE Help"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -11112,7 +11804,6 @@
"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",
@@ -11256,6 +11947,7 @@
"homepage": "https://github.com/ClinicalTrialOntology/CTO/",
"keywords": [
"biomedical science",
+ "disease",
"neurobiology",
"obo",
"ontology",
@@ -11293,7 +11985,8 @@
"preferred_prefix": "ctri",
"references": [
"https://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=82487"
- ]
+ ],
+ "uri_format": "https://trialsearch.who.int/Trial2.aspx?TrialID=$1"
},
"cubedb": {
"comment": "website down as of 2021-10-04",
@@ -11303,6 +11996,7 @@
"homepage": "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html",
"mappings": {
"biocontext": "CUBEDB",
+ "integbio": "nbdc02094",
"miriam": "cubedb",
"n2t": "cubedb"
},
@@ -11355,6 +12049,7 @@
"homepage": "https://github.com/OpenLHS/CVDO",
"keywords": [
"cardiology",
+ "cardiovascular disease",
"obo",
"ontology"
],
@@ -11391,7 +12086,8 @@
},
"name": "Vaccine administered code set",
"pattern": "^\\d+$",
- "preferred_prefix": "cvx"
+ "preferred_prefix": "cvx",
+ "uri_format": "https://biopragmatics.github.io/providers/cvx/$1"
},
"d1id": {
"description": "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences.",
@@ -11434,7 +12130,6 @@
"dandi": {
"contact": {
"email": "yoh@dartmouth.edu",
- "github": null,
"name": "Yaroslav Halchenko",
"orcid": "0000-0003-3456-2493"
},
@@ -11486,7 +12181,6 @@
"dashr": {
"contact": {
"email": "dashr@lisanwanglab.org",
- "github": null,
"name": "Li-San Wang",
"orcid": "0000-0002-3684-0031"
},
@@ -11548,7 +12242,11 @@
"example": "AgentIdentifierScheme",
"homepage": "http://www.sparontologies.net/ontologies/datacite",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
"ontology",
+ "report",
"subject agnostic"
],
"mappings": {
@@ -11636,6 +12334,7 @@
"biocontext": "DATF",
"miriam": "datf",
"n2t": "datf",
+ "pathguide": "518",
"prefixcommons": "datf"
},
"name": "Database of Arabidopsis Transcription Factors",
@@ -11665,6 +12364,7 @@
"edam": "2716",
"miriam": "dbd",
"n2t": "dbd",
+ "pathguide": "496",
"prefixcommons": "dbd"
},
"name": "Transcription Factor Database",
@@ -11694,6 +12394,7 @@
"biocontext": "DBEST",
"edam": "1105",
"fairsharing": "FAIRsharing.v9fya8",
+ "integbio": "nbdc00413",
"miriam": "dbest",
"n2t": "dbest",
"ncbi": "dbEST",
@@ -11729,7 +12430,6 @@
"publications": [
{
"doi": "10.1038/ng0893-332",
- "pmc": null,
"pubmed": "8401577",
"title": "dbEST--database for \"expressed sequence tags\"",
"year": 1993
@@ -11776,7 +12476,7 @@
"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",
+ "homepage": "https://www.ncbi.nlm.nih.gov/gap/",
"keywords": [
"biomedical science",
"epigenetics",
@@ -11786,6 +12486,7 @@
"biocontext": "DBGAP",
"cellosaurus": "dbGAP",
"fairsharing": "FAIRsharing.88v2k0",
+ "integbio": "nbdc00414",
"miriam": "dbgap",
"n2t": "dbgap"
},
@@ -11810,6 +12511,18 @@
],
"uri_format": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"
},
+ "dblp.author": {
+ "description": "identifier for author entries in the DBLP computer science bibliography (use portion of DBLP person key after pid/)",
+ "example": "199/2168",
+ "homepage": "https://dblp.org/",
+ "mappings": {
+ "wikidata": "P2456"
+ },
+ "name": "DBLP author ID",
+ "preferred_prefix": "dblp.author",
+ "rdf_uri_format": "https://dblp.org/pid/$1.rdf",
+ "uri_format": "https://dblp.org/pid/$1"
+ },
"dbmhc": {
"appears_in": [
"cellosaurus"
@@ -11819,7 +12532,8 @@
"example": "48439",
"homepage": "https://www.ncbi.nlm.nih.gov/gv/mhc/",
"mappings": {
- "cellosaurus": "dbMHC"
+ "cellosaurus": "dbMHC",
+ "integbio": "nbdc01831"
},
"name": "Database of human Major Histocompatibility Complex",
"pattern": "^\\d+$",
@@ -11840,6 +12554,9 @@
"dbpedia",
"ontology"
],
+ "mappings": {
+ "zazuko": "dbo"
+ },
"name": "DBPedia Ontology",
"preferred_prefix": "dbo",
"uri_format": "https://dbpedia.org/ontology/$1"
@@ -11888,11 +12605,13 @@
"fairsharing": "FAIRsharing.edxb58",
"go": "dbSNP",
"hl7": "2.16.840.1.113883.6.284",
+ "integbio": "nbdc00206",
"miriam": "dbsnp",
"n2t": "dbsnp",
"ncbi": "dbSNP",
"prefixcommons": "dbsnp",
"re3data": "r3d100010652",
+ "togoid": "Dbsnp",
"uniprot": "DB-0013",
"wikidata": "P6861"
},
@@ -11916,6 +12635,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkaa892",
+ "pubmed": "33095870"
+ },
{
"doi": "10.1093/nar/gkl1031",
"pmc": "PMC1781113",
@@ -11971,7 +12694,6 @@
"dc": {
"contact": {
"email": "kdurante@stanford.edu",
- "github": null,
"name": "Kim Durante",
"orcid": "0000-0001-9052-2854"
},
@@ -11983,13 +12705,18 @@
},
"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": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_elements.rdf",
+ "download_owl": "http://aber-owl.net/media/ontologies/dcelements/1/dcelements.owl",
+ "download_rdf": "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": [
+ "annotation",
"biomedical science",
"life science",
+ "metadata",
+ "metadata standardization",
"ontology",
+ "resource metadata",
"subject agnostic"
],
"mappings": {
@@ -11997,7 +12724,9 @@
"biocontext": "dc",
"bioportal": "DC",
"fairsharing": "FAIRsharing.3nx7t",
- "ols": "dc"
+ "lov": "dce",
+ "ols": "dc",
+ "zazuko": "dc11"
},
"name": "Dublin Core Elements (1.1)",
"preferred_prefix": "dc",
@@ -12011,7 +12740,6 @@
"dc_cl": {
"contact": {
"email": "Lindsay.Cowell@utsouthwestern.edu",
- "github": null,
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
@@ -12035,7 +12763,6 @@
"dcat": {
"contact": {
"email": "kdurante@stanford.edu",
- "github": null,
"name": "Kim Durante",
"orcid": "0000-0001-9052-2854"
},
@@ -12052,14 +12779,17 @@
"keywords": [
"data management",
"ontology",
- "subject agnostic"
+ "subject agnostic",
+ "w3c rec"
],
"mappings": {
"aberowl": "DCAT",
"biocontext": "dcat",
"biolink": "dcat",
"bioportal": "DCAT",
- "fairsharing": "FAIRsharing.h4j3qm"
+ "fairsharing": "FAIRsharing.h4j3qm",
+ "lov": "dcat",
+ "zazuko": "dcat"
},
"name": "Data Catalog",
"preferred_prefix": "dcat",
@@ -12069,9 +12799,7 @@
"dcterms": {
"contact": {
"email": "futo@stanford.edu",
- "github": null,
- "name": "Michelle Futornick",
- "orcid": null
+ "name": "Michelle Futornick"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -12080,11 +12808,15 @@
"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": "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/dublin_core_terms.rdf",
+ "download_owl": "http://aber-owl.net/media/ontologies/dcterms/1/dcterms.owl",
+ "download_rdf": "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": [
+ "metadata",
+ "metadata standardization",
"ontology",
+ "resource metadata",
"subject agnostic"
],
"mappings": {
@@ -12093,7 +12825,9 @@
"biolink": "dct",
"bioportal": "DCTERMS",
"fairsharing": "FAIRsharing.9vtwjs",
- "ols": "dcterms"
+ "lov": "dcterms",
+ "ols": "dcterms",
+ "zazuko": "dcterms"
},
"name": "Dublin Core Metadata Initiative Terms",
"preferred_prefix": "dcterms",
@@ -12127,13 +12861,14 @@
"name": "Petra Fey",
"orcid": "0000-0002-4532-2703"
},
- "description": "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum",
+ "description": "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum.",
"download_obo": "http://purl.obolibrary.org/obo/ddanat.obo",
"download_owl": "http://purl.obolibrary.org/obo/ddanat.owl",
"example": "0000006",
"homepage": "http://dictybase.org/",
"keywords": [
"anatomy",
+ "cell",
"life science",
"obo",
"ontology",
@@ -12175,18 +12910,38 @@
"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",
- "version": "2020-04-13"
+ "uri_format": "http://purl.obolibrary.org/obo/DDANAT_$1"
+ },
+ "ddc": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "The Dewey Decimal Classification (DDC) system, devised by library pioneer Melvil Dewey in the 1870s and owned by OCLC since 1988, provides a dynamic structure for the organization of library collections. Now in its 23rd edition, and available in print and Web versions, the DDC is the world's most widely used library classification system.",
+ "example": "325.4",
+ "example_extras": [
+ "325.4-325.9",
+ "325",
+ "32",
+ "3"
+ ],
+ "homepage": "http://www.oclc.org/dewey/",
+ "mappings": {
+ "bartoc": "241"
+ },
+ "name": "Dewey Decimal Classification",
+ "pattern": "^(([0-9][0-9]?|[0-9]{3}(-[0-9]{3})?|[0-9]{3}(-[0-9]{3}(:[0-9]+)?)?|[0-9]{3}\\.[0-9]+(-[0-9]{3}\\.[0-9]+(:[0-9]+)?)?|T[1-9][A-Z]?--[0-9]+(-T[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?|[1-9][A-Z]?--[0-9]+(-[1-9][A-Z]?--[0-9]+(:[0-9]+)?)?)?)$",
+ "preferred_prefix": "ddc"
},
"ddinter.drug": {
"contact": {
"email": "oriental-cds@163.com",
- "github": null,
"name": "Dongsheng Cao",
"orcid": "0000-0003-3604-3785"
},
"contributor": {
- "email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
@@ -12215,7 +12970,6 @@
"ddinter.interaction": {
"contact": {
"email": "oriental-cds@163.com",
- "github": null,
"name": "Dongsheng Cao",
"orcid": "0000-0003-3604-3785"
},
@@ -12257,7 +13011,8 @@
"keywords": [
"life science",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"license": "CC0-1.0",
"mappings": {
@@ -12292,7 +13047,7 @@
"repository": "https://github.com/obophenotype/dicty-phenotype-ontology",
"twitter": "dictybase",
"uri_format": "http://purl.obolibrary.org/obo/DDPHENO_$1",
- "version": "2023-02-19"
+ "version": "2023-08-26"
},
"debio": {
"contact": {
@@ -12318,7 +13073,7 @@
],
"name": "Decentralized Biomedical Ontology",
"pattern": "^\\d{7}$",
- "preferred_prefix": "DeBiO",
+ "preferred_prefix": "debio",
"providers": [
{
"code": "obo2",
@@ -12328,6 +13083,9 @@
"uri_format": "http://purl.obolibrary.org/obo/debio_$1"
}
],
+ "synonyms": [
+ "DeBiO"
+ ],
"uri_format": "https://biopragmatics.github.io/debio/$1"
},
"decipher": {
@@ -12400,25 +13158,22 @@
"example": "Reference",
"homepage": "http://www.sparontologies.net/ontologies/deo",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
+ "spar",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.39fd58"
+ "fairsharing": "FAIRsharing.39fd58",
+ "lov": "deo"
},
"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,
- "pubmed": null,
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
@@ -12437,6 +13192,7 @@
"description": "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells.",
"example": "ACH-000001",
"homepage": "https://depmap.org/portal",
+ "license": "CC-BY-4.0",
"mappings": {
"cellosaurus": "DepMap"
},
@@ -12448,7 +13204,6 @@
"depod": {
"contact": {
"email": "depod@embl.de",
- "github": null,
"name": "General Enquiries",
"orcid": "0000-0003-3562-7869"
},
@@ -12463,6 +13218,7 @@
"fairsharing": "FAIRsharing.q9j2e3",
"miriam": "depod",
"n2t": "depod",
+ "pathguide": "584",
"re3data": "r3d100011936",
"uniprot": "DB-0190"
},
@@ -12487,7 +13243,6 @@
},
{
"doi": "10.1126/scisignal.2003203",
- "pmc": null,
"pubmed": "23674824",
"title": "Elucidating human phosphatase-substrate networks",
"year": 2013
@@ -12514,6 +13269,7 @@
"homepage": "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x",
"keywords": [
"dermatology",
+ "disease",
"ontology"
],
"mappings": {
@@ -12549,6 +13305,41 @@
"preferred_prefix": "dev.ga4ghdos",
"uri_format": "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"
},
+ "devtox": {
+ "contact": {
+ "email": "rupert.kellner@item.fraunhofer.de",
+ "name": "Rupert Kellner",
+ "orcid": "0000-0002-6807-8731"
+ },
+ "contributor": {
+ "github": "bgyori",
+ "name": "Benjamin M. Gyori",
+ "orcid": "0000-0001-9439-5346"
+ },
+ "description": "The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with the aid of photographs, and provides a historical control database of developmental effects in laboratory animals.",
+ "example": "311935300",
+ "github_request_issue": 989,
+ "homepage": "https://www.devtox.org/",
+ "name": "DevTox",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "devtox",
+ "publications": [
+ {
+ "doi": "10.1016/j.reprotox.2019.07.003",
+ "pmc": "PMC8865445",
+ "pubmed": "31288076",
+ "title": "Update of the DevTox data database for harmonized risk assessment and alternative methodologies in developmental toxicology: Report of the 9th Berlin Workshop on Developmental Toxicity",
+ "year": 2019
+ }
+ ],
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://www.devtox.org/nomenclature/ml_manus.php?mno=$1"
+ },
"dg.4503": {
"description": "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org",
"example": "0000ffeb-36e0-4a29-b21d-84423bda979d",
@@ -12621,12 +13412,31 @@
"preferred_prefix": "dg5b0d",
"uri_format": "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"
},
+ "dggr": {
+ "description": "Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]",
+ "example": "918902",
+ "homepage": "http://kyotofly.kit.jp/cgi-bin/stocks/data_search.cgi",
+ "keywords": [
+ "drosophila",
+ "genetic resource",
+ "genomics",
+ "organism supplier"
+ ],
+ "mappings": {
+ "rrid": "DGGR"
+ },
+ "name": "Kyoto Stock Center",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "dggr",
+ "uri_format": "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1"
+ },
"dgrc": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "215",
"homepage": "https://dgrc.bio.indiana.edu/cells/Catalog",
"mappings": {
- "cellosaurus": "DGRC"
+ "cellosaurus": "DGRC",
+ "integbio": "nbdc00048"
},
"name": "Drosophila Genomics Resource Center",
"pattern": "^\\d+$",
@@ -12655,7 +13465,6 @@
"dicom": {
"contact": {
"email": "dclunie@dclunie.com",
- "github": null,
"name": "David Clunie",
"orcid": "0000-0002-2406-1145"
},
@@ -12688,14 +13497,13 @@
},
{
"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",
"year": 2005
}
],
"uri_format": "http://dicom.nema.org/resources/ontology/DCM/$1",
- "version": "2023b_20230403"
+ "version": "2024b_20240331"
},
"dictybase": {
"description": "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics",
@@ -12711,6 +13519,7 @@
"biocontext": "dictyBase",
"fairsharing": "FAIRsharing.4shj9c",
"go": "dictyBase",
+ "integbio": "nbdc00420",
"ncbi": "dictyBase",
"prefixcommons": "dictybase",
"re3data": "r3d100010586",
@@ -12813,6 +13622,9 @@
"homepage": "https://github.com/DIDEO/DIDEO",
"keywords": [
"biochemistry",
+ "drug interaction",
+ "evidence",
+ "natural product",
"obo",
"ontology"
],
@@ -12838,7 +13650,6 @@
"year": 2018
},
{
- "doi": null,
"pmc": "PMC5765984",
"pubmed": "29295242",
"title": "Formalizing Evidence Type Definitions for Drug-Drug Interaction Studies to Improve Evidence Base Curation",
@@ -12846,8 +13657,6 @@
},
{
"doi": "10.1016/j.knosys.2016.10.006",
- "pmc": null,
- "pubmed": null,
"title": "Conceptual models of drug-drug interactions: A summary of recent efforts",
"year": 2016
}
@@ -12855,14 +13664,12 @@
"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"
+ "version": "2023-10-16"
},
"dinto": {
"contact": {
"email": "maria.herrero@kcl.ac.uk",
- "github": null,
- "name": "Maria Herrero",
- "orcid": null
+ "name": "Maria Herrero"
},
"deprecated": true,
"description": "A formal represention for drug-drug interactions knowledge.",
@@ -12885,7 +13692,6 @@
"publications": [
{
"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",
"year": 2015
@@ -12908,8 +13714,10 @@
"biocontext": "DIP",
"edam": "2616",
"fairsharing": "FAIRsharing.qje0v8",
+ "integbio": "nbdc00049",
"miriam": "dip",
"n2t": "dip",
+ "pathguide": "3",
"prefixcommons": "dip",
"re3data": "r3d100010670",
"uniprot": "DB-0016"
@@ -12959,15 +13767,15 @@
"uri_format": "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"
},
"discoverx": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "95-0166C6",
- "homepage": "https://www.discoverx.com/products-applications/cell-lines",
+ "homepage": "https://www.discoverx.com/product-category/cell-lines-primary-cells/",
"mappings": {
"cellosaurus": "DiscoverX"
},
"name": "DiscoverX cell line products",
"preferred_prefix": "discoverx",
- "uri_format": "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"
+ "uri_format": "https://www.discoverx.com/?post_type=product&s=$1"
},
"disdriv": {
"contact": {
@@ -12998,7 +13806,8 @@
"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"
+ "uri_format": "http://purl.obolibrary.org/obo/DISDRIV_$1",
+ "version": "2023-12-15"
},
"diseaseclass": {
"appears_in": [
@@ -13043,7 +13852,6 @@
"disprot": {
"contact": {
"email": "silvio.tosatto@unipd.it",
- "github": null,
"name": "Silvio C.E. Tosatto",
"orcid": "0000-0003-4525-7793"
},
@@ -13111,7 +13919,6 @@
},
{
"doi": "10.1093/bioinformatics/bth476",
- "pmc": null,
"pubmed": "15310560",
"title": "DisProt: a database of protein disorder",
"year": 2004
@@ -13183,8 +13990,7 @@
"contact": {
"email": "edd@usefulinc.com",
"github": "ewilderj",
- "name": "Edd Wilder-James",
- "orcid": null
+ "name": "Edd Wilder-James"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -13199,8 +14005,13 @@
"keywords": [
"metadata",
"rdf",
- "semantic web"
+ "semantic web",
+ "society"
],
+ "mappings": {
+ "lov": "doap",
+ "zazuko": "doap"
+ },
"name": "Description of a Project",
"preferred_prefix": "doap",
"references": [
@@ -13226,27 +14037,24 @@
"example": "Paragraph",
"homepage": "http://www.sparontologies.net/ontologies/doco",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
+ "spar",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.162003"
+ "fairsharing": "FAIRsharing.162003",
+ "lov": "doco"
},
"name": "Document Components Ontology",
"preferred_prefix": "DoCO",
"publications": [
{
"doi": "10.3233/sw-150177",
- "pmc": null,
- "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",
@@ -13264,7 +14072,6 @@
"orcid": "0000-0002-6601-2165"
},
{
- "email": null,
"github": "dhimmel",
"name": "Daniel Himmelstein",
"orcid": "0000-0002-3012-7446"
@@ -13282,6 +14089,7 @@
"homepage": "https://www.doi.org/",
"keywords": [
"bibliography",
+ "centrally registered identifier",
"knowledge and information systems"
],
"mappings": {
@@ -13370,9 +14178,15 @@
"homepage": "http://www.disease-ontology.org",
"keywords": [
"biomedical science",
+ "classification",
"disease",
+ "disease phenotype",
+ "disease process modeling",
+ "genetic disorder",
"human",
+ "infection",
"life science",
+ "mental health",
"obo",
"ontology"
],
@@ -13384,12 +14198,14 @@
"biocontext": "DOID",
"bioportal": "DOID",
"fairsharing": "FAIRsharing.8b6wfq",
+ "integbio": "nbdc00261",
"miriam": "doid",
"n2t": "doid",
"obofoundry": "doid",
"ols": "doid",
"ontobee": "DOID",
"prefixcommons": "do",
+ "togoid": "Doid",
"wikidata": "P699"
},
"name": "Human Disease Ontology",
@@ -13420,6 +14236,12 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkad1051",
+ "pubmed": "37953304",
+ "title": "The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem",
+ "year": 2023
+ },
{
"doi": "10.1093/nar/gkab1063",
"pmc": "PMC8728220",
@@ -13441,13 +14263,6 @@
"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",
@@ -13518,13 +14333,6 @@
"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",
@@ -13539,8 +14347,8 @@
"do"
],
"twitter": "diseaseontology",
- "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/doid/terms?obo_id=DOID:$1",
- "version": "2023-05-31"
+ "uri_format": "http://purl.obolibrary.org/obo/DOID_$1",
+ "version": "2024-04-30"
},
"dolce": {
"comment": "This resource doesn't exist anymore",
@@ -13554,6 +14362,7 @@
"description": "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use.",
"homepage": "http://www.loa.istc.cnr.it/dolce/overview.html",
"keywords": [
+ "classification",
"computer science",
"knowledge and information systems",
"linguistics",
@@ -13572,7 +14381,8 @@
"mappings": {
"biocontext": "DOMMINO",
"miriam": "dommino",
- "n2t": "dommino"
+ "n2t": "dommino",
+ "pathguide": "423"
},
"name": "Database of Macromolecular Interactions",
"pattern": "^[0-9][A-Za-z0-9]{3}$",
@@ -13636,7 +14446,6 @@
"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
@@ -13673,7 +14482,6 @@
"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
@@ -13722,7 +14530,7 @@
"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": "2023-05-03"
+ "version": "2024-04-25"
},
"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.",
@@ -13734,6 +14542,7 @@
],
"mappings": {
"biocontext": "DPV",
+ "integbio": "nbdc02410",
"miriam": "dpv",
"n2t": "dpv",
"prefixcommons": "dpvweb"
@@ -13857,6 +14666,7 @@
{
"code": "alt1",
"description": "German Language Provider",
+ "first_party": true,
"homepage": "http://drks.de",
"name": "German Language Provider",
"uri_format": "https://drks.de/search/de/trial/$1"
@@ -13864,6 +14674,7 @@
{
"code": "alt2",
"description": "Legacy Provider",
+ "first_party": true,
"homepage": "http://drks.de",
"name": "Legacy Provider",
"uri_format": "http://drks.de/en/trial/$1"
@@ -13888,9 +14699,12 @@
"example": "00023232",
"homepage": "https://github.com/ufbmi/dron",
"keywords": [
+ "approved drug",
"biomedical science",
+ "drug",
"obo",
- "ontology"
+ "ontology",
+ "small molecule"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -13931,7 +14745,7 @@
"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": "2023-06-11"
+ "version": "2024-03-03"
},
"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. ",
@@ -13962,7 +14776,6 @@
"drugbank": {
"contact": {
"email": "david.wishart@ualberta.ca",
- "github": null,
"name": "David Wishart",
"orcid": "0000-0002-3207-2434"
},
@@ -13982,10 +14795,13 @@
"cheminf": "000406",
"edam": "2326",
"fairsharing": "FAIRsharing.353yat",
+ "integbio": "nbdc01071",
"miriam": "drugbank",
"n2t": "drugbank",
+ "pathguide": "221",
"prefixcommons": "drugbank",
"re3data": "r3d100010544",
+ "togoid": "Drugbank",
"uniprot": "DB-0019",
"wikidata": "P715"
},
@@ -14002,6 +14818,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkx1037",
+ "pubmed": "29126136"
+ },
{
"doi": "10.1093/nar/gkt1068",
"pmc": "PMC3965102",
@@ -14038,6 +14858,25 @@
"twitter": "DrugBankDB",
"uri_format": "http://www.drugbank.ca/drugs/$1"
},
+ "drugbank.bioentity": {
+ "description": "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database.",
+ "example": "BE0000048",
+ "homepage": "http://www.drugbank.ca/targets",
+ "mappings": {
+ "biocontext": "DRUGBANKV4.TARGET",
+ "miriam": "drugbankv4.target",
+ "n2t": "drugbankv4.target"
+ },
+ "name": "DrugBank Target v4",
+ "part_of": "drugbank",
+ "pattern": "^BE\\d{7}$",
+ "preferred_prefix": "drugbank.bioentity",
+ "synonyms": [
+ "drugbank.target",
+ "drugbankv4.target"
+ ],
+ "uri_format": "https://go.drugbank.com/bio_entities/$1"
+ },
"drugbank.category": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -14060,6 +14899,51 @@
"preferred_prefix": "drugbank.category",
"uri_format": "https://www.drugbank.ca/categories/$1"
},
+ "drugbank.condition": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Indications and other conditions in drugbank",
+ "example": "DBCOND0066902",
+ "homepage": "https://go.drugbank.com",
+ "name": "DrugBank Condition",
+ "pattern": "^DBCOND\\d+$",
+ "preferred_prefix": "drugbank.condition",
+ "uri_format": "https://go.drugbank.com/indications/$1"
+ },
+ "drugbank.metabolite": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Metabolites in drugbank",
+ "example": "DBMET02292",
+ "homepage": "https://go.drugbank.com",
+ "name": "DrugBank Metabolite",
+ "pattern": "^DBMET\\d+$",
+ "preferred_prefix": "drugbank.metabolite",
+ "uri_format": "https://go.drugbank.com/metabolites/$1"
+ },
+ "drugbank.reaction": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Reactions in drugbank",
+ "example": "1537",
+ "homepage": "https://go.drugbank.com",
+ "name": "DrugBank Reaction",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "drugbank.reaction",
+ "uri_format": "https://go.drugbank.com/reactions/$1"
+ },
"drugbank.salt": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -14070,37 +14954,15 @@
"description": "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets.",
"example": "DBSALT001211",
"homepage": "http://www.drugbank.ca",
- "mappings": {
- "biocontext": "DRUGBANK.TARGET"
- },
"name": "DrugBank Salts",
"part_of": "drugbank",
"pattern": "^DBSALT\\d{6}$",
"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/$1"
- },
"drugcentral": {
"contact": {
"email": "toprea@salud.unm.edu",
- "github": null,
"name": "Tudor Oprea",
"orcid": "0000-0002-6195-6976"
},
@@ -14125,6 +14987,7 @@
"mappings": {
"biolink": "DrugCentral",
"fairsharing": "FAIRsharing.3me82d",
+ "integbio": "nbdc02192",
"miriam": "drugcentral",
"uniprot": "DB-0239",
"wikidata": "P11198"
@@ -14208,15 +15071,22 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines).",
+ "description": "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line",
"example": "ACC-1",
+ "example_extras": [
+ "DSM-2",
+ "RT-0753",
+ "PC-0754",
+ "AS-0753",
+ "PV-0998"
+ ],
"homepage": "https://www.dsmz.de",
"mappings": {
- "cellosaurus": "DSMZ",
+ "cellosaurus": "DSMZCellDive",
"re3data": "r3d100010219"
},
"name": "Deutsche Sammlung von Mikroorganismen und Zellkulturen",
- "pattern": "^ACC-\\d+$",
+ "pattern": "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$",
"preferred_prefix": "dsmz",
"synonyms": [
"DSMZCellDive"
@@ -14254,9 +15124,7 @@
],
"contact": {
"email": "sschurer@med.miami.edu",
- "github": null,
- "name": "Stephan Schurer",
- "orcid": null
+ "name": "Stephan Schurer"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -14270,8 +15138,11 @@
"homepage": "https://github.com/DrugTargetOntology/DTO",
"keywords": [
"biomedical science",
+ "disease",
"drug discovery",
- "ontology"
+ "drug target",
+ "ontology",
+ "protein"
],
"mappings": {
"aberowl": "DTO",
@@ -14313,11 +15184,13 @@
"homepage": "https://github.com/EBISPOT/DUO",
"keywords": [
"biomedical science",
+ "metadata standardization",
"obo",
"ontology",
"subject agnostic"
],
"license": "CC-BY-4.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmdCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--9a42083efa91d79ee5c7ed8e7868db0f7faf0b76/DUO_logo_white_background.png?disposition=inline",
"mappings": {
"aberowl": "DUO",
"biocontext": "DUO",
@@ -14400,7 +15273,7 @@
"uri_format": "https://easychair.org/cfp/topic.cgi?tid=$1"
},
"ebisc": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "ESi007-A",
"example_extras": [
"EDi008-B"
@@ -14467,7 +15340,7 @@
"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_$1",
- "version": "2020-05-22"
+ "version": "2024-02-20"
},
"eccode": {
"contact": {
@@ -14498,20 +15371,26 @@
"homepage": "https://www.enzyme-database.org/",
"keywords": [
"biochemistry",
+ "centrally registered identifier",
"classification",
"enzyme",
+ "enzyme commission number",
"enzymology"
],
+ "license": "CC-BY-4.0",
"mappings": {
"bartoc": "671",
"biocontext": "EC-CODE",
"edam": "1011",
"fairsharing": "FAIRsharing.rfLD2u",
"go": "EC",
+ "integbio": "nbdc00508",
"miriam": "ec-code",
"n2t": "ec-code",
+ "pathguide": "106",
"prefixcommons": "intenz",
"re3data": "r3d100010803",
+ "togoid": "Ec",
"uniprot": "DB-0024",
"wikidata": "P591"
},
@@ -14581,7 +15460,6 @@
"ecg": {
"contact": {
"email": "rwinslow@jhu.edu",
- "github": null,
"name": "Raimond Winslow",
"orcid": "0000-0003-1719-1651"
},
@@ -14597,6 +15475,8 @@
"homepage": "https://bioportal.bioontology.org/ontologies/ECG",
"keywords": [
"biomedical science",
+ "electrocardiography",
+ "heart",
"ontology"
],
"mappings": {
@@ -14610,7 +15490,6 @@
"publications": [
{
"doi": "10.1016/j.jbi.2010.08.007",
- "pmc": null,
"pubmed": "20800107",
"title": "Using an ECG reference ontology for semantic interoperability of ECG data",
"year": 2010
@@ -14631,6 +15510,9 @@
"description": "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species.",
"example": "23159291",
"homepage": "https://www.echinobase.org",
+ "mappings": {
+ "integbio": "nbdc01512"
+ },
"name": "Echinobase",
"pattern": "^\\d+$",
"preferred_prefix": "echinobase",
@@ -14686,6 +15568,9 @@
"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",
+ "mappings": {
+ "pathguide": "386"
+ },
"name": "E. coli Metabolite Database",
"pattern": "^ECMDB\\d+$",
"preferred_prefix": "ecmdb",
@@ -14730,10 +15615,20 @@
"example": "0007807",
"homepage": "https://www.evidenceontology.org",
"keywords": [
+ "assay",
+ "biocuration",
+ "biological sample annotation",
"computational biology",
+ "curated information",
+ "digital curation",
+ "evidence",
"life science",
+ "literature curation",
"obo",
- "ontology"
+ "ontology",
+ "resource metadata",
+ "study design",
+ "text mining"
],
"license": "CC0-1.0",
"logo": "https://avatars1.githubusercontent.com/u/12802432",
@@ -14752,7 +15647,7 @@
"prefixcommons": "eco",
"wikidata": "P3811"
},
- "name": "Evidence ontology",
+ "name": "Evidence and Conclusion Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "ECO",
@@ -14796,7 +15691,6 @@
},
{
"doi": "10.1142/9789812704856_0019",
- "pmc": null,
"pubmed": "14992503",
"title": "An evidence ontology for use in pathway/genome databases",
"year": 2004
@@ -14804,8 +15698,8 @@
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/ECO_$1",
"repository": "https://github.com/evidenceontology/evidenceontology",
- "uri_format": "http://www.evidenceontology.org/browse/#ECO_$1",
- "version": "2023-04-07"
+ "uri_format": "http://purl.obolibrary.org/obo/ECO_$1",
+ "version": "2024-03-25"
},
"ecocore": {
"contact": {
@@ -14870,7 +15764,9 @@
"mappings": {
"fairsharing": "FAIRsharing.65dmtr",
"go": "EcoCyc",
+ "integbio": "nbdc00262",
"ncbi": "ECOCYC",
+ "pathguide": "9",
"re3data": "r3d100011277"
},
"name": "EcoCyc",
@@ -14906,10 +15802,7 @@
},
{
"doi": "10.1128/ecosalplus.ESP-0009-2013",
- "pmc": null,
- "pubmed": null,
- "title": "The EcoCyc Database.",
- "year": null
+ "title": "The EcoCyc Database."
}
],
"uri_format": "https://ecocyc.org/gene?id=$1"
@@ -14986,6 +15879,7 @@
"biocontext": "ECOLIWIKI",
"fairsharing": "FAIRsharing.tx95wa",
"go": "EcoliWiki",
+ "integbio": "nbdc02041",
"miriam": "ecoliwiki",
"n2t": "ecoliwiki"
},
@@ -15016,6 +15910,7 @@
"homepage": "http://bioportal.bioontology.org/ontologies/ECSO",
"keywords": [
"earth science",
+ "ecosystem",
"ecosystem science",
"ontology"
],
@@ -15059,6 +15954,9 @@
"example": "0000001",
"homepage": "https://github.com/EnvironmentOntology/environmental-exposure-ontology",
"keywords": [
+ "diet",
+ "environmental science",
+ "exposure",
"obo",
"ontology"
],
@@ -15066,8 +15964,10 @@
"logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/ecto-logos/ecto-logo_black-banner.png",
"mappings": {
"aberowl": "ECTO",
+ "agroportal": "ECTO",
"biolink": "ECTO",
"bioportal": "ECTO",
+ "fairsharing": "FAIRsharing.6b77ac",
"obofoundry": "ecto",
"ols": "ecto",
"ontobee": "ECTO"
@@ -15075,6 +15975,14 @@
"name": "Environmental conditions, treatments and exposures ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "ECTO",
+ "publications": [
+ {
+ "doi": "10.1186/s13326-023-00283-x",
+ "pubmed": "36823605",
+ "title": "The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond",
+ "year": 2023
+ }
+ ],
"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",
@@ -15150,10 +16058,14 @@
"example": "data_1664",
"homepage": "http://edamontology.org",
"keywords": [
+ "analysis",
"bioinformatics",
+ "data acquisition",
+ "data transformation",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "subject agnostic"
],
"mappings": {
"aberowl": "EDAM",
@@ -15186,6 +16098,16 @@
"pubmed": "23479348",
"title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats",
"year": 2013
+ },
+ {
+ "doi": "10.7490/f1000research.1118900.1",
+ "title": "EDAM: the bioscientific data analysis ontology (update 2021)",
+ "year": 2021
+ },
+ {
+ "doi": "10.5281/zenodo.3899895",
+ "title": "edamontology/edamontology: EDAM 1.25",
+ "year": 2020
}
],
"rdf_uri_format": "http://edamontology.org/$1",
@@ -15320,7 +16242,6 @@
"edda": {
"contact": {
"email": "tanja.bekhuis@tcbinfosci.com",
- "github": null,
"name": "Tanja Bekhuis",
"orcid": "0000-0002-8537-9077"
},
@@ -15354,8 +16275,14 @@
"example": "0005147",
"homepage": "http://www.ebi.ac.uk/efo",
"keywords": [
+ "assay",
+ "experimental condition",
+ "experimental measurement",
"functional genomics",
- "ontology"
+ "genome-wide association study",
+ "independent variable",
+ "ontology",
+ "study design"
],
"license": "Apache-2.0",
"mappings": {
@@ -15377,8 +16304,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^\\d{7}$",
@@ -15403,7 +16329,7 @@
],
"repository": "https://github.com/EBISPOT/efo/",
"uri_format": "http://www.ebi.ac.uk/efo/EFO_$1",
- "version": "3.55.0"
+ "version": "3.65.0"
},
"ega.dataset": {
"description": "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.",
@@ -15428,8 +16354,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^EGAD\\d{11}$",
@@ -15505,6 +16430,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkac1022",
+ "pubmed": "36399505"
+ },
{
"doi": "10.1093/nar/gkp951",
"pmc": "PMC2808932",
@@ -15525,9 +16454,7 @@
"ehda": {
"contact": {
"email": "J.Bard@ed.ac.uk",
- "github": null,
- "name": "Jonathan Bard",
- "orcid": null
+ "name": "Jonathan Bard"
},
"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.",
@@ -15566,9 +16493,7 @@
"ehdaa": {
"contact": {
"email": "J.Bard@ed.ac.uk",
- "github": null,
- "name": "Jonathan Bard",
- "orcid": null
+ "name": "Jonathan Bard"
},
"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.",
@@ -15607,9 +16532,7 @@
"ehdaa2": {
"contact": {
"email": "J.Bard@ed.ac.uk",
- "github": null,
- "name": "Jonathan Bard",
- "orcid": null
+ "name": "Jonathan Bard"
},
"depends_on": [
"aeo",
@@ -15624,7 +16547,9 @@
"homepage": "https://github.com/obophenotype/human-developmental-anatomy-ontology",
"keywords": [
"anatomy",
+ "animal organ development",
"biomedical science",
+ "life cycle stage",
"life science",
"obo",
"ontology"
@@ -15788,7 +16713,6 @@
"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
@@ -15809,8 +16733,6 @@
},
{
"doi": "10.1016/b978-0-12-800043-4.00023-3",
- "pmc": null,
- "pubmed": null,
"title": "Textual Anatomics",
"year": 2016
}
@@ -15820,8 +16742,8 @@
"synonyms": [
"EMAPA_RETIRED"
],
- "uri_format": "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1",
- "version": "2023-05-05"
+ "uri_format": "http://purl.obolibrary.org/obo/EMAPA_$1",
+ "version": "2023-11-14"
},
"emaps": {
"contact": {
@@ -15857,7 +16779,6 @@
"emdb": {
"contact": {
"email": "help@emdatabank.org",
- "github": null,
"name": "Ardan Patwardhan",
"orcid": "0000-0001-7663-9028"
},
@@ -15875,15 +16796,15 @@
"fairsharing": "FAIRsharing.651n9j",
"miriam": "emdb",
"n2t": "emdb",
- "re3data": "r3d100010562"
+ "re3data": "r3d100010562",
+ "uniprot": "DB-0272"
},
"name": "Electron Microscopy Data Bank",
"owners": [
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^EMD-\\d{4,5}$",
@@ -15905,21 +16826,30 @@
},
{
"doi": "10.1016/s0968-0004(02)02176-x",
- "pmc": null,
"pubmed": "12417136",
"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
+ "title": "New electron microscopy database and deposition system"
}
],
"uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"
},
+ "emea": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Product number for the European Medicines Agency",
+ "example": "EMEA/H/C/000181",
+ "homepage": "https://www.ema.europa.eu/en/medicines",
+ "name": "European Medicines Evaluation Agency",
+ "preferred_prefix": "emea"
+ },
"emmo": {
"banana": "EMMO",
"banana_peel": "_",
@@ -15939,7 +16869,16 @@
"download_rdf": "https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl",
"example": "03212fd7_abfd_4828_9c8e_62c293052d4b",
"homepage": "https://emmo-repo.github.io",
+ "keywords": [
+ "communication science",
+ "philosophy",
+ "physics"
+ ],
"license": "CC-BY-4.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdmtEIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69489934048fba98feded162d24a8e3b36c9d370/EMMO.jpg?disposition=inline",
+ "mappings": {
+ "fairsharing": "FAIRsharing.1bdf3c"
+ },
"name": "Elementary Multiperspective Material Ontology",
"preferred_prefix": "emmo",
"repository": "https://github.com/emmo-repo/EMMO",
@@ -16015,8 +16954,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^\\d+$",
@@ -16024,7 +16962,6 @@
"publications": [
{
"doi": "10.1038/nmeth.3806",
- "pmc": null,
"pubmed": "27067018",
"title": "EMPIAR: a public archive for raw electron microscopy image data",
"year": 2016
@@ -16063,12 +17000,12 @@
"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",
+ "has_canonical": "insdc.run",
"homepage": "https://www.ebi.ac.uk/ena/",
"keywords": [
"biodiversity",
@@ -16084,6 +17021,7 @@
"biocontext": "ENA.EMBL",
"fairsharing": "FAIRsharing.dj8nt8",
"go": "ENA",
+ "integbio": "nbdc00432",
"miriam": "ena.embl",
"n2t": "ena.embl",
"prefixcommons": "ena",
@@ -16095,8 +17033,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^[A-Z]+[0-9]+(\\.\\d+)?$",
@@ -16177,7 +17114,6 @@
"encode": {
"contact": {
"email": "gabdank@stanford.edu",
- "github": null,
"name": "Idan Gabdank",
"orcid": "0000-0001-5025-5886"
},
@@ -16300,7 +17236,6 @@
},
{
"doi": "10.1126/science.1105136",
- "pmc": null,
"pubmed": "15499007",
"title": "The ENCODE (ENCyclopedia Of DNA Elements) Project",
"year": 2004
@@ -16311,16 +17246,18 @@
"enm": {
"contact": {
"email": "egon.willighagen@maastrichtuniversity.nl",
- "github": null,
"name": "Egon Willighagen",
"orcid": "0000-0001-7542-0286"
},
"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",
+ "download_owl": "http://enanomapper.github.io/ontologies/releases/10.0/enanomapper.owl",
"example": "8000221",
"homepage": "http://www.enanomapper.net/",
"keywords": [
+ "chemical entity",
"health science",
+ "nanoparticle",
+ "nanosafety",
"ontology"
],
"mappings": {
@@ -16342,7 +17279,7 @@
}
],
"uri_format": "http://purl.enanomapper.org/onto/ENM_$1",
- "version": "9.0"
+ "version": "10.0"
},
"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.",
@@ -16366,6 +17303,7 @@
"edam": "2610",
"fairsharing": "FAIRsharing.fx0mw7",
"go": "ENSEMBL",
+ "integbio": "nbdc00054",
"miriam": "ensembl",
"n2t": "ensembl",
"ncbi": "ENSEMBL",
@@ -16663,7 +17601,6 @@
},
{
"doi": "10.1093/bfgp/elm025",
- "pmc": null,
"pubmed": "17967807",
"title": "Genome browsing with Ensembl: a practical overview",
"year": 2007
@@ -16698,7 +17635,6 @@
},
{
"doi": "10.1016/j.tig.2004.04.002",
- "pmc": null,
"pubmed": "15145580",
"title": "Genome information resources - developments at Ensembl",
"year": 2004
@@ -16761,10 +17697,7 @@
},
{
"doi": "doi:10.1093/nar/gku1010",
- "pmc": null,
- "pubmed": null,
- "title": "Ensembl 2015",
- "year": null
+ "title": "Ensembl 2015"
}
],
"rdf_uri_format": "http://rdf.ebi.ac.uk/resource/ensembl/$1",
@@ -16786,6 +17719,7 @@
"mappings": {
"biocontext": "ENSEMBL.BACTERIA",
"fairsharing": "FAIRsharing.zsgmvd",
+ "integbio": "nbdc00433",
"miriam": "ensembl.bacteria",
"n2t": "ensembl.bacteria",
"prefixcommons": "ensembl.bacteria",
@@ -16844,6 +17778,7 @@
"biocontext": "ENSEMBL.FUNGI",
"fairsharing": "FAIRsharing.bg5xqs",
"go": "EnsemblFungi",
+ "integbio": "nbdc00434",
"miriam": "ensembl.fungi",
"n2t": "ensembl.fungi",
"prefixcommons": "ensembl.fungi",
@@ -16895,6 +17830,7 @@
"biocontext": "ENSEMBL.METAZOA",
"fairsharing": "FAIRsharing.c23cqq",
"go": "EnsemblMetazoa",
+ "integbio": "nbdc00435",
"miriam": "ensembl.metazoa",
"n2t": "ensembl.metazoa",
"prefixcommons": "ensembl.metazoa",
@@ -17006,7 +17942,6 @@
"envipath": {
"contact": {
"email": "admin@envipath.org",
- "github": null,
"name": "Jörg Wicker",
"orcid": "0000-0003-0533-3368"
},
@@ -17018,6 +17953,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.g0c5qn",
+ "integbio": "nbdc02011",
"miriam": "envipath",
"re3data": "r3d100012715"
},
@@ -17034,7 +17970,6 @@
},
{
"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",
"year": 2017
@@ -17048,10 +17983,7 @@
},
{
"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
+ "title": "Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data"
}
],
"twitter": "envipath",
@@ -17067,7 +17999,8 @@
"ons",
"pco",
"rbo",
- "scdo"
+ "scdo",
+ "uberon"
],
"banana": "ENVO",
"contact": {
@@ -17094,9 +18027,12 @@
"homepage": "http://environmentontology.org/",
"keywords": [
"ecology",
+ "environmental material",
"environmental science",
"epidemiology",
"life science",
+ "marine metagenome",
+ "microbiome",
"nutritional science",
"obo",
"ontology"
@@ -17153,7 +18089,7 @@
"repository": "https://github.com/EnvironmentOntology/envo",
"twitter": "envoTweets",
"uri_format": "http://purl.obolibrary.org/obo/ENVO_$1",
- "version": "2023-02-13"
+ "version": "2024-02-16"
},
"enzo": {
"contributor": {
@@ -17215,6 +18151,13 @@
"pattern": "^\\d{7}$",
"preferred_prefix": "EO",
"providers": [
+ {
+ "code": "CURATOR_REVIEW",
+ "description": "Plant Environment Ontology through Gramene",
+ "homepage": "http://archive.gramene.org/db/ontology/search_term?id=EO:0007359",
+ "name": "Plant Environment Ontology through Gramene",
+ "uri_format": "http://archive.gramene.org/db/ontology/search?query=EO:$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.",
@@ -17234,12 +18177,11 @@
],
"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"
+ "uri_format": "http://purl.obolibrary.org/obo/EO_$1"
},
"eol": {
"contact": {
"email": "pylebail@rennes.inra.fr",
- "github": null,
"name": "Pierre-Yves LeBail",
"orcid": "0000-0002-8310-5195"
},
@@ -17257,7 +18199,9 @@
"agriculture",
"animal husbandry",
"environmental science",
- "ontology"
+ "livestock",
+ "ontology",
+ "species-environment interaction"
],
"mappings": {
"aberowl": "EOL",
@@ -17276,7 +18220,6 @@
"eolife": {
"contact": {
"email": "secretariat@eol.org",
- "github": null,
"name": "EOL Secretariat",
"orcid": "0000-0002-9943-2342"
},
@@ -17325,7 +18268,6 @@
"epd": {
"contact": {
"email": "Philipp.Bucher@sib.swiss",
- "github": null,
"name": "Philipp Bucher",
"orcid": "0000-0002-0816-7775"
},
@@ -17348,6 +18290,7 @@
"biocontext": "EPD",
"edam": "2386",
"fairsharing": "FAIRsharing.yk1krv",
+ "integbio": "nbdc00438",
"miriam": "epd",
"n2t": "epd",
"ncbi": "EPD",
@@ -17472,7 +18415,6 @@
"epo": {
"contributor_extras": [
{
- "email": null,
"github": "djinnome",
"name": "Jeremy Zucker",
"orcid": "0000-0002-7276-9009"
@@ -17499,7 +18441,6 @@
"epso": {
"contact": {
"email": "satyasahoo@ieee.org",
- "github": null,
"name": "Satya S. Sahoo",
"orcid": "0000-0001-9190-4256"
},
@@ -17508,8 +18449,10 @@
"example": "0000400",
"homepage": "http://prism.case.edu/prism/index.php/EpilepsyOntology",
"keywords": [
+ "epilepsy",
"neurology",
- "ontology"
+ "ontology",
+ "patient care"
],
"mappings": {
"aberowl": "EPSO",
@@ -17543,6 +18486,7 @@
"example": "ERM00000044",
"homepage": "https://nanocommons.github.io/identifiers/",
"keywords": [
+ "chemical entity",
"materials informatics",
"nanotechnology"
],
@@ -17555,6 +18499,15 @@
"name": "European Registry of Materials",
"pattern": "^ERM[0-9]{8}$",
"preferred_prefix": "erm",
+ "providers": [
+ {
+ "code": "erm.database",
+ "description": "Database that provides links to onlnie information about materials with an European Registry of Materials (ERM) identifier",
+ "homepage": "https://nanocommons.github.io/erm-database/",
+ "name": "ERM Identifier Database",
+ "uri_format": "https://nanocommons.github.io/erm-database/substance/erm/$1"
+ }
+ ],
"publications": [
{
"doi": "10.1186/s13321-022-00614-7",
@@ -17570,7 +18523,6 @@
"ero": {
"contact": {
"email": "Marc_Ciriello@hms.harvard.edu",
- "github": null,
"name": "Marc Ciriello",
"orcid": "0000-0002-3734-1859"
},
@@ -17580,10 +18532,14 @@
"example": "0001655",
"homepage": "https://open.med.harvard.edu/wiki/display/eaglei/Ontology",
"keywords": [
+ "biological sample",
"biomedical science",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "protocol",
+ "reagent",
+ "study design"
],
"license": "CC BY 2.0",
"mappings": {
@@ -17606,13 +18562,6 @@
"title": "Automating data citation: the eagle-i experience",
"year": 2017
},
- {
- "doi": "10.1109/JCDL.2017.7991571",
- "pmc": "PMC5868434",
- "pubmed": "29599662",
- "title": "Automating data citation: the eagle-i experience",
- "year": null
- },
{
"doi": "10.1093/database/bar067",
"pmc": "PMC3308157",
@@ -17633,6 +18582,7 @@
"protein"
],
"mappings": {
+ "integbio": "nbdc00265",
"prefixcommons": "eropmoscow"
},
"name": "Endogenous Regulatory OligoPeptide knowledgebase-Moscow",
@@ -17711,8 +18661,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^\\d{3}$",
@@ -17753,7 +18702,6 @@
"eugenes": {
"contact": {
"email": "eugenes@iubio.bio.indiana.edu",
- "github": null,
"name": "Don Gilbert",
"orcid": "0000-0002-6646-7274"
},
@@ -17802,11 +18750,12 @@
"scdo"
],
"contact": {
- "email": "jiezheng@pennmedicine.upenn.edu",
+ "email": "jiezhen@med.umich.edu",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
},
+ "deprecated": true,
"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",
@@ -17815,6 +18764,7 @@
"biomedical science",
"epidemiology",
"functional genomics",
+ "microbiome",
"obo",
"ontology",
"population genetics"
@@ -17836,8 +18786,6 @@
"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
}
@@ -17866,13 +18814,11 @@
],
"contact": {
"email": "evoc@sanbi.ac.za",
- "github": null,
- "name": "eVOC mailing list",
- "orcid": null
+ "name": "eVOC mailing list"
},
"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",
+ "example": "0100011",
"homepage": "http://www.evocontology.org/",
"keywords": [
"anatomy",
@@ -17888,6 +18834,7 @@
"prefixcommons": "evoc"
},
"name": "eVOC (Expressed Sequence Annotation for Humans)",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "EV",
"providers": [
{
@@ -17977,8 +18924,10 @@
"example": "0000078",
"homepage": "https://github.com/CTDbase/exposure-ontology",
"keywords": [
+ "disease",
"environmental science",
"epigenetics",
+ "exposure",
"obo",
"ontology",
"toxicology"
@@ -18032,34 +18981,32 @@
"example": "d4e2515",
"homepage": "https://github.com/sparontologies/fabio",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
"ontology",
+ "protocol",
+ "publication",
+ "report",
+ "spar",
"subject agnostic"
],
"mappings": {
"aberowl": "FaBiO",
"biolink": "fabio",
- "fairsharing": "FAIRsharing.2f3180"
+ "fairsharing": "FAIRsharing.2f3180",
+ "lov": "fabio"
},
"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
}
],
+ "rdf_uri_format": "http://purl.org/spar/fabio/$1",
"repository": "https://github.com/sparontologies/fabio",
"twitter": "sparontologies",
"uri_format": "https://sparontologies.github.io/fabio/current/fabio.html#$1"
@@ -18078,6 +19025,7 @@
"mappings": {
"biocontext": "FACEBASE",
"fairsharing": "FAIRsharing.mqvqde",
+ "integbio": "nbdc02022",
"miriam": "facebase",
"n2t": "facebase",
"re3data": "r3d100013263"
@@ -18099,7 +19047,6 @@
"fairsharing": {
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
- "github": null,
"name": "Allyson Lister",
"orcid": "0000-0002-7702-4495"
},
@@ -18150,8 +19097,6 @@
},
{
"doi": "10.5281/zenodo.5106255",
- "pmc": null,
- "pubmed": null,
"title": "FAIRsharing, a FAIR-enabling service for repositories, standards and policies",
"year": 2021
}
@@ -18207,9 +19152,7 @@
"faldo": {
"contact": {
"email": "faldo@googlegroups.com",
- "github": null,
- "name": "FALDO group",
- "orcid": null
+ "name": "FALDO group"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -18222,15 +19165,22 @@
"example": "ForwardStrandPosition",
"homepage": "http://biohackathon.org/resource/faldo",
"keywords": [
+ "binding site",
+ "gene feature",
"genetics",
- "ontology"
+ "geography",
+ "nucleic acid sequence",
+ "ontology",
+ "sequence annotation",
+ "sequence feature"
],
"mappings": {
"aberowl": "FALDO",
"agroportal": "FALDO",
"biocontext": "faldo",
"bioportal": "FALDO",
- "fairsharing": "FAIRsharing.haxp7g"
+ "fairsharing": "FAIRsharing.haxp7g",
+ "lov": "faldo"
},
"name": "Feature Annotation Location Description Ontology ",
"preferred_prefix": "faldo",
@@ -18297,7 +19247,6 @@
"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"
@@ -18328,14 +19277,17 @@
"name": "Willy Wong",
"orcid": "0000-0002-8841-5870"
},
+ "deprecated": true,
"description": "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research.",
"download_obo": "http://aber-owl.net/media/ontologies/FBbi/14/fbbi.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbbi.owl",
"example": "00000268",
"homepage": "http://cellimagelibrary.org/",
"keywords": [
+ "assay",
"biomedical science",
"experiment",
+ "image",
"imaging",
"life science",
"obo",
@@ -18379,7 +19331,7 @@
"name": "Clare Pilgrim",
"orcid": "0000-0002-1373-1705"
},
- "description": "An ontology of Drosophila melanogaster anatomy.",
+ "description": "An ontology representing the gross anatomy of Drosophila melanogaster.",
"download_json": "http://purl.obolibrary.org/obo/fbbt.json",
"download_obo": "http://purl.obolibrary.org/obo/fbbt.obo",
"download_owl": "http://purl.obolibrary.org/obo/fbbt.owl",
@@ -18389,9 +19341,13 @@
"anatomy",
"developmental biology",
"fly",
+ "gene expression",
+ "image",
+ "life cycle stage",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -18406,7 +19362,6 @@
"prefixcommons": "fbbt"
},
"name": "Drosophila gross anatomy",
- "part_of": "flybase",
"pattern": "^\\d{8}$",
"preferred_prefix": "FBbt",
"providers": [
@@ -18428,14 +19383,12 @@
},
{
"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
@@ -18454,8 +19407,8 @@
"FBbt",
"FBbt_root"
],
- "uri_format": "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1",
- "version": "2023-05-03"
+ "uri_format": "http://purl.obolibrary.org/obo/FBbt_$1",
+ "version": "2024-04-25"
},
"fbcv": {
"appears_in": [
@@ -18475,10 +19428,12 @@
"homepage": "http://purl.obolibrary.org/obo/fbcv",
"keywords": [
"descriptor",
+ "expression data",
"fly",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -18519,7 +19474,7 @@
"FBcv"
],
"uri_format": "http://purl.obolibrary.org/obo/FBcv_$1",
- "version": "2023-05-04"
+ "version": "2024-04-25"
},
"fbdv": {
"contact": {
@@ -18538,6 +19493,8 @@
"development",
"developmental biology",
"fly",
+ "life cycle",
+ "life cycle stage",
"life science",
"obo",
"ontology"
@@ -18548,6 +19505,7 @@
"biocontext": "FBdv",
"bioportal": "FB-DV",
"fairsharing": "FAIRsharing.p52pzj",
+ "go": "FBdv",
"obofoundry": "fbdv",
"ols": "fbdv",
"ontobee": "FBdv",
@@ -18571,7 +19529,7 @@
"FBdv"
],
"uri_format": "http://purl.obolibrary.org/obo/FBdv_$1",
- "version": "2023-05-03"
+ "version": "2024-04-25"
},
"fbol": {
"comment": "Website down, checked on 2021-10-07",
@@ -18661,6 +19619,9 @@
"description": "The cell line vocabulary inside FlyBase",
"example": "0000190",
"homepage": "https://flybase.org",
+ "mappings": {
+ "cellosaurus": "FlyBase_Cell_line"
+ },
"name": "Flybase Cell Line",
"part_of": "flybase",
"pattern": "^\\d{7}$",
@@ -18742,7 +19703,7 @@
"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",
- "version": "2023-02-01"
+ "version": "2023-12-18"
},
"fishbase.species": {
"contributor": {
@@ -18755,6 +19716,7 @@
"example": "6472",
"homepage": "http://fishbase.org",
"mappings": {
+ "integbio": "nbdc00270",
"re3data": "r3d100010912",
"wikidata": "P938"
},
@@ -18783,6 +19745,10 @@
"example": "hasOpenAccessRating",
"homepage": "http://www.sparontologies.net/ontologies/fivestars",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
"subject agnostic"
],
"mappings": {
@@ -18793,8 +19759,6 @@
"publications": [
{
"doi": "10.1045/january2012-shotton",
- "pmc": null,
- "pubmed": null,
"title": "The Five Stars of Online Journal Articles - a Framework for Article Evaluation",
"year": 2012
}
@@ -18805,9 +19769,7 @@
"fix": {
"contact": {
"email": "chebi-help@ebi.ac.uk",
- "github": null,
- "name": "chEBI",
- "orcid": null
+ "name": "chEBI"
},
"deprecated": true,
"description": "An ontology of physico-chemical methods and properties.",
@@ -18818,9 +19780,11 @@
"keywords": [
"chemistry",
"experiment",
+ "experimental measurement",
"obo",
"ontology",
- "property"
+ "property",
+ "protocol"
],
"mappings": {
"aberowl": "FIX",
@@ -18837,8 +19801,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"part_of": "chebi",
@@ -18858,6 +19821,9 @@
"version": "2020-04-13"
},
"flopo": {
+ "appears_in": [
+ "gallont"
+ ],
"contact": {
"email": "robert.hoehndorf@kaust.edu.sa",
"github": "leechuck",
@@ -18871,8 +19837,10 @@
"keywords": [
"biodiversity",
"botany",
+ "life cycle stage",
"obo",
"ontology",
+ "phenotype",
"plant anatomy"
],
"license": "CC0-1.0",
@@ -18903,13 +19871,6 @@
"pubmed": "25057255",
"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",
@@ -18919,7 +19880,6 @@
"flowrepository": {
"contact": {
"email": "rbrinkman@bccrc.ca",
- "github": null,
"name": "Ryan Brinkman",
"orcid": "0000-0002-9765-2990"
},
@@ -18933,6 +19893,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.veg2d6",
+ "integbio": "nbdc01698",
"miriam": "flowrepository",
"n2t": "flowrepository",
"re3data": "r3d100011280"
@@ -18943,14 +19904,12 @@
"publications": [
{
"doi": "10.1002/cyto.a.22106",
- "pmc": null,
"pubmed": "22887982",
"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)",
"year": 2012
@@ -18961,7 +19920,6 @@
"flu": {
"contact": {
"email": "burkesquires@gmail.com",
- "github": null,
"name": "R. Burke Squires",
"orcid": "0000-0001-9666-6285"
},
@@ -18991,30 +19949,53 @@
"example": "FBgn0011293",
"homepage": "http://flybase.org/",
"keywords": [
+ "allele",
"anatomy",
+ "bio.tools",
"bioinformatics",
+ "blast",
"comparative genomics",
+ "controlled term",
"dna",
+ "drosophilidae",
+ "expression",
+ "faseb list",
"functional genomics",
+ "gene",
"genetics",
"genome",
"genomics",
+ "genotype",
+ "image",
+ "image collection",
"interaction",
"life science",
+ "life-cycle",
"molecular biology",
- "molecular genetics"
+ "molecular genetics",
+ "movie",
+ "mutant",
+ "phenotype",
+ "rna-seq",
+ "sequence",
+ "stock",
+ "video resource"
],
+ "license": "CC-BY-4.0",
"mappings": {
"biocontext": "FlyBase",
"cellosaurus": "FlyBase",
"edam": "1089",
"fairsharing": "FAIRsharing.wrvze3",
"go": "FB",
+ "integbio": "nbdc00064",
"miriam": "fb",
"n2t": "fb",
"ncbi": "FLYBASE",
+ "pathguide": "460",
"prefixcommons": "flybase",
"re3data": "r3d100010591",
+ "rrid": "FlyBase",
"uniprot": "DB-0026",
"wikidata": "P3852"
},
@@ -19066,6 +20047,9 @@
"title": "FlyBase: the Drosophila database",
"year": 1996
},
+ {
+ "pubmed": "8578603"
+ },
{
"doi": "10.1093/nar/22.17.3456",
"pmc": "PMC308301",
@@ -19075,7 +20059,6 @@
},
{
"doi": "10.1242/dev.120.7.2077",
- "pmc": null,
"pubmed": "7925011",
"title": "FlyBase--the Drosophila genetic database",
"year": 1994
@@ -19180,7 +20163,6 @@
},
{
"doi": "10.1007/978-1-59745-583-1_3",
- "pmc": null,
"pubmed": "18641940",
"title": "FlyBase : a database for the Drosophila research community",
"year": 2008
@@ -19227,12 +20209,12 @@
"title": "The FlyBase database of the Drosophila genome projects and community literature",
"year": 2002
},
+ {
+ "pubmed": "11465064"
+ },
{
"doi": "10.1093/nar/gkn788.",
- "pmc": null,
- "pubmed": null,
- "title": "FlyBase: enhancing Drosophila Gene Ontology annotations.",
- "year": null
+ "title": "FlyBase: enhancing Drosophila Gene Ontology annotations."
}
],
"synonyms": [
@@ -19252,6 +20234,9 @@
"description": "A database of fly neurons and pathways with an associated 3D viewer.",
"example": "10531",
"homepage": "https://flybrain-ndb.virtualflybrain.org",
+ "mappings": {
+ "integbio": "nbdc01446"
+ },
"name": "FlyBrain Neuron Database",
"pattern": "^\\d+$",
"preferred_prefix": "flybrain.ndb",
@@ -19292,9 +20277,7 @@
"banana": "FMA",
"contact": {
"email": "mejino@u.washington.edu",
- "github": null,
- "name": "Onard Mejino",
- "orcid": null
+ "name": "Onard Mejino"
},
"deprecated": true,
"description": "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.",
@@ -19304,13 +20287,16 @@
"keywords": [
"anatomy",
"biomedical science",
+ "brain imaging",
"human",
"obo",
"ontology",
"owl",
+ "phenotype",
"radiology"
],
"license": "CC-BY-3.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBYTg9IiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--16f323877b0cea5b9b3df9ea964ed441ad10cff1/fma.png?disposition=inline",
"mappings": {
"aberowl": "FMA",
"bartoc": "571",
@@ -19320,6 +20306,7 @@
"fairsharing": "FAIRsharing.x56jsy",
"go": "FMA",
"hl7": "2.16.840.1.113883.6.119",
+ "integbio": "nbdc00273",
"miriam": "fma",
"n2t": "fma",
"obofoundry": "fma",
@@ -19365,13 +20352,11 @@
},
{
"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",
"year": 2004
},
{
- "doi": null,
"pmc": "PMC1560487",
"pubmed": "16779026",
"title": "Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study",
@@ -19379,7 +20364,6 @@
},
{
"doi": "10.1016/j.jbi.2003.11.007",
- "pmc": null,
"pubmed": "14759820",
"title": "A reference ontology for biomedical informatics: the Foundational Model of Anatomy",
"year": 2003
@@ -19397,9 +20381,7 @@
"foaf": {
"contact": {
"email": "rafael.goncalves@stanford.edu",
- "github": null,
- "name": "Rafael Gonçalves",
- "orcid": null
+ "name": "Rafael Gonçalves"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -19412,13 +20394,16 @@
"example": "familyName",
"homepage": "http://xmlns.com/foaf/spec/",
"keywords": [
- "ontology"
+ "ontology",
+ "people"
],
"mappings": {
"aberowl": "foaf",
"biocontext": "foaf",
"biolink": "foaf",
- "bioportal": "FOAF"
+ "bioportal": "FOAF",
+ "lov": "foaf",
+ "zazuko": "foaf"
},
"name": "Friend of a Friend",
"preferred_prefix": "foaf",
@@ -19471,7 +20456,6 @@
"publications": [
{
"doi": "10.1093/bioinformatics/btab626",
- "pmc": null,
"pubmed": "34601570",
"title": "The fobitools framework: the first steps towards food enrichment analysis",
"year": 2021
@@ -19528,18 +20512,16 @@
},
"foodex2": {
"contact": {
- "email": "datex@efsa.europa.eu",
- "github": null,
- "name": "European Food Safety Authority",
- "orcid": null
+ "email": "data@food.gov.uk",
+ "name": "UK Food Standard Agency"
},
- "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.",
+ "description": "Food Type identifiers, supporting codes and vocabularies based on the EFSA FoodEx2 (https://www.efsa.europa.eu/en/data/data-standardisation) that are being tested in the development of the FSA's code and data standards repository. These codes may be used within FSA data.",
"example": "A0TMC",
- "homepage": "http://www.efsa.europa.eu/",
+ "homepage": "https://data.food.gov.uk/codes/_foodtype",
"mappings": {
"agroportal": "FOODEX2"
},
- "name": "Food Classification and Description System",
+ "name": "Food Classification and Description System (from FSA Food Type identifiers)",
"preferred_prefix": "foodex2",
"uri_format": "http://data.food.gov.uk/codes/foodtype/id/$1"
},
@@ -19577,10 +20559,13 @@
"keywords": [
"agriculture",
"botany",
+ "disease",
"environmental science",
+ "food",
"medicine",
"obo",
- "ontology"
+ "ontology",
+ "sustainability"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -19617,8 +20602,7 @@
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/FOODON_$1",
"repository": "https://github.com/FoodOntology/foodon",
- "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/foodon/terms?obo_id=FOODON:$1",
- "version": "2023-05-03"
+ "uri_format": "http://purl.obolibrary.org/obo/FOODON_$1"
},
"fossilworks.journal": {
"contributor": {
@@ -19727,6 +20711,7 @@
"keywords": [
"ontology"
],
+ "license": "CC0-1.0",
"mappings": {
"aberowl": "FPLX",
"biocontext": "FPLX",
@@ -19768,6 +20753,10 @@
"example": "ReviewVersion",
"homepage": "http://www.sparontologies.net/ontologies/fr",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
"subject agnostic"
],
"mappings": {
@@ -19795,11 +20784,18 @@
"example": "Grant",
"homepage": "http://www.sparontologies.net/ontologies/frapo",
"keywords": [
+ "academy",
+ "data model",
+ "funding bodies",
+ "grant application",
+ "report",
+ "research project",
"subject agnostic"
],
"mappings": {
"aberowl": "FRAPO",
- "fairsharing": "FAIRsharing.0a2576"
+ "fairsharing": "FAIRsharing.0a2576",
+ "lov": "frapo"
},
"name": "Funding, Research Administration and Projects Ontology",
"preferred_prefix": "FRAPO",
@@ -19824,10 +20820,17 @@
"example": "Expression",
"homepage": "http://www.sparontologies.net/ontologies/frbr",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "frbr",
+ "report",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.b34b43"
+ "fairsharing": "FAIRsharing.b34b43",
+ "lov": "frbr",
+ "zazuko": "frbr"
},
"name": "Functional Requirements for Bibliographic Records",
"preferred_prefix": "FRBR",
@@ -19846,6 +20849,12 @@
"download_rdf": "http://iflastandards.info/ns/fr/frbr/frbrer.jsonld",
"example": "1001",
"homepage": "https://www.iflastandards.info/fr/frbr/frbrer",
+ "keywords": [
+ "frbr"
+ ],
+ "mappings": {
+ "lov": "frbrer"
+ },
"name": "Functional Requirements for Bibliographic Records Entity-Relationship Model",
"part_of": "frbr",
"preferred_prefix": "frbrer",
@@ -19989,7 +20998,6 @@
"fungidb": {
"contact": {
"email": "jason.stajich@ucr.edu",
- "github": null,
"name": "Jason E. Stajich",
"orcid": "0000-0002-7591-0020"
},
@@ -20012,7 +21020,6 @@
"publications": [
{
"doi": "10.1016/j.fgb.2016.04.002",
- "pmc": null,
"pubmed": "27259951",
"title": "Database whiplash, crowdsourcing, and FungiDB",
"year": 2016
@@ -20033,10 +21040,7 @@
},
{
"doi": "10.1128/EC.00083-14",
- "pmc": null,
- "pubmed": null,
- "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus.",
- "year": null
+ "title": "Literature-based gene curation and proposed genetic nomenclature for cryptococcus."
}
],
"twitter": "fungidb",
@@ -20125,10 +21129,12 @@
"example": "0001707",
"homepage": "https://github.com/pombase/fypo",
"keywords": [
+ "gene ontology enrichment",
"genetics",
"life science",
"obo",
"ontology",
+ "phenotype",
"phylogenetics"
],
"license": "CC-BY-4.0",
@@ -20159,7 +21165,7 @@
"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": "2023-06-21"
+ "version": "2024-04-27"
},
"ga4ghdos": {
"description": "Assists in resolving data across cloud resources.",
@@ -20240,9 +21246,7 @@
"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
+ "name": "Julian Seidenberg"
},
"deprecated": true,
"description": "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic.",
@@ -20260,7 +21264,54 @@
"preferred_prefix": "galen",
"uri_format": "http://www.co-ode.org/ontologies/galen#$1"
},
+ "gallont": {
+ "contact": {
+ "email": "adeans@psu.edu",
+ "github": "adeans",
+ "name": "Andy Deans",
+ "orcid": "0000-0002-2119-4663"
+ },
+ "depends_on": [
+ "caro",
+ "flopo",
+ "ncbitaxon",
+ "obi",
+ "pato",
+ "po",
+ "poro",
+ "ro"
+ ],
+ "description": "Ontology of plant gall phenotypes. Plant galls are novel plant structures, generated by plants in response to biotic stressors. This ontology is used to annotate gall phenotypes (e.g., their colors, textures, sizes, locations on the plant) in a semantic way, in order to facilitate discoveries about the genetic and physiologic mechanisms responsible for such phenotypes. The ontology can also be used as a controlled vocabulary for natural language descriptions of plant galls.",
+ "download_json": "http://purl.obolibrary.org/obo/gallont.json",
+ "download_obo": "http://purl.obolibrary.org/obo/gallont.obo",
+ "download_owl": "http://purl.obolibrary.org/obo/gallont.owl",
+ "example": "0000001",
+ "homepage": "https://adeans.github.io/gallont/",
+ "keywords": [
+ "obo",
+ "ontology"
+ ],
+ "license": "CC0-1.0",
+ "mappings": {
+ "aberowl": "GALLONT",
+ "agroportal": "GALLONT",
+ "obofoundry": "gallont",
+ "ontobee": "GALLONT"
+ },
+ "name": "Plant Gall Ontology",
+ "pattern": "^\\d{7}$",
+ "preferred_prefix": "GALLONT",
+ "rdf_uri_format": "http://purl.obolibrary.org/obo/GALLONT_$1",
+ "repository": "https://github.com/adeans/gallont",
+ "uri_format": "http://purl.obolibrary.org/obo/GALLONT_$1"
+ },
"gard": {
+ "contact": {
+ "email": "eric.sid@nih.gov",
+ "github": "ericsid",
+ "name": "Eric Sid",
+ "orcid": "0000-0001-7697-3026"
+ },
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -20276,6 +21327,21 @@
"name": "Genetic and Rare Diseases Information Center",
"pattern": "^\\d+$",
"preferred_prefix": "gard",
+ "publications": [
+ {
+ "doi": "10.1080/02763869.2022.2131143",
+ "pubmed": "36394913",
+ "title": "Genetic and Rare Diseases Information Center (GARD)",
+ "year": 2022
+ },
+ {
+ "doi": "10.3233/trd-170011",
+ "pmc": "PMC5685198",
+ "pubmed": "29152459",
+ "title": "Marking 15 years of the Genetic and Rare Diseases Information Center",
+ "year": 2017
+ }
+ ],
"synonyms": [
"GARD",
"Genetic and Rare Diseases Information Center"
@@ -20305,13 +21371,14 @@
"orcid": "0000-0001-8910-9851"
},
"deprecated": true,
- "description": "A gazetteer constructed on ontological principles",
+ "description": "A gazetteer constructed on ontological principles. The countries are actively maintained.",
"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",
+ "geographical location",
"obo",
"ontology"
],
@@ -20360,6 +21427,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.zv11j3",
+ "integbio": "nbdc00069",
"re3data": "r3d100000039",
"wikidata": "P846"
},
@@ -20414,8 +21482,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^GCST\\d{6}\\d*$",
@@ -20495,11 +21562,14 @@
"example": "0000044",
"homepage": "https://github.com/IHCC-cohorts/GECKO",
"keywords": [
+ "biological sample",
+ "experimental measurement",
"genomics",
"life science",
"obo",
"ontology",
- "statistics"
+ "statistics",
+ "survey"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -20521,9 +21591,7 @@
"gemet": {
"contact": {
"email": "helpdesk@eionet.europa.eu",
- "github": null,
- "name": "Eionet Helpdesk",
- "orcid": null
+ "name": "Eionet Helpdesk"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -20562,6 +21630,7 @@
"mappings": {
"biocontext": "GENATLAS",
"fairsharing": "FAIRsharing.pmg2vd",
+ "integbio": "nbdc00275",
"miriam": "genatlas",
"n2t": "genatlas",
"prefixcommons": "genatlas",
@@ -20582,14 +21651,12 @@
"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
@@ -20624,6 +21691,7 @@
"edam": "2292",
"fairsharing": "FAIRsharing.9kahy4",
"go": "GenBank",
+ "integbio": "nbdc00276",
"prefixcommons": "genbank",
"re3data": "r3d100010528",
"uniprot": "DB-0028"
@@ -20776,7 +21844,6 @@
"genecards": {
"contact": {
"email": "marilyn.safran@weizmann.ac.il",
- "github": null,
"name": "Marilyn Safran",
"orcid": "0000-0001-5424-1393"
},
@@ -20792,6 +21859,7 @@
"mappings": {
"biocontext": "GENECARDS",
"fairsharing": "FAIRsharing.g7jbvn",
+ "integbio": "nbdc00242",
"miriam": "genecards",
"n2t": "genecards",
"prefixcommons": "genecards",
@@ -20813,7 +21881,6 @@
"publications": [
{
"doi": "10.1016/s0168-9525(97)01103-7",
- "pmc": null,
"pubmed": "9097728",
"title": "GeneCards: integrating information about genes, proteins and diseases",
"year": 1997
@@ -20827,7 +21894,6 @@
},
{
"doi": "10.1002/cpbi.5",
- "pmc": null,
"pubmed": "27322403",
"title": "The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses",
"year": 2016
@@ -20862,17 +21928,13 @@
},
{
"doi": "10.1093/bioinformatics/18.11.1542",
- "pmc": null,
"pubmed": "12424129",
"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
+ "title": "GeneCards: integrating information about genes, proteins and diseases."
}
],
"uri_format": "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"
@@ -20966,6 +22028,7 @@
"edam": "1035",
"fairsharing": "FAIRsharing.j7esqq",
"go": "GeneDB",
+ "integbio": "nbdc00469",
"miriam": "genedb",
"n2t": "genedb",
"ncbi": "GeneDB",
@@ -21057,14 +22120,18 @@
"homepage": "http://genepio.org/",
"keywords": [
"epidemiology",
+ "food",
+ "genome",
"genomics",
"obo",
- "ontology"
+ "ontology",
+ "pathogen"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "GENEPIO",
"biocontext": "GENEPIO",
+ "bioportal": "GENEPIO",
"fairsharing": "FAIRsharing.y1mmbv",
"obofoundry": "genepio",
"ols": "genepio",
@@ -21076,7 +22143,7 @@
"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"
+ "version": "2023-08-19"
},
"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.",
@@ -21135,6 +22202,7 @@
"mappings": {
"biocontext": "GENEWIKI",
"fairsharing": "FAIRsharing.t3snf",
+ "integbio": "nbdc00834",
"miriam": "genewiki",
"n2t": "genewiki",
"uniprot": "DB-0180"
@@ -21190,7 +22258,9 @@
"example": "0000632",
"homepage": "https://github.com/monarch-initiative/GENO-ontology/",
"keywords": [
+ "disease phenotype",
"genomics",
+ "genotype",
"obo",
"ontology"
],
@@ -21210,7 +22280,7 @@
"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_$1",
- "version": "2023-02-21"
+ "version": "2023-10-08"
},
"genpept": {
"description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.",
@@ -21245,8 +22315,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^GenProp\\d+$",
@@ -21265,7 +22334,6 @@
"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/5/geo.owl",
"example": "GDS1234",
"homepage": "https://www.ncbi.nlm.nih.gov/geo/",
"keywords": [
@@ -21276,17 +22344,15 @@
"genomics",
"life science",
"omics",
- "ontology",
"phenomics",
"transcriptomics"
],
"mappings": {
- "aberowl": "GEO",
- "biocontext": "GEO",
"cellosaurus": "GEO",
"edam": "1147",
"fairsharing": "FAIRsharing.5hc8vt",
"go": "GEO",
+ "integbio": "nbdc00080",
"miriam": "geo",
"n2t": "geo",
"prefixcommons": "geo",
@@ -21328,15 +22394,12 @@
},
{
"doi": "10.1038/35001676",
- "pmc": null,
"pubmed": "10693778",
"title": "One-stop shop for microarray data",
"year": 2000
},
{
"doi": "10.5281/zenodo.5706412",
- "pmc": null,
- "pubmed": null,
"title": "MINSEQE: Minimum Information about a high-throughput Nucleotide SeQuencing Experiment - a proposal for standards in functional genomic data reporting",
"year": 2012
}
@@ -21357,6 +22420,7 @@
"example": "000000021",
"homepage": "https://github.com/ufbmi/geographical-entity-ontology/wiki",
"keywords": [
+ "geographical location",
"human geography",
"obo",
"ontology",
@@ -21364,6 +22428,7 @@
],
"license": "CC-BY-4.0",
"mappings": {
+ "aberowl": "GEO",
"biocontext": "GEO",
"bioportal": "GEO",
"fairsharing": "FAIRsharing.27rndz",
@@ -21392,6 +22457,7 @@
"example": "3532759",
"homepage": "https://www.geonames.org",
"keywords": [
+ "geographical location",
"geography",
"geoinformatics"
],
@@ -21432,8 +22498,11 @@
"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",
+ "download_rdf": "http://www.bio.ntnu.no/ontology/GeXO/gexo.rdf",
"homepage": "http://www.semantic-systems-biology.org/apo",
"keywords": [
+ "expression data",
+ "gene expression",
"life science",
"ontology"
],
@@ -21459,9 +22528,7 @@
"gfo": {
"contact": {
"email": "heinrich.herre@imise.uni-leipzig.de",
- "github": null,
- "name": "Heinrich Herre",
- "orcid": null
+ "name": "Heinrich Herre"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -21476,6 +22543,7 @@
"keywords": [
"biomedical science",
"life science",
+ "modeling and simulation",
"ontology"
],
"mappings": {
@@ -21513,6 +22581,7 @@
"mappings": {
"biocontext": "GIARDIADB",
"fairsharing": "FAIRsharing.e7skwg",
+ "integbio": "nbdc01782",
"miriam": "giardiadb",
"n2t": "giardiadb",
"prefixcommons": "giardiadb",
@@ -21659,6 +22728,7 @@
"homepage": "https://www.glycoepitope.jp/epitopes/",
"mappings": {
"biocontext": "GLYCOEPITOPE",
+ "integbio": "nbdc00087",
"miriam": "glycoepitope",
"n2t": "glycoepitope"
},
@@ -21711,6 +22781,7 @@
"biocontext": "GLYCOMEDB",
"edam": "2664",
"fairsharing": "FAIRsharing.k5k0yh",
+ "integbio": "nbdc00899",
"miriam": "glycomedb",
"n2t": "glycomedb",
"prefixcommons": "glycomedb",
@@ -21738,7 +22809,6 @@
},
{
"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
@@ -21756,7 +22826,6 @@
"glyconavi": {
"contact": {
"email": "issaku@noguchi.or.jp",
- "github": null,
"name": "Issaku Yamada",
"orcid": "0000-0001-9504-189X"
},
@@ -21774,6 +22843,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.wvp1t7",
+ "integbio": "nbdc01174",
"miriam": "glyconavi"
},
"name": "GlycoNAVI",
@@ -21840,6 +22910,12 @@
"uri_format": "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1"
},
"glygen": {
+ "contact": {
+ "email": "jeetvora@gwmail.gwu.edu",
+ "github": "jeet-vora",
+ "name": "Jeet Vora",
+ "orcid": "0000-0002-5317-1458"
+ },
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -21847,17 +22923,29 @@
"orcid": "0000-0003-4423-4370"
},
"description": "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data.",
- "example": "G24361QY",
- "homepage": "https://glygen.org/glycan/",
+ "example": "G17689DH",
+ "homepage": "https://glygen.org/",
"keywords": [
+ "genomics",
"glycomics",
- "life science"
+ "glycoproteomics",
+ "life science",
+ "proteomics"
],
"mappings": {
"fairsharing": "FAIRsharing.aI1J5W",
+ "integbio": "nbdc02434",
"uniprot": "DB-0254"
},
- "name": "Computational and Informatics Resources for Glycoscience",
+ "name": "GlyGen Computational and Informatics Resources for Glycoscience",
+ "owners": [
+ {
+ "name": "George Washington University",
+ "partnered": false,
+ "ror": "00y4zzh67"
+ }
+ ],
+ "pattern": "^G[0-9]{5}[A-Z]{2}$",
"preferred_prefix": "glygen",
"publications": [
{
@@ -21869,12 +22957,10 @@
},
{
"doi": "cwz080",
- "pmc": null,
- "pubmed": null,
- "title": "GlyGen: Computational and Informatics Resources for Glycoscience.",
- "year": null
+ "title": "GlyGen: Computational and Informatics Resources for Glycoscience."
}
],
+ "repository": "https://github.com/glygener",
"twitter": "gly_gen",
"uri_format": "https://glygen.org/glycan/$1"
},
@@ -21889,9 +22975,11 @@
"mappings": {
"biocontext": "GLYTOUCAN",
"fairsharing": "FAIRsharing.5Pze7l",
+ "integbio": "nbdc01535",
"miriam": "glytoucan",
"n2t": "glytoucan",
- "re3data": "r3d100012388"
+ "re3data": "r3d100012388",
+ "togoid": "Glytoucan"
},
"name": "GlyTouCan",
"pattern": "^G[0-9]{5}[A-Z]{2}$",
@@ -21943,10 +23031,7 @@
},
{
"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
+ "title": "Decision tree supported substructure prediction of metabolites from GC-MS profiles"
}
],
"uri_format": "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"
@@ -22036,6 +23121,7 @@
"keywords": [
"culture",
"knowledge and information systems",
+ "publication",
"social science"
],
"mappings": {
@@ -22099,8 +23185,6 @@
"publications": [
{
"doi": "10.5281/zenodo.6678278",
- "pmc": null,
- "pubmed": null,
"title": "GNOme - Glycan Naming and Subsumption Ontology",
"year": 2021
}
@@ -22111,7 +23195,7 @@
"gnome"
],
"uri_format": "http://purl.obolibrary.org/obo/GNO_$1",
- "version": "2023-05-08"
+ "version": "2024-04-17"
},
"gnomad": {
"contact": {
@@ -22135,6 +23219,9 @@
"github_request_issue": 695,
"homepage": "https://gnomad.broadinstitute.org",
"license": "CC0-1.0",
+ "mappings": {
+ "integbio": "nbdc02561"
+ },
"name": "Genome Aggregation Database",
"preferred_prefix": "gnomad",
"publications": [
@@ -22158,7 +23245,6 @@
"gnpis": {
"contact": {
"email": "urgi-contact@versailles.inra.fr",
- "github": null,
"name": "URGI Contact",
"orcid": "0000-0003-3001-4908"
},
@@ -22240,6 +23326,14 @@
"name": "Suzi Aleksander",
"orcid": "0000-0001-6787-2901"
},
+ "contributor_extras": [
+ {
+ "email": "jmcl@ebi.ac.uk",
+ "github": "jamesamcl",
+ "name": "James Alastair McLaughlin",
+ "orcid": "0000-0002-8361-2795"
+ }
+ ],
"depends_on": [
"cl",
"ncbitaxon",
@@ -22253,10 +23347,23 @@
"example": "0032571",
"homepage": "http://geneontology.org/",
"keywords": [
+ "annotation",
+ "biocuration",
+ "biological process",
+ "cellular component",
+ "data model",
+ "expression data",
"gene",
+ "gene functional annotation",
+ "gene ontology enrichment",
+ "knowledge representation",
"life science",
+ "molecular function",
"obo",
- "ontology"
+ "ontology",
+ "protein",
+ "sequence annotation",
+ "transcript"
],
"license": "CC-BY-4.0",
"logo": "https://obofoundry.org/images/go_logo.png",
@@ -22270,14 +23377,17 @@
"fairsharing": "FAIRsharing.6xq0ee",
"go": "GO",
"hl7": "2.16.840.1.113883.6.128",
+ "integbio": "nbdc00074",
"miriam": "go",
"n2t": "go",
"ncbi": "GO",
"obofoundry": "go",
"ols": "go",
"ontobee": "GO",
+ "pathguide": "272",
"prefixcommons": "go",
"re3data": "r3d100014165",
+ "togoid": "Go",
"uniprot": "DB-0037",
"wikidata": "P686"
},
@@ -22294,13 +23404,6 @@
"name": "GO Browser",
"uri_format": "http://www.informatics.jax.org/searches/GO.cgi?id=GO:$1"
},
- {
- "code": "CURATOR_REVIEW",
- "description": "GO through PANTHER",
- "homepage": "http://www.pantherdb.org/",
- "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.",
@@ -22336,11 +23439,25 @@
"name": "neXtProt GO Browser",
"uri_format": "https://www.nextprot.org/term/GO:$1"
},
+ {
+ "code": "pantherdb",
+ "description": "GO Browser in PantherDB",
+ "homepage": "http://www.pantherdb.org/panther",
+ "name": "PatherDB",
+ "uri_format": "http://www.pantherdb.org/panther/category.do?categoryAcc=GO:$1"
+ },
{
"code": "quickgo",
+ "description": "Gene Ontology browser from the EBI",
+ "homepage": "https://www.ebi.ac.uk/QuickGO/",
+ "name": "QuickGO",
+ "uri_format": "https://www.ebi.ac.uk/QuickGO/term/GO:$1"
+ },
+ {
+ "code": "quickgo.legacy",
"description": "QuickGO (Gene Ontology browser)",
"homepage": "https://www.ebi.ac.uk/QuickGO/",
- "name": "QuickGO (Gene Ontology browser)",
+ "name": "QuickGO (Legacy URL)",
"uri_format": "https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:$1"
}
],
@@ -22420,8 +23537,8 @@
"gomfid"
],
"twitter": "news4go",
- "uri_format": "http://amigo.geneontology.org/amigo/term/GO:$1",
- "version": "2023-06-11"
+ "uri_format": "http://purl.obolibrary.org/obo/GO_$1",
+ "version": "2024-04-24"
},
"go.gpi": {
"contributor": {
@@ -22432,7 +23549,6 @@
},
"contributor_extras": [
{
- "email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
@@ -22520,6 +23636,7 @@
"mappings": {
"biocontext": "GOA",
"fairsharing": "FAIRsharing.7zffgc",
+ "integbio": "nbdc00468",
"miriam": "goa",
"n2t": "goa",
"ncbi": "GOA",
@@ -22613,6 +23730,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.5q1p14",
+ "integbio": "nbdc00483",
"miriam": "gold",
"prefixcommons": "gold",
"re3data": "r3d100010808"
@@ -22667,17 +23785,13 @@
},
{
"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
},
{
"doi": "11125068",
- "pmc": null,
- "pubmed": null,
- "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.",
- "year": null
+ "title": "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide."
}
],
"uri_format": "https://gold.jgi.doe.gov/resolver?id=$1"
@@ -22830,7 +23944,6 @@
"gpcrdb": {
"contact": {
"email": "david.gloriam@sund.ku.dk",
- "github": null,
"name": "David Gloriam",
"orcid": "0000-0002-4299-7561"
},
@@ -22846,6 +23959,7 @@
"mappings": {
"biocontext": "GPCRDB",
"fairsharing": "FAIRsharing.e4n3an",
+ "integbio": "nbdc00484",
"miriam": "gpcrdb",
"n2t": "gpcrdb",
"prefixcommons": "gpcrdb",
@@ -22984,7 +24098,6 @@
"publications": [
{
"doi": "10.1021/pr049882h",
- "pmc": null,
"pubmed": "15595733",
"title": "Open source system for analyzing, validating, and storing protein identification data",
"year": 2004
@@ -23043,9 +24156,7 @@
"banana": "GRO",
"contact": {
"email": "po-discuss@plantontology.org",
- "github": null,
- "name": "Plant Ontology Administrators",
- "orcid": null
+ "name": "Plant Ontology Administrators"
},
"deprecated": true,
"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 collection refers to growth stage ontology information in Gramene.",
@@ -23176,7 +24287,6 @@
"greengenes": {
"contact": {
"email": "GLAndersen@lbl.gov",
- "github": null,
"name": "Gary L Andersen",
"orcid": "0000-0002-1618-9827"
},
@@ -23191,6 +24301,7 @@
"mappings": {
"biocontext": "GREENGENES",
"fairsharing": "FAIRsharing.bpxgb6",
+ "integbio": "nbdc01824",
"miriam": "greengenes",
"n2t": "greengenes",
"ncbi": "Greengenes",
@@ -23219,10 +24330,7 @@
},
{
"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
+ "title": "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB."
}
],
"uri_format": "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"
@@ -23296,9 +24404,7 @@
"gro": {
"contact": {
"email": "vlee@ebi.ac.uk",
- "github": null,
- "name": "Vivian Lee",
- "orcid": null
+ "name": "Vivian Lee"
},
"deprecated": true,
"description": "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes.",
@@ -23468,17 +24574,13 @@
},
{
"doi": "10.1681/asn.2007101078",
- "pmc": null,
"pubmed": "18287559",
"title": "GUDMAP: the genitourinary developmental molecular anatomy project",
"year": 2008
},
{
"doi": "10.1681/ASN.2007101078",
- "pmc": null,
- "pubmed": null,
- "title": "GUDMAP: the genitourinary developmental molecular anatomy project.",
- "year": null
+ "title": "GUDMAP: the genitourinary developmental molecular anatomy project."
}
],
"twitter": "GUDMAP",
@@ -23554,8 +24656,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^[AEP]-\\w{4}-\\d+$",
@@ -23585,8 +24686,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^\\w+$",
@@ -23596,7 +24696,6 @@
"habronattus": {
"contact": {
"email": "peteremidford@yahoo.com",
- "github": null,
"name": "Peter Midford",
"orcid": "0000-0001-6512-3296"
},
@@ -23699,7 +24798,6 @@
"hamap": {
"contact": {
"email": "alan.bridge@isb-sib.ch",
- "github": null,
"name": "Alan Bridge",
"orcid": "0000-0003-2148-9135"
},
@@ -23752,7 +24850,7 @@
},
"hancestro": {
"contact": {
- "email": "danielle.welter@uni.lu",
+ "email": "dwelter.ontologist@gmail.com",
"github": "daniwelter",
"name": "Danielle Welter",
"orcid": "0000-0003-1058-2668"
@@ -23760,9 +24858,10 @@
"description": "Human ancestry ontology for the NHGRI GWAS Catalog",
"download_owl": "http://purl.obolibrary.org/obo/hancestro.owl",
"example": "0290",
- "homepage": "https://github.com/EBISPOT/ancestro",
+ "homepage": "https://ebispot.github.io/hancestro/",
"keywords": [
"demographics",
+ "genome-wide association study",
"human genetics",
"obo",
"ontology",
@@ -23783,8 +24882,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^\\d{4}$",
@@ -23810,7 +24908,7 @@
"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": "2023-06-20"
+ "version": "2024-04-25"
},
"hao": {
"contact": {
@@ -23826,6 +24924,7 @@
"homepage": "http://hymao.org",
"keywords": [
"anatomy",
+ "image",
"life science",
"obo",
"ontology"
@@ -23965,6 +25064,21 @@
],
"uri_format": "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"
},
+ "hc.trial": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]",
+ "example": "239287",
+ "homepage": "https://health-products.canada.ca/ctdb-bdec",
+ "name": "Health Canada Clinical Trials Database",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "hc.trial",
+ "uri_format": "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"
+ },
"hcao": {
"description": "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas.",
"download_owl": "http://ontology.data.humancellatlas.org/ontologies/hcao/releases/2023-05-16/hcao.owl",
@@ -23979,12 +25093,22 @@
"no_own_terms": true,
"preferred_prefix": "hcao"
},
+ "hco": {
+ "description": "The Human Chromosome Ontology (HCO) provides simple and stable URIs for human reference genome versions to semantically identify human chromosomes.",
+ "example": "MT",
+ "homepage": "https://dbcls.rois.ac.jp/",
+ "mappings": {
+ "miriam": "hco"
+ },
+ "name": "Human Chromosome Ontology",
+ "pattern": "^.+$",
+ "preferred_prefix": "hco",
+ "uri_format": "http://biohackathon.org/resource/hco#$1"
+ },
"hcpcs": {
"contact": {
"email": "Cynthia.Hake@cms.hhs.gov",
- "github": null,
- "name": "Cynthia Hake",
- "orcid": null
+ "name": "Cynthia Hake"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -24051,6 +25175,7 @@
],
"homepage": "https://www.handle.net/",
"keywords": [
+ "centrally registered identifier",
"subject agnostic"
],
"mappings": {
@@ -24075,6 +25200,7 @@
"biocontext": "HDR",
"miriam": "hdr",
"n2t": "hdr",
+ "pathguide": "307",
"prefixcommons": "hdr"
},
"name": "Homeodomain Research",
@@ -24119,8 +25245,7 @@
{
"name": "Université de Sherbrooke",
"partnered": false,
- "ror": "00kybxq39",
- "wikidata": null
+ "ror": "00kybxq39"
}
],
"pattern": "^\\d{7}$",
@@ -24159,6 +25284,7 @@
"mappings": {
"biocontext": "HGMD",
"edam": "3265",
+ "integbio": "nbdc00097",
"miriam": "hgmd",
"n2t": "hgmd"
},
@@ -24170,7 +25296,6 @@
"hgnc": {
"contact": {
"email": "elspeth@genenames.org",
- "github": null,
"name": "Elspeth Bruford",
"orcid": "0000-0002-8380-5247"
},
@@ -24181,9 +25306,14 @@
"keywords": [
"classification",
"gene",
+ "gene name",
"life science",
- "ontology"
+ "non-coding rna",
+ "ontology",
+ "protein",
+ "pseudogene"
],
+ "license": "CC0-1.0",
"mappings": {
"aberowl": "HGNC",
"biocontext": "HGNC",
@@ -24197,6 +25327,7 @@
"n2t": "hgnc",
"ncbi": "HGNC",
"prefixcommons": "hgnc",
+ "togoid": "Hgnc",
"uniprot": "DB-0042",
"wikidata": "P354"
},
@@ -24243,7 +25374,6 @@
},
{
"doi": "10.1159/000131404",
- "pmc": null,
"pubmed": "295268",
"title": "International system for human gene nomenclature (1979) ISGN (1979)",
"year": 1979
@@ -24291,6 +25421,7 @@
"biocontext": "HGNC.SYMBOL",
"miriam": "hgnc.symbol",
"n2t": "hgnc.symbol",
+ "togoid": "HgncSymbol",
"wikidata": "P353"
},
"name": "HGNC gene symbol",
@@ -24319,7 +25450,73 @@
"uri_format": "https://apps.pathwaycommons.org/interactions?source=$1"
}
],
- "uri_format": "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"
+ "uri_format": "https://www.genenames.org/data/gene-symbol-report/#!/symbol/$1"
+ },
+ "hgvs": {
+ "contact": {
+ "email": "reecehart@gmail.com",
+ "github": "reece",
+ "name": "Reece Hart",
+ "orcid": "0000-0003-3463-0775"
+ },
+ "contributor": {
+ "email": "miseming@sfu.ca",
+ "github": "miseminger",
+ "name": "Madeline Iseminger",
+ "orcid": "0000-0002-0548-891X"
+ },
+ "description": "The HGVS Nomenclature is an internationally-recognized standard for the description of DNA, RNA and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases. The HGVS Nomenclature is administered by the [HGVS Variant Nomenclature Committee (HVNC)](https://hgvs-nomenclature.org/stable/hvnc/) under the auspices of the [Human Genome Organization (HUGO)](https://hugo-int.org/).",
+ "example": "NP_003997.1:p.Trp24Cys",
+ "example_extras": [
+ "NG_012337.3(NM_003002.4):c.274G>T",
+ "NG_012337.3(NM_003002.4):r.(274g>u)",
+ "NC_000011.10:g.112088970del",
+ "NC_000011.10(NM_001276503.2):c.169+998del",
+ "GRCh38(chr11):g.112088970del"
+ ],
+ "github_request_issue": 1032,
+ "homepage": "https://hgvs-nomenclature.org/stable/background/simple/",
+ "mappings": {
+ "hl7": "2.16.840.1.113883.6.282",
+ "wikidata": "P3331"
+ },
+ "name": "Human Genome Variation Society Nomenclature",
+ "preferred_prefix": "hgvs",
+ "providers": [
+ {
+ "code": "mutalyzer",
+ "description": " The Mutalyzer tool suite is designed to be of help when working with HGVS sequence variant nomenclature descriptions.",
+ "homepage": "https://mutalyzer.nl",
+ "name": "LUMC Mutalyzer 3",
+ "uri_format": "https://mutalyzer.nl/api/description_to_model/$1"
+ }
+ ],
+ "publications": [
+ {
+ "doi": "10.1002/humu.22981",
+ "pubmed": "26931183",
+ "title": "HGVS Recommendations for the Description of Sequence Variants: 2016 Update",
+ "year": 2016
+ },
+ {
+ "doi": "10.1093/bioinformatics/btu630",
+ "pmc": "PMC4287946",
+ "pubmed": "25273102",
+ "title": "A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature",
+ "year": 2014
+ }
+ ],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/460"
+ ],
+ "repository": "https://github.com/HGVSnomenclature/hgvs-nomenclature",
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "http://reg.clinicalgenome.org/allele?hgvs=$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.",
@@ -24375,7 +25572,7 @@
"uri_format": "https://www.hipsci.org/lines/#/lines/$1"
},
"hivreagentprogram": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "ARP-1513",
"homepage": "https://www.hivreagentprogram.org/",
"mappings": {
@@ -24437,10 +25634,13 @@
"cheminf": "000408",
"edam": "2622",
"fairsharing": "FAIRsharing.sye5js",
+ "integbio": "nbdc00909",
"miriam": "hmdb",
"n2t": "hmdb",
+ "pathguide": "244",
"prefixcommons": "hmdb",
"re3data": "r3d100011285",
+ "togoid": "Hmdb",
"wikidata": "P2057"
},
"name": "Human Metabolome Database",
@@ -24486,10 +25686,7 @@
},
{
"doi": "10.1093/nar/gkn810",
- "pmc": null,
- "pubmed": null,
- "title": "HMDB: a knowledgebase for the human metabolome",
- "year": null
+ "title": "HMDB: a knowledgebase for the human metabolome"
}
],
"synonyms": [
@@ -24571,7 +25768,6 @@
"hoelzel": {
"contact": {
"email": "info@hoelzel.de",
- "github": null,
"name": "Carsten Linder",
"orcid": "0009-0009-3816-8777"
},
@@ -24635,6 +25831,7 @@
"mappings": {
"biocontext": "HOGENOM",
"fairsharing": "FAIRsharing.qe8tz8",
+ "integbio": "nbdc01858",
"miriam": "hogenom",
"n2t": "hogenom",
"prefixcommons": "hogenom",
@@ -24669,10 +25866,7 @@
},
{
"doi": "10.1186/1471-2105-10-S6-S3",
- "pmc": null,
- "pubmed": null,
- "title": "Databases of homologous gene families for comparative genomics.",
- "year": null
+ "title": "Databases of homologous gene families for comparative genomics."
}
],
"uri_format": "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"
@@ -24728,7 +25922,10 @@
"homepage": "https://github.com/BgeeDB/homology-ontology",
"keywords": [
"anatomy",
+ "homologous",
+ "life cycle stage",
"life science",
+ "molecular entity",
"obo",
"ontology"
],
@@ -24748,7 +25945,6 @@
"publications": [
{
"doi": "10.1016/j.tig.2009.12.012",
- "pmc": null,
"pubmed": "20116127",
"title": "An ontology to clarify homology-related concepts",
"year": 2010
@@ -24846,9 +26042,11 @@
"mappings": {
"biocontext": "HOMOLOGENE",
"fairsharing": "FAIRsharing.mzc066",
+ "integbio": "nbdc00101",
"miriam": "homologene",
"n2t": "homologene",
"prefixcommons": "homologene",
+ "togoid": "Homologene",
"wikidata": "P593"
},
"name": "HomoloGene",
@@ -24882,7 +26080,7 @@
"uri_format": "https://www.ncbi.nlm.nih.gov/homologene/$1"
},
"horizon_discovery": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "HD+118-001",
"homepage": "https://horizondiscovery.com/",
"mappings": {
@@ -24924,7 +26122,6 @@
"hovergen": {
"contact": {
"email": "duret@biomserv.univ-lyon1.fr",
- "github": null,
"name": "Laurent Duret",
"orcid": "0000-0003-2836-3463"
},
@@ -24940,6 +26137,7 @@
"mappings": {
"biocontext": "HOVERGEN",
"fairsharing": "FAIRsharing.dg1f0e",
+ "integbio": "nbdc00284",
"miriam": "hovergen",
"n2t": "hovergen",
"prefixcommons": "hovergen"
@@ -24959,7 +26157,6 @@
"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
@@ -24988,10 +26185,13 @@
"homepage": "http://www.human-phenotype-ontology.org/",
"keywords": [
"biomedical science",
+ "disease",
"genetics",
+ "industry",
"obo",
"ontology",
"phenomics",
+ "phenotype",
"preclinical studies"
],
"license": "hpo",
@@ -25003,6 +26203,8 @@
"bioportal": "HP_O",
"fairsharing": "FAIRsharing.kbtt7f",
"hl7": "2.16.840.1.113883.6.339",
+ "integbio": "nbdc02559",
+ "lov": "hpo",
"miriam": "hp",
"n2t": "hp",
"obofoundry": "hp",
@@ -25023,13 +26225,6 @@
"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",
@@ -25053,7 +26248,6 @@
},
{
"doi": "10.1111/j.1399-0004.2010.01436.x",
- "pmc": null,
"pubmed": "20412080",
"title": "The human phenotype ontology",
"year": 2010
@@ -25072,13 +26266,12 @@
"hpo"
],
"twitter": "hp_ontology",
- "uri_format": "https://hpo.jax.org/app/browse/term/HP:$1",
- "version": "2023-06-17"
+ "uri_format": "http://purl.obolibrary.org/obo/HP_$1",
+ "version": "2024-04-26"
},
"hpa": {
"contact": {
"email": "mathias.uhlen@scilifelab.se",
- "github": null,
"name": "Mathias Uhlen",
"orcid": "0000-0002-4858-8056"
},
@@ -25118,14 +26311,12 @@
"publications": [
{
"doi": "10.1126/science.aan2507",
- "pmc": null,
"pubmed": "28818916",
"title": "A pathology atlas of the human cancer transcriptome",
"year": 2017
},
{
"doi": "10.1126/science.aal3321",
- "pmc": null,
"pubmed": "28495876",
"title": "A subcellular map of the human proteome",
"year": 2017
@@ -25139,87 +26330,82 @@
},
{
"doi": "10.1126/science.1260419",
- "pmc": null,
"pubmed": "25613900",
"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",
"year": 2010
},
{
"doi": "10.1002/path.2440",
- "pmc": null,
"pubmed": "18853439",
"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",
"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",
"year": 2005
},
{
"doi": "eaal3321",
- "pmc": null,
- "pubmed": null,
- "title": "A subcellular map of the human proteome.",
- "year": null
+ "title": "A subcellular map of the human proteome."
},
{
"doi": "10.1074/mcp.R800013-MCP200",
- "pmc": null,
- "pubmed": null,
- "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies.",
- "year": null
+ "title": "A genecentric Human Protein Atlas for expression profiles based on antibodies."
},
{
"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
+ "title": "A human protein atlas for normal and cancer tissues based on antibody proteomics."
}
],
"twitter": "ProteinAtlas",
"uri_format": "http://www.proteinatlas.org/$1"
},
"hpath": {
- "description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.",
- "download_owl": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo",
+ "comment": "This ontology used to be available in OLS3, but is no longer available in OLS4.\n\nThe URI format string in this resource takes the form of an OBO PURL, but it is not itself registered with the OBO Foundry, and terms therefore redirect into http://ontologies.berkeleybop.org. This happens because the data is curated natively in the OBO Flat File Format from which CURIEs are automatically assumed to expand to OBO PURLs",
+ "contact": {
+ "email": "carlo.ravagli@novartis.com",
+ "github": "carloravagli",
+ "name": "Carlo Ravagli",
+ "orcid": "0000-0001-8372-8387"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species.\n\nThe original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]",
+ "download_obo": "https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo",
"example": "2000191",
"homepage": "https://github.com/Novartis/hpath",
"keywords": [
- "microbiology",
- "ontology",
- "taxonomy"
+ "ontology"
],
- "mappings": {
- "fairsharing": "FAIRsharing.kj336a",
- "ols": "hpath"
- },
"name": "Histopathology Ontology",
"pattern": "^\\d+$",
"preferred_prefix": "hpath",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/927"
+ ],
"repository": "https://github.com/Novartis/hpath",
"synonyms": [
"MC"
],
- "uri_format": "http://purl.obolibrary.org/obo/MC_$1",
- "version": "2019-07-05"
+ "uri_format": "http://purl.obolibrary.org/obo/MC_$1"
},
"hpm.peptide": {
"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.",
@@ -25253,7 +26439,6 @@
"hprd": {
"contact": {
"email": "pandey@jhmi.edu",
- "github": null,
"name": "Akhilesh Pandey",
"orcid": "0000-0001-9943-6127"
},
@@ -25267,8 +26452,10 @@
"mappings": {
"biocontext": "HPRD",
"fairsharing": "FAIRsharing.y2qws7",
+ "integbio": "nbdc00103",
"miriam": "hprd",
"n2t": "hprd",
+ "pathguide": "14",
"prefixcommons": "hprd",
"re3data": "r3d100010978"
},
@@ -25298,7 +26485,6 @@
"hpscreg": {
"contact": {
"email": "stefanie.seltmann@ibmt.fraunhofer.de",
- "github": null,
"name": "Stefanie Seltmann",
"orcid": "0000-0002-8411-3226"
},
@@ -25322,7 +26508,6 @@
"publications": [
{
"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)",
"year": 2020
@@ -25336,7 +26521,6 @@
},
{
"doi": "10.1016/j.scr.2019.101539",
- "pmc": null,
"pubmed": "31450190",
"title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC",
"year": 2019
@@ -25357,31 +26541,19 @@
},
{
"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
+ "title": "A Manually Curated Database on Clinical Studies Involving Cell Products Derived from Human Pluripotent Stem Cells."
},
{
"doi": "S2213-6711(17)30531-3",
- "pmc": null,
- "pubmed": null,
- "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.",
- "year": null
+ "title": "A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells."
},
{
"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
+ "title": "Access to stem cell data and registration of pluripotent cell lines: The Human Pluripotent Stem Cell Registry (hPSCreg)."
},
{
"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
+ "title": "A pathway for attesting ethical provenance of cell lines: Lessons from the European human pluripotent stem cell registry (hPSC(reg))."
}
],
"uri_format": "https://hpscreg.eu/cell-line/$1"
@@ -25404,6 +26576,7 @@
"keywords": [
"anatomy",
"developmental biology",
+ "life cycle stage",
"obo",
"ontology"
],
@@ -25426,8 +26599,7 @@
"synonyms": [
"HsapDv"
],
- "uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1",
- "version": "2020-03-10"
+ "uri_format": "http://purl.obolibrary.org/obo/HsapDv_$1"
},
"hsdb": {
"contributor": {
@@ -25440,6 +26612,7 @@
"example": "5621",
"homepage": "https://pubchem.ncbi.nlm.nih.gov/source/hsdb",
"mappings": {
+ "integbio": "nbdc00930",
"wikidata": "P2062"
},
"name": "Hazardous Substances Data Bank",
@@ -25538,7 +26711,6 @@
"year": 1996
},
{
- "doi": null,
"pmc": "PMC308328",
"pubmed": "7937066",
"title": "The HSSP database of protein structure-sequence alignments",
@@ -25591,6 +26763,7 @@
"mappings": {
"biocontext": "HUGE",
"fairsharing": "FAIRsharing.zx2ztd",
+ "integbio": "nbdc00104",
"miriam": "huge",
"n2t": "huge",
"prefixcommons": "huge",
@@ -25629,12 +26802,13 @@
"fovt",
"labo",
"maxo",
+ "mcro",
"pco",
"psdo",
"xpo"
],
"contact": {
- "email": "jiezheng@pennmedicine.upenn.edu",
+ "email": "zhengj2007@gmail.com",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
@@ -25645,11 +26819,18 @@
"example": "0000030",
"homepage": "https://github.com/information-artifact-ontology/IAO/",
"keywords": [
+ "assay",
"biomedical science",
+ "data identity and mapping",
"data management",
+ "drug report",
+ "experimental measurement",
"knowledge and information systems",
"obo",
"ontology",
+ "protocol",
+ "reagent",
+ "study design",
"subject agnostic"
],
"license": "CC-BY-4.0",
@@ -25681,7 +26862,6 @@
"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
@@ -25695,13 +26875,10 @@
"icd10": {
"contact": {
"email": "info@who.int",
- "github": null,
- "name": "World Health Organization",
- "orcid": null
+ "name": "World Health Organization"
},
"contributor_extras": [
{
- "email": null,
"github": "joeflack4",
"name": "Joe Flack",
"orcid": "0000-0002-2906-7319"
@@ -25741,6 +26918,7 @@
"keywords": [
"biomedical science",
"classification",
+ "diagnosis",
"disease",
"epidemiology",
"global health",
@@ -25748,6 +26926,7 @@
"ontology",
"taxonomy"
],
+ "license": "https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf",
"mappings": {
"aberowl": "ICD10",
"bartoc": "447",
@@ -25827,9 +27006,7 @@
"icd10cm": {
"contact": {
"email": "pbrooks@hcfa.gov",
- "github": null,
- "name": "Patricia Brooks",
- "orcid": null
+ "name": "Patricia Brooks"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -25859,8 +27036,12 @@
"homepage": "https://www.icd10data.com/ICD10CM",
"keywords": [
"biomedical science",
+ "diagnosis",
+ "disease",
+ "electronic health record",
"health science",
"medicine",
+ "morbidity",
"ontology"
],
"mappings": {
@@ -25890,9 +27071,7 @@
"icd10pcs": {
"contact": {
"email": "patricia.brooks2@cms.hhs.gov",
- "github": null,
- "name": "Pat Brooks",
- "orcid": null
+ "name": "Pat Brooks"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -25905,8 +27084,14 @@
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS",
"keywords": [
"biomedical science",
+ "classification",
+ "diagnosis",
+ "disease",
+ "electronic health record",
"epidemiology",
"health science",
+ "hospital",
+ "morbidity",
"ontology"
],
"mappings": {
@@ -25933,18 +27118,27 @@
"homepage": "https://icd.who.int/",
"keywords": [
"biomedical science",
+ "diagnosis",
+ "disease",
+ "electronic health record",
"epidemiology",
"global health",
- "health science"
+ "health science",
+ "morbidity"
],
+ "license": "CC-BY-ND-3.0-IGO",
"mappings": {
"fairsharing": "FAIRsharing.97805c",
"hl7": "2.16.840.1.113883.6.347",
+ "integbio": "nbdc02556",
"wikidata": "P7807"
},
"name": "International Classification of Diseases, 11th Revision",
"pattern": "^[1-9]\\d*$",
"preferred_prefix": "icd11",
+ "references": [
+ "https://icd.who.int/docs/icd-api/license/"
+ ],
"synonyms": [
"ICD-11"
],
@@ -25978,9 +27172,7 @@
"icd9cm": {
"contact": {
"email": "pbrooks@hcfa.gov",
- "github": null,
- "name": "Patricia Brooks",
- "orcid": null
+ "name": "Patricia Brooks"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -25993,9 +27185,12 @@
"homepage": "https://www.cdc.gov/nchs/icd/icd9cm.htm",
"keywords": [
"biomedical science",
+ "diagnosis",
+ "disease",
"epidemiology",
"health science",
"medicine",
+ "morbidity",
"ontology",
"preclinical studies"
],
@@ -26021,7 +27216,6 @@
"icdc": {
"contact": {
"email": "annika.jahnke-bornemann@uni-hamburg.de",
- "github": null,
"name": "Annika Jahnke-Bornemann",
"orcid": "0000-0001-7815-151X"
},
@@ -26055,14 +27249,9 @@
"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",
@@ -26285,11 +27474,8 @@
"preferred_prefix": "icepo",
"publications": [
{
- "doi": null,
"pmc": "PMC4823818",
- "pubmed": null,
- "title": "ICEPO: the ion channel electrophysiology ontology",
- "year": null
+ "title": "ICEPO: the ion channel electrophysiology ontology"
}
],
"twitter": "neXtProt_news",
@@ -26299,9 +27485,7 @@
"comment": "This might be possible to roll directly into ICD11",
"contact": {
"email": "info@who.int",
- "github": null,
- "name": "The World Health Organization",
- "orcid": null
+ "name": "The World Health Organization"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -26315,6 +27499,7 @@
"homepage": "https://icd.who.int/dev11/l-icf/en",
"keywords": [
"biomedical science",
+ "electronic health record",
"health science",
"medicine",
"ontology",
@@ -26332,7 +27517,7 @@
"uri_format": "http://id.who.int/icd/entity/$1"
},
"iclc": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "ATL98012",
"homepage": "http://www.iclc.it",
"mappings": {
@@ -26346,7 +27531,6 @@
"icldb": {
"contact": {
"email": "surjeet.arya@uky.edu",
- "github": null,
"name": "Surjeet Kumar Arya",
"orcid": "0000-0002-2212-4771"
},
@@ -26359,6 +27543,9 @@
"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",
+ "mappings": {
+ "cellosaurus": "ICLDB"
+ },
"name": "Insect Cell Line Database",
"preferred_prefix": "icldb",
"uri_format": "https://entomology.ca.uky.edu/content/$1"
@@ -26413,8 +27600,10 @@
"mappings": {
"biocontext": "IDEAL",
"fairsharing": "FAIRsharing.h3y42f",
+ "integbio": "nbdc01456",
"miriam": "ideal",
"n2t": "ideal",
+ "pathguide": "701",
"uniprot": "DB-0251"
},
"name": "Intrinsically Disordered proteins with Extensive Annotations and Literature",
@@ -26441,12 +27630,23 @@
"name": "Lindsay Cowell",
"orcid": "0000-0003-1617-8244"
},
+ "contributor_extras": [
+ {
+ "email": "github@yohannparis.com",
+ "github": "YohannParis",
+ "name": "Yohann Paris",
+ "orcid": "0009-0006-6049-1392"
+ }
+ ],
"description": "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases.",
"download_owl": "http://purl.obolibrary.org/obo/ido.owl",
"example": "0000504",
"homepage": "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology",
"keywords": [
"biomedical science",
+ "classification",
+ "disease",
+ "disease process modeling",
"molecular infection biology",
"obo",
"ontology",
@@ -26465,7 +27665,7 @@
"ontobee": "IDO"
},
"name": "Infectious Disease Ontology",
- "pattern": "^[0-9]+$",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "IDO",
"providers": [
{
@@ -26487,7 +27687,7 @@
],
"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/ols4/ontologies/ido/terms?obo_id=IDO:$1",
+ "uri_format": "http://purl.obolibrary.org/obo/IDO_$1",
"version": "2017-11-03"
},
"idocovid19": {
@@ -26528,7 +27728,6 @@
"idoden": {
"contact": {
"email": "elvira@imbb.forth.gr",
- "github": null,
"name": "Elvira Mitraka",
"orcid": "0000-0003-0719-3485"
},
@@ -26562,7 +27761,6 @@
"idog": {
"contact": {
"email": "baoym@big.ac.cn",
- "github": null,
"name": "Yiming Bao",
"orcid": "0000-0002-9922-9723"
},
@@ -26577,6 +27775,7 @@
"homepage": "https://ngdc.cncb.ac.cn/idog/",
"license": "CC-BY-4.0",
"mappings": {
+ "integbio": "nbdc02480",
"re3data": "r3d100012176"
},
"name": "Integrated Resource for Domestic Dog",
@@ -26602,7 +27801,6 @@
],
"contact": {
"email": "topalis@imbb.forth.gr",
- "github": null,
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
@@ -26617,10 +27815,14 @@
"homepage": "https://www.vectorbase.org/ontology-browser",
"keywords": [
"biomedical science",
+ "disease",
+ "intervention design",
"life science",
+ "malaria",
"molecular infection biology",
"obo",
- "ontology"
+ "ontology",
+ "pathogen"
],
"license": "CC0-1.0",
"mappings": {
@@ -26714,7 +27916,6 @@
"idr": {
"contact": {
"email": "j.a.moore@dundee.ac.uk",
- "github": null,
"name": "Josh Moore",
"orcid": "0000-0003-4028-811X"
},
@@ -26759,6 +27960,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.c886cd",
+ "integbio": "nbdc00924",
"miriam": "iedb",
"prefixcommons": "tied",
"re3data": "r3d100012702"
@@ -26798,8 +28000,6 @@
"year": 2009
},
{
- "doi": null,
- "pmc": null,
"pubmed": "16312048",
"title": "The immune epitope database and analysis resource: from vision to blueprint",
"year": 2004
@@ -26880,8 +28080,15 @@
"example": "AU124",
"homepage": "http://www.geosamples.org/",
"keywords": [
- "subject agnostic"
+ "citation",
+ "earth science",
+ "environmental science",
+ "geochemistry",
+ "geology",
+ "hydrogeology",
+ "physical samples"
],
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaVVDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--4d19e53906f86cdaca6a9752fde1dd82276b7f22/igsn-original.jpg?disposition=inline",
"mappings": {
"fairsharing": "FAIRsharing.c7f365",
"miriam": "igsn",
@@ -26890,6 +28097,33 @@
"name": "International Geo Sample Number",
"pattern": "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$",
"preferred_prefix": "igsn",
+ "publications": [
+ {
+ "doi": "10.5334/dsj-2023-005",
+ "title": "Scaling Identifiers and their Metadata to Gigascale: An Architecture to Tackle the Challenges of Volume and Variety",
+ "year": 2023
+ },
+ {
+ "doi": "10.5334/dsj-2021-033",
+ "title": "Towards Globally Unique Identification of Physical Samples: Governance and Technical Implementation of the IGSN Global Sample Number",
+ "year": 2021
+ },
+ {
+ "doi": "10.5334/dsj-2017-002",
+ "title": "Utilizing the International Geo Sample Number Concept in Continental Scientific Drilling During ICDP Expedition COSC-1",
+ "year": 2017
+ },
+ {
+ "doi": "10.5281/zenodo.5118289",
+ "title": "IGSN 2040 Summary Report: Defining the Future of the IGSN as a Global Persistent Identifier for Material Samples",
+ "year": 2021
+ },
+ {
+ "doi": "10.1007/978-3-030-85040-1_162",
+ "title": "International Generic Sample Number",
+ "year": 2023
+ }
+ ],
"uri_format": "http://igsn.org/$1"
},
"igsr": {
@@ -26964,7 +28198,7 @@
]
},
"imanis": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "CL070",
"homepage": "https://www.imanislife.com/collections/cell-lines/",
"mappings": {
@@ -27007,6 +28241,7 @@
"biocontext": "IMEX",
"miriam": "imex",
"n2t": "imex",
+ "pathguide": "422",
"prefixcommons": "imex",
"re3data": "r3d100010669"
},
@@ -27015,8 +28250,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^\\d+(-\\d+)?$",
@@ -27047,7 +28281,6 @@
"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
@@ -27132,7 +28365,6 @@
"imgt.hla": {
"contact": {
"email": "steven.marsh@ucl.ac.uk",
- "github": null,
"name": "Steven G. E. Marsh",
"orcid": "0000-0003-2855-4120"
},
@@ -27153,6 +28385,7 @@
"edam": "2773",
"fairsharing": "FAIRsharing.e28v7g",
"go": "IMGT_HLA",
+ "integbio": "nbdc00106",
"miriam": "imgt.hla",
"n2t": "imgt.hla",
"ncbi": "IMGT/HLA",
@@ -27164,8 +28397,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^[A-Z0-9*:]+$",
@@ -27203,14 +28435,12 @@
},
{
"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
@@ -27238,7 +28468,6 @@
},
{
"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
@@ -27329,6 +28558,7 @@
"protein"
],
"mappings": {
+ "pathguide": "207",
"prefixcommons": "imotdb"
},
"name": "Database of Spatially Interacting Motifs in Proteins",
@@ -27353,9 +28583,7 @@
"imr": {
"contact": {
"email": "curator@inoh.org",
- "github": null,
- "name": "INOH curators",
- "orcid": null
+ "name": "INOH curators"
},
"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.",
@@ -27387,9 +28615,87 @@
"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=$1"
},
+ "imsr.apb": {
+ "description": "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]",
+ "example": "7345",
+ "homepage": "https://pb.apf.edu.au/phenbank/homePage.html",
+ "keywords": [
+ "allele",
+ "alteration",
+ "chromosome",
+ "database",
+ "embryo",
+ "gene",
+ "live mouse",
+ "murine",
+ "mutation",
+ "phenotype",
+ "sperm",
+ "strain",
+ "transgene",
+ "transgenic"
+ ],
+ "mappings": {
+ "rrid": "IMSR_APB"
+ },
+ "name": "NHMRC Australian PhenomeBank",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "imsr.apb",
+ "uri_format": "https://pb.apf.edu.au/phenbank/strain.html?id=$1"
+ },
+ "imsr_em": {
+ "description": "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]",
+ "example": "11478",
+ "homepage": "https://www.infrafrontier.eu/emma/",
+ "keywords": [
+ "mouse",
+ "mutant mouse repository",
+ "mutant mouse strain",
+ "mutant strain"
+ ],
+ "mappings": {
+ "rrid": "IMSR_EM"
+ },
+ "name": "European Mouse Mutant Archive",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "imsr_em",
+ "publications": [
+ {
+ "pubmed": "19783817"
+ },
+ {
+ "pubmed": "17709347"
+ }
+ ],
+ "uri_format": "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1"
+ },
+ "imsr_tac": {
+ "description": "Supplier of mice for research purposes. [from RRID]",
+ "example": "1178",
+ "homepage": "https://www.taconic.com/",
+ "keywords": [
+ "gene",
+ "genetic engineering",
+ "knockout",
+ "mice",
+ "model",
+ "mouse",
+ "repository",
+ "research",
+ "strain",
+ "subject",
+ "supply",
+ "transgenic"
+ ],
+ "mappings": {
+ "rrid": "IMSR_TAC"
+ },
+ "name": "Taconic Biosciences",
+ "preferred_prefix": "imsr_tac",
+ "uri_format": "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1"
+ },
"inaturalist.observation": {
"contributor": {
- "email": null,
"github": "oolonek",
"name": "Pierre-Marie Allard",
"orcid": "0000-0003-3389-2191"
@@ -27471,9 +28777,15 @@
"example": "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3",
"homepage": "http://www.chemspider.com/",
"keywords": [
+ "centrally registered identifier",
+ "chemical descriptor",
+ "chemical entity",
+ "chemical structure",
"cheminformatics",
"chemistry",
- "knowledge and information systems"
+ "knowledge and information systems",
+ "molecular entity",
+ "molecular structure"
],
"mappings": {
"biocontext": "INCHI",
@@ -27516,13 +28828,6 @@
"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",
@@ -27532,7 +28837,6 @@
},
{
"doi": "10.1007/s10822-015-9854-3",
- "pmc": null,
"pubmed": "26081259",
"title": "Many InChIs and quite some feat",
"year": 2015
@@ -27549,6 +28853,7 @@
"biocontext": "INCHIKEY",
"miriam": "inchikey",
"n2t": "inchikey",
+ "togoid": "InchiKey",
"wikidata": "P235"
},
"name": "InChIKey",
@@ -27576,7 +28881,9 @@
"description": "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology.",
"homepage": "https://www.goreni.org/gr3_nomenclature.php",
"keywords": [
- "biomedical science"
+ "biomedical science",
+ "disease",
+ "toxicity"
],
"mappings": {
"fairsharing": "FAIRsharing.9gqfpm"
@@ -27587,7 +28894,6 @@
"publications": [
{
"doi": "10.1177/0192623309353423",
- "pmc": null,
"pubmed": "20032296",
"title": "Proliferative and nonproliferative lesions of the rat and mouse respiratory tract",
"year": 2009
@@ -27629,6 +28935,8 @@
],
"mappings": {
"fairsharing": "FAIRsharing.rb2drw",
+ "integbio": "nbdc01870",
+ "pathguide": "264",
"prefixcommons": "innatedb",
"re3data": "r3d100010676"
},
@@ -27674,6 +28982,8 @@
"homepage": "https://github.com/INO-ontology/ino",
"keywords": [
"life science",
+ "molecular interaction",
+ "network model",
"obo",
"ontology"
],
@@ -27711,13 +29021,6 @@
"pubmed": "21624163",
"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_$1",
@@ -27734,9 +29037,11 @@
],
"mappings": {
"biocontext": "INSDC",
+ "integbio": "nbdc02567",
"miriam": "insdc",
"n2t": "insdc",
- "prefixcommons": "insdc"
+ "prefixcommons": "insdc",
+ "togoid": "Insdc"
},
"name": "Nucleotide Sequence Database",
"pattern": "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$",
@@ -27795,7 +29100,6 @@
},
{
"doi": "10.1126/science.298.5597.1333b",
- "pmc": null,
"pubmed": "12436968",
"title": "Nucleotide sequence database policies",
"year": 2002
@@ -27844,8 +29148,8 @@
"miriam": "insdc.gca",
"n2t": "insdc.gca"
},
- "name": "Genome assembly database",
- "pattern": "^GC[AF]_[0-9]{9}\\.[0-9]+$",
+ "name": "Genome assembly database - INSDC accessions",
+ "pattern": "^GCA_[0-9]{9}(\\.[0-9]+)?$",
"preferred_prefix": "insdc.gca",
"providers": [
{
@@ -27858,8 +29162,24 @@
],
"uri_format": "https://www.ebi.ac.uk/ena/data/view/$1"
},
+ "insdc.gcf": {
+ "description": "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database RefSeq accessions does not extend to viroids and bacteriophage.",
+ "example": "GCF_000001405",
+ "has_canonical": "ncbi.assembly",
+ "homepage": "https://www.ncbi.nlm.nih.gov/",
+ "mappings": {
+ "miriam": "refseq.gcf"
+ },
+ "name": "Genome assembly database - RefSeq accessions",
+ "pattern": "^GCF_[0-9]{9}(\\.[0-9]+)?$",
+ "preferred_prefix": "insdc.gcf",
+ "synonyms": [
+ "insdc.gcf"
+ ],
+ "uri_format": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"
+ },
"insdc.run": {
- "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation here: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --",
+ "comment": "https://www.insdc.org/ is the authoritative source for INSDC. However, confusingly, they don't mention runs in this table. I think we should ask them to include. ENA is a partner and they have documentation [here](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html). Runs | (E\\|D\\|S)RR[0-9]{6,} | ERR123456 -- | -- | --",
"contributor": {
"email": "cjmungall@lbl.gov",
"github": "cmungall",
@@ -27869,7 +29189,6 @@
"description": "An experimental run, served thrugh the ENA",
"example": "ERR436051",
"github_request_issue": 131,
- "has_canonical": "ena.embl",
"homepage": "https://www.insdc.org/",
"name": "International Nucleotide Sequence Database Collaboration (INSDC) Run",
"pattern": "^(E|D|S)RR[0-9]{6,}$",
@@ -27906,9 +29225,9 @@
{
"code": "ddbj",
"description": "DDBJ Sequence Read Archive (DRA)",
- "homepage": "http://trace.ddbj.nig.ac.jp/dra/",
+ "homepage": "https://www.ddbj.nig.ac.jp/dra/index-e.html",
"name": "DDBJ Sequence Read Archive (DRA)",
- "uri_format": "http://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=$1"
+ "uri_format": "https://ddbj.nig.ac.jp/resource/sra-experiment/$1"
},
{
"code": "ebi",
@@ -27946,7 +29265,6 @@
"intact": {
"contact": {
"email": "orchard@ebi.ac.uk",
- "github": null,
"name": "Sandra Orchard",
"orcid": "0000-0002-8878-3972"
},
@@ -27958,14 +29276,18 @@
"interaction",
"protein"
],
+ "license": "CC-BY-4.0",
"mappings": {
"biocontext": "INTACT",
"fairsharing": "FAIRsharing.d05nwx",
"go": "IntAct",
+ "integbio": "nbdc00507",
"miriam": "intact",
"n2t": "intact",
+ "pathguide": "111",
"prefixcommons": "intact",
"re3data": "r3d100010671",
+ "togoid": "Intact",
"uniprot": "DB-0051"
},
"name": "IntAct protein interaction database",
@@ -27973,8 +29295,7 @@
{
"name": "European Bioinformatics Institute",
"partnered": false,
- "ror": "02catss52",
- "wikidata": null
+ "ror": "02catss52"
}
],
"pattern": "^EBI\\-[0-9]+$",
@@ -28042,6 +29363,29 @@
"preferred_prefix": "intact.molecule",
"uri_format": "https://www.ebi.ac.uk/intact/search?query=$1"
},
+ "integbio": {
+ "contact": {
+ "email": "kwsm@dbcls.rois.ac.jp",
+ "github": "skwsm",
+ "name": "Shuichi Kawashima",
+ "orcid": "0000-0001-7883-3756"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). (from https://integbio.jp/dbcatalog/en/about)",
+ "example": "nbdc01071",
+ "homepage": "https://integbio.jp/en/",
+ "license": "CC0-1.0",
+ "logo": "https://integbio.jp/templates/integbio/images/logo/logo.png",
+ "name": "Integbio",
+ "pattern": "^nbdc\\d+$",
+ "preferred_prefix": "integbio",
+ "uri_format": "https://integbio.jp/dbcatalog/en/record/$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",
@@ -28078,6 +29422,8 @@
"keywords": [
"anatomy",
"biomedical science",
+ "brain",
+ "imaging",
"neurobiology"
],
"mappings": {
@@ -28108,9 +29454,7 @@
"interpro": {
"contact": {
"email": "interhelp@ebi.ac.uk",
- "github": null,
- "name": "InterPro Help",
- "orcid": null
+ "name": "InterPro Help"
},
"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",
@@ -28129,12 +29473,14 @@
"edam": "1133",
"fairsharing": "FAIRsharing.pda11d",
"go": "InterPro",
+ "integbio": "nbdc00108",
"miriam": "interpro",
"n2t": "interpro",
"ncbi": "InterPro",
"obofoundry": "ipr",
"prefixcommons": "interpro",
"re3data": "r3d100010798",
+ "togoid": "Interpro",
"uniprot": "DB-0052",
"wikidata": "P2926"
},
@@ -28195,7 +29541,7 @@
"InterPro"
],
"twitter": "InterProDB",
- "uri_format": "https://www.ebi.ac.uk/interpro/entry/$1"
+ "uri_format": "http://purl.obolibrary.org/obo/IPR_$1"
},
"iobc": {
"contact": {
@@ -28226,8 +29572,6 @@
"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
}
@@ -28245,6 +29589,7 @@
],
"mappings": {
"biocontext": "IPI",
+ "integbio": "nbdc00911",
"prefixcommons": "ipi"
},
"name": "International Protein Index",
@@ -28261,7 +29606,6 @@
"publications": [
{
"doi": "10.1002/pmic.200300721",
- "pmc": null,
"pubmed": "15221759",
"title": "The International Protein Index: an integrated database for proteomics experiments",
"year": 2004
@@ -28337,6 +29681,7 @@
"fairsharing": "FAIRsharing.t31wcb",
"miriam": "irefweb",
"n2t": "irefweb",
+ "pathguide": "300",
"prefixcommons": "irefweb",
"re3data": "r3d100012725"
},
@@ -28375,6 +29720,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.kd39j4",
+ "integbio": "nbdc01752",
"prefixcommons": "iresite"
},
"name": "Database of experimentally verified IRES structures",
@@ -28501,6 +29847,7 @@
"mappings": {
"biocontext": "ISFINDER",
"fairsharing": "FAIRsharing.xhpc3h",
+ "integbio": "nbdc00510",
"miriam": "isfinder",
"n2t": "isfinder",
"ncbi": "ISFinder",
@@ -28534,6 +29881,7 @@
"example": "000000012281955X",
"homepage": "http://www.isni.org",
"mappings": {
+ "bartoc": "20464",
"biolink": "isni",
"miriam": "isni",
"n2t": "isni"
@@ -28627,7 +29975,6 @@
"itis": {
"contact": {
"email": "itiswebmaster@itis.gov",
- "github": null,
"name": "Gerald Guala",
"orcid": "0000-0002-4972-3782"
},
@@ -28648,6 +29995,7 @@
"mappings": {
"bartoc": "17791",
"fairsharing": "FAIRsharing.t19hpa",
+ "integbio": "nbdc00916",
"re3data": "r3d100011213",
"wikidata": "P815"
},
@@ -28676,7 +30024,6 @@
"banana_peel": "_",
"contact": {
"email": "matthias.samwald@meduniwien.ac.at",
- "github": null,
"name": "Matthias Samwald",
"orcid": "0000-0002-4855-2571"
},
@@ -28686,6 +30033,8 @@
"homepage": "https://openbiolink.github.io/ITOExplorer/",
"keywords": [
"artificial intelligence",
+ "machine learning",
+ "natural language processing",
"ontology"
],
"mappings": {
@@ -28707,24 +30056,13 @@
},
{
"doi": "10.5281/zenodo.5561989",
- "pmc": null,
- "pubmed": null,
"title": "Intelligence Task Ontology and Knowledge Graph (ITO)",
"year": 2022
},
{
"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": 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
}
],
"repository": "https://github.com/OpenBioLink/ITO",
@@ -28737,6 +30075,7 @@
"keywords": [
"protein"
],
+ "license": "CC-BY-SA-4.0",
"mappings": {
"biocontext": "IUPHAR.FAMILY",
"miriam": "iuphar.family",
@@ -28764,11 +30103,13 @@
"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.",
"example": "1755",
"homepage": "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all",
+ "license": "CC-BY-SA-4.0",
"mappings": {
"biocontext": "IUPHAR.LIGAND",
"biolink": "GTOPDB",
"miriam": "iuphar.ligand",
"n2t": "iuphar.ligand",
+ "togoid": "IupharLigand",
"wikidata": "P595"
},
"name": "Guide to Pharmacology Ligand",
@@ -28784,6 +30125,7 @@
"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 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.",
"example": "101",
"homepage": "http://www.guidetopharmacology.org/targets.jsp",
+ "license": "CC-BY-SA-4.0",
"mappings": {
"biocontext": "IUPHAR.RECEPTOR",
"go": "IUPHAR_RECEPTOR",
@@ -28853,11 +30195,23 @@
"example": "004435",
"homepage": "https://www.jax.org/strain",
"keywords": [
- "life science"
+ "gene",
+ "genetic engineering",
+ "knockout",
+ "life science",
+ "mice",
+ "model",
+ "mouse",
+ "repository",
+ "research",
+ "strain",
+ "subject",
+ "supply"
],
"mappings": {
"biocontext": "JAX",
- "fairsharing": "FAIRsharing.5701h1"
+ "fairsharing": "FAIRsharing.5701h1",
+ "rrid": "IMSR_JAX"
},
"name": "Jackson Laboratories Strain",
"pattern": "^\\d{6}$",
@@ -28884,6 +30238,7 @@
"homepage": "http://jcggdb.jp/index_en.html",
"mappings": {
"biocontext": "JCGGDB",
+ "integbio": "nbdc01164",
"miriam": "jcggdb",
"n2t": "jcggdb"
},
@@ -28930,7 +30285,7 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "JCRB1355",
"homepage": "https://cellbank.nibiohn.go.jp",
"mappings": {
@@ -28942,6 +30297,14 @@
"uri_format": "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"
},
"jcsd": {
+ "contributor_extras": [
+ {
+ "email": "b.gyori@northeastern.edu",
+ "github": "bgyori",
+ "name": "Benjamin M. Gyori",
+ "orcid": "0000-0001-9439-5346"
+ }
+ ],
"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/",
@@ -28972,7 +30335,6 @@
"jgi.proposal": {
"contact": {
"email": "sewilson@lbl.gov",
- "github": null,
"name": "Steven E. Wilson",
"orcid": "0000-0002-8489-208X"
},
@@ -29096,7 +30458,6 @@
"publications": [
{
"doi": "10.1093/bioinformatics/bth200",
- "pmc": null,
"pubmed": "15072998",
"title": "Web-based kinetic modelling using JWS Online",
"year": 2004
@@ -29125,7 +30486,7 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "10020.2",
"homepage": "https://cellbank.snu.ac.kr/english",
"mappings": {
@@ -29163,8 +30524,10 @@
"biolink": "KEGG",
"cheminf": "000409",
"go": "KEGG",
+ "integbio": "nbdc00530",
"miriam": "kegg",
"n2t": "kegg",
+ "pathguide": "16",
"uniprot": "DB-0053"
},
"name": "Kyoto Encyclopedia of Genes and Genomes",
@@ -29195,6 +30558,7 @@
],
"mappings": {
"biolink": "KEGG.BRITE",
+ "integbio": "nbdc00115",
"prefixcommons": "kegg.brite"
},
"name": "KEGG BRITE",
@@ -29221,6 +30585,7 @@
"mappings": {
"biocontext": "KEGG.COMPOUND",
"edam": "2605",
+ "integbio": "nbdc00814",
"miriam": "kegg.compound",
"n2t": "kegg.compound",
"prefixcommons": "kegg.compound",
@@ -29242,7 +30607,6 @@
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
- "pmc": null,
"pubmed": "22700311",
"title": "Using the KEGG database resource",
"year": 2012
@@ -29288,6 +30652,7 @@
],
"mappings": {
"biocontext": "KEGG.DISEASE",
+ "integbio": "nbdc00813",
"miriam": "kegg.disease",
"n2t": "kegg.disease",
"prefixcommons": "kegg.disease"
@@ -29317,6 +30682,7 @@
"mappings": {
"biocontext": "KEGG.DRUG",
"edam": "2609",
+ "integbio": "nbdc00812",
"miriam": "kegg.drug",
"n2t": "kegg.drug",
"prefixcommons": "kegg.drug",
@@ -29357,6 +30723,7 @@
"homepage": "http://www.genome.jp/kegg/drug/environ.html",
"mappings": {
"biocontext": "KEGG.ENVIRON",
+ "integbio": "nbdc01059",
"miriam": "kegg.environ",
"n2t": "kegg.environ"
},
@@ -29429,6 +30796,7 @@
"homepage": "http://www.genome.jp/kegg/catalog/org_list.html",
"mappings": {
"biocontext": "KEGG.GENOME",
+ "integbio": "nbdc00816",
"miriam": "kegg.genome",
"n2t": "kegg.genome",
"prefixcommons": "kegg.genome",
@@ -29472,6 +30840,7 @@
"mappings": {
"biocontext": "KEGG.GLYCAN",
"edam": "2613",
+ "integbio": "nbdc00533",
"miriam": "kegg.glycan",
"n2t": "kegg.glycan",
"prefixcommons": "kegg.glycan"
@@ -29492,7 +30861,6 @@
"publications": [
{
"doi": "10.1093/glycob/cwj010",
- "pmc": null,
"pubmed": "16014746",
"title": "KEGG as a glycome informatics resource",
"year": 2005
@@ -29555,6 +30923,7 @@
"homepage": "http://www.kegg.jp/kegg/module.html",
"mappings": {
"biocontext": "KEGG.MODULE",
+ "integbio": "nbdc01428",
"miriam": "kegg.module",
"n2t": "kegg.module"
},
@@ -29626,7 +30995,6 @@
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
- "pmc": null,
"pubmed": "22700311",
"title": "Using the KEGG database resource",
"year": 2012
@@ -29649,7 +31017,8 @@
"example": "RC00001",
"homepage": "http://www.genome.jp/kegg/reaction/",
"mappings": {
- "biolink": "KEGG.RCLASS"
+ "biolink": "KEGG.RCLASS",
+ "integbio": "nbdc00860"
},
"name": "KEGG Reaction Class",
"part_of": "kegg",
@@ -29675,6 +31044,7 @@
"biocontext": "KEGG.REACTION",
"edam": "2608",
"go": "KEGG_REACTION",
+ "integbio": "nbdc00818",
"miriam": "kegg.reaction",
"n2t": "kegg.reaction",
"prefixcommons": "kegg.reaction",
@@ -29696,7 +31066,6 @@
"publications": [
{
"doi": "10.1002/0471250953.bi0112s38",
- "pmc": null,
"pubmed": "22700311",
"title": "Using the KEGG database resource",
"year": 2012
@@ -29709,7 +31078,7 @@
"uri_format": "https://www.kegg.jp/entry/$1"
},
"kerafast": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "EJH014",
"homepage": "https://www.kerafast.com/",
"mappings": {
@@ -29746,6 +31115,7 @@
"homepage": "http://www.knapsackfamily.com/KNApSAcK/",
"mappings": {
"biocontext": "KNAPSACK",
+ "integbio": "nbdc00545",
"miriam": "knapsack",
"n2t": "knapsack",
"wikidata": "P2064"
@@ -29777,7 +31147,7 @@
]
},
"kyinno": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "KC-0979",
"homepage": "https://www.kyinno.com/",
"mappings": {
@@ -29824,8 +31194,6 @@
"publications": [
{
"doi": "10.5281/zenodo.6522019",
- "pmc": null,
- "pubmed": null,
"title": "LABO: An ontology for laboratory test prescription and reporting",
"year": 2019
}
@@ -30048,7 +31416,6 @@
"licebase": {
"contact": {
"email": "Inge.Jonassen@uib.no",
- "github": null,
"name": "Inge Jonassen",
"orcid": "0000-0003-4110-0748"
},
@@ -30061,6 +31428,7 @@
"mappings": {
"biocontext": "LICEBASE",
"fairsharing": "FAIRsharing.c7w81a",
+ "integbio": "nbdc02217",
"miriam": "licebase",
"n2t": "licebase",
"re3data": "r3d100013547"
@@ -30089,6 +31457,7 @@
"homepage": "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en",
"mappings": {
"biocontext": "LIGANDBOX",
+ "integbio": "nbdc00551",
"miriam": "ligandbox",
"n2t": "ligandbox"
},
@@ -30100,7 +31469,6 @@
"ligandexpo": {
"contact": {
"email": "jwest@rcsb.rutgers.edu",
- "github": null,
"name": "John Westbrook",
"orcid": "0000-0002-6686-5475"
},
@@ -30118,8 +31486,10 @@
"mappings": {
"biocontext": "LIGANDEXPO",
"fairsharing": "FAIRsharing.2ma4gq",
+ "integbio": "nbdc01864",
"miriam": "ligandexpo",
"n2t": "ligandexpo",
+ "pathguide": "154",
"prefixcommons": "ligandexpo"
},
"name": "Ligand Expo",
@@ -30144,7 +31514,6 @@
"publications": [
{
"doi": "10.1093/bioinformatics/bth214",
- "pmc": null,
"pubmed": "15059838",
"title": "Ligand Depot: a data warehouse for ligands bound to macromolecules",
"year": 2004
@@ -30291,8 +31660,6 @@
"publications": [
{
"doi": "10.5281/zenodo.5598314",
- "pmc": null,
- "pubmed": null,
"title": "linkml/linkml-model: v1.5.2",
"year": 2023
}
@@ -30315,6 +31682,7 @@
"biocontext": "LIPIDBANK",
"edam": "2665",
"fairsharing": "FAIRsharing.bdn9br",
+ "integbio": "nbdc00126",
"miriam": "lipidbank",
"n2t": "lipidbank",
"prefixcommons": "lipidbank"
@@ -30333,8 +31701,6 @@
],
"publications": [
{
- "doi": null,
- "pmc": null,
"pubmed": "12058481",
"title": "[LIPIDBANK for Web, the newly developed lipid database]",
"year": 2002
@@ -30362,8 +31728,10 @@
"fairsharing": "FAIRsharing.cpneh8",
"miriam": "lipidmaps",
"n2t": "lipidmaps",
+ "pathguide": "503",
"prefixcommons": "lipidmaps",
"re3data": "r3d100012315",
+ "togoid": "Lipidmaps",
"wikidata": "P2063"
},
"name": "LIPID MAPS",
@@ -30409,17 +31777,13 @@
},
{
"doi": "10.1194/jlr.e400004-jlr200",
- "pmc": null,
"pubmed": "15722563",
"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
+ "title": "Update of the LIPID MAPS comprehensive classification system for lipids."
}
],
"synonyms": [
@@ -30433,7 +31797,6 @@
"lipro": {
"contact": {
"email": "bakerc@unb.ca",
- "github": null,
"name": "Christopher Baker",
"orcid": "0000-0003-4004-6479"
},
@@ -30500,7 +31863,6 @@
"loggerhead": {
"contact": {
"email": "peteremidford@yahoo.com",
- "github": null,
"name": "Peter Midford",
"orcid": "0000-0001-6512-3296"
},
@@ -30522,9 +31884,7 @@
"loinc": {
"contact": {
"email": "loinc@regenstrief.org",
- "github": null,
- "name": "LOINC Support",
- "orcid": null
+ "name": "LOINC Support"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -30536,11 +31896,17 @@
"example": "LL379-9",
"homepage": "https://loinc.org/",
"keywords": [
+ "assay",
"biomedical science",
+ "diagnosis",
+ "genetic disorder",
+ "genetic polymorphism",
"life science",
"ontology",
+ "phenotype",
"preclinical studies"
],
+ "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "LOINC",
"bartoc": "1897",
@@ -30556,7 +31922,6 @@
"publications": [
{
"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)",
"year": 1998
@@ -30691,7 +32056,8 @@
"homepage": "https://github.com/AnimalGenome/livestock-product-trait-ontology",
"keywords": [
"animal husbandry",
- "ontology"
+ "ontology",
+ "phenotype"
],
"mappings": {
"aberowl": "LPT",
@@ -30715,8 +32081,10 @@
"mappings": {
"biocontext": "LRG",
"hl7": "2.16.840.1.113883.6.283",
+ "integbio": "nbdc02566",
"miriam": "lrg",
- "n2t": "lrg"
+ "n2t": "lrg",
+ "togoid": "Lrg"
},
"name": "Locus Reference Genomic",
"pattern": "^\\d+$",
@@ -30788,6 +32156,59 @@
"preferred_prefix": "lter",
"uri_format": "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"
},
+ "m4i": {
+ "contact": {
+ "email": "dorothea.iglezakis@ub.uni-stuttgart.de",
+ "github": "doigl",
+ "name": "Dorothea Iglezakis",
+ "orcid": "0000-0002-8524-0569"
+ },
+ "contributor": {
+ "email": "giacomo.lanza@ptb.de",
+ "github": "Zack-83",
+ "name": "Giacomo Lanza",
+ "orcid": "0000-0002-2239-3955"
+ },
+ "description": "The ontology Metadata4Ing is developed within the NFDI Consortium NFDI4Ing with the aim of providing a thorough framework for the semantic description of research data, with a particular focus on engineering sciences and neighbouring disciplines. This ontology allows a description of the whole data generation process (experiment, observation, simulation), embracing the object of investigation, all sample and data manipulation procedures, a summary of the data files and the information contained, and all personal and institutional roles. The subordinate classes and relations can be built according to the two principles of inheritance and modularity. \"Inheritance\" means that a subclass inherits all properties of its superordinate class, possibly adding some new ones. Modularity means that all expansions are independent of each other; this makes possible for instance to generate expanded ontologies for any possible combinations of method × object of research.",
+ "download_owl": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.xml",
+ "download_rdf": "https://nfdi4ing.pages.rwth-aachen.de/metadata4ing/metadata4ing/ontology.ttl",
+ "example": "Method",
+ "github_request_issue": 970,
+ "homepage": "https://w3id.org/nfdi4ing/metadata4ing/",
+ "keywords": [
+ "academy",
+ "engineering science",
+ "metadata",
+ "ontology"
+ ],
+ "license": "CC-BY-4.0",
+ "mappings": {
+ "bartoc": "20402",
+ "fairsharing": "FAIRsharing.f8b3ec",
+ "lov": "m4i",
+ "wikidata": "Q111516803",
+ "zazuko": "m4i"
+ },
+ "mastodon": "nfdi4ing@nfdi.social",
+ "name": "Metadata4Ing",
+ "owners": [
+ {
+ "name": "Nationale Forschungsdateninfrastruktur",
+ "partnered": false,
+ "ror": "05qj6w324"
+ }
+ ],
+ "pattern": "^\\w+$",
+ "preferred_prefix": "m4i",
+ "repository": "https://git.rwth-aachen.de/nfdi4ing/metadata4ing/metadata4ing/",
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "http://w3id.org/nfdi4ing/metadata4ing#$1"
+ },
"ma": {
"banana": "MA",
"contact": {
@@ -30805,7 +32226,9 @@
"anatomy",
"mouse",
"obo",
- "ontology"
+ "ontology",
+ "organ",
+ "tissue"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -30845,7 +32268,7 @@
],
"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",
+ "uri_format": "http://purl.obolibrary.org/obo/MA_$1",
"version": "2017-02-07"
},
"macie": {
@@ -30895,6 +32318,18 @@
],
"uri_format": "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"
},
+ "maggot": {
+ "description": "Sharing descriptive Metadata is the first essential step towards Open Scientific Data. With this in mind, Maggot was specifically designed to annotate datasets by creating a metadata file to attach to the storage space. Indeed, it allows users to easily add descriptive metadata to datasets produced within a collective of people (research unit, platform, multi-partner project, etc.). This approach fits perfectly into a data management plan as it addresses the issues of data organization and documentation, data storage and frictionless metadata sharing within this same collective and beyond.",
+ "example": "frim1",
+ "homepage": "https://eng-bfp.bordeaux-aquitaine.hub.inrae.fr/resources/metabolome-platform",
+ "mappings": {
+ "miriam": "maggot"
+ },
+ "name": "Maggot",
+ "pattern": "^[A-Za-z0-9]+$",
+ "preferred_prefix": "maggot",
+ "uri_format": "https://pmb-bordeaux.fr/maggot/metadata/$1"
+ },
"maizegdb.locus": {
"description": "MaizeGDB is the maize research community's central repository for genetics and genomics information.",
"example": "25011",
@@ -30910,6 +32345,7 @@
"biocontext": "MAIZEGDB.LOCUS",
"fairsharing": "FAIRsharing.aq280w",
"go": "MaizeGDB_Locus",
+ "integbio": "nbdc00129",
"miriam": "maizegdb.locus",
"n2t": "maizegdb.locus",
"ncbi": "MaizeGDB",
@@ -30930,6 +32366,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1186/s12870-021-03173-5",
+ "pubmed": "34416864"
+ },
{
"doi": "10.3389/fpls.2019.01050",
"pmc": "PMC6724615",
@@ -30946,7 +32386,6 @@
},
{
"doi": "10.1007/978-1-4939-3167-5_9",
- "pmc": null,
"pubmed": "26519406",
"title": "MaizeGDB: The Maize Genetics and Genomics Database",
"year": 2016
@@ -30983,18 +32422,19 @@
"banana_peel": "_",
"contact": {
"email": "n.lenovere@gmail.com",
- "github": null,
"name": "Nicolas Le Novere",
"orcid": "0000-0002-6309-7327"
},
"deprecated": true,
"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.",
"download_owl": "http://purl.obolibrary.org/obo/mamo.owl",
+ "download_rdf": "https://raw.githubusercontent.com/EBISPOT/mamo/main/mamo.rdf",
"example": "0000026",
"homepage": "http://sourceforge.net/p/mamo-ontology/wiki/Home/",
"keywords": [
"computational biology",
"mathematics",
+ "modeling and simulation",
"obo",
"ontology",
"systems biology"
@@ -31017,7 +32457,7 @@
"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_$1",
- "version": "2020-08-24"
+ "version": "2023-02-03"
},
"mampol": {
"description": "The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches).",
@@ -31051,13 +32491,11 @@
"mao": {
"contact": {
"email": "julie@igbmc.u-strasbg.fr",
- "github": null,
- "name": "Julie Thompson",
- "orcid": null
+ "name": "Julie Thompson"
},
"deprecated": true,
"description": "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment.",
- "example": "MAO:0000061",
+ "example": "0000061",
"homepage": "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html",
"keywords": [
"alignment",
@@ -31071,6 +32509,7 @@
"prefixcommons": "mao"
},
"name": "Multiple alignment",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "MAO",
"providers": [
{
@@ -31102,6 +32541,7 @@
"mappings": {
"biocontext": "MASSBANK",
"fairsharing": "FAIRsharing.dk451a",
+ "integbio": "nbdc00298",
"miriam": "massbank",
"n2t": "massbank",
"wikidata": "P6689"
@@ -31121,7 +32561,6 @@
"publications": [
{
"doi": "10.1002/jms.1777",
- "pmc": null,
"pubmed": "20623627",
"title": "MassBank: a public repository for sharing mass spectral data for life sciences",
"year": 2010
@@ -31133,7 +32572,6 @@
"massive": {
"contact": {
"email": "miw023@ucsd.edu",
- "github": null,
"name": "Mingxun Wang",
"orcid": "0000-0001-7647-6097"
},
@@ -31210,9 +32648,7 @@
"mat": {
"contact": {
"email": "j.bard@ed.ac.uk",
- "github": null,
- "name": "Jonathan Bard",
- "orcid": null
+ "name": "Jonathan Bard"
},
"deprecated": true,
"description": "Minimal set of terms for anatomy",
@@ -31255,6 +32691,8 @@
],
"mappings": {
"fairsharing": "FAIRsharing.91yrz6",
+ "integbio": "nbdc01222",
+ "pathguide": "298",
"prefixcommons": "matrixdb",
"re3data": "r3d100010672"
},
@@ -31315,6 +32753,48 @@
"preferred_prefix": "matrixdb.association",
"uri_format": "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"
},
+ "mavedb": {
+ "comment": "This is an interesting one as the full IDs as they appear on the page are of the form `urn:mavedb:00000011-a` suggesting this is the preferred URI expansion for identification purposes. However, mavedb hasn't been registered with IANA https://www.iana.org/assignments/urn-namespaces/urn-namespaces.xhtml",
+ "contact": {
+ "email": "alan.rubin@wehi.edu.au",
+ "github": "afrubin",
+ "name": "Alan Rubin",
+ "orcid": "0000-0003-1474-605X"
+ },
+ "contributor": {
+ "email": "cjmungall@lbl.gov",
+ "github": "cmungall",
+ "name": "Chris Mungall",
+ "orcid": "0000-0002-6601-2165"
+ },
+ "description": "Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a",
+ "example": "00000011-a",
+ "example_extras": [
+ "00000011"
+ ],
+ "github_request_issue": 1045,
+ "homepage": "https://www.mavedb.org",
+ "name": "Multiplexed Assays of Variant Effect Database",
+ "pattern": "^\\S+$",
+ "preferred_prefix": "mavedb",
+ "publications": [
+ {
+ "doi": "10.1186/s13059-019-1845-6",
+ "pmc": "PMC6827219",
+ "pubmed": "31679514",
+ "title": "MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect",
+ "year": 2019
+ }
+ ],
+ "repository": "https://github.com/VariantEffect/mavedb-api",
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://www.mavedb.org/#/experiments/urn:mavedb:$1"
+ },
"maxo": {
"appears_in": [
"ecto"
@@ -31343,8 +32823,10 @@
"example": "0000008",
"homepage": "https://github.com/monarch-initiative/MAxO",
"keywords": [
+ "medicine",
"obo",
- "ontology"
+ "ontology",
+ "rare disease"
],
"license": "CC-BY-4.0",
"logo": "https://raw.githubusercontent.com/jmcmurry/closed-illustrations/master/logos/maxo-logos/maxo_logo_black-banner.png",
@@ -31352,6 +32834,8 @@
"aberowl": "MAXO",
"biolink": "MAXO",
"bioportal": "MAXO",
+ "fairsharing": "FAIRsharing.945c78",
+ "miriam": "maxo",
"obofoundry": "maxo",
"ols": "maxo",
"ontobee": "MAXO"
@@ -31359,18 +32843,24 @@
"name": "Medical Action Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "MAXO",
+ "publications": [
+ {
+ "doi": "10.1101/2023.07.13.23292612",
+ "pubmed": "37503136",
+ "title": "The Medical Action Ontology: A Tool for Annotating and Analyzing Treatments and Clinical Management of Human Disease",
+ "year": 2023
+ }
+ ],
"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": "2023-06-06"
+ "version": "2024-02-05"
},
"mba": {
"contact": {
"email": "chinhda@alleninstitute.org",
- "github": null,
- "name": "Allen Institute for Brain Science",
- "orcid": null
+ "name": "Allen Institute for Brain Science"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -31396,9 +32886,7 @@
"mcc": {
"contact": {
"email": "usha@molecularconnections.com",
- "github": null,
- "name": "Usha Mahadevan",
- "orcid": null
+ "name": "Usha Mahadevan"
},
"deprecated": true,
"description": "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.",
@@ -31462,10 +32950,50 @@
"uri_format": "http://purl.obolibrary.org/obo/MCO_$1",
"version": "2019-05-15"
},
+ "mcro": {
+ "banana": "MCRO",
+ "contact": {
+ "email": "muamith@utmb.edu",
+ "github": "ProfTuan",
+ "name": "Tuan Amith",
+ "orcid": "0000-0003-4333-1857"
+ },
+ "depends_on": [
+ "iao",
+ "swo"
+ ],
+ "description": "An ontology representing the model card structure, he aim of this work is to describe machine learning models to communicate information about specific details about the model (trade offs, intended users, licensing, etc.). ",
+ "download_owl": "http://purl.obolibrary.org/obo/mcro.owl",
+ "example": "0000001",
+ "homepage": "https://github.com/UTHealth-Ontology/MCRO",
+ "keywords": [
+ "obo",
+ "ontology"
+ ],
+ "license": "CC-BY-4.0",
+ "mappings": {
+ "aberowl": "MCRO",
+ "miriam": "mcro",
+ "obofoundry": "mcro",
+ "ontobee": "MCRO"
+ },
+ "name": "Model Card Report Ontology",
+ "namespace_in_lui": true,
+ "pattern": "^\\d{7}$",
+ "preferred_prefix": "MCRO",
+ "publications": [
+ {
+ "doi": "10.1186/s12859-022-04797-6",
+ "title": "Toward a standard formal semantic representation of the model card report"
+ }
+ ],
+ "rdf_uri_format": "http://purl.obolibrary.org/obo/MCRO_$1",
+ "repository": "https://github.com/UTHealth-Ontology/MCRO",
+ "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mcro/classes?obo_id=MCRO:$1"
+ },
"mdm": {
"contact": {
"email": "bernd.mueller@zbmed.de",
- "github": null,
"name": "Bernd Müller",
"orcid": "0000-0003-3062-8192"
},
@@ -31505,15 +33033,14 @@
"meddra": {
"contact": {
"email": "mssohelp@meddra.org",
- "github": null,
- "name": "MedDRA MSSO",
- "orcid": null
+ "name": "MedDRA MSSO"
},
"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).",
"example": "10015919",
"homepage": "http://bioportal.bioontology.org/ontologies/MEDDRA",
"keywords": [
"biomedical science",
+ "disease",
"medicine",
"ontology",
"preclinical studies"
@@ -31525,8 +33052,10 @@
"bioportal": "MEDDRA",
"fairsharing": "FAIRsharing.ad3137",
"hl7": "2.16.840.1.113883.6.163",
+ "integbio": "nbdc02564",
"miriam": "meddra",
"n2t": "meddra",
+ "togoid": "Meddra",
"wikidata": "P3201"
},
"name": "Medical Dictionary for Regulatory Activities Terminology",
@@ -31535,14 +33064,12 @@
"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
@@ -31564,27 +33091,103 @@
"mappings": {
"biocontext": "MedGen",
"biolink": "medgen",
+ "integbio": "nbdc02560",
"miriam": "medgen",
"n2t": "medgen",
- "ncbi": "MedGen"
+ "ncbi": "MedGen",
+ "togoid": "Medgen"
},
"name": "Human Medical Genetics",
"pattern": "^[CN]*\\d{4,7}$",
"preferred_prefix": "medgen",
"uri_format": "https://www.ncbi.nlm.nih.gov/medgen/$1"
},
+ "mediadive.ingredient": {
+ "contact": {
+ "email": "joerg.overmann@dsmz.de",
+ "name": "Jörg Overmann",
+ "orcid": "0000-0003-3909-7201"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]",
+ "example": "13",
+ "github_request_issue": 941,
+ "homepage": "https://mediadive.dsmz.de/solutions",
+ "license": "CC-BY-4.0",
+ "name": "MediaDive Ingredient",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "mediadive.ingredient",
+ "uri_format": "https://mediadive.dsmz.de/ingredients/$1"
+ },
+ "mediadive.medium": {
+ "contact": {
+ "email": "joerg.overmann@dsmz.de",
+ "name": "Jörg Overmann",
+ "orcid": "0000-0003-3909-7201"
+ },
+ "contributor": {
+ "email": "cjmungall@lbl.gov",
+ "github": "cmungall",
+ "name": "Chris Mungall",
+ "orcid": "0000-0002-6601-2165"
+ },
+ "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]",
+ "example": "77",
+ "example_extras": [
+ "54b"
+ ],
+ "github_request_issue": 941,
+ "homepage": "https://mediadive.dsmz.de/media",
+ "license": "CC-BY-4.0",
+ "name": "MediaDive Medium",
+ "pattern": "^\\d+\\w?$",
+ "preferred_prefix": "mediadive.medium",
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://mediadive.dsmz.de/medium/$1"
+ },
+ "mediadive.solution": {
+ "contact": {
+ "email": "joerg.overmann@dsmz.de",
+ "name": "Jörg Overmann",
+ "orcid": "0000-0003-3909-7201"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]",
+ "example": "S6",
+ "github_request_issue": 941,
+ "homepage": "https://mediadive.dsmz.de/solutions",
+ "license": "CC-BY-4.0",
+ "name": "MediaDive Solution",
+ "pattern": "^S\\d+$",
+ "preferred_prefix": "mediadive.solution",
+ "uri_format": "https://mediadive.dsmz.de/solutions/$1"
+ },
"medlineplus": {
"contact": {
- "email": "custserv@nlm.nih.gov",
- "github": null,
- "name": "NLM Customer Service",
- "orcid": null
+ "email": "willisj@mail.nlm.nih.gov",
+ "name": "Jan Willis, NLM"
},
"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.",
"example": "002804",
"homepage": "http://www.nlm.nih.gov/medlineplus/",
"keywords": [
"biomedical science",
+ "disease",
"health science",
"medicine",
"ontology"
@@ -31595,6 +33198,7 @@
"bioportal": "MEDLINEPLUS",
"fairsharing": "FAIRsharing.bf8dsb",
"hl7": "2.16.840.1.113883.6.173",
+ "integbio": "nbdc00836",
"miriam": "medlineplus",
"n2t": "medlineplus"
},
@@ -31763,10 +33367,15 @@
"mesh": {
"contact": {
"email": "custserv@nlm.nih.gov",
- "github": null,
- "name": "NLM Customer Service",
- "orcid": null
+ "name": "NLM Customer Service"
},
+ "contributor_extras": [
+ {
+ "github": "rombaum",
+ "name": "Roman Baum",
+ "orcid": "0000-0001-5246-9351"
+ }
+ ],
"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": [
@@ -31777,12 +33386,16 @@
"bioinformatics",
"biomedical science",
"classification",
+ "data model",
+ "data retrieval",
"life science",
+ "literature curation",
"metascience",
"ontology",
"topics"
],
"license": "CC0-1.0",
+ "logo": "https://meshb.nlm.nih.gov/public/img/meshLogo.jpg",
"mappings": {
"aberowl": "MESH",
"bartoc": "391",
@@ -31794,9 +33407,11 @@
"fairsharing": "FAIRsharing.qnkw45",
"go": "MeSH",
"hl7": "2.16.840.1.113883.6.177",
+ "integbio": "nbdc00132",
"miriam": "mesh",
"n2t": "mesh",
"prefixcommons": "mesh",
+ "togoid": "Mesh",
"wikidata": "P486"
},
"name": "Medical Subject Headings",
@@ -31809,11 +33424,41 @@
"homepage": "https://bio2rdf.org",
"name": "Bio2RDF",
"uri_format": "http://bio2rdf.org/mesh:$1"
+ },
+ {
+ "code": "bioportal.purl",
+ "description": "The BioPortal version of MeSH. Should be re-coded to `bioportal`, see https://github.com/biopragmatics/bioregistry/pull/1066.",
+ "homepage": "https://bioportal.bioontology.org/ontologies/MESH",
+ "name": "BioPortal",
+ "uri_format": "http://purl.bioontology.org/ontology/MESH/$1"
+ },
+ {
+ "code": "mesh.json-ld",
+ "description": "The MeSH version in JSON-LD.",
+ "first_party": true,
+ "homepage": "http://id.nlm.nih.gov/mesh/",
+ "name": "Medical Subject Headings (JSON-LD)",
+ "uri_format": "https://id.nlm.nih.gov/mesh/$1.json-ld"
+ },
+ {
+ "code": "mesh.n3",
+ "description": "The MeSH version in N3.",
+ "first_party": true,
+ "homepage": "http://id.nlm.nih.gov/mesh/",
+ "name": "Medical Subject Headings (N3)",
+ "uri_format": "https://id.nlm.nih.gov/mesh/$1.n3"
+ },
+ {
+ "code": "mesh.ttl",
+ "description": "The MeSH version in TTL.",
+ "first_party": true,
+ "homepage": "http://id.nlm.nih.gov/mesh/",
+ "name": "Medical Subject Headings (TTL)",
+ "uri_format": "https://id.nlm.nih.gov/mesh/$1.ttl"
}
],
"publications": [
{
- "doi": null,
"pmc": "PMC197951",
"pubmed": "13982385",
"title": "Medical subject headings",
@@ -31891,6 +33536,7 @@
"mappings": {
"biocontext": "METABOLIGHTS",
"cellosaurus": "MetaboLights",
+ "integbio": "nbdc02124",
"miriam": "metabolights",
"n2t": "metabolights",
"re3data": "r3d100011556",
@@ -31911,6 +33557,12 @@
"uri_format": "https://www.ebi.ac.uk/metabolights/$1"
},
"metacyc.compound": {
+ "contact": {
+ "email": "pkarp@ai.sri.com",
+ "github": "pkarp111",
+ "name": "Peter Karp",
+ "orcid": "0000-0002-5876-6418"
+ },
"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",
@@ -31924,8 +33576,10 @@
"biolink": "MetaCyc",
"fairsharing": "FAIRsharing.yytevr",
"go": "MetaCyc",
+ "integbio": "nbdc00907",
"miriam": "metacyc.compound",
"n2t": "metacyc.compound",
+ "pathguide": "10",
"re3data": "r3d100011294"
},
"name": "Metabolic Encyclopedia of metabolic and other pathways",
@@ -31960,7 +33614,56 @@
"twitter": "BioCyc",
"uri_format": "https://metacyc.org/compound?orgid=META&id=$1"
},
+ "metacyc.pathway": {
+ "contact": {
+ "email": "pkarp@ai.sri.com",
+ "github": "pkarp111",
+ "name": "Peter Karp",
+ "orcid": "0000-0002-5876-6418"
+ },
+ "contributor": {
+ "github": "hrshdhgd",
+ "name": "Harshad Hegde",
+ "orcid": "0000-0002-2411-565X"
+ },
+ "description": "MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data.\n\nMetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number",
+ "example": "12DICHLORETHDEG-PWY",
+ "github_request_issue": 1012,
+ "homepage": "https://metacyc.org",
+ "name": "Metabolic Encyclopedia for Pathway/Genome Databases",
+ "preferred_prefix": "metacyc.pathway",
+ "publications": [
+ {
+ "pubmed": "31586394",
+ "title": "The MetaCyc database of metabolic pathways and enzymes - a 2019 update",
+ "year": 2019
+ },
+ {
+ "pubmed": "23746312",
+ "title": "The challenge of constructing, classifying, and representing metabolic pathways",
+ "year": 2013
+ },
+ {
+ "pubmed": "21523460",
+ "title": "A survey of metabolic databases emphasizing the MetaCyc family",
+ "year": 2011
+ }
+ ],
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://metacyc.org/META/NEW-IMAGE?object=$1"
+ },
"metacyc.reaction": {
+ "contact": {
+ "email": "pkarp@ai.sri.com",
+ "github": "pkarp111",
+ "name": "Peter Karp",
+ "orcid": "0000-0002-5876-6418"
+ },
"description": "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.",
"example": "RXN-14904",
"homepage": "https://metacyc.org",
@@ -32155,6 +33858,7 @@
"small molecule"
],
"mappings": {
+ "pathguide": "234",
"prefixcommons": "metnetdb"
},
"name": "Metabolic Network Exchange Database",
@@ -32212,7 +33916,9 @@
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"keywords": [
"biomedical science",
+ "cognition",
"cognitive neuroscience",
+ "mental health",
"obo",
"ontology"
],
@@ -32244,6 +33950,7 @@
"depends_on": [
"uberon"
],
+ "deprecated": true,
"description": "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors.",
"download_owl": "http://purl.obolibrary.org/obo/mfmo.owl",
"example": "0000208",
@@ -32291,7 +33998,7 @@
"description": "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.",
"download_obo": "http://aber-owl.net/media/ontologies/MFO/14/mfo.obo",
"download_owl": "http://purl.obolibrary.org/obo/mfo.owl",
- "example": "MFO_0000001",
+ "example": "0000001",
"homepage": "http://ani.embl.de:8080/mepd/",
"keywords": [
"anatomy",
@@ -32308,6 +34015,7 @@
"prefixcommons": "mfo"
},
"name": "Medaka fish anatomy and development",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "MFO",
"providers": [
{
@@ -32334,6 +34042,8 @@
"homepage": "https://github.com/jannahastings/emotion-ontology",
"keywords": [
"biomedical science",
+ "emotion",
+ "mental health",
"obo",
"ontology"
],
@@ -32376,6 +34086,7 @@
"example": "0000046",
"homepage": "https://github.com/jannahastings/mental-functioning-ontology",
"keywords": [
+ "disease",
"obo",
"ontology",
"psychiatry"
@@ -32413,6 +34124,7 @@
"biocontext": "ACLAME",
"edam": "2631",
"fairsharing": "FAIRsharing.5tfcy8",
+ "integbio": "nbdc00355",
"miriam": "mge",
"n2t": "mge",
"prefixcommons": "aclame"
@@ -32457,23 +34169,48 @@
"example": "6017782",
"homepage": "http://www.informatics.jax.org/",
"keywords": [
+ "animal model",
+ "blast",
+ "data analysis service",
"expression",
+ "function",
+ "gene",
+ "gene expression",
+ "genetics",
+ "genome",
+ "genotype",
+ "gold standard",
+ "human disease",
+ "human health",
+ "image",
"life science",
+ "model",
+ "molecular neuroanatomy resource",
"ontology and terminology",
+ "orthology",
+ "pathology",
+ "pathway",
"phenotype",
- "sequence"
+ "recombinase",
+ "sequence",
+ "single nucleotide polymorphism",
+ "strain",
+ "tumor"
],
+ "license": "CC-BY-4.0",
"mappings": {
"biocontext": "MGI",
"cellosaurus": "MGI",
"edam": "3274",
"fairsharing": "FAIRsharing.fcwyhz",
"go": "MGI",
+ "integbio": "nbdc00568",
"miriam": "mgi",
"n2t": "mgi",
"ncbi": "MGI",
"prefixcommons": "mgi",
"re3data": "r3d100010266",
+ "rrid": "MGI",
"uniprot": "DB-0060",
"wikidata": "P671"
},
@@ -32507,7 +34244,6 @@
"publications": [
{
"doi": "10.1126/science.8091224",
- "pmc": null,
"pubmed": "8091224",
"title": "A database for mouse development",
"year": 1994
@@ -32535,7 +34271,6 @@
},
{
"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
@@ -32568,6 +34303,12 @@
"title": "The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse",
"year": 2011
},
+ {
+ "pubmed": "19274630"
+ },
+ {
+ "pubmed": "18428715"
+ },
{
"doi": "10.1093/nar/gki113",
"pmc": "PMC540067",
@@ -32640,9 +34381,12 @@
"keywords": [
"interaction",
"life science",
+ "molecular interaction",
"molecule",
"obo",
- "ontology"
+ "ontology",
+ "protein",
+ "protein interaction"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -32675,7 +34419,6 @@
"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
@@ -32686,7 +34429,7 @@
"synonyms": [
"PSI-MI"
],
- "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/mi/terms?obo_id=MI:$1"
+ "uri_format": "http://purl.obolibrary.org/obo/MI_$1"
},
"miaa": {
"comment": "same as MAT",
@@ -32763,10 +34506,13 @@
"example": "0002999",
"homepage": "https://github.com/carrineblank/MicrO",
"keywords": [
+ "assay",
"bioinformatics",
+ "cell culture",
"microbiology",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"license": "CC BY 2.0",
"mappings": {
@@ -32861,7 +34607,7 @@
"uri_format": "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"
},
"millipore": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "SCC111",
"homepage": "https://www.merckmillipore.com/",
"mappings": {
@@ -32925,17 +34671,42 @@
"uri_format": "http://immunet.cn/bdb/index.php/mimoset/$1"
},
"minid": {
+ "contact": {
+ "email": "foster@uchicago.edu",
+ "name": "Ian Foster",
+ "orcid": "0000-0003-2129-5269"
+ },
"description": "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation.",
"example": "b97957",
"homepage": "https://fair-research.org",
+ "keywords": [
+ "citation",
+ "data retrieval",
+ "publication",
+ "subject agnostic"
+ ],
"mappings": {
"biocontext": "MINID",
+ "fairsharing": "FAIRsharing.d099fb",
"miriam": "minid",
"n2t": "minid"
},
"name": "Minimal Viable Identifier",
"pattern": "^[A-Za-z0-9]+$",
"preferred_prefix": "minid",
+ "publications": [
+ {
+ "doi": "10.1371/journal.pone.0213013",
+ "pubmed": "30973881",
+ "title": "Reproducible big data science: A case study in continuous FAIRness",
+ "year": 2019
+ },
+ {
+ "doi": "10.1371/journal.pone.0294883",
+ "title": "Correction: Reproducible big data science: A case study in continuous FAIRness",
+ "year": 2023
+ }
+ ],
"uri_format": "https://hdl.handle.net/hdl:20.500.12582/$1"
},
"minid.test": {
@@ -32955,7 +34726,6 @@
"banana_peel": "-",
"contact": {
"email": "luana.licata@gmail.com",
- "github": null,
"name": "Luana Licata",
"orcid": "0000-0001-5084-9000"
},
@@ -32974,6 +34744,7 @@
"fairsharing": "FAIRsharing.2bdvmk",
"miriam": "mint",
"n2t": "mint",
+ "pathguide": "17",
"prefixcommons": "mint",
"re3data": "r3d100010414",
"uniprot": "DB-0158"
@@ -32982,19 +34753,19 @@
"pattern": "^\\d{1,7}$",
"preferred_prefix": "mint",
"providers": [
+ {
+ "code": "CURATOR_REVIEW",
+ "description": "The Molecular INTeraction database (MINT)",
+ "homepage": "http://mint.bio.uniroma2.it/mint/",
+ "name": "The Molecular INTeraction database (MINT)",
+ "uri_format": "http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$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/mint:$1"
- },
- {
- "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": [
@@ -33021,7 +34792,6 @@
},
{
"doi": "10.1016/s0014-5793(01)03293-8",
- "pmc": null,
"pubmed": "11911893",
"title": "MINT: a Molecular INTeraction database",
"year": 2002
@@ -33097,11 +34867,14 @@
"biolink": "mirbase",
"edam": "2642",
"fairsharing": "FAIRsharing.hmgte8",
+ "integbio": "nbdc00136",
"miriam": "mirbase",
"n2t": "mirbase",
"ncbi": "miRBase",
+ "pathguide": "210",
"prefixcommons": "mirbase",
"re3data": "r3d100010566",
+ "togoid": "Mirbase",
"wikidata": "P2870"
},
"name": "miRBase pre-miRNA",
@@ -33221,6 +34994,7 @@
"mappings": {
"biocontext": "MIREX",
"fairsharing": "FAIRsharing.q3b39v",
+ "integbio": "nbdc02064",
"miriam": "mirex",
"n2t": "mirex"
},
@@ -33248,7 +35022,6 @@
"miriam": {
"contact": {
"email": "n.lenovere@gmail.com",
- "github": null,
"name": "Nicolas Le Novère",
"orcid": "0000-0002-6309-7327"
},
@@ -33285,7 +35058,6 @@
},
{
"doi": "10.1038/nbt1156",
- "pmc": null,
"pubmed": "16333295",
"title": "Minimum information requested in the annotation of biochemical models (MIRIAM)",
"year": 2005
@@ -33355,7 +35127,6 @@
"mirnao": {
"contact": {
"email": "topalis@imbb.forth.gr",
- "github": null,
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
@@ -33393,6 +35164,7 @@
"mappings": {
"biocontext": "MIRNEST",
"fairsharing": "FAIRsharing.5pfx4r",
+ "integbio": "nbdc01703",
"miriam": "mirnest",
"n2t": "mirnest",
"prefixcommons": "mirnest"
@@ -33430,7 +35202,6 @@
"miro": {
"contact": {
"email": "louis@imbb.forth.gr",
- "github": null,
"name": " Christos Louis",
"orcid": "0000-0003-2497-2210"
},
@@ -33441,9 +35212,12 @@
"example": "40000617",
"homepage": "https://github.com/VEuPathDB-ontology/MIRO",
"keywords": [
+ "insecticide resistance",
"life science",
+ "mutation",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"mappings": {
"aberowl": "MIRO",
@@ -33474,27 +35248,77 @@
"mirtarbase": {
"contact": {
"email": "ken.sd.hsu@gmail.com",
- "github": null,
"name": "Sheng-Da Hsu",
"orcid": "0000-0002-8214-1696"
},
+ "contributor_extras": [
+ {
+ "email": "benjamin_gyori@hms.harvard.edu",
+ "github": "bgyori",
+ "name": "Benjamin M. Gyori",
+ "orcid": "0000-0001-9439-5346"
+ },
+ {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ }
+ ],
"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/",
+ "homepage": "https://mirtarbase.cuhk.edu.cn/",
"keywords": [
"life science"
],
"mappings": {
"biocontext": "MIRTARBASE",
"fairsharing": "FAIRsharing.f0bxfg",
+ "integbio": "nbdc01217",
"miriam": "mirtarbase",
"n2t": "mirtarbase",
+ "pathguide": "715",
"wikidata": "P2646"
},
"name": "mirTarBase",
"pattern": "^MIRT\\d{6}$",
"preferred_prefix": "mirtarbase",
"publications": [
+ {
+ "doi": "10.1093/nar/gkab1079",
+ "pmc": "PMC8728135",
+ "pubmed": "34850920",
+ "title": "miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions",
+ "year": 2022
+ },
+ {
+ "doi": "10.1093/nar/gkz896",
+ "pmc": "PMC7145596 ",
+ "pubmed": "31647101",
+ "title": "miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database",
+ "year": 2020
+ },
+ {
+ "doi": "10.1093/nar/gkx1067",
+ "pmc": "PMC5753222 ",
+ "pubmed": "29126174",
+ "title": "miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions",
+ "year": 2018
+ },
+ {
+ "doi": "10.1093/nar/gkv1258",
+ "pmc": "PMC4702890",
+ "pubmed": "26590260",
+ "title": "miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database",
+ "year": 2016
+ },
+ {
+ "doi": "10.1093/nar/gkt1266",
+ "pmc": "PMC3965058",
+ "pubmed": "24304892",
+ "title": "miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions",
+ "year": 2014
+ },
{
"doi": "10.1093/nar/gkq1107",
"pmc": "PMC3013699",
@@ -33503,7 +35327,10 @@
"year": 2010
}
],
- "uri_format": "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/940"
+ ],
+ "uri_format": "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"
},
"mirte": {
"contributor": {
@@ -33538,12 +35365,18 @@
"github": "only1chunts",
"name": "Chris Hunter",
"orcid": "0000-0002-1335-0881"
+ },
+ {
+ "email": "lindsey.anderson@pnnl.gov",
+ "github": "lnanderson",
+ "name": "Lindsey N. Anderson",
+ "orcid": "0000-0002-8741-7823"
}
],
"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/",
+ "homepage": "https://www.gensc.org/pages/standards/all-terms.html",
"keywords": [
"ontology"
],
@@ -33609,6 +35442,7 @@
"edam": "2667",
"miriam": "mmdb",
"n2t": "mmdb",
+ "pathguide": "508",
"prefixcommons": "mmdb"
},
"name": "Molecular Modeling Database",
@@ -33682,8 +35516,10 @@
"keywords": [
"biomedical science",
"life science",
+ "model organism",
"obo",
"ontology",
+ "phenotype",
"preclinical studies"
],
"license": "CC0-1.0",
@@ -33719,7 +35555,7 @@
"repository": "https://github.com/rat-genome-database/MMO-Measurement-Method-Ontology",
"twitter": "ratgenome",
"uri_format": "http://purl.obolibrary.org/obo/MMO_$1",
- "version": "2.39"
+ "version": "2.132"
},
"mmp.cat": {
"description": "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.",
@@ -33780,7 +35616,17 @@
"example": "70",
"homepage": "https://www.mmrrc.org",
"keywords": [
- "biology"
+ "biology",
+ "cryopreserved",
+ "database",
+ "embryonic stem cell",
+ "embryonic stem cell line",
+ "faseb list",
+ "mouse strain",
+ "mutant",
+ "mutant mouse strain",
+ "stem cell",
+ "transgenic"
],
"mappings": {
"biocontext": "MMRRC",
@@ -33788,15 +35634,14 @@
"fairsharing": "FAIRsharing.9dpd18",
"miriam": "mmrrc",
"n2t": "mmrrc",
- "re3data": "r3d100013715"
+ "re3data": "r3d100013715",
+ "rrid": "MMRRC"
},
"name": "Mutant Mouse Resource and Research Centers",
"pattern": "^\\d+$",
"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
@@ -33871,6 +35716,7 @@
"anatomy",
"developmental biology",
"embryology",
+ "life cycle stage",
"obo",
"ontology"
],
@@ -33893,13 +35739,11 @@
"synonyms": [
"MmusDv"
],
- "uri_format": "http://purl.obolibrary.org/obo/MmusDv_$1",
- "version": "2020-03-10"
+ "uri_format": "http://purl.obolibrary.org/obo/MmusDv_$1"
},
"mo": {
"contact": {
"email": "stoeckrt@pcbi.upenn.edu",
- "github": null,
"name": "Chris Stoeckert",
"orcid": "0000-0002-5714-991X"
},
@@ -33923,22 +35767,12 @@
"name": "Microarray experimental conditions",
"pattern": "^\\w+$",
"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"
- }
- ],
"rdf_uri_format": "http://purl.obolibrary.org/obo/MO_$1",
- "uri_format": "http://purl.obolibrary.org/obo/MO_$1"
+ "uri_format": "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1"
},
"mobidb": {
"contact": {
"email": "silvio.tosatto@unipd.it",
- "github": null,
"name": "Silvio C.E. Tosatto",
"orcid": "0000-0003-4525-7793"
},
@@ -33952,8 +35786,10 @@
"mappings": {
"biocontext": "MOBIDB",
"fairsharing": "FAIRsharing.jwra3e",
+ "integbio": "nbdc01956",
"miriam": "mobidb",
"n2t": "mobidb",
+ "pathguide": "623",
"uniprot": "DB-0183"
},
"name": "MobiDB",
@@ -33979,8 +35815,7 @@
"doi": "10.1093/bioinformatics/bts327",
"pmc": "PMC5753340",
"pubmed": "29136219",
- "title": "MobiDB: a comprehensive database of intrinsic protein disorder annotations.",
- "year": null
+ "title": "MobiDB: a comprehensive database of intrinsic protein disorder annotations."
},
{
"doi": "10.1093/nar/gku982",
@@ -33991,7 +35826,6 @@
},
{
"doi": "10.1093/bioinformatics/bts327",
- "pmc": null,
"pubmed": "22661649",
"title": "MobiDB: a comprehensive database of intrinsic protein disorder annotations",
"year": 2012
@@ -34013,6 +35847,7 @@
"example": "01467",
"homepage": "http://www.psidev.info/MOD",
"keywords": [
+ "enzymatic reaction",
"life science",
"molecule",
"obo",
@@ -34050,7 +35885,6 @@
"publications": [
{
"doi": "10.1038/nbt0808-864",
- "pmc": null,
"pubmed": "18688235",
"title": "The PSI-MOD community standard for representation of protein modification data",
"year": 2008
@@ -34061,7 +35895,7 @@
"synonyms": [
"PSI-MOD"
],
- "uri_format": "http://bioportal.bioontology.org/ontologies/1041?p=terms&conceptid=MOD:$1",
+ "uri_format": "http://purl.obolibrary.org/obo/MOD_$1",
"version": "1.031.6"
},
"modeldb": {
@@ -34077,6 +35911,7 @@
"biocontext": "MODELDB",
"edam": "2669",
"fairsharing": "FAIRsharing.5rb3fk",
+ "integbio": "nbdc02085",
"miriam": "modeldb",
"n2t": "modeldb",
"prefixcommons": "modeldb",
@@ -34125,17 +35960,11 @@
},
{
"doi": "10.1385/NI:1:1:135",
- "pmc": null,
- "pubmed": null,
- "title": "ModelDB: making models publicly accessible to support computational neuroscience.",
- "year": null
+ "title": "ModelDB: making models publicly accessible to support computational neuroscience."
},
{
"doi": "10.1023/B:JCNS.0000023869.22017.2e",
- "pmc": null,
- "pubmed": null,
- "title": "ModelDB: A Database to Support Computational Neuroscience.",
- "year": null
+ "title": "ModelDB: A Database to Support Computational Neuroscience."
}
],
"twitter": "SenseLabProject",
@@ -34231,6 +36060,7 @@
"structure"
],
"mappings": {
+ "integbio": "nbdc00573",
"prefixcommons": "molmovdb"
},
"name": "Database of Macromolecular Movements",
@@ -34266,6 +36096,7 @@
"example": "0000001",
"homepage": "https://monarch-initiative.github.io/mondo",
"keywords": [
+ "biocuration",
"infectious disease medicine",
"medicine",
"obo",
@@ -34278,9 +36109,11 @@
"biocontext": "MONDO",
"bioportal": "MONDO",
"fairsharing": "FAIRsharing.b2979t",
+ "integbio": "nbdc02563",
"obofoundry": "mondo",
"ols": "mondo",
"ontobee": "MONDO",
+ "togoid": "Mondo",
"wikidata": "P5270"
},
"mastodon": "monarch_initiative@genomic.social",
@@ -34288,10 +36121,14 @@
"pattern": "^\\d{7}$",
"preferred_prefix": "MONDO",
"publications": [
+ {
+ "doi": "10.1093/nar/gkw1128",
+ "pubmed": "27899636",
+ "title": "The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species",
+ "year": 2016
+ },
{
"doi": "10.1101/2022.04.13.22273750",
- "pmc": null,
- "pubmed": null,
"title": "Mondo: Unifying diseases for the world, by the world",
"year": 2022
}
@@ -34300,7 +36137,7 @@
"repository": "https://github.com/monarch-initiative/mondo",
"twitter": "MonarchInit",
"uri_format": "http://purl.obolibrary.org/obo/MONDO_$1",
- "version": "2023-06-01"
+ "version": "2024-04-02"
},
"mop": {
"contact": {
@@ -34317,11 +36154,13 @@
"keywords": [
"molecular chemistry",
"obo",
- "ontology"
+ "ontology",
+ "reaction data"
],
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "MOP",
+ "bartoc": "20466",
"biocontext": "MOP",
"bioportal": "MOP",
"fairsharing": "FAIRsharing.mct09a",
@@ -34404,8 +36243,9 @@
"download_obo": "http://purl.obolibrary.org/obo/mp.obo",
"download_owl": "http://purl.obolibrary.org/obo/mp.owl",
"example": "0005452",
- "homepage": "http://www.informatics.jax.org/searches/MP_form.shtml",
+ "homepage": "https://www.informatics.jax.org/vocab/mp_ontology/",
"keywords": [
+ "behavior",
"developmental biology",
"life science",
"mammalian",
@@ -34415,6 +36255,7 @@
"physiology"
],
"license": "CC-BY-4.0",
+ "logo": "https://raw.githubusercontent.com/mgijax/mammalian-phenotype-ontology/main/logo/2024_MP_logo_RGB_ICON_color.png",
"mappings": {
"aberowl": "MP",
"biocontext": "MP",
@@ -34425,13 +36266,21 @@
"obofoundry": "mp",
"ols": "mp",
"ontobee": "MP",
- "prefixcommons": "mp"
+ "prefixcommons": "mp",
+ "togoid": "Mp"
},
"name": "Mammalian Phenotype Ontology",
"namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "MP",
"providers": [
+ {
+ "code": "CURATOR_REVIEW",
+ "description": "Mammalian Phenotype Ontology at The Jackson Lab",
+ "homepage": "http://www.informatics.jax.org/",
+ "name": "Mammalian Phenotype Ontology at The Jackson Lab",
+ "uri_format": "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$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.",
@@ -34479,7 +36328,8 @@
],
"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"
+ "uri_format": "http://purl.obolibrary.org/obo/MP_$1",
+ "version": "2024-04-23"
},
"mpath": {
"contact": {
@@ -34496,7 +36346,11 @@
"keywords": [
"anatomy",
"biomedical science",
+ "disease",
+ "genetic strain",
+ "histology",
"mouse",
+ "mutation",
"obo",
"ontology",
"phenotype"
@@ -34507,6 +36361,7 @@
"biocontext": "MPATH",
"bioportal": "MPATH",
"fairsharing": "FAIRsharing.3wbgm0",
+ "integbio": "nbdc01568",
"obofoundry": "mpath",
"ols": "mpath",
"ontobee": "MPATH",
@@ -34556,6 +36411,7 @@
"fairsharing": "FAIRsharing.eyjkws",
"miriam": "mpid",
"n2t": "mpid",
+ "pathguide": "559",
"prefixcommons": "mpi"
},
"name": "Microbial Protein Interaction Database",
@@ -34621,7 +36477,7 @@
"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"
+ "version": "2023-10-17"
},
"mro": {
"contact": {
@@ -34635,7 +36491,9 @@
"example": "0000634",
"homepage": "https://github.com/IEDB/MRO",
"keywords": [
+ "immune system",
"immunology",
+ "major histocompatibility complex",
"obo",
"ontology"
],
@@ -34664,7 +36522,7 @@
"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": "2023-06-06"
+ "version": "2023-12-21"
},
"ms": {
"banana": "MS",
@@ -34714,7 +36572,7 @@
"rdf_uri_format": "http://purl.obolibrary.org/obo/MS_$1",
"repository": "https://github.com/HUPO-PSI/psi-ms-CV",
"uri_format": "http://purl.obolibrary.org/obo/MS_$1",
- "version": "4.1.127"
+ "version": "4.1.152"
},
"msigdb": {
"contributor": {
@@ -34727,7 +36585,8 @@
"example": "M1",
"homepage": "https://www.gsea-msigdb.org",
"mappings": {
- "biolink": "MSigDB"
+ "biolink": "MSigDB",
+ "integbio": "nbdc02550"
},
"name": "Molecular Signatures Database",
"pattern": "^M\\d+$",
@@ -34738,19 +36597,40 @@
"uri_format": "https://biopragmatics.github.io/providers/msigdb/$1"
},
"msio": {
+ "contact": {
+ "email": "philippe.rocca-serra@oerc.ox.ac.uk",
+ "name": "Philippe Rocca-Serra",
+ "orcid": "0000-0001-9853-5668"
+ },
"description": "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies.",
"download_owl": "https://raw.githubusercontent.com/MSI-Metabolomics-Standards-Initiative/MSIO/master/releases/latest_release/MSIO-merged-reasoned.owl",
"example": "0000111",
"homepage": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"keywords": [
+ "annotation",
+ "experimental measurement",
+ "mass spectrum",
+ "metabolomics",
+ "nmr",
+ "nuclear magnetic resonance (nmr) spectroscopy",
+ "omics",
+ "omics data analysis",
"ontology"
],
"mappings": {
+ "fairsharing": "FAIRsharing.4c7f91",
"ols": "msio"
},
"name": "Metabolomics Standards Initiative Ontology",
"pattern": "^\\d{7}$",
"preferred_prefix": "msio",
+ "publications": [
+ {
+ "doi": "10.1007/s11306-007-0069-z",
+ "title": "Metabolomics standards initiative: ontology working group work in progress",
+ "year": 2007
+ }
+ ],
"repository": "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO",
"uri_format": "http://purl.obolibrary.org/obo/MSIO_$1",
"version": "1.0.1"
@@ -34788,7 +36668,6 @@
"multicellds": {
"contact": {
"email": "samuel.friedman@cammlab.org",
- "github": null,
"name": "Samuel Friedman",
"orcid": "0000-0001-8003-6860"
},
@@ -34856,6 +36735,31 @@
"preferred_prefix": "multicellds.snapshot",
"uri_format": "http://multicellds.org/MultiCellDB/$1"
},
+ "mvx": {
+ "contributor": {
+ "email": "lindsey.anderson@pnnl.gov",
+ "github": "lnanderson",
+ "name": "Lindsey Anderson",
+ "orcid": "0000-0002-8741-7823"
+ },
+ "description": "The CDC's National Center for Immunization and Respiratory Diseases ([NCIRD](https://www.cdc.gov/ncird/)) developed and maintains HL7 Table 0227, Manufacturers of Vaccines (MVX). It includes both active and inactive manufacturers of vaccines in the US. Inactive MVX codes allow transmission of historical immunization records. When [MVX code is paired with a CVX code](https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename) (vaccine administered code), the specific trade named vaccine may be indicated.",
+ "example": "ASZ",
+ "github_request_issue": 986,
+ "homepage": "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=mvx",
+ "mappings": {
+ "hl7": "2.16.840.1.113883.6.60"
+ },
+ "name": "Manufacturers of Vaccines",
+ "pattern": "^\\w+$",
+ "preferred_prefix": "mvx",
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.12.227&code=$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",
@@ -35009,7 +36913,6 @@
"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
@@ -35063,12 +36966,31 @@
},
"mzspec": {
"banana": "mzspec",
+ "contact": {
+ "email": "gerhard.mayer@rub.de",
+ "github": "germa",
+ "name": "Gerhard Mayer",
+ "orcid": "0000-0002-1767-2343"
+ },
+ "contributor_extras": [
+ {
+ "email": "lindsey.anderson@pnnl.gov",
+ "github": "lnanderson",
+ "name": "Lindsey N. Anderson",
+ "orcid": "0000-0002-8741-7823"
+ }
+ ],
"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/",
+ "example": "PXD002255:ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2",
+ "homepage": "http://www.psidev.info/usi",
"keywords": [
"data governance",
+ "data identity and mapping",
+ "data retrieval",
+ "lipidomics",
+ "mass spectrum",
"metabolomics",
+ "omics data analysis",
"proteomics"
],
"mappings": {
@@ -35088,6 +37010,13 @@
"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"
+ },
+ {
+ "code": "ebi",
+ "description": "PRIDE is a database of PRoteomics IDEntifications. It contains protein and peptide identifications (including details of post-translational modifications) together with the mass spectrometric evidence supporting these identifications. PRIDE acts as a repository for mass spectrometry data, specifically the fragment ion spectra used to identify peptide sequences.",
+ "homepage": "https://www.ebi.ac.uk/pride",
+ "name": "PRIDE",
+ "uri_format": "https://www.ebi.ac.uk/pride/archive/usi?usi=mzspec:$1"
}
],
"publications": [
@@ -35099,6 +37028,7 @@
"year": 2021
}
],
+ "repository": "https://github.com/HUPO-PSI/usi",
"uri_format": "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"
},
"n2t": {
@@ -35136,15 +37066,12 @@
"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
}
@@ -35156,11 +37083,22 @@
},
"nando": {
"banana": "NANDO",
+ "contact": {
+ "email": "kninomiya-mope@g.ecc.u-tokyo.ac.jp",
+ "name": "Kota Ninomiya"
+ },
"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.",
+ "download_owl": "http://aber-owl.net/media/ontologies/NANDO/14/nando.owl",
"example": "1200031",
"homepage": "https://nanbyodata.jp/",
+ "keywords": [
+ "ontology"
+ ],
"mappings": {
- "miriam": "nando"
+ "aberowl": "NANDO",
+ "bioportal": "NANDO",
+ "miriam": "nando",
+ "togoid": "Nando"
},
"name": "Nanbyo Disease Ontology",
"namespace_in_lui": true,
@@ -35171,7 +37109,6 @@
"napdi": {
"contact": {
"email": "rdb20@pitt.edu",
- "github": null,
"name": "Richard Boyce",
"orcid": "0000-0002-2993-2085"
},
@@ -35205,7 +37142,6 @@
"napp": {
"contact": {
"email": "daniel.gautheret@u-psud.fr",
- "github": null,
"name": "Daniel Gautheret",
"orcid": "0000-0002-1508-8469"
},
@@ -35264,6 +37200,7 @@
"mappings": {
"biocontext": "NARCIS",
"fairsharing": "FAIRsharing.f63h4k",
+ "integbio": "nbdc01862",
"miriam": "narcis",
"n2t": "narcis"
},
@@ -35275,7 +37212,6 @@
"nasc": {
"contact": {
"email": "sean@arabidopsis.org.uk",
- "github": null,
"name": "Sean May",
"orcid": "0000-0001-5282-3250"
},
@@ -35337,7 +37273,8 @@
"ecto",
"maxo",
"pcl",
- "scdo"
+ "scdo",
+ "uberon"
],
"contact": {
"email": "g.gkoutos@bham.ac.uk",
@@ -35351,8 +37288,10 @@
"example": "0000564",
"homepage": "https://github.com/obo-behavior/behavior-ontology/",
"keywords": [
+ "behavior",
"obo",
"ontology",
+ "phenotype",
"social and behavioural science",
"systemic neuroscience"
],
@@ -35372,30 +37311,21 @@
"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
- },
- {
- "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": "2023-05-02"
+ "version": "2023-07-04"
},
"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.",
@@ -35431,12 +37361,10 @@
"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"
@@ -35484,13 +37412,11 @@
"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"
@@ -35576,7 +37502,27 @@
"preferred_prefix": "ncbibook",
"uri_format": "https://www.ncbi.nlm.nih.gov/books/$1"
},
+ "ncbidrs": {
+ "description": "This is the namespace for the archive of sequence and other files provided by NCBI e.g. in SRA and dbGaP. These files are related to objects in the sequencing data model managed under the insdc.sra namespace. ",
+ "example": "72ff6ff882ec447f12df018e6183de59",
+ "homepage": "https://www.ncbi.nlm.nih.gov/",
+ "mappings": {
+ "miriam": "ncbidrs"
+ },
+ "name": "NCBI Data Repository Service",
+ "pattern": "^[0-9a-fA-F]{32}$",
+ "preferred_prefix": "ncbidrs",
+ "uri_format": "https://locate.be-md.ncbi.nlm.nih.gov/ga4gh/drs/v1/objects/$1"
+ },
"ncbigene": {
+ "contributor_extras": [
+ {
+ "email": "rcameron@sfu.com",
+ "github": "cmrn-rhi",
+ "name": "Rhiannon Cameron",
+ "orcid": "0000-0002-9578-0788"
+ }
+ ],
"description": "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis.",
"example": "100010",
"homepage": "https://www.ncbi.nlm.nih.gov/gene",
@@ -35594,11 +37540,13 @@
"fairsharing": "FAIRsharing.5h3maw",
"go": "NCBIGene",
"hl7": "2.16.840.1.113883.6.340",
+ "integbio": "nbdc00073",
"miriam": "ncbigene",
"n2t": "ncbigene",
"ncbi": "GeneID",
"prefixcommons": "ncbigene",
"re3data": "r3d100010650",
+ "togoid": "Ncbigene",
"uniprot": "DB-0118",
"wikidata": "P351"
},
@@ -35607,8 +37555,7 @@
{
"name": "National Center for Biotechnology Information",
"partnered": false,
- "ror": "02meqm098",
- "wikidata": null
+ "ror": "02meqm098"
}
],
"pattern": "^\\d+$",
@@ -35644,6 +37591,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gku1055",
+ "pubmed": "25355515"
+ },
{
"doi": "10.1093/nar/gkq1237",
"pmc": "PMC3013746",
@@ -35660,13 +37611,17 @@
}
],
"rdf_uri_format": "http://purl.uniprot.org/geneid/$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/983"
+ ],
"synonyms": [
"EGID",
"EntrezGene",
"NCBIGene",
"NCBI_GeneID",
"entrez",
- "entrez gene/locuslink"
+ "entrez gene/locuslink",
+ "nihgeneid"
],
"uri_format": "https://www.ncbi.nlm.nih.gov/gene/$1"
},
@@ -35692,8 +37647,7 @@
{
"name": "National Center for Biotechnology Information",
"partnered": false,
- "ror": "02meqm098",
- "wikidata": null
+ "ror": "02meqm098"
}
],
"pattern": "^\\d+$",
@@ -35718,6 +37672,7 @@
"mappings": {
"biocontext": "NCBIProtein",
"go": "NCBI_NP",
+ "integbio": "nbdc00636",
"miriam": "ncbiprotein",
"n2t": "ncbiprotein",
"prefixcommons": "ncbi.protein",
@@ -35728,8 +37683,7 @@
{
"name": "National Center for Biotechnology Information",
"partnered": false,
- "ror": "02meqm098",
- "wikidata": null
+ "ror": "02meqm098"
}
],
"pattern": "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$",
@@ -35754,6 +37708,7 @@
"ecto",
"envo",
"foodon",
+ "gallont",
"genepio",
"go",
"hso",
@@ -35761,13 +37716,14 @@
"ons",
"pcl",
"pco",
+ "uberon",
"vbo"
],
"contact": {
- "email": "frederic.bastian@unil.ch",
+ "email": "schoch2@ncbi.nlm.nih.gov",
"github": "fbastian",
- "name": "Frederic Bastian",
- "orcid": "0000-0002-9415-5104"
+ "name": "Conrad L Schoch",
+ "orcid": "0000-0003-1839-5322"
},
"description": "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined.",
"download_json": "http://purl.obolibrary.org/obo/ncbitaxon.json",
@@ -35784,6 +37740,7 @@
"phylogenetics",
"protein",
"structure",
+ "taxonomic classification",
"taxonomy"
],
"license": "CC0-1.0",
@@ -35806,6 +37763,7 @@
"ontobee": "NCBITaxon",
"prefixcommons": "taxonomy",
"re3data": "r3d100010415",
+ "togoid": "Taxonomy",
"wikidata": "P685"
},
"name": "NCBI Taxonomy",
@@ -35813,8 +37771,7 @@
{
"name": "National Center for Biotechnology Information",
"partnered": false,
- "ror": "02meqm098",
- "wikidata": null
+ "ror": "02meqm098"
}
],
"pattern": "^\\d+$",
@@ -35894,8 +37851,8 @@
"taxonomy",
"uniprot.taxonomy"
],
- "uri_format": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1",
- "version": "2023-06-20"
+ "uri_format": "http://purl.obolibrary.org/obo/NCBITaxon_$1",
+ "version": "2024-03-26"
},
"nci.drug": {
"description": "identifier of an entry in the NCI Drug Dictionary",
@@ -35922,8 +37879,7 @@
{
"name": "National Cancer Institute",
"partnered": false,
- "ror": "040gcmg81",
- "wikidata": null
+ "ror": "040gcmg81"
}
],
"pattern": "^C\\d+$",
@@ -35950,6 +37906,8 @@
"homepage": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition",
"keywords": [
"biomedical science",
+ "cancer",
+ "disease",
"obo",
"ontology",
"preclinical studies",
@@ -35977,8 +37935,7 @@
{
"name": "National Cancer Institute",
"partnered": false,
- "ror": "040gcmg81",
- "wikidata": null
+ "ror": "040gcmg81"
}
],
"pattern": "^C\\d+$",
@@ -36009,7 +37966,6 @@
},
{
"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",
"year": 2004
@@ -36022,6 +37978,7 @@
"NCI2004_11_17",
"NCIT",
"NCIT_Thesaurus",
+ "NCIThesaurus",
"NCITm",
"NCITt",
"NCI_Thesaurus",
@@ -36029,8 +37986,8 @@
"NCit",
"ncithesaurus"
],
- "uri_format": "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1",
- "version": "2022-08-19"
+ "uri_format": "http://purl.obolibrary.org/obo/NCIT_$1",
+ "version": "2023-10-19"
},
"ncro": {
"contact": {
@@ -36046,6 +38003,7 @@
"homepage": "http://omnisearch.soc.southalabama.edu/w/index.php/Ontology",
"keywords": [
"genomics",
+ "non-coding rna",
"obo",
"ontology"
],
@@ -36103,9 +38061,7 @@
"nddf": {
"contact": {
"email": "cs@firstdatabank.com",
- "github": null,
- "name": "First DataBank Customer Support",
- "orcid": null
+ "name": "First DataBank Customer Support"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -36118,9 +38074,12 @@
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF",
"keywords": [
"biomedical science",
+ "chemical entity",
+ "drug",
"medicinal chemistry",
"ontology"
],
+ "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "NDDF",
"biolink": "NDDF",
@@ -36136,7 +38095,6 @@
"ndex": {
"contact": {
"email": "rpillich@ucsd.edu",
- "github": null,
"name": "Rudolf T. Pillich",
"orcid": "0000-0001-8682-0568"
},
@@ -36177,7 +38135,6 @@
},
{
"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",
"year": 2017
@@ -36191,10 +38148,7 @@
},
{
"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
+ "title": "NDEx 2.0: A Clearinghouse for Research on Cancer Pathways."
}
],
"repository": "https://github.com/ndexbio",
@@ -36204,9 +38158,7 @@
"ndfrt": {
"contact": {
"email": "michael.lincoln@va.gov",
- "github": null,
- "name": "Michael J. Lincoln MD",
- "orcid": null
+ "name": "Michael J. Lincoln MD"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -36219,6 +38171,8 @@
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT",
"keywords": [
"biomedical science",
+ "chemical entity",
+ "drug name",
"health science",
"medicine",
"ontology",
@@ -36247,7 +38201,6 @@
],
"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",
@@ -36309,7 +38262,6 @@
"nemo2": {
"contact": {
"email": "gfrishkoff@gsu.edu",
- "github": null,
"name": "Gwen Frishkoff",
"orcid": "0000-0003-0612-0970"
},
@@ -36318,9 +38270,15 @@
"example": "0000196",
"homepage": "http://aimlab.cs.uoregon.edu/NEMO/web/index.html",
"keywords": [
+ "brain",
+ "cognition",
"cognitive neuroscience",
+ "electroencephalography",
+ "imaging",
+ "interoperability",
"life science",
"neurobiology",
+ "neuron",
"ontology"
],
"mappings": {
@@ -36340,8 +38298,6 @@
},
{
"doi": "10.1038/npre.2009.3458.1",
- "pmc": null,
- "pubmed": null,
"title": "Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials",
"year": 2009
}
@@ -36430,7 +38386,6 @@
"publications": [
{
"doi": "10.1038/nrn1885",
- "pmc": null,
"pubmed": "16552417",
"title": "Mobilizing the base of neuroscience data: the case of neuronal morphologies",
"year": 2006
@@ -36539,6 +38494,7 @@
"mappings": {
"biocontext": "NEXTDB",
"fairsharing": "FAIRsharing.xz5m1a",
+ "integbio": "nbdc00594",
"miriam": "nextdb",
"n2t": "nextdb",
"ncbi": "NextDB",
@@ -36561,7 +38517,6 @@
"nextprot": {
"contact": {
"email": "monique.zahn@sib.swiss",
- "github": null,
"name": "Monique Zahn",
"orcid": "0000-0001-7961-6091"
},
@@ -36575,6 +38530,7 @@
"mappings": {
"biocontext": "NEXTPROT",
"fairsharing": "FAIRsharing.62evqh",
+ "integbio": "nbdc02107",
"miriam": "nextprot",
"n2t": "nextprot",
"uniprot": "DB-0161"
@@ -36606,7 +38562,6 @@
},
{
"doi": "10.1021/pr300830v",
- "pmc": null,
"pubmed": "23205526",
"title": "neXtProt: organizing protein knowledge in the context of human proteome projects",
"year": 2012
@@ -36620,24 +38575,15 @@
},
{
"doi": "10.1093/nar/gkw1062.",
- "pmc": null,
- "pubmed": null,
- "title": "The neXtProt knowledgebase on human proteins: 2017 update.",
- "year": null
+ "title": "The neXtProt knowledgebase on human proteins: 2017 update."
},
{
"doi": "10.1093/nar/gku1178.",
- "pmc": null,
- "pubmed": null,
- "title": "The neXtProt knowledgebase on human proteins: current status.",
- "year": null
+ "title": "The neXtProt knowledgebase on human proteins: current status."
},
{
"doi": "10.1021/pr300830v.",
- "pmc": null,
- "pubmed": null,
- "title": "neXtProt: organizing protein knowledge in the context of human proteome projects.",
- "year": null
+ "title": "neXtProt: organizing protein knowledge in the context of human proteome projects."
}
],
"synonyms": [
@@ -36665,38 +38611,6 @@
"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_$1",
- "version": "0.2"
- },
"nfdi4chem.ontocape": {
"comment": "This ontology ecosystem is near unusable",
"contributor": {
@@ -36750,6 +38664,7 @@
"ontobee": "NGBO"
},
"name": "Next Generation Biobanking Ontology",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "NGBO",
"rdf_uri_format": "http://purl.obolibrary.org/obo/NGBO_$1",
"repository": "https://github.com/Dalalghamdi/NGBO",
@@ -36771,7 +38686,7 @@
"uri_format": "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"
},
"nhcdr": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "ND50028",
"homepage": "https://stemcells.nindsgenetics.org",
"mappings": {
@@ -36784,7 +38699,6 @@
"niaest": {
"contact": {
"email": "dawood@helix.nih.gov",
- "github": null,
"name": "Dawood B. Dudekula",
"orcid": "0000-0002-4054-1827"
},
@@ -36818,7 +38732,6 @@
"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",
"year": 2003
@@ -36828,7 +38741,7 @@
},
"niaid.chemdb": {
"description": "ID in NIAID ChemDB",
- "example": "112081",
+ "example": "059486",
"homepage": "http://chemdb.niaid.nih.gov",
"mappings": {
"wikidata": "P2065"
@@ -36840,7 +38753,6 @@
"nif.cell": {
"contact": {
"email": "smtifahim@gmail.com",
- "github": null,
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
@@ -36867,7 +38779,6 @@
"nif.dysfunction": {
"contact": {
"email": "smtifahim@gmail.com",
- "github": null,
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
@@ -36924,7 +38835,6 @@
"nif.grossanatomy": {
"contact": {
"email": "smtifahim@gmail.com",
- "github": null,
"name": "Fahim Imam",
"orcid": "0000-0003-4752-543X"
},
@@ -37007,6 +38917,9 @@
"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",
+ "mappings": {
+ "cellosaurus": "NIHhESC"
+ },
"name": "NIH Human Embryonic Stem Cell Registry",
"preferred_prefix": "nihhesc",
"uri_format": "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"
@@ -37050,6 +38963,17 @@
"NIST Chemistry WebBook"
]
},
+ "nist.codata": {
+ "description": "identifier for a physical constant",
+ "example": "c",
+ "homepage": "http://physics.nist.gov/cuu/Constants/index.html",
+ "mappings": {
+ "wikidata": "P1645"
+ },
+ "name": "NIST/CODATA ID",
+ "preferred_prefix": "nist.codata",
+ "uri_format": "http://physics.nist.gov/cgi-bin/cuu/Value?$1"
+ },
"nkos": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -37593,6 +39517,14 @@
"name": "Donny Winston",
"orcid": "0000-0002-8424-0604"
},
+ "contributor_extras": [
+ {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ }
+ ],
"description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.",
"example": "y3ax-8bq3-60",
"homepage": "https://microbiomedata.org/",
@@ -37603,15 +39535,28 @@
"miriam": "nmdc"
},
"name": "National Microbiome Data Collaborative",
- "pattern": "^[\\w\\-.]{3,}$",
+ "pattern": "^.{2,}$",
"preferred_prefix": "nmdc",
+ "providers": [
+ {
+ "code": "web",
+ "description": "Direct link",
+ "homepage": "https://drs.microbiomedata.org",
+ "name": "NMDC Web Page",
+ "uri_format": "https://drs.microbiomedata.org/objects/$1"
+ }
+ ],
+ "rdf_uri_format": "https://w3id.org/nmdc/$1",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/982"
+ ],
"reviewer": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "uri_format": "https://drs.microbiomedata.org/objects/$1"
+ "uri_format": "https://w3id.org/nmdc/$1"
},
"nmpdr": {
"comment": "This resource doesn't exist on the web anymore",
@@ -37691,16 +39636,23 @@
"synonyms": [
"nmrcv"
],
- "uri_format": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1",
+ "uri_format": "https://www.ebi.ac.uk/ols4/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"
},
+ "contributor_extras": [
+ {
+ "email": "b.gyori@northeastern.edu",
+ "github": "bgyori",
+ "name": "Benjamin M. Gyori",
+ "orcid": "0000-0001-9439-5346"
+ }
+ ],
"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",
@@ -37710,6 +39662,7 @@
"mappings": {
"fairsharing": "FAIRsharing.nYaZ1N",
"miriam": "nmrshiftdb2",
+ "re3data": "r3d100010316",
"wikidata": "P9405"
},
"name": "NMRShiftDB structure",
@@ -37718,26 +39671,26 @@
"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
}
],
+ "synonyms": [
+ "NMRShiftDB"
+ ],
"uri_format": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"
},
"noaa": {
@@ -37945,6 +39898,23 @@
"pattern": "^NPC\\d+$",
"preferred_prefix": "npass"
},
+ "npm": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "A repository of software packages written in Javascript, TypeScript, and related.",
+ "example": "@biopragmatics/curies",
+ "example_extras": [
+ "ansi-pad"
+ ],
+ "homepage": "https://www.npmjs.com",
+ "name": "Node Package Manager",
+ "preferred_prefix": "npm",
+ "uri_format": "https://www.npmjs.com/package/$1"
+ },
"npo": {
"contact": {
"email": "nathan.baker@pnnl.gov",
@@ -37964,7 +39934,10 @@
"homepage": "https://bioportal.bioontology.org/ontologies/NPO",
"keywords": [
"life science",
- "ontology"
+ "molecular entity",
+ "nanoparticle",
+ "ontology",
+ "structure"
],
"mappings": {
"aberowl": "NPO",
@@ -37996,6 +39969,9 @@
"description": "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)",
"example": "NRFC051",
"homepage": "https://mail.nbfgr.res.in/nrfc/index.php",
+ "mappings": {
+ "cellosaurus": "NRFC"
+ },
"name": "National Repository of Fish Cell Lines",
"pattern": "^NRFC\\d+$",
"preferred_prefix": "nrfc"
@@ -38036,6 +40012,37 @@
"preferred_prefix": "nsf.award",
"uri_format": "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1"
},
+ "nsrrc": {
+ "description": "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]",
+ "example": "0005",
+ "homepage": "http://www.nsrrc.missouri.edu/",
+ "keywords": [
+ "biomaterial manufacture",
+ "breeding",
+ "consulting",
+ "cryopreservation",
+ "fetal fibroblast",
+ "fetus",
+ "fibroblast",
+ "genetically modified pig",
+ "genetics",
+ "genome",
+ "genotyping",
+ "health monitoring",
+ "live animal",
+ "phenotyping",
+ "pig",
+ "reproduction",
+ "tissue"
+ ],
+ "mappings": {
+ "rrid": "NSRRC"
+ },
+ "name": "National Swine Resource and Research Center",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "nsrrc",
+ "uri_format": "https://nsrrc.missouri.edu/nsrrc$1info/"
+ },
"nucc.characteristic": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -38082,6 +40089,7 @@
],
"mappings": {
"biocontext": "NUCLEARBD",
+ "integbio": "nbdc00599",
"miriam": "nuclearbd",
"n2t": "nuclearbd",
"prefixcommons": "nucleardb"
@@ -38118,6 +40126,7 @@
"has_canonical": "insdc",
"homepage": "https://www.ncbi.nlm.nih.gov/",
"mappings": {
+ "integbio": "nbdc00600",
"miriam": "nucleotide"
},
"name": "Nucleotide",
@@ -38125,6 +40134,57 @@
"preferred_prefix": "nucleotide",
"uri_format": "https://www.ncbi.nlm.nih.gov/nuccore/$1"
},
+ "nxr": {
+ "description": "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]",
+ "example": "0024",
+ "homepage": "http://www.mbl.edu/xenopus/",
+ "keywords": [
+ "laevis",
+ "tropicalis",
+ "xenopus"
+ ],
+ "mappings": {
+ "rrid": "NXR"
+ },
+ "name": "National Xenopus Resource",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "nxr",
+ "uri_format": "https://scicrunch.org/resolver/RRID:NXR_$1"
+ },
+ "nztcs": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "contributor_extras": [
+ {
+ "email": "sumirp77@gmail.com",
+ "github": "SumirHPandit",
+ "name": "Sumir Pandit",
+ "orcid": "0000-0002-1216-4761"
+ }
+ ],
+ "description": "identifier for species classified under the New Zealand Threat Classification System",
+ "example": "11061",
+ "homepage": "https://nztcs.org.nz/",
+ "keywords": [
+ "taxon",
+ "taxonomy"
+ ],
+ "license": "CC-BY-4.0",
+ "mappings": {
+ "wikidata": "P9889"
+ },
+ "name": "New Zealand Threat Classification System",
+ "pattern": "^[1-9]\\d{3,7}$",
+ "preferred_prefix": "nztcs",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1083"
+ ],
+ "uri_format": "https://nztcs.org.nz/nztcs-species/$1"
+ },
"oa": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -38137,12 +40197,15 @@
"example": "sourceDateStart",
"homepage": "http://www.w3.org/ns/oa",
"keywords": [
- "ontology"
+ "ontology",
+ "quality"
],
"mappings": {
"aberowl": "OA",
"biocontext": "oa",
- "bioportal": "OA"
+ "bioportal": "OA",
+ "lov": "oa",
+ "zazuko": "oa"
},
"name": "Web Annotation Ontology",
"preferred_prefix": "oa",
@@ -38160,9 +40223,12 @@
"example": "0002959",
"homepage": "https://github.com/OAE-ontology/OAE/",
"keywords": [
+ "adverse reaction",
"biomedical science",
+ "drug",
"obo",
- "ontology"
+ "ontology",
+ "vaccine"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -38224,7 +40290,6 @@
"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
@@ -38262,6 +40327,7 @@
"license": "CC0-1.0",
"mappings": {
"aberowl": "OBA",
+ "agroportal": "OBA",
"biocontext": "OBA",
"bioportal": "OBA",
"fairsharing": "FAIRsharing.mp0rwf",
@@ -38275,7 +40341,6 @@
"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
@@ -38291,7 +40356,7 @@
"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": "2023-06-07"
+ "version": "2024-03-27"
},
"oban": {
"contributor": {
@@ -38319,13 +40384,14 @@
"uri_format": "http://purl.org/oban/$1"
},
"obcs": {
+ "banana": "OBCS",
"contact": {
- "email": "jiezheng@pennmedicine.upenn.edu",
+ "email": "jiezhen@med.umich.edu",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
},
- "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012.",
+ "description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI)",
"download_owl": "http://purl.obolibrary.org/obo/obcs.owl",
"example": "0000121",
"homepage": "https://github.com/obcs/obcs",
@@ -38336,19 +40402,22 @@
"medicine",
"obo",
"ontology",
- "statistics"
+ "statistics",
+ "vaccine"
],
- "license": "CC-BY-3.0",
+ "license": "CC-BY-4.0",
"mappings": {
"aberowl": "OBCS",
"biocontext": "OBCS",
"bioportal": "OBCS",
"fairsharing": "FAIRsharing.5p12xh",
+ "miriam": "obcs",
"obofoundry": "obcs",
"ols": "obcs",
"ontobee": "OBCS"
},
"name": "Ontology of Biological and Clinical Statistics",
+ "namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "OBCS",
"publications": [
@@ -38363,12 +40432,13 @@
"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": "2018-02-22"
+ "version": "2023-12-08"
},
"obi": {
"appears_in": [
"agro",
"foodon",
+ "gallont",
"hso",
"labo",
"maxo",
@@ -38393,11 +40463,18 @@
"example": "0400109",
"homepage": "http://obi-ontology.org",
"keywords": [
+ "assay",
"biomedical science",
+ "data transformation",
+ "device",
"functional genomics",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "protocol",
+ "reagent",
+ "report",
+ "study design"
],
"license": "CC-BY-4.0",
"logo": "https://svn.code.sf.net/p/obi/code/trunk/web/htdocs/images/obi-lotext.png",
@@ -38449,13 +40526,6 @@
"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",
@@ -38469,32 +40539,26 @@
"pubmed": "20626927",
"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": "2023-03-10"
+ "version": "2024-01-09"
},
"obib": {
"contact": {
- "email": "jiezheng@pennmedicine.upenn.edu",
- "github": "zhengj2007",
- "name": "Jie Zheng",
- "orcid": "0000-0002-2999-0103"
+ "email": "jmwhorton@uams.edu",
+ "github": "jmwhorton",
+ "name": "Justin Whorton",
+ "orcid": "0009-0003-4268-6207"
},
"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": [
+ "biobank",
"health science",
"obo",
"ontology"
@@ -38541,11 +40605,15 @@
],
"homepage": "http://www.obofoundry.org/",
"keywords": [
+ "biology",
+ "health",
"ontology and terminology"
],
"mappings": {
"biocontext": "OBO",
- "fairsharing": "FAIRsharing.847069"
+ "fairsharing": "FAIRsharing.847069",
+ "integbio": "nbdc00305",
+ "lov": "obo"
},
"name": "Open Biological and Biomedical Ontologies",
"preferred_prefix": "obo",
@@ -38568,6 +40636,12 @@
"uri_format": "http://purl.obolibrary.org/obo/$1"
},
"oboinowl": {
+ "contact": {
+ "email": "cjmungall@lbl.gov",
+ "github": "cmungall",
+ "name": "Chris Mungall",
+ "orcid": "0000-0002-6601-2165"
+ },
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -38575,9 +40649,14 @@
"orcid": "0000-0003-4423-4370"
},
"description": "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties",
- "download_obo": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo",
- "download_owl": "https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.owl",
+ "download_obo": "http://www.geneontology.org/formats/oboInOwl.obo",
+ "download_owl": "http://www.geneontology.org/formats/oboInOwl.owl",
"example": "hasDbXref",
+ "example_extras": [
+ "hasExactSynonym",
+ "hasBroadSynonym",
+ "hasNarrowSynonym"
+ ],
"homepage": "https://github.com/geneontology/go-ontology/tree/master/contrib",
"keywords": [
"life science",
@@ -38590,7 +40669,12 @@
"ols": "oboinowl"
},
"name": "OBO in OWL",
+ "pattern": "^\\w+$",
"preferred_prefix": "oboInOwl",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/973",
+ "https://github.com/geneontology/go-site/issues/2157"
+ ],
"repository": "https://github.com/geneontology/go-ontology",
"synonyms": [
"oboformat",
@@ -38624,6 +40708,35 @@
"preferred_prefix": "occ",
"uri_format": "https://w3id.org/oc/corpus/$1"
},
+ "occo": {
+ "contact": {
+ "email": "zhengj2007@gmail.com",
+ "github": "zhengj2007",
+ "name": "Jie Zheng",
+ "orcid": "0000-0002-2999-0103"
+ },
+ "description": "An ontology representing occupations. It is designed to facilitate harmonization of existing occupation standards, such as the US Bureau of Labor Statistics Standard Occupational Classification (US SOC), the International Standard Classification of Occupations (ISCO), the UK National Statistics Standard Occupational Classification (UK SOC), and the European Skills, Competences, Qualifications and Occupations (ESCO) of the European Union.",
+ "download_owl": "http://purl.obolibrary.org/obo/occo.owl",
+ "example": "00000001",
+ "homepage": "https://github.com/Occupation-Ontology/OccO",
+ "keywords": [
+ "obo",
+ "ontology"
+ ],
+ "license": "CC-BY-4.0",
+ "mappings": {
+ "aberowl": "OCCO",
+ "bioportal": "OCCO",
+ "obofoundry": "occo",
+ "ontobee": "OCCO"
+ },
+ "name": "Occupation Ontology",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "OCCO",
+ "rdf_uri_format": "http://purl.obolibrary.org/obo/OCCO_$1",
+ "repository": "https://github.com/Occupation-Ontology/OccO",
+ "uri_format": "http://purl.obolibrary.org/obo/OCCO_$1"
+ },
"oci": {
"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",
@@ -38681,7 +40794,6 @@
"odc.sci": {
"contact": {
"email": "jgrethe@ucsd.edu",
- "github": null,
"name": "Jeffrey Grethe",
"orcid": "0000-0001-5212-7052"
},
@@ -38754,10 +40866,7 @@
},
{
"doi": "S0014-4886(17)30137-1",
- "pmc": null,
- "pubmed": null,
- "title": "Developing a data sharing community for spinal cord injury research.",
- "year": null
+ "title": "Developing a data sharing community for spinal cord injury research."
}
],
"uri_format": "https://odc-sci.org/data/$1"
@@ -38799,10 +40908,40 @@
"download_rdf": "https://www.w3.org/ns/odrl/2/ODRL22.rdf",
"example": "assetConcepts",
"homepage": "http://www.w3.org/ns/odrl/2",
+ "keywords": [
+ "metadata"
+ ],
+ "mappings": {
+ "lov": "odrl"
+ },
"name": "Open Digital Rights Language Ontology",
"preferred_prefix": "odrl",
"uri_format": "http://www.w3.org/ns/odrl/2/$1"
},
+ "oecd.template": {
+ "comment": "The identifiers have two numbers separated by a dot. The first one corresponds to the template number which can be found on the homepage. The second number referes to the row within the corresponding spreadsheet.",
+ "contributor": {
+ "github": "bgyori",
+ "name": "Benjamin M. Gyori",
+ "orcid": "0000-0001-9439-5346"
+ },
+ "description": "The Organisation for Economic Co-operation and Development (OECD) Harmonised Templates (OHTs) are standard data formats for reporting information used for the risk assessment of chemicals, mainly studies done on chemicals to determine their properties or effects on human health and the environment, but also for storing data on use and exposure.",
+ "example": "74.186",
+ "github_request_issue": 997,
+ "homepage": "https://www.oecd.org/ehs/templates/",
+ "name": "OECD Harmonised Templates",
+ "pattern": "^\\d+\\.\\d+$",
+ "preferred_prefix": "oecd.template",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/991"
+ ],
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ }
+ },
"ogg": {
"contact": {
"email": "yongqunh@med.umich.edu",
@@ -38816,6 +40955,9 @@
"homepage": "https://bitbucket.org/hegroup/ogg",
"keywords": [
"biology",
+ "gene",
+ "gene name",
+ "genome",
"life science",
"obo",
"ontology"
@@ -38890,6 +41032,10 @@
"homepage": "https://github.com/OGMS/ogms",
"keywords": [
"biomedical science",
+ "cancer",
+ "diagnosis",
+ "disease",
+ "disease phenotype",
"medicine",
"obo",
"ontology"
@@ -38911,8 +41057,6 @@
"preferred_prefix": "OGMS",
"publications": [
{
- "doi": null,
- "pmc": null,
"pubmed": "25991121",
"title": "Biomarkers in the ontology for general medical science",
"year": 2015
@@ -38925,7 +41069,6 @@
"year": 2013
},
{
- "doi": null,
"pmc": "PMC3041577",
"pubmed": "21347182",
"title": "Toward an ontological treatment of disease and diagnosis",
@@ -38947,13 +41090,17 @@
"name": "Asiyah Yu Lin",
"orcid": "0000-0002-5379-5359"
},
+ "deprecated": true,
"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": [
+ "adverse reaction",
"biomedical science",
+ "disease",
"epidemiology",
+ "genetic disorder",
"genetics",
"obo",
"ontology"
@@ -38980,8 +41127,6 @@
"year": 2014
},
{
- "doi": null,
- "pmc": null,
"pubmed": "20847592",
"title": "Ontology driven modeling for the knowledge of genetic susceptibility to disease",
"year": 2009
@@ -39035,7 +41180,7 @@
"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": "2023-04-14"
+ "version": "2024-03-01"
},
"ohmi": {
"contact": {
@@ -39049,7 +41194,9 @@
"example": "0000460",
"homepage": "https://github.com/ohmi-ontology/ohmi",
"keywords": [
+ "host",
"life science",
+ "microbiome",
"obo",
"ontology"
],
@@ -39085,8 +41232,11 @@
"keywords": [
"bioinformatics",
"biomedical science",
+ "host",
+ "infection",
"obo",
- "ontology"
+ "ontology",
+ "pathogen"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -39169,6 +41319,7 @@
"name": "Frédéric Bastian",
"orcid": "0000-0002-9415-5104"
},
+ "deprecated": true,
"description": "Life cycle stages for Medaka",
"download_obo": "http://purl.obolibrary.org/obo/olatdv.obo",
"download_owl": "http://purl.obolibrary.org/obo/olatdv.owl",
@@ -39177,6 +41328,7 @@
"keywords": [
"aquaculture",
"developmental biology",
+ "life cycle stage",
"life science",
"obo",
"ontology"
@@ -39196,18 +41348,16 @@
"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",
- "version": "2020-03-10"
+ "uri_format": "http://purl.obolibrary.org/obo/OlatDv_$1"
},
"om": {
"contact": {
"email": "hajo.rijgersberg@wur.nl",
- "github": null,
- "name": "Hajo Rijgersberg",
- "orcid": null
+ "name": "Hajo Rijgersberg"
},
"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",
+ "download_owl": "http://aber-owl.net/media/ontologies/OM/29/om.owl",
+ "download_rdf": "https://raw.githubusercontent.com/HajoRijgersberg/OM/master/om-2.0.rdf",
"example": "Dimension",
"homepage": "https://github.com/HajoRijgersberg/OM",
"keywords": [
@@ -39223,7 +41373,7 @@
"preferred_prefix": "om",
"repository": "https://github.com/HajoRijgersberg/OM",
"uri_format": "http://www.ontology-of-units-of-measure.org/resource/om-2/$1",
- "version": "2.0.39"
+ "version": "2.0.55"
},
"oma.grp": {
"description": "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs.",
@@ -39260,7 +41410,8 @@
"mappings": {
"biocontext": "OMA.PROTEIN",
"miriam": "oma.protein",
- "n2t": "oma.protein"
+ "n2t": "oma.protein",
+ "togoid": "OmaProtein"
},
"name": "OMA Protein",
"pattern": "^[A-Z0-9]{5}\\d+$",
@@ -39282,8 +41433,8 @@
"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",
+ "description": "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in more than 500 vertebrate animal species (other than human, mouse, rats, zebrafish and western clawed frog, which have their own resources).",
+ "example": "001000",
"homepage": "https://omia.org",
"keywords": [
"classification",
@@ -39294,12 +41445,13 @@
],
"mappings": {
"biocontext": "OMIA",
+ "integbio": "nbdc00153",
"miriam": "omia",
"n2t": "omia",
"prefixcommons": "omia"
},
"name": "Online Mendelian Inheritance in Animals",
- "pattern": "^\\d+$",
+ "pattern": "^\\d{6}$",
"preferred_prefix": "omia",
"providers": [
{
@@ -39318,7 +41470,6 @@
],
"contact": {
"email": "mbrochhausen@gmail.com",
- "github": null,
"name": "Mathias Brochhausen",
"orcid": "0000-0003-1834-3856"
},
@@ -39372,10 +41523,16 @@
"homepage": "https://omim.org/",
"keywords": [
"biomedical science",
+ "disease",
+ "disease process modeling",
"gene",
"gene expression",
- "ontology"
+ "genetic disorder",
+ "genotype",
+ "ontology",
+ "phenotype"
],
+ "license": "https://www.omim.org/help/agreement",
"mappings": {
"aberowl": "OMIM",
"biocontext": "OMIM",
@@ -39384,6 +41541,7 @@
"fairsharing": "FAIRsharing.b084yh",
"go": "OMIM",
"hl7": "2.16.840.1.113883.6.174",
+ "integbio": "nbdc00154",
"miriam": "mim",
"n2t": "mim",
"ncbi": "MIM",
@@ -39486,7 +41644,6 @@
},
"contributor_extras": [
{
- "email": null,
"github": "sierra-moxon",
"name": "Sierra Moxon",
"orcid": "0000-0002-8719-7760"
@@ -39495,6 +41652,7 @@
"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",
+ "license": "https://www.omim.org/help/agreement",
"mappings": {
"biolink": "OMIM.PS"
},
@@ -39535,10 +41693,20 @@
"example": "0000069",
"homepage": "http://omit.cis.usouthal.edu/",
"keywords": [
+ "annotation",
"biology",
+ "cell",
+ "computational biological predictions",
+ "gene",
+ "gene prediction",
"life science",
+ "micro rna",
+ "molecular entity",
+ "molecular interaction",
"obo",
- "ontology"
+ "ontology",
+ "protein",
+ "regulation of gene expression"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -39572,7 +41740,6 @@
},
{
"doi": "10.1007/s11095-011-0573-8",
- "pmc": null,
"pubmed": "21879385",
"title": "OMIT: a domain-specific knowledge base for microRNA target prediction",
"year": 2011
@@ -39583,12 +41750,13 @@
"synonyms": [
"OMIT"
],
- "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/omit/terms?short_form=OMIT_$1",
+ "uri_format": "http://purl.obolibrary.org/obo/OMIT_$1",
"version": "dev"
},
"omo": {
"appears_in": [
- "pcl"
+ "pcl",
+ "uberon"
],
"contact": {
"email": "cjmungall@lbl.gov",
@@ -39598,6 +41766,7 @@
},
"description": "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO).",
"download_owl": "http://purl.obolibrary.org/obo/omo.owl",
+ "example": "0003003",
"homepage": "https://github.com/information-artifact-ontology/ontology-metadata",
"keywords": [
"obo",
@@ -39612,12 +41781,12 @@
"ontobee": "OMO"
},
"name": "OBO Metadata Ontology",
- "no_own_terms": true,
+ "pattern": "^\\d{7}$",
"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": "2023-06-09"
+ "version": "2023-11-02"
},
"omop": {
"contributor": {
@@ -39686,7 +41855,8 @@
"data mining",
"microbiology",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -39713,7 +41883,7 @@
"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_$1",
- "version": "2023-06-09"
+ "version": "2024-03-25"
},
"omrse": {
"appears_in": [
@@ -39725,18 +41895,20 @@
"name": "Bill Hogan",
"orcid": "0000-0002-9881-1017"
},
- "description": "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations.",
+ "description": "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations.",
"download_json": "http://purl.obolibrary.org/obo/omrse.json",
"download_obo": "https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo",
"download_owl": "http://purl.obolibrary.org/obo/omrse.owl",
"example": "00000022",
- "homepage": "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview",
+ "homepage": "https://github.com/mcwdsi/OMRSE/wiki/OMRSE-Overview",
"keywords": [
"biomedical science",
"demographics",
"health science",
+ "hospital",
"obo",
"ontology",
+ "patient care",
"social science"
],
"license": "CC-BY-4.0",
@@ -39749,7 +41921,7 @@
"ols": "omrse",
"ontobee": "OMRSE"
},
- "name": "Ontology of Medically Related Social Entities",
+ "name": "Ontology for Modeling and Representation of Social Entities",
"pattern": "^\\d{8}$",
"preferred_prefix": "OMRSE",
"publications": [
@@ -39762,9 +41934,24 @@
}
],
"rdf_uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1",
- "repository": "https://github.com/ufbmi/OMRSE",
+ "repository": "https://github.com/mcwdsi/OMRSE",
"uri_format": "http://purl.obolibrary.org/obo/OMRSE_$1",
- "version": "2023-05-19"
+ "version": "2024-03-22"
+ },
+ "omx.dataset": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "OncoMX is a knowledgebase for exploring cancer biomarkers in the context of related cancer and healthy data. This resource is for datasets within OncoMX.",
+ "example": "000059",
+ "homepage": "https://data.oncomx.org",
+ "name": "OncoMX Dataset",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "omx.dataset",
+ "uri_format": "https://data.oncomx.org/OMX_$1"
},
"oncotree": {
"appears_in": [
@@ -39805,8 +41992,9 @@
"example": "0001021",
"homepage": "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies",
"keywords": [
+ "diet",
"epidemiology",
- "life science",
+ "metabolomics",
"nutritional science",
"obo",
"ontology"
@@ -39869,6 +42057,7 @@
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "ONS",
+ "agroportal": "ONS",
"bioportal": "ONS",
"fairsharing": "FAIRsharing.rfec93",
"obofoundry": "ons",
@@ -39911,7 +42100,9 @@
"homepage": "https://ontology.iedb.org/",
"keywords": [
"immunology",
+ "infection",
"life science",
+ "major histocompatibility complex",
"ontology"
],
"mappings": {
@@ -39957,6 +42148,12 @@
"name": "Ontology for Avida digital evolution platform",
"pattern": "^\\d{8}$",
"preferred_prefix": "ONTOAVIDA",
+ "publications": [
+ {
+ "doi": "10.1038/s41597-023-02514-3",
+ "title": "Ontology for the Avida digital evolution platform"
+ }
+ ],
"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",
@@ -39974,6 +42171,7 @@
"example": "00000098",
"homepage": "http://ontoneo.com",
"keywords": [
+ "electronic health record",
"obo",
"obstetrics",
"ontology"
@@ -39994,8 +42192,6 @@
"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": 2017
}
@@ -40037,14 +42233,13 @@
"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": "2023-03-30"
+ "version": "2024-01-25"
},
"opb": {
"banana": "OPB",
"banana_peel": "_",
"contact": {
"email": "maxneal@gmail.com",
- "github": null,
"name": "Maxwell L. Neal",
"orcid": "0000-0002-2390-6572"
},
@@ -40061,7 +42256,10 @@
"example": "00573",
"homepage": "http://bioportal.bioontology.org/ontologies/OPB",
"keywords": [
+ "concentration",
+ "kinetic model",
"life science",
+ "mathematical model",
"ontology",
"physics",
"structure"
@@ -40113,7 +42311,6 @@
"orcid": "0000-0003-1613-5981"
},
"contributor": {
- "email": null,
"github": "dhimmel",
"name": "Daniel Himmelstein",
"orcid": "0000-0002-3012-7446"
@@ -40137,23 +42334,55 @@
},
"uri_format": "https://openalex.org/$1"
},
+ "openwemi": {
+ "contact": {
+ "email": "kcoyle@kcoyle.net",
+ "github": "kcoyle",
+ "name": "Karen Coyle",
+ "orcid": "0000-0002-1085-7089"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "openWEMI is a minimally constrained vocabulary for describing created resources using the concepts of Work, Expression, Manifestation, Item.",
+ "example": "Endeavor",
+ "homepage": "https://dcmi.github.io/openwemi/",
+ "license": "CC0-1.0",
+ "name": "openWEMI Vocabulary",
+ "pattern": "^\\w+$",
+ "preferred_prefix": "openwemi",
+ "references": [
+ "https://journal.code4lib.org/articles/16491",
+ "http://archive.ifla.org/VII/s13/frbr/frbr_2008.pdf"
+ ],
+ "repository": "https://github.com/dcmi/openwemi",
+ "uri_format": "https://dcmi.github.io/openwemi/ns#$1"
+ },
"opl": {
+ "banana": "OPL",
"contact": {
- "email": "jiezheng@pennmedicine.upenn.edu",
+ "email": "zhengj2007@gmail.com",
"github": "zhengj2007",
"name": "Jie Zheng",
"orcid": "0000-0002-2999-0103"
},
- "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.",
+ "description": "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc.",
"download_owl": "http://purl.obolibrary.org/obo/opl.owl",
"example": "0000319",
"homepage": "https://github.com/OPL-ontology/OPL",
"keywords": [
"anatomy",
"developmental biology",
+ "host",
+ "life cycle",
+ "life cycle stage",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "parasite"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -40161,11 +42390,13 @@
"biocontext": "OPL",
"bioportal": "OPL",
"fairsharing": "FAIRsharing.ez2nhb",
+ "miriam": "opl",
"obofoundry": "opl",
"ols": "opl",
"ontobee": "OPL"
},
"name": "Ontology for Parasite LifeCycle",
+ "namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "OPL",
"publications": [
@@ -40180,7 +42411,7 @@
"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": "2023-06-23"
+ "version": "2023-08-28"
},
"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.",
@@ -40218,6 +42449,7 @@
"homepage": "https://github.com/OPMI/opmi",
"keywords": [
"clinical studies",
+ "disease",
"obo",
"omics",
"ontology"
@@ -40237,7 +42469,7 @@
"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": "1.0.161"
+ "version": "1.0.166"
},
"orcid": {
"contact": {
@@ -40247,7 +42479,7 @@
"orcid": "0000-0003-4654-1403"
},
"description": "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.",
- "example": "0000-0002-5355-2576",
+ "example": "0000-0003-4423-4370",
"homepage": "https://orcid.org",
"keywords": [
"person",
@@ -40279,15 +42511,11 @@
"publications": [
{
"doi": "10.23640/07243.16687207.v1",
- "pmc": null,
- "pubmed": null,
"title": "From Vision to Value: ORCID's 2022–2025 Strategic Plan",
"year": 2021
},
{
"doi": "10.23640/07243.12009255.v3",
- "pmc": null,
- "pubmed": null,
"title": "ORCID's 2025 Vision",
"year": 2020
}
@@ -40315,6 +42543,7 @@
"fairsharing": "FAIRsharing.6375zh",
"miriam": "ordb",
"n2t": "ordb",
+ "pathguide": "65",
"prefixcommons": "ordb"
},
"name": "Olfactory Receptor Database",
@@ -40416,6 +42645,7 @@
},
"orphanet": {
"description": "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.",
+ "download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl",
"example": "85163",
"homepage": "http://www.orpha.net/consor/",
"keywords": [
@@ -40423,12 +42653,15 @@
"drug",
"human",
"life science",
+ "ontology",
"ontology and terminology"
],
+ "license": "CC-BY-4.0",
"mappings": {
"biocontext": "Orphanet",
"biolink": "orphanet",
"fairsharing": "FAIRsharing.6bd5k6",
+ "integbio": "nbdc01422",
"miriam": "orphanet",
"n2t": "orphanet",
"prefixcommons": "orphanet",
@@ -40456,8 +42689,6 @@
],
"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
@@ -40474,7 +42705,6 @@
"banana_peel": "_",
"contact": {
"email": "ordo.orphanet@inserm.fr",
- "github": null,
"name": "Ana Rath",
"orcid": "0000-0003-4308-6337"
},
@@ -40484,12 +42714,18 @@
"example_extras": [
"478"
],
- "homepage": "https://www.ebi.ac.uk/ols/ontologies/ordo",
+ "homepage": "https://www.ebi.ac.uk/ols4/ontologies/ordo",
"keywords": [
"biomedical science",
+ "diagnosis",
+ "disease",
+ "gene",
"health science",
- "ontology"
+ "ontology",
+ "phenotype",
+ "rare disease"
],
+ "license": "CC-BY-4.0",
"mappings": {
"aberowl": "ordo",
"biocontext": "ORPHANET.ORDO",
@@ -40506,8 +42742,6 @@
"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
@@ -40517,7 +42751,7 @@
"ordo"
],
"uri_format": "http://www.orpha.net/ORDO/Orphanet_$1",
- "version": "4.2"
+ "version": "4.4"
},
"orth": {
"contact": {
@@ -40532,7 +42766,13 @@
"homepage": "https://github.com/qfo/OrthologyOntology",
"keywords": [
"comparative genomics",
- "ontology"
+ "gene",
+ "homologous",
+ "ontology",
+ "orthologous",
+ "paralogous",
+ "protein",
+ "sequence"
],
"mappings": {
"aberowl": "ORTH",
@@ -40683,9 +42923,7 @@
"oslc": {
"contact": {
"email": "jamsden@us.ibm.com",
- "github": null,
- "name": "Jim Amsden",
- "orcid": null
+ "name": "Jim Amsden"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -40696,10 +42934,52 @@
"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",
+ "keywords": [
+ "plm"
+ ],
+ "mappings": {
+ "lov": "oslc"
+ },
"name": "OASIS Open Services for Lifecycle Collaboration Core Vocabulary",
"preferred_prefix": "oslc",
"uri_format": "http://open-services.net/ns/core#$1"
},
+ "osti.article": {
+ "comment": "Corresponding GitHub linked to software registrations is located at https://github.com/doecode. All related contact information can be found here https://www.osti.gov/contact",
+ "contributor": {
+ "email": "Lindsey.Anderson@pnnl.gov",
+ "github": "lnanderson",
+ "name": "Lindsey Anderson",
+ "orcid": "0000-0002-8741-7823"
+ },
+ "description": "The U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) is the main metadata archive for permanent storage of registered [DOE DOI products](https://www.osti.gov/pids/doi-services/doe-data-id-service) (datasets, code, articles, patents, multimedia, etc.). When a DOI is minted a unique OSTI identifier for each record [{osti_id}](https://www.osti.gov/api/v1/docs#endpoints-singlerecord) is provided as the suffix in the DOI schema ([{site-specific-prefix}/{user-supplied-doi-infix}/{osti_id}](https://www.osti.gov/pids/doi-services)) and can be alternatively used as the main product identifier endpoint when [searching OSTI.GOV](https://www.osti.gov/search-tools) registry archive (see example below). OSTI.GOV is the primary registry and search tool for all Department of Energy (DOE) funded science, technology, and engineering research and development (R&D) results and the organizational hub for information about the DOE Office of Scientific and Technical Information (OSTI. **Data Product Type Example:** - https://www.osti.gov/biblio/1668761 - https://www.osti.gov/search/semantic:1668761 - https://www.osti.gov/dataexplorer/biblio/dataset/1668761 - https://www.osti.gov/api/v1/records/1668761 - https://doi.org/10.11578/1668761 **Other Core Product Registry Examples:** - Journal Articles: https://www.osti.gov/pages/biblio - Datasets: https://www.osti.gov/dataexplorer/biblio/dataset/ - Software: https://www.osti.gov/doecode/biblio/ - Patents: https://www.osti.gov/doepatents/biblio/ - Multimedia: https://www.osti.gov/sciencecinema/biblio/",
+ "example": "1668761",
+ "github_request_issue": 1050,
+ "homepage": "https://www.osti.gov/",
+ "keywords": [
+ "article",
+ "articles",
+ "publication",
+ "publications"
+ ],
+ "license": "https://www.osti.gov/disclaim",
+ "mappings": {
+ "wikidata": "P3894"
+ },
+ "name": "Office of Scientific and Technical Information (OSTI)",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "osti.article",
+ "references": [
+ "https://www.energy.gov/doe-public-access-plan"
+ ],
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://www.osti.gov/biblio/$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",
@@ -40737,10 +43017,7 @@
},
{
"doi": "17947330",
- "pmc": null,
- "pubmed": null,
- "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."
}
],
"uri_format": "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"
@@ -40782,9 +43059,11 @@
"example": "0000609",
"homepage": "http://www.violinet.org/ovae/",
"keywords": [
+ "adverse reaction",
"biomedical science",
"obo",
- "ontology"
+ "ontology",
+ "vaccine"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -40816,7 +43095,6 @@
"owl": {
"contact": {
"email": "rmrich5@gmail.com",
- "github": null,
"name": "Rafael Richards",
"orcid": "0000-0001-5699-0515"
},
@@ -40835,12 +43113,16 @@
"informatics",
"ontology",
"ontology and terminology",
- "subject agnostic"
+ "subject agnostic",
+ "w3c rec"
],
"mappings": {
"biocontext": "owl",
"fairsharing": "FAIRsharing.atygwy",
- "ols": "owl"
+ "integbio": "nbdc00307",
+ "lov": "owl",
+ "ols": "owl",
+ "zazuko": "owl"
},
"name": "Web Ontology Language",
"preferred_prefix": "owl",
@@ -40916,6 +43198,20 @@
"preferred_prefix": "p3db.site",
"uri_format": "http://www.p3db.org/phosphosite.php?id=$1&ref=0"
},
+ "packagist": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "A repository of software packages written in PHP.",
+ "example": "florianv/swap",
+ "homepage": "https://packagist.org",
+ "name": "Packagist",
+ "preferred_prefix": "packagist",
+ "uri_format": "https://packagist.org/packages/$1"
+ },
"pactr": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -40971,6 +43267,7 @@
"structure"
],
"mappings": {
+ "integbio": "nbdc00607",
"prefixcommons": "pandit",
"re3data": "r3d100011232"
},
@@ -40997,7 +43294,6 @@
"panorama": {
"contact": {
"email": "brendanx@uw.edu",
- "github": null,
"name": "Brendan MacLean",
"orcid": "0000-0002-9575-0255"
},
@@ -41037,10 +43333,7 @@
},
{
"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
+ "title": "Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline."
}
],
"uri_format": "https://panoramaweb.org/$1.url"
@@ -41177,6 +43470,7 @@
],
"mappings": {
"biocontext": "PASS2",
+ "integbio": "nbdc02108",
"miriam": "pass2",
"n2t": "pass2",
"prefixcommons": "pass2"
@@ -41227,7 +43521,8 @@
"transcriptomics"
],
"mappings": {
- "fairsharing": "FAIRsharing.3xwMon"
+ "fairsharing": "FAIRsharing.3xwMon",
+ "togoid": "Pathbank"
},
"name": "PathBank",
"pattern": "^(SMP|PW)\\d+$",
@@ -41235,6 +43530,12 @@
"uri_format": "https://pathbank.org/view/$1"
},
"pathguide": {
+ "contact": {
+ "email": "gary.bader@utoronto.ca",
+ "github": "gbader",
+ "name": "Gary Bader",
+ "orcid": "0000-0003-0185-8861"
+ },
"description": "Pathguide contains information about 325 biological related resources and molecular interaction related resources.",
"example": "49",
"homepage": "http://pathguide.org",
@@ -41246,9 +43547,11 @@
"small molecule"
],
"mappings": {
+ "integbio": "nbdc00608",
"prefixcommons": "pathguide"
},
"name": "Pathguide",
+ "pattern": "^\\d+$",
"preferred_prefix": "pathguide",
"providers": [
{
@@ -41279,6 +43582,7 @@
"small molecule"
],
"mappings": {
+ "pathguide": "333",
"prefixcommons": "pathoplant"
},
"name": "PathoPlant®",
@@ -41328,6 +43632,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkz946/5606621",
+ "pubmed": "31647099"
+ },
{
"doi": "10.1093/nar/gkq1039",
"pmc": "PMC3013659",
@@ -41348,6 +43656,7 @@
"ecocore",
"ecto",
"fovt",
+ "gallont",
"lepao",
"mco",
"ms",
@@ -41357,6 +43666,7 @@
"planp",
"proco",
"rbo",
+ "uberon",
"xpo",
"zp"
],
@@ -41442,12 +43752,11 @@
"rdf_uri_format": "http://purl.obolibrary.org/obo/PATO_$1",
"repository": "https://github.com/pato-ontology/pato",
"uri_format": "http://purl.obolibrary.org/obo/PATO_$1",
- "version": "2023-05-18"
+ "version": "2024-03-28"
},
"pav": {
"contact": {
"email": "stian@soiland-reyes.com",
- "github": null,
"name": "Stian Soiland-Reyes",
"orcid": "0000-0001-9842-9718"
},
@@ -41471,8 +43780,11 @@
"github_request_issue": 186,
"homepage": "https://pav-ontology.github.io/pav/",
"keywords": [
+ "citation",
"data management",
"ontology",
+ "quality",
+ "resource metadata",
"subject agnostic"
],
"mappings": {
@@ -41480,7 +43792,8 @@
"biocontext": "pav",
"biolink": "pav",
"bioportal": "PAV",
- "fairsharing": "FAIRsharing.nbfwwv"
+ "fairsharing": "FAIRsharing.nbfwwv",
+ "lov": "pav"
},
"name": "Provenance, Authoring, and Versioning Vocabulary",
"pattern": "^[a-z][a-zA-Z]+$",
@@ -41534,7 +43847,6 @@
"pazar": {
"contact": {
"email": "wyeth@cmmt.ubc.ca",
- "github": null,
"name": "Wyeth W. Wasserman",
"orcid": "0000-0001-6098-6412"
},
@@ -41550,8 +43862,10 @@
"mappings": {
"biocontext": "PAZAR",
"fairsharing": "FAIRsharing.33yggg",
+ "integbio": "nbdc00611",
"miriam": "pazar",
"n2t": "pazar",
+ "pathguide": "521",
"prefixcommons": "pazar"
},
"name": "Pazar Transcription Factor",
@@ -41632,6 +43946,8 @@
"homepage": "https://github.com/obophenotype/provisional_cell_ontology",
"keywords": [
"anatomy",
+ "annotation",
+ "cell",
"cell biology",
"life science",
"obo",
@@ -41652,8 +43968,6 @@
"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
}
@@ -41661,7 +43975,7 @@
"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_$1",
- "version": "2023-02-27"
+ "version": "2024-01-04"
},
"pco": {
"appears_in": [
@@ -41693,6 +44007,7 @@
"biodiversity",
"community care",
"ecology",
+ "evolution",
"obo",
"ontology",
"population genetics",
@@ -41743,7 +44058,6 @@
"pdb": {
"contact": {
"email": "harukin@protein.osaka-u.ac.jp",
- "github": null,
"name": "Haruki Nakamura",
"orcid": "0000-0001-6690-5863"
},
@@ -41764,11 +44078,14 @@
"edam": "1127",
"fairsharing": "FAIRsharing.rs2815",
"go": "PDB",
+ "integbio": "nbdc00613",
"miriam": "pdb",
"n2t": "pdb",
"ncbi": "PDB",
+ "pathguide": "398",
"prefixcommons": "pdbj",
"re3data": "r3d100010910",
+ "togoid": "Pdb",
"uniprot": "DB-0172",
"wikidata": "P638"
},
@@ -41850,7 +44167,6 @@
},
{
"doi": "10.1007/s10822-011-9460-y",
- "pmc": null,
"pubmed": "21796434",
"title": "Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr",
"year": 2011
@@ -41863,8 +44179,6 @@
"year": 2010
},
{
- "doi": null,
- "pmc": null,
"pubmed": "12099029",
"title": "[Development of PDBj: Advanced database for protein structures]",
"year": 2002
@@ -41906,7 +44220,8 @@
"biocontext": "PDB-CCD",
"miriam": "pdb-ccd",
"n2t": "pdb-ccd",
- "prefixcommons": "ccd"
+ "prefixcommons": "ccd",
+ "togoid": "PdbCcd"
},
"name": "Chemical Component Dictionary",
"pattern": "^\\w{1,3}$",
@@ -41923,7 +44238,6 @@
"publications": [
{
"doi": "10.1038/nsb1203-980",
- "pmc": null,
"pubmed": "14634627",
"title": "Announcing the worldwide Protein Data Bank",
"year": 2003
@@ -41948,6 +44262,7 @@
"biocontext": "PDB.LIGAND",
"miriam": "pdb.ligand",
"n2t": "pdb.ligand",
+ "pathguide": "169",
"prefixcommons": "pdbligand",
"wikidata": "P3636"
},
@@ -41978,7 +44293,6 @@
"pdbsum": {
"contact": {
"email": "roman@ebi.ac.uk",
- "github": null,
"name": "Roman Laskowski",
"orcid": "0000-0001-5528-0087"
},
@@ -41993,6 +44307,8 @@
],
"mappings": {
"fairsharing": "FAIRsharing.7vjq5t",
+ "integbio": "nbdc00308",
+ "pathguide": "461",
"prefixcommons": "pdbsum",
"uniprot": "DB-0119"
},
@@ -42073,6 +44389,7 @@
"example": "0010039",
"homepage": "https://github.com/OpenLHS/PDRO",
"keywords": [
+ "drug",
"obo",
"ontology",
"primary health care"
@@ -42120,6 +44437,7 @@
"name": "Frédéric Bastian",
"orcid": "0000-0002-9415-5104"
},
+ "deprecated": true,
"description": "Life cycle stages for Platynereis dumerilii",
"download_obo": "http://purl.obolibrary.org/obo/pdumdv.obo",
"download_owl": "http://purl.obolibrary.org/obo/pdumdv.owl",
@@ -42127,6 +44445,7 @@
"homepage": "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv",
"keywords": [
"developmental biology",
+ "life cycle stage",
"life science",
"obo",
"ontology"
@@ -42149,8 +44468,7 @@
"synonyms": [
"PdumDv"
],
- "uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1",
- "version": "2020-03-10"
+ "uri_format": "http://purl.obolibrary.org/obo/PdumDv_$1"
},
"peco": {
"appears_in": [
@@ -42170,8 +44488,12 @@
"homepage": "http://planteome.org/",
"keywords": [
"botany",
+ "experimental condition",
+ "experimental measurement",
+ "experimentally determined",
"obo",
- "ontology"
+ "ontology",
+ "study design"
],
"license": "CC-BY-4.0",
"logo": "http://planteome.org/sites/default/files/garland_logo.PNG",
@@ -42200,7 +44522,7 @@
"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"
+ "version": "2023-07-25"
},
"ped": {
"description": "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins.",
@@ -42212,6 +44534,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.4ef690",
+ "integbio": "nbdc02490",
"miriam": "ped"
},
"name": "Protein Ensemble Database",
@@ -42283,6 +44606,7 @@
"structure"
],
"mappings": {
+ "pathguide": "235",
"prefixcommons": "pepbank"
},
"name": "PepBank Peptide Database",
@@ -42307,7 +44631,7 @@
"peptideatlas": {
"contact": {
"email": "edeutsch@systemsbiology.org",
- "github": null,
+ "github": "edeutsch",
"name": "Eric W. Deutsch",
"orcid": "0000-0001-8732-0928"
},
@@ -42324,6 +44648,7 @@
"biocontext": "PEPTIDEATLAS",
"edam": "2626",
"fairsharing": "FAIRsharing.dvyrsz",
+ "integbio": "nbdc01812",
"miriam": "peptideatlas",
"n2t": "peptideatlas",
"prefixcommons": "peptideatlas",
@@ -42359,10 +44684,7 @@
},
{
"doi": "10.1038/embor.2008.56.",
- "pmc": null,
- "pubmed": null,
- "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.",
- "year": null
+ "title": "PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows."
}
],
"uri_format": "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"
@@ -42381,7 +44703,7 @@
"uri_format": "http://www.peptideatlas.org/PASS/$1"
},
"perkinelmer": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "SCC111",
"homepage": "https://www.perkinelmer.com/",
"mappings": {
@@ -42394,9 +44716,8 @@
"peroxibase": {
"contact": {
"email": "dunand@lrsv.ups-tlse.fr",
- "github": null,
"name": "Christophe Dunand",
- "orcid": "0000-0003-1637-404"
+ "orcid": "0000-0003-1637-4042"
},
"description": "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.",
"example": "5282",
@@ -42410,6 +44731,7 @@
"mappings": {
"biocontext": "PEROXIBASE",
"fairsharing": "FAIRsharing.z1czxj",
+ "integbio": "nbdc01869",
"miriam": "peroxibase",
"n2t": "peroxibase",
"prefixcommons": "peroxibase",
@@ -42437,7 +44759,6 @@
},
{
"doi": "10.1093/jxb/ern317",
- "pmc": null,
"pubmed": "19112168",
"title": "PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae",
"year": 2008
@@ -42474,7 +44795,6 @@
"pfam": {
"contact": {
"email": "agb@ebi.ac.uk",
- "github": null,
"name": "Alex Bateman",
"orcid": "0000-0002-6982-4660"
},
@@ -42491,11 +44811,13 @@
"edam": "1138",
"fairsharing": "FAIRsharing.y3scf6",
"go": "Pfam",
+ "integbio": "nbdc00163",
"miriam": "pfam",
"n2t": "pfam",
"ncbi": "PFAM",
"prefixcommons": "pfam",
"re3data": "r3d100012850",
+ "togoid": "Pfam",
"uniprot": "DB-0073",
"wikidata": "P3519"
},
@@ -42542,7 +44864,6 @@
},
{
"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",
"year": 1997
@@ -42693,9 +45014,7 @@
"pgdso": {
"contact": {
"email": "po-discuss@plantontology.org",
- "github": null,
- "name": "Plant Ontology Administrators",
- "orcid": null
+ "name": "Plant Ontology Administrators"
},
"deprecated": true,
"homepage": "http://www.plantontology.org",
@@ -42787,14 +45106,12 @@
},
{
"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
@@ -42891,7 +45208,6 @@
},
{
"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
@@ -42937,7 +45253,6 @@
},
{
"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
@@ -42987,7 +45302,6 @@
},
{
"doi": "10.1385/1-59259-957-5:179",
- "pmc": null,
"pubmed": "16100408",
"title": "PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base",
"year": 2005
@@ -43034,7 +45348,6 @@
},
{
"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
@@ -43101,9 +45414,7 @@
"phenx": {
"contact": {
"email": "yingqin@rti.org",
- "github": null,
- "name": "PhenX Admin",
- "orcid": null
+ "name": "PhenX Admin"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -43118,14 +45429,18 @@
"homepage": "https://www.phenxtoolkit.org/",
"keywords": [
"biomedical science",
+ "disease",
"environmental science",
+ "exposure",
"life science",
- "ontology"
+ "ontology",
+ "phenotype"
],
"mappings": {
"aberowl": "PHENX",
"bioportal": "PHENX",
- "fairsharing": "FAIRsharing.y5jcwa"
+ "fairsharing": "FAIRsharing.y5jcwa",
+ "integbio": "nbdc02244"
},
"name": "PhenX Toolkit",
"pattern": "^\\d+$",
@@ -43151,13 +45466,6 @@
"pubmed": "20154612",
"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": [
@@ -43207,7 +45515,7 @@
"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": "2023-06-22"
+ "version": "2024-04-04"
},
"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.",
@@ -43291,6 +45599,20 @@
"orcid": "0000-0003-4423-4370"
}
},
+ "phrr": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]",
+ "example": "4195",
+ "homepage": "https://registry.healthresearch.ph",
+ "name": "Philippine Health Research Registry",
+ "preferred_prefix": "phrr",
+ "uri_format": "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"
+ },
"phylomedb": {
"description": "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins.",
"example": "Phy000CLXM_RAT",
@@ -43307,6 +45629,7 @@
"mappings": {
"biocontext": "PHYLOMEDB",
"fairsharing": "FAIRsharing.7hxxc4",
+ "integbio": "nbdc01764",
"miriam": "phylomedb",
"n2t": "phylomedb",
"prefixcommons": "phylomedb",
@@ -43384,6 +45707,7 @@
"structure"
],
"mappings": {
+ "pathguide": "183",
"prefixcommons": "pibase"
},
"name": "Database of structurally defined protein interfaces",
@@ -43438,6 +45762,7 @@
"fairsharing": "FAIRsharing.ncgh1j",
"miriam": "pid.pathway",
"n2t": "pid.pathway",
+ "pathguide": "119",
"prefixcommons": "pid"
},
"name": "NCI Pathway Interaction Database: Pathway",
@@ -43498,7 +45823,6 @@
"pina": {
"contact": {
"email": "wujm@bjmu.edu.cn",
- "github": null,
"name": "Jianmin Wu",
"orcid": "0000-0002-8876-128X"
},
@@ -43513,7 +45837,8 @@
"biocontext": "PINA",
"fairsharing": "FAIRsharing.7q4gsz",
"miriam": "pina",
- "n2t": "pina"
+ "n2t": "pina",
+ "pathguide": "348"
},
"name": "Protein Interaction Network Analysis",
"pattern": "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$",
@@ -43536,7 +45861,6 @@
},
{
"doi": "10.1038/nmeth.1282",
- "pmc": null,
"pubmed": "19079255",
"title": "Integrated network analysis platform for protein-protein interactions",
"year": 2008
@@ -43604,7 +45928,6 @@
"pkdb": {
"contact": {
"email": "konigmatt@googlemail.com",
- "github": null,
"name": "Matthias König",
"orcid": "0000-0003-1725-179X"
},
@@ -43663,7 +45986,10 @@
"developmental biology",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "organ",
+ "organelle",
+ "tissue"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -43748,6 +46074,7 @@
"fairsharing": "FAIRsharing.ex3fqk",
"miriam": "planttfdb",
"n2t": "planttfdb",
+ "pathguide": "497",
"prefixcommons": "planttfdb",
"re3data": "r3d100011301"
},
@@ -43801,9 +46128,11 @@
"biocontext": "PLASMODB",
"fairsharing": "FAIRsharing.g4n8sw",
"go": "PlasmoDB",
+ "integbio": "nbdc01783",
"miriam": "plasmodb",
"n2t": "plasmodb",
"ncbi": "ApiDB_PlasmoDB",
+ "pathguide": "514",
"prefixcommons": "plasmodb",
"re3data": "r3d100011569"
},
@@ -43837,9 +46166,7 @@
"plo": {
"contact": {
"email": "mb4@sanger.ac.uk",
- "github": null,
- "name": "Matt Berriman",
- "orcid": null
+ "name": "Matt Berriman"
},
"deprecated": true,
"homepage": "http://www.sanger.ac.uk/Users/mb4/PLO/",
@@ -43933,22 +46260,30 @@
"uri_format": "http://substrate.burnham.org/protein/annotation/$1/html"
},
"pmc": {
+ "comment": "Note that the Europe PMC instance redirects canonical local unique identifiers from https://europepmc.org/articles/PMC3084216 to https://europepmc.org/article/PMC/3084216. However, this is an implementation detail and does not reflect the official format of a PMC identifier, which indeed does include `PMC` at the beginning of the local unique identifier",
+ "contact": {
+ "email": "beck@ncbi.nlm.nih.gov",
+ "github": "jeffbeckncbi",
+ "name": "Jeff Beck",
+ "orcid": "0000-0002-1798-9797"
+ },
"description": "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature.",
"example": "PMC3084216",
+ "example_extras": [
+ "PMC7418728",
+ "PMC7418728.1",
+ "PMC7418728.2"
+ ],
"homepage": "http://europepmc.org/",
"keywords": [
"bibliography",
- "biomedical science",
- "earth science",
- "environmental science",
- "epidemiology",
- "life science",
- "virology"
+ "centrally registered identifier",
+ "knowledge and information systems"
],
"mappings": {
"biocontext": "PMCID",
"biolink": "PMC",
- "fairsharing": "FAIRsharing.wpt5mp",
+ "fairsharing": "FAIRsharing.2b4316",
"go": "PMCID",
"miriam": "pmc",
"n2t": "pmc",
@@ -43956,7 +46291,7 @@
"wikidata": "P932"
},
"name": "PubMed Central",
- "pattern": "^PMC\\d+$",
+ "pattern": "^PMC\\d+(\\.\\d+)?$",
"preferred_prefix": "pmc",
"providers": [
{
@@ -43967,11 +46302,11 @@
"uri_format": "http://bio2rdf.org/pmc:$1"
},
{
- "code": "ncbi",
+ "code": "ncbi.pmc",
"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"
+ "uri_format": "https://www.ncbi.nlm.nih.gov/pmc/articles/$1"
}
],
"publications": [
@@ -43990,6 +46325,9 @@
"year": 2010
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/965"
+ ],
"synonyms": [
"PMC",
"PMCID"
@@ -44048,6 +46386,7 @@
"biocontext": "PMP",
"miriam": "pmp",
"n2t": "pmp",
+ "pathguide": "438",
"prefixcommons": "pmp"
},
"name": "Protein Model Portal",
@@ -44077,7 +46416,6 @@
"pmr": {
"contact": {
"email": "laia.subirats@gmail.com",
- "github": null,
"name": "Laia Subirats",
"orcid": "0000-0001-8646-5463"
},
@@ -44119,7 +46457,6 @@
},
{
"doi": "10.1093/bioinformatics/btq723",
- "pmc": null,
"pubmed": "21216774",
"title": "The Physiome Model Repository 2",
"year": 2011
@@ -44133,24 +46470,19 @@
},
{
"doi": "10.1093/bioinformatics/btn390",
- "pmc": null,
"pubmed": "18658182",
"title": "The CellML Model Repository",
"year": 2008
},
{
"doi": "10.1109/iembs.2006.260202",
- "pmc": null,
"pubmed": "17947072",
"title": "Toward a curated CellML model repository",
"year": 2006
},
{
"doi": "10.1109/IEMBS.2006.260202",
- "pmc": null,
- "pubmed": null,
- "title": "Toward a curated CellML model repository.",
- "year": null
+ "title": "Toward a curated CellML model repository."
}
],
"twitter": "physiomeproject",
@@ -44173,6 +46505,7 @@
"agro",
"ecocore",
"envo",
+ "gallont",
"genepio"
],
"banana": "PO",
@@ -44190,10 +46523,13 @@
"keywords": [
"botany",
"classification",
+ "expression data",
+ "life cycle",
"life science",
"obo",
"ontology",
"plant anatomy",
+ "plant development stage",
"structure"
],
"license": "CC-BY-4.0",
@@ -44218,6 +46554,13 @@
"pattern": "^\\d+$",
"preferred_prefix": "PO",
"providers": [
+ {
+ "code": "amigo",
+ "description": "Plant Ontology through Amigo",
+ "homepage": "http://www.plantontology.org/",
+ "name": "Plant Ontology through Amigo",
+ "uri_format": "http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$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.",
@@ -44236,7 +46579,6 @@
},
{
"doi": "10.1007/978-1-4939-3167-5_5",
- "pmc": null,
"pubmed": "26519402",
"title": "The Plant Ontology: A Tool for Plant Genomics",
"year": 2016
@@ -44280,8 +46622,8 @@
"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",
- "version": "2021-08-13"
+ "uri_format": "http://purl.obolibrary.org/obo/PO_$1",
+ "version": "2024-04-17"
},
"pocketome": {
"description": "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries.",
@@ -44294,7 +46636,8 @@
"biocontext": "POCKETOME",
"fairsharing": "FAIRsharing.tc6df8",
"miriam": "pocketome",
- "n2t": "pocketome"
+ "n2t": "pocketome",
+ "pathguide": "537"
},
"name": "Pocketome",
"pattern": "^[A-Za-z_0-9]+$",
@@ -44328,6 +46671,7 @@
"mappings": {
"biocontext": "POLBASE",
"fairsharing": "FAIRsharing.s9ztmd",
+ "integbio": "nbdc02079",
"miriam": "polbase",
"n2t": "polbase"
},
@@ -44357,6 +46701,7 @@
"biolink": "PomBase",
"fairsharing": "FAIRsharing.8jsya3",
"go": "PomBase",
+ "integbio": "nbdc00332",
"miriam": "pombase",
"n2t": "pombase",
"ncbi": "PomBase",
@@ -44448,6 +46793,9 @@
"uri_format": "https://www.pombase.org/gene/$1"
},
"poro": {
+ "appears_in": [
+ "gallont"
+ ],
"contact": {
"email": "robert.thacker@stonybrook.edu",
"github": "bobthacker",
@@ -44468,6 +46816,7 @@
"obo",
"ontology",
"phylogeny",
+ "taxonomic classification",
"taxonomy"
],
"license": "CC-BY-3.0",
@@ -44500,7 +46849,6 @@
"ppdb": {
"contact": {
"email": "ppdb@gifu-u.ac.jp",
- "github": null,
"name": "Yoshiharu Y. Yamamoto",
"orcid": "0000-0002-9667-0572"
},
@@ -44517,7 +46865,8 @@
"life science"
],
"mappings": {
- "fairsharing": "FAIRsharing.7k8zh0"
+ "fairsharing": "FAIRsharing.7k8zh0",
+ "integbio": "nbdc01041"
},
"name": "Pesticide Properties DataBase",
"pattern": "^\\d+$",
@@ -44553,8 +46902,11 @@
"homepage": "https://github.com/PlantPhenoOntology/PPO",
"keywords": [
"botany",
+ "life cycle",
"obo",
- "ontology"
+ "ontology",
+ "phenology",
+ "phenotype"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -44636,16 +46988,40 @@
"name": "Darren Natale",
"orcid": "0000-0001-5809-9523"
},
+ "contributor_extras": [
+ {
+ "email": "dan5@georgetown.edu",
+ "github": "nataled",
+ "name": "Darren Natale",
+ "orcid": "0000-0001-5809-9523"
+ }
+ ],
"description": "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.",
"download_obo": "http://purl.obolibrary.org/obo/pr.obo",
"download_owl": "http://purl.obolibrary.org/obo/pr.owl",
"example": "000000024",
+ "example_extras": [
+ "P0DP23",
+ "Q15796",
+ "Q15796-1",
+ "A0A0G2QC33",
+ "A0A0G2QC33-2"
+ ],
"homepage": "http://proconsortium.org",
"keywords": [
+ "annotation",
+ "biocuration",
"biology",
+ "data model",
+ "glycosylation",
+ "methylation",
"obo",
"ontology",
- "protein"
+ "phosphorylation",
+ "protein",
+ "protein acetylation",
+ "protein-containing complex",
+ "ptm site prediction"
],
"license": "CC-BY-4.0",
"logo": "https://raw.githubusercontent.com/PROconsortium/logo/master/PROlogo_small.png",
@@ -44656,6 +47032,7 @@
"bioportal": "PR",
"fairsharing": "FAIRsharing.4ndncv",
"go": "PR",
+ "integbio": "nbdc01630",
"miriam": "pr",
"n2t": "pr",
"obofoundry": "pr",
@@ -44667,9 +47044,16 @@
},
"name": "Protein Ontology",
"namespace_in_lui": true,
- "pattern": "^\\d+$",
+ "pattern": "^(?:\\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\\d+)?)$",
"preferred_prefix": "PR",
"providers": [
+ {
+ "code": "CURATOR_REVIEW",
+ "description": "Protein Ontology at Georgetown",
+ "homepage": "https://proconsortium.org/",
+ "name": "Protein Ontology at Georgetown",
+ "uri_format": "https://proconsortium.org/app/entry/PR:$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.",
@@ -44720,23 +47104,19 @@
"pubmed": "18047702",
"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",
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/959"
+ ],
"repository": "https://github.com/PROconsortium/PRoteinOntology",
"synonyms": [
"PR",
"PRO"
],
- "uri_format": "https://proconsortium.org/app/entry/PR:$1",
- "version": "68.0"
+ "uri_format": "http://purl.obolibrary.org/obo/PR_$1",
+ "version": "69.0"
},
"prefixcommons": {
"contributor": {
@@ -44759,8 +47139,9 @@
"name": "Yasset Perez-Riverol",
"orcid": "0000-0001-6579-6941"
},
+ "deprecated": true,
"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 experiments and assays.",
- "download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo",
+ "download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.owl",
"example": "0000006",
"homepage": "https://github.com/PRIDE-Utilities/pride-ontology",
"keywords": [
@@ -44772,6 +47153,7 @@
"aberowl": "PRIDE",
"biocontext": "PRIDE",
"fairsharing": "FAIRsharing.e1byny",
+ "integbio": "nbdc00630",
"miriam": "pride",
"n2t": "pride",
"ols": "pride",
@@ -44815,7 +47197,6 @@
},
{
"doi": "10.1002/pmic.201400120",
- "pmc": null,
"pubmed": "25047258",
"title": "How to submit MS proteomics data to ProteomeXchange via the PRIDE database",
"year": 2014
@@ -44836,7 +47217,6 @@
},
{
"doi": "10.1002/0471250953.bi1308s21",
- "pmc": null,
"pubmed": "18428683",
"title": "Using the Proteomics Identifications Database (PRIDE)",
"year": 2008
@@ -44857,7 +47237,6 @@
},
{
"doi": "10.1002/pmic.200401303",
- "pmc": null,
"pubmed": "16041671",
"title": "PRIDE: the proteomics identifications database",
"year": 2005
@@ -44905,6 +47284,7 @@
"biocontext": "PRINTS",
"fairsharing": "FAIRsharing.h8r843",
"go": "PRINTS",
+ "integbio": "nbdc00039",
"miriam": "prints",
"n2t": "prints",
"prefixcommons": "sprint",
@@ -44946,7 +47326,6 @@
},
{
"doi": "10.1093/bioinformatics/15.10.799",
- "pmc": null,
"pubmed": "10705433",
"title": "FingerPRINTScan: intelligent searching of the PRINTS motif database",
"year": 1999
@@ -44967,7 +47346,6 @@
"probesanddrugs": {
"contact": {
"email": "ctibor.skuta@img.cas.cz",
- "github": null,
"name": "Ctibor Škuta",
"orcid": "0000-0001-5325-4934"
},
@@ -44999,7 +47377,7 @@
"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": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/probonto.ttl",
+ "download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/probonto.ttl",
"example": "c0000005",
"example_extras": [
"k0001285"
@@ -45008,7 +47386,6 @@
"keywords": [
"computational biology",
"mathematics",
- "ontology",
"statistics",
"systems biology"
],
@@ -45085,6 +47462,7 @@
"mappings": {
"biocontext": "PRODOM",
"fairsharing": "FAIRsharing.a8z6gz",
+ "integbio": "nbdc00174",
"miriam": "prodom",
"n2t": "prodom",
"prefixcommons": "prodom"
@@ -45111,7 +47489,6 @@
},
{
"doi": "10.1093/bib/3.3.246",
- "pmc": null,
"pubmed": "12230033",
"title": "ProDom: automated clustering of homologous domains",
"year": 2002
@@ -45136,7 +47513,6 @@
"propreo": {
"contact": {
"email": "satyasahoo@ieee.org",
- "github": null,
"name": "Satya S. Sahoo",
"orcid": "0000-0001-9190-4256"
},
@@ -45185,9 +47561,11 @@
"biocontext": "PROSITE",
"fairsharing": "FAIRsharing.vwc6bd",
"go": "Prosite",
+ "integbio": "nbdc00241",
"miriam": "prosite",
"n2t": "prosite",
"prefixcommons": "prosite",
+ "togoid": "Prosite",
"uniprot": "DB-0084",
"wikidata": "P4355"
},
@@ -45280,6 +47658,7 @@
"structure"
],
"mappings": {
+ "pathguide": "242",
"prefixcommons": "protcom"
},
"name": "Database of protein-protein complexes",
@@ -45412,17 +47791,20 @@
"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": "https://www.w3.org/ns/prov-o",
+ "download_owl": "http://aber-owl.net/media/ontologies/PROV/1/prov.owl",
"example": "Activity",
"homepage": "https://www.w3.org/ns/prov",
"keywords": [
- "ontology"
+ "ontology",
+ "w3c rec"
],
"mappings": {
"aberowl": "PROV",
"biocontext": "prov",
"biolink": "prov",
- "ols": "prov"
+ "lov": "prov",
+ "ols": "prov",
+ "zazuko": "prov"
},
"name": "PROV Namespace",
"preferred_prefix": "prov",
@@ -45438,6 +47820,7 @@
"mappings": {
"biocontext": "PSCDB",
"fairsharing": "FAIRsharing.3d4jx0",
+ "integbio": "nbdc01636",
"miriam": "pscdb",
"n2t": "pscdb"
},
@@ -45454,7 +47837,6 @@
},
{
"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
@@ -45502,9 +47884,8 @@
"pseudogene": {
"contact": {
"email": "mark@gersteinlab.org",
- "github": null,
"name": "Mark Gerstein",
- "orcid": "0000-0002-9746-371"
+ "orcid": "0000-0002-9746-3719"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -45521,6 +47902,7 @@
],
"mappings": {
"bioportal": "pseudo",
+ "integbio": "nbdc00178",
"prefixcommons": "pseudogene"
},
"name": "PseudoGene",
@@ -45586,7 +47968,9 @@
"example": "0000013",
"homepage": "https://github.com/Planteome/plant-stress-ontology",
"keywords": [
+ "hospital",
"medical informatics",
+ "monitoring",
"obo",
"occupational medicine",
"ontology"
@@ -45594,6 +47978,7 @@
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "PSO",
+ "agroportal": "PSO",
"bioportal": "PSO",
"fairsharing": "FAIRsharing.dyj433",
"obofoundry": "pso",
@@ -45615,7 +48000,7 @@
"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"
+ "version": "2023-11-14"
},
"pspub": {
"contributor": {
@@ -45640,6 +48025,7 @@
"biocontext": "PUBCHEM.BIOASSAY",
"edam": "2638",
"go": "PubChem_BioAssay",
+ "integbio": "nbdc00640",
"miriam": "pubchem.bioassay",
"n2t": "pubchem.bioassay",
"prefixcommons": "pubchem.bioassay"
@@ -45735,10 +48121,13 @@
"edam": "2639",
"fairsharing": "FAIRsharing.qt3w7z",
"go": "PubChem_Compound",
+ "integbio": "nbdc02626",
"miriam": "pubchem.compound",
"n2t": "pubchem.compound",
+ "pathguide": "361",
"prefixcommons": "pubchem.compound",
"re3data": "r3d100010129",
+ "togoid": "PubchemCompound",
"wikidata": "P662"
},
"name": "PubChem CID",
@@ -45864,9 +48253,11 @@
"biocontext": "PUBCHEM.SUBSTANCE",
"cheminf": "000141",
"go": "PubChem_Substance",
+ "integbio": "nbdc00642",
"miriam": "pubchem.substance",
"n2t": "pubchem.substance",
"prefixcommons": "pubchem.substance",
+ "togoid": "PubchemSubstance",
"wikidata": "P2153"
},
"name": "PubChem Substance ID (SID)",
@@ -45900,7 +48291,7 @@
},
"publons.publication": {
"description": "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)",
- "example": "507568",
+ "example": "18466622",
"homepage": "https://publons.com",
"mappings": {
"wikidata": "P3431"
@@ -45928,27 +48319,33 @@
"uri_format": "https://publons.com/researcher/$1"
},
"pubmed": {
+ "contact": {
+ "email": "beck@ncbi.nlm.nih.gov",
+ "github": "jeffbeckncbi",
+ "name": "Jeff Beck",
+ "orcid": "0000-0002-1798-9797"
+ },
"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"
+ "citation",
+ "publication"
],
"mappings": {
"biocontext": "PUBMED",
"cellosaurus": "PubMed",
"cheminf": "000302",
"edam": "1187",
- "fairsharing": "FAIRsharing.a5sv8m",
+ "fairsharing": "FAIRsharing.2b9b61",
"go": "PMID",
+ "integbio": "nbdc00179",
"miriam": "pubmed",
"n2t": "pubmed",
"prefixcommons": "pubmed",
+ "togoid": "Pubmed",
"wikidata": "P698"
},
"name": "PubMed",
@@ -46047,6 +48444,10 @@
"example": "RoleInTime",
"homepage": "http://www.sparontologies.net/ontologies/pro",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
"subject agnostic"
],
"mappings": {
@@ -46057,8 +48458,6 @@
"publications": [
{
"doi": "10.1145/2362499.2362502",
- "pmc": null,
- "pubmed": null,
"title": "Scholarly publishing and linked data",
"year": 2012
}
@@ -46081,12 +48480,21 @@
"example": "0000423",
"homepage": "http://rgd.mcw.edu/rgdweb/ontology/search.html",
"keywords": [
+ "biological regulation",
+ "disease",
+ "drug",
"drug metabolism",
+ "enzymatic reaction",
"human",
"life science",
+ "mathematical model",
+ "molecular entity",
+ "network model",
"obo",
"ontology",
- "pathway"
+ "pathway",
+ "pathway model",
+ "signaling"
],
"license": "CC-BY-4.0",
"logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif",
@@ -46149,8 +48557,8 @@
"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": "7.52"
+ "uri_format": "http://purl.obolibrary.org/obo/PW_$1",
+ "version": "7.82"
},
"pwo": {
"contact": {
@@ -46169,25 +48577,22 @@
"example": "Workflow",
"homepage": "http://www.sparontologies.net/ontologies/pwo",
"keywords": [
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
+ "spar",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.c4e46c"
+ "fairsharing": "FAIRsharing.c4e46c",
+ "lov": "pwo"
},
"name": "Publishing Workflow Ontology",
"preferred_prefix": "PWO",
"publications": [
- {
- "doi": "https://doi.org/10.3233/SW-160230",
- "pmc": null,
- "pubmed": null,
- "title": "The Publishing Workflow Ontology (PWO)",
- "year": null
- },
{
"doi": "10.3233/sw-160230",
- "pmc": null,
- "pubmed": null,
"title": "The Publishing Workflow Ontology (PWO)",
"year": 2017
}
@@ -46239,6 +48644,14 @@
"download_rdf": "http://purl.org/linked-data/cube#",
"example": "Observation",
"homepage": "https://www.w3.org/TR/vocab-data-cube",
+ "keywords": [
+ "methods",
+ "w3c rec"
+ ],
+ "mappings": {
+ "lov": "qb",
+ "zazuko": "qb"
+ },
"name": "The data cube vocabulary",
"pattern": "^\\w+$",
"preferred_prefix": "qb",
@@ -46271,14 +48684,19 @@
"homepage": "https://qudt.org",
"keywords": [
"astrophysics and astronomy",
- "ontology"
+ "experimental measurement",
+ "methods",
+ "ontology",
+ "unit"
],
"mappings": {
"aberowl": "QUDT",
"bartoc": "18206",
"biolink": "qud",
"bioportal": "QUDT",
- "fairsharing": "FAIRsharing.d3pqw7"
+ "fairsharing": "FAIRsharing.d3pqw7",
+ "lov": "qudt",
+ "zazuko": "qudt"
},
"name": "Quantities, Units, Dimensions, and Types Ontology",
"preferred_prefix": "qudt",
@@ -46297,7 +48715,6 @@
"radiomics": {
"contact": {
"email": "alberto.traverso@maastro.nl",
- "github": null,
"name": "Alberto Traverso",
"orcid": "0000-0001-6183-4429"
},
@@ -46317,9 +48734,7 @@
"radlex": {
"contact": {
"email": "radlex-feedback@lists.rsna.org",
- "github": null,
- "name": "Radiological Society of North America",
- "orcid": null
+ "name": "Radiological Society of North America"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -46335,6 +48750,8 @@
"anatomy",
"biomedical science",
"clinical studies",
+ "diagnosis",
+ "medical imaging",
"medical informatics",
"ontology",
"radiology"
@@ -46352,21 +48769,18 @@
"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
@@ -46481,10 +48895,7 @@
},
{
"doi": "10.1681/ASN.2016101077",
- "pmc": null,
- "pubmed": null,
- "title": "(Re)Building a Kidney.",
- "year": null
+ "title": "(Re)Building a Kidney."
}
],
"repository": "https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Create-citable-datasets",
@@ -46533,7 +48944,7 @@
"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_$1",
- "version": "2023-06-15"
+ "version": "2024-02-29"
},
"rcb": {
"contributor": {
@@ -46545,18 +48956,48 @@
"description": "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center.",
"example": "RCB0002",
"homepage": "https://cell.brc.riken.jp/en/rcb",
+ "keywords": [
+ "animal",
+ "bioresource",
+ "cell",
+ "cell line",
+ "cultured cell",
+ "cultured cell line",
+ "dna",
+ "embryo",
+ "experimental animal",
+ "experimental plant",
+ "faseb list",
+ "gene",
+ "genetic material",
+ "organ",
+ "plant",
+ "recombinant host",
+ "seed",
+ "sperm",
+ "tissue",
+ "virus"
+ ],
"mappings": {
- "cellosaurus": "RCB"
+ "cellosaurus": "RCB",
+ "rrid": "IMSR_RBRC"
},
"name": "RIKEN Bioresource Center Cell Bank",
"pattern": "^RCB\\d+$",
"preferred_prefix": "rcb",
+ "publications": [
+ {
+ "pubmed": "34532769"
+ },
+ {
+ "pubmed": "19448331"
+ }
+ ],
"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"
},
@@ -46567,24 +49008,54 @@
"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",
+ "example": "type",
"homepage": "http://www.w3.org/1999/02/22-rdf-syntax-ns",
"keywords": [
"computer science",
- "subject agnostic"
+ "subject agnostic",
+ "w3c rec"
],
"mappings": {
"biocontext": "rdf",
- "fairsharing": "FAIRsharing.p77ph9"
+ "fairsharing": "FAIRsharing.p77ph9",
+ "lov": "rdf",
+ "zazuko": "rdf"
},
"name": "Resource Description Framework",
"preferred_prefix": "rdf",
"uri_format": "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"
},
+ "rdfa": {
+ "contact": {
+ "email": "ivan@w3.org",
+ "github": "iherman",
+ "name": "Ivan Herman",
+ "orcid": "0000-0003-0782-2704"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "RDFa Core is a specification for attributes to express structured data in any markup language. The embedded data already available in the markup language (e.g., HTML) can often be reused by the RDFa markup, so that publishers don't need to repeat significant data in the document content. (from https://www.w3.org/TR/rdfa-core/)",
+ "download_rdf": "http://www.w3.org/ns/rdfa.ttl",
+ "example": "PrefixOrTermMapping",
+ "homepage": "http://www.w3.org/ns/rdfa",
+ "keywords": [
+ "rdf"
+ ],
+ "mappings": {
+ "lov": "rdfa",
+ "zazuko": "rdfa"
+ },
+ "name": "RDFa Vocabulary for Term and Prefix Assignment, and for Processor Graph Reporting",
+ "preferred_prefix": "rdfa",
+ "uri_format": "http://www.w3.org/ns/rdfa#$1"
+ },
"rdfs": {
"contact": {
"email": "danbri@w3.org",
- "github": null,
"name": "Dan Brickley",
"orcid": "0000-0002-6450-7041"
},
@@ -46603,14 +49074,17 @@
"life science",
"linguistics",
"ontology",
- "ontology and terminology"
+ "ontology and terminology",
+ "w3c rec"
],
"mappings": {
"aberowl": "RDFS",
"biocontext": "rdfs",
"bioportal": "RDFS",
"fairsharing": "FAIRsharing.v9n3gk",
- "ols": "rdfs"
+ "lov": "rdfs",
+ "ols": "rdfs",
+ "zazuko": "rdfs"
},
"name": "RDF Schema",
"preferred_prefix": "rdfs",
@@ -46650,6 +49124,20 @@
"uri_format": "https://www.re3data.org/repository/$1"
},
"reactome": {
+ "contact": {
+ "email": "deustp01@med.nyu.edu",
+ "github": "deustp01",
+ "name": "Peter D'Eustachio",
+ "orcid": "0000-0002-5494-626X"
+ },
+ "contributor_extras": [
+ {
+ "email": "smoxon@lbl.gov",
+ "github": "sierra-moxon",
+ "name": "Sierra Moxon",
+ "orcid": "0000-0002-8719-7760"
+ }
+ ],
"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/",
@@ -46663,10 +49151,13 @@
"cheminf": "000411",
"edam": "1155",
"go": "Reactome",
+ "integbio": "nbdc00185",
"miriam": "reactome",
"n2t": "reactome",
+ "pathguide": "103",
"prefixcommons": "reactome",
"re3data": "r3d100010861",
+ "togoid": "ReactomePathway",
"wikidata": "P3937"
},
"name": "Reactome",
@@ -46680,6 +49171,13 @@
"name": "Bio2RDF",
"uri_format": "http://bio2rdf.org/reactome:$1"
},
+ {
+ "code": "browser",
+ "description": "An interactive view over pathways.",
+ "homepage": "https://reactome.org/PathwayBrowser/",
+ "name": "Reactome Pathway Browser",
+ "uri_format": "https://reactome.org/PathwayBrowser/#/$1"
+ },
{
"code": "pathwaycommons",
"description": "Pathway diagram drawn with Cytoscape",
@@ -46697,9 +49195,13 @@
"year": 2005
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/pull/1086"
+ ],
"synonyms": [
"RE",
- "REACT"
+ "REACT",
+ "reactome.pathway"
],
"uri_format": "https://reactome.org/content/detail/$1"
},
@@ -46744,8 +49246,10 @@
"edam": "2325",
"fairsharing": "FAIRsharing.9sb9qh",
"go": "REBASE",
+ "integbio": "nbdc00648",
"miriam": "rebase",
"n2t": "rebase",
+ "pathguide": "72",
"prefixcommons": "rebase",
"re3data": "r3d100012171",
"uniprot": "DB-0089",
@@ -46835,6 +49339,7 @@
"regulation"
],
"mappings": {
+ "pathguide": "265",
"prefixcommons": "redfly"
},
"name": "Regulatory Elements Database for Drosophila",
@@ -46859,7 +49364,6 @@
"refseq": {
"contributor_extras": [
{
- "email": null,
"github": "slobentanzer",
"name": "Sebastian Lobentanzer",
"orcid": "0000-0003-3399-6695"
@@ -46886,6 +49390,7 @@
"fairsharing": "FAIRsharing.4jg0qw",
"go": "RefSeq",
"hl7": "2.16.840.1.113883.6.280",
+ "integbio": "nbdc00187",
"miriam": "refseq",
"n2t": "refseq",
"prefixcommons": "refseq",
@@ -47007,12 +49512,11 @@
"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",
+ "download_owl": "http://aber-owl.net/media/ontologies/REPRODUCE-ME/7/reproduce-me.owl",
"example": "MicrobeamManipulation",
"homepage": "https://w3id.org/reproduceme/research",
"keywords": [
@@ -47031,7 +49535,6 @@
"resid": {
"contact": {
"email": "john.garavelli@ebi.ac.uk",
- "github": null,
"name": "John Garavelli",
"orcid": "0000-0002-4131-735X"
},
@@ -47070,7 +49573,6 @@
"publications": [
{
"doi": "10.1002/pmic.200300764",
- "pmc": null,
"pubmed": "15174124",
"title": "Annotation of post-translational modifications in the Swiss-Prot knowledge base",
"year": 2004
@@ -47082,17 +49584,18 @@
"reto": {
"contact": {
"email": "vladimir.n.mironov@gmail.com",
- "github": null,
- "name": "Vladimir Mironov",
- "orcid": null
+ "name": "Vladimir Mironov"
},
"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",
+ "download_rdf": "http://www.bio.ntnu.no/ontology/ReTO/reto.rdf",
"homepage": "http://www.semantic-systems-biology.org/apo",
"keywords": [
"life science",
"ontology",
+ "regulation of gene expression",
+ "transcript",
"transcriptomics"
],
"mappings": {
@@ -47108,9 +49611,7 @@
"rex": {
"contact": {
"email": "chebi-help@ebi.ac.uk",
- "github": null,
- "name": "Chebi Administrators",
- "orcid": null
+ "name": "Chebi Administrators"
},
"deprecated": true,
"description": "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.",
@@ -47120,9 +49621,11 @@
"keywords": [
"biochemistry",
"chemistry",
+ "enzymatic reaction",
"life science",
"obo",
- "ontology"
+ "ontology",
+ "reaction data"
],
"mappings": {
"aberowl": "REX",
@@ -47161,10 +49664,14 @@
"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",
+ "download_rdf": "http://www.bio.ntnu.no/ontology/ReXO/rexo.rdf",
"homepage": "http://www.semantic-systems-biology.org/apo",
"keywords": [
+ "expression data",
"life science",
- "ontology"
+ "ontology",
+ "orthologous",
+ "regulation of gene expression"
],
"mappings": {
"aberowl": "REXO",
@@ -47188,7 +49695,7 @@
"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/",
+ "homepage": "https://rfam.org/",
"keywords": [
"genetics"
],
@@ -47197,6 +49704,7 @@
"edam": "2356",
"fairsharing": "FAIRsharing.fex4c8",
"go": "Rfam",
+ "integbio": "nbdc00654",
"miriam": "rfam",
"n2t": "rfam",
"ncbi": "RFAM"
@@ -47221,7 +49729,7 @@
}
],
"twitter": "RfamDB",
- "uri_format": "https://rfam.xfam.org/family/$1"
+ "uri_format": "https://rfam.org/family/$1"
},
"rfc": {
"contributor": {
@@ -47285,7 +49793,6 @@
"rgd": {
"contact": {
"email": "jrsmith@mcw.edu",
- "github": null,
"name": "Jennifer R Smith",
"orcid": "0000-0002-6443-9376"
},
@@ -47293,19 +49800,51 @@
"example": "7499841",
"homepage": "http://rgd.mcw.edu/",
"keywords": [
+ "behavior",
"biomedical science",
"comparative genomics",
+ "congenic rat",
+ "data analysis service",
+ "disease",
"dna",
+ "est",
+ "faseb list",
+ "function",
"gene",
+ "genetic",
"genome",
+ "genomic",
"genomics",
+ "genotype",
+ "gold standard",
+ "human",
+ "immunology",
+ "inbred rat strain",
+ "knockout",
+ "map",
+ "marker",
+ "model organism",
"molecular medicine",
+ "mouse",
+ "mutant",
"ontology",
+ "organism supplier",
+ "pathway",
"phenomics",
+ "phenotype",
+ "physiology",
+ "proteomics",
+ "qtl",
"quantitative genetics",
+ "rat",
+ "recombinant inbred rat",
+ "sequence",
+ "strain",
"translational medicine",
+ "variation",
"veterinary medicine"
],
+ "license": "CC-BY-4.0",
"mappings": {
"aberowl": "RGD",
"biocontext": "RGD",
@@ -47314,11 +49853,15 @@
"edam": "2620",
"fairsharing": "FAIRsharing.pfg82t",
"go": "RGD",
+ "integbio": "nbdc00188",
"miriam": "rgd",
"n2t": "rgd",
"ncbi": "RGD",
+ "pathguide": "267",
"prefixcommons": "rgd",
"re3data": "r3d100010417",
+ "rrid": "RGD",
+ "togoid": "Rgd",
"uniprot": "DB-0091",
"wikidata": "P3853"
},
@@ -47365,21 +49908,18 @@
},
{
"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
@@ -47461,6 +50001,9 @@
"title": "PhenoMiner: quantitative phenotype curation at the rat genome database",
"year": 2013
},
+ {
+ "pubmed": "23434633"
+ },
{
"doi": "10.1371/journal.pcbi.1000582",
"pmc": "PMC2775909",
@@ -47468,6 +50011,9 @@
"title": "The rat genome database curators: who, what, where, why",
"year": 2009
},
+ {
+ "pubmed": "18996890"
+ },
{
"doi": "10.1093/nar/gkl988",
"pmc": "PMC1761441",
@@ -47476,8 +50022,6 @@
"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
@@ -47522,7 +50066,6 @@
"rhea": {
"contact": {
"email": "anne.morgat@sib.swiss",
- "github": null,
"name": "Anne Morgat",
"orcid": "0000-0002-1216-2969"
},
@@ -47540,10 +50083,13 @@
"edam": "2644",
"fairsharing": "FAIRsharing.pn1sr5",
"go": "RHEA",
+ "integbio": "nbdc02083",
"miriam": "rhea",
"n2t": "rhea",
+ "pathguide": "310",
"prefixcommons": "rhea",
- "re3data": "r3d100010891"
+ "re3data": "r3d100010891",
+ "togoid": "Rhea"
},
"name": "Rhea, the Annotated Reactions Database",
"pattern": "^\\d{5}$",
@@ -47610,7 +50156,6 @@
"ribocentre": {
"contact": {
"email": "huanglin36@mail.sysu.edu.cn",
- "github": null,
"name": "Lin Huang",
"orcid": "0000-0002-2121-365X"
},
@@ -47657,6 +50202,7 @@
"pathway"
],
"mappings": {
+ "pathguide": "227",
"prefixcommons": "ricecyc"
},
"name": "Rice Metabolic Pathways",
@@ -47823,6 +50369,7 @@
"edam": "3856",
"fairsharing": "FAIRsharing.KcCjL7",
"go": "RNAcentral",
+ "integbio": "nbdc01215",
"miriam": "rnacentral",
"n2t": "rnacentral",
"ncbi": "RNAcentral",
@@ -47979,7 +50526,6 @@
"rnao": {
"contact": {
"email": "BatchelorC@rsc.org",
- "github": null,
"name": "Colin Batchelor",
"orcid": "0000-0001-5985-7429"
},
@@ -47992,8 +50538,12 @@
"keywords": [
"biochemistry",
"life science",
+ "molecular structure",
"obo",
- "ontology"
+ "ontology",
+ "ribonucleic acid",
+ "rna secondary structure",
+ "sequence motif"
],
"license": "CC0-1.0",
"mappings": {
@@ -48028,17 +50578,8 @@
},
{
"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
- },
- {
- "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",
@@ -48086,6 +50627,7 @@
"envo",
"foodon",
"fovt",
+ "gallont",
"genepio",
"go",
"hso",
@@ -48102,6 +50644,7 @@
"psdo",
"pso",
"rbo",
+ "uberon",
"upa",
"xpo",
"zp"
@@ -48183,7 +50726,7 @@
"oborel"
],
"uri_format": "http://purl.obolibrary.org/obo/RO_$1",
- "version": "2023-02-22"
+ "version": "2024-04-24"
},
"roleo": {
"banana": "RoleO",
@@ -48245,6 +50788,7 @@
"ontology"
],
"mappings": {
+ "bartoc": "20474",
"fairsharing": "FAIRsharing.1jKfji",
"miriam": "ror",
"n2t": "ror"
@@ -48269,6 +50813,7 @@
"mappings": {
"biocontext": "ROUGE",
"fairsharing": "FAIRsharing.vdbagq",
+ "integbio": "nbdc00672",
"miriam": "rouge",
"n2t": "rouge",
"prefixcommons": "rouge",
@@ -48314,12 +50859,32 @@
},
"rrid": {
"banana": "RRID",
+ "contact": {
+ "email": "bandrow@gmail.com",
+ "github": "bandrow",
+ "name": "Anita Bandrowski",
+ "orcid": "0000-0002-5497-0243"
+ },
+ "contributor_extras": [
+ {
+ "email": "bandrow@gmail.com",
+ "github": "bandrow",
+ "name": "Anita Bandrowski",
+ "orcid": "0000-0002-5497-0243"
+ }
+ ],
"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",
+ "homepage": "https://rrid.site",
"keywords": [
+ "annotation",
+ "centrally registered identifier",
"chemistry",
- "life science"
+ "citation",
+ "data retrieval",
+ "knowledge and information systems",
+ "life science",
+ "resource metadata"
],
"mappings": {
"biocontext": "RRID",
@@ -48332,9 +50897,44 @@
"pattern": "^[a-zA-Z]+.+$",
"preferred_prefix": "rrid",
"publications": [
+ {
+ "doi": "10.1093/nar/gkac927",
+ "pmc": "PMC9825422",
+ "pubmed": "36370112",
+ "title": "The Antibody Registry: ten years of registering antibodies",
+ "year": 2023
+ },
+ {
+ "doi": "10.1093/gigascience/giac058",
+ "pmc": "PMC9197678",
+ "pubmed": "35701373",
+ "title": "A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?",
+ "year": 2022
+ },
+ {
+ "doi": "10.1371/journal.pcbi.1008967",
+ "pmc": "PMC8189493",
+ "pubmed": "34043624",
+ "title": "Antibody Watch: Text mining antibody specificity from the literature",
+ "year": 2021
+ },
+ {
+ "doi": "10.1002/cnr2.1150",
+ "pmc": "PMC7941525",
+ "pubmed": "32721132",
+ "title": "Improving transparency and scientific rigor in academic publishing",
+ "year": 2018
+ },
+ {
+ "doi": "10.7554/elife.41676",
+ "pmc": "PMC6351100",
+ "pubmed": "30693867",
+ "title": "Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines",
+ "year": 2019
+ },
{
"doi": "10.1038/nmeth.3995",
- "pmc": null,
+ "pmc": "PMC10335836",
"pubmed": "27595404",
"title": "A proposal for validation of antibodies",
"year": 2016
@@ -48370,6 +50970,51 @@
],
"uri_format": "https://scicrunch.org/resolver/RRID:$1"
},
+ "rrrc": {
+ "description": "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]",
+ "example": "961",
+ "homepage": "http://www.rrrc.us/",
+ "keywords": [
+ "animal",
+ "biomedical",
+ "catalog",
+ "cell line",
+ "cryopreserved",
+ "database",
+ "disease",
+ "drug",
+ "embryo",
+ "embryonic stem cell",
+ "gamete",
+ "genome",
+ "genotyping",
+ "germplasma",
+ "human",
+ "hybrid",
+ "inbred",
+ "infectious",
+ "molecular",
+ "mutant",
+ "nuclear",
+ "ovarian",
+ "pathogen",
+ "protocol",
+ "rat",
+ "rat model",
+ "reagent",
+ "research",
+ "stem cell",
+ "strain",
+ "tissue"
+ ],
+ "mappings": {
+ "rrid": "RRRC"
+ },
+ "name": "Rat Resource and Research Center",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "rrrc",
+ "uri_format": "https://www.rrrc.us/Strain/?x=$1"
+ },
"rs": {
"contact": {
"email": "sjwang@mcw.edu",
@@ -48383,7 +51028,9 @@
"example": "0001807",
"homepage": "http://rgd.mcw.edu/rgdweb/search/strains.html",
"keywords": [
+ "genetic strain",
"life science",
+ "mutation",
"obo",
"ontology"
],
@@ -48431,7 +51078,7 @@
"repository": "https://github.com/rat-genome-database/RS-Rat-Strain-Ontology",
"twitter": "ratgenome",
"uri_format": "http://purl.obolibrary.org/obo/RS_$1",
- "version": "6.107"
+ "version": "6.221"
},
"rtecs": {
"contributor": {
@@ -48453,8 +51100,6 @@
"publications": [
{
"doi": "10.1016/s1074-9098%2899%2900058-1",
- "pmc": null,
- "pubmed": null,
"title": "An overview of the Registry of Toxic Effects of Chemical Substances (RTECS): Critical information on chemical hazards",
"year": 1999
}
@@ -48464,6 +51109,20 @@
"https://www.cdc.gov/niosh/npg/npgdrtec.html"
]
},
+ "rubygems": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "A repository of software packages written in Ruby.",
+ "example": "bel",
+ "homepage": "https://rubygems.org",
+ "name": "RubyGems",
+ "preferred_prefix": "rubygems",
+ "uri_format": "https://rubygems.org/gems/$1"
+ },
"runbiosimulations": {
"description": "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive.",
"example": "5fde96bdc5f1aa9ff0cce18a",
@@ -48491,7 +51150,8 @@
"keywords": [
"molecular chemistry",
"obo",
- "ontology"
+ "ontology",
+ "reaction data"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -48509,15 +51169,13 @@
"preferred_prefix": "RXNO",
"rdf_uri_format": "http://purl.obolibrary.org/obo/RXNO_$1",
"repository": "https://github.com/rsc-ontologies/rxno",
- "uri_format": "http://www.rsc.org/publishing/journals/prospect/ontology.asp?id=$1",
+ "uri_format": "http://purl.obolibrary.org/obo/RXNO_$1",
"version": "2021-12-16"
},
"rxnorm": {
"contact": {
- "email": "custserv@nlm.nih.gov",
- "github": null,
- "name": "NLM Customer Service",
- "orcid": null
+ "email": "willisj@mail.nlm.nih.gov",
+ "name": "Jan Willis, NLM"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -48530,9 +51188,12 @@
"homepage": "https://www.nlm.nih.gov/research/umls/rxnorm/",
"keywords": [
"biomedical science",
+ "drug",
+ "drug name",
"ontology",
"preclinical studies"
],
+ "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "RXNORM",
"biocontext": "RXCUI",
@@ -48563,7 +51224,6 @@
"year": 2011
},
{
- "doi": null,
"pmc": "PMC2655997",
"pubmed": "18998891",
"title": "RxTerms - a drug interface terminology derived from RxNorm",
@@ -48571,17 +51231,8 @@
},
{
"doi": "10.1109/mitp.2005.122",
- "pmc": null,
- "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": [
@@ -48597,6 +51248,8 @@
"protein"
],
"mappings": {
+ "integbio": "nbdc00674",
+ "pathguide": "47",
"prefixcommons": "s_mart_db"
},
"name": "The S/MAR transaction DataBase",
@@ -48659,8 +51312,6 @@
"provides": "eccode",
"publications": [
{
- "doi": null,
- "pmc": null,
"pubmed": "17822389",
"title": "Storing and annotating of kinetic data",
"year": 2007
@@ -48698,8 +51349,6 @@
],
"publications": [
{
- "doi": null,
- "pmc": null,
"pubmed": "17822389",
"title": "Storing and annotating of kinetic data",
"year": 2007
@@ -48724,6 +51373,7 @@
"fairsharing": "FAIRsharing.cwx04e",
"miriam": "sabiork.reaction",
"n2t": "sabiork.reaction",
+ "pathguide": "226",
"prefixcommons": "sabiork.reaction",
"re3data": "r3d100011052",
"uniprot": "DB-0177"
@@ -48741,6 +51391,10 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkx1065",
+ "pubmed": "29092055"
+ },
{
"doi": "10.1093/nar/gkr1046",
"pmc": "PMC3245076",
@@ -48819,9 +51473,7 @@
"sao": {
"contact": {
"email": "slarson@ncmir.ucsd.edu",
- "github": null,
- "name": "Stephen Larson",
- "orcid": null
+ "name": "Stephen Larson"
},
"deprecated": true,
"description": "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules.",
@@ -48885,7 +51537,6 @@
"sasbdb": {
"contact": {
"email": "a.kikhney@embl-hamburg.de",
- "github": null,
"name": "Al Kikhney",
"orcid": "0000-0003-1321-3956"
},
@@ -48943,8 +51594,12 @@
"example": "0000485",
"homepage": "http://www.ebi.ac.uk/sbo/",
"keywords": [
+ "mathematical model",
+ "modeling and simulation",
+ "molecular interaction",
"obo",
"ontology",
+ "pathway model",
"systems biology"
],
"license": "Artistic License 2.0",
@@ -48999,7 +51654,7 @@
"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/ols4/ontologies/sbo/terms?obo_id=SBO:$1",
+ "uri_format": "http://purl.obolibrary.org/obo/SBO_$1",
"version": "2021-08-28"
},
"scdo": {
@@ -49049,10 +51704,13 @@
"homepage": "https://scdontology.h3abionet.org/",
"keywords": [
"biomedical science",
+ "genetic disorder",
"obo",
- "ontology"
+ "ontology",
+ "sickle cell disease"
],
"license": "GPL-3.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbWtCIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--69320a8be8ca6a407eaf142714307b4c7e6b5f45/cropped-Screenshot-from-2020-05-23-20-20-32-2.png?disposition=inline",
"mappings": {
"aberowl": "SCDO",
"bioportal": "SCDO",
@@ -49107,6 +51765,7 @@
"chemistry",
"selventa"
],
+ "license": "Apache-2.0",
"name": "Selventa Chemicals",
"pattern": "^A\\d{4}$",
"preferred_prefix": "schem",
@@ -49115,9 +51774,7 @@
"schema": {
"contact": {
"email": "johardi@stanford.edu",
- "github": null,
- "name": "Josef Hardi",
- "orcid": null
+ "name": "Josef Hardi"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -49126,11 +51783,13 @@
"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": "https://schema.org/version/latest/schemaorg-all-http.rdf",
+ "download_owl": "http://aber-owl.net/media/ontologies/SCHEMAORG/2/schemaorg.owl",
+ "download_rdf": "https://schema.org/version/latest/schemaorg-all-http.rdf",
"example": "Person",
"homepage": "https://schema.org",
"keywords": [
"computer science",
+ "general & upper",
"ontology",
"subject agnostic"
],
@@ -49139,7 +51798,9 @@
"biolink": "schema",
"bioportal": "SCHEMA",
"fairsharing": "FAIRsharing.hzdzq8",
- "ols": "schemaorg_http"
+ "lov": "schema",
+ "ols": "schemaorg_http",
+ "zazuko": "schema"
},
"name": "Schema.org",
"preferred_prefix": "schema",
@@ -49195,6 +51856,7 @@
"protein complexes",
"selventa"
],
+ "license": "Apache-2.0",
"name": "Selventa Complexes",
"pattern": "^C\\d{4}$",
"preferred_prefix": "scomp",
@@ -49277,7 +51939,6 @@
},
{
"doi": "10.1107/s0907444998009172",
- "pmc": null,
"pubmed": "10089491",
"title": "SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data",
"year": 1998
@@ -49435,25 +52096,22 @@
"example": "IntellectualContribution",
"homepage": "http://www.sparontologies.net/ontologies/scoro",
"keywords": [
+ "academy",
+ "bibliography",
+ "citation",
+ "data model",
+ "report",
"subject agnostic"
],
"mappings": {
- "fairsharing": "FAIRsharing.c86b48"
+ "fairsharing": "FAIRsharing.c86b48",
+ "lov": "scoro"
},
"name": "Scholarly Contributions and Roles Ontology",
"preferred_prefix": "SCoRO",
"publications": [
- {
- "doi": "https://doi.org/10.3233/SW-150177",
- "pmc": null,
- "pubmed": null,
- "title": "The Document Components Ontology (DoCO)",
- "year": null
- },
{
"doi": "10.3233/sw-150177",
- "pmc": null,
- "pubmed": null,
"title": "The Document Components Ontology (DoCO)",
"year": 2016
}
@@ -49473,6 +52131,7 @@
"rna"
],
"mappings": {
+ "pathguide": "130",
"prefixcommons": "scpd"
},
"name": "Saccharomyces cerevisiae promoter database",
@@ -49506,11 +52165,16 @@
"github_request_issue": 421,
"homepage": "https://scicrunch.org/browse/resourcedashboard",
"keywords": [
+ "interactive portal",
"life science",
- "neurobiology"
+ "neurobiology",
+ "nih initiative",
+ "rrid"
],
"mappings": {
- "fairsharing": "FAIRsharing.kj4pvk"
+ "fairsharing": "FAIRsharing.kj4pvk",
+ "integbio": "nbdc01937",
+ "rrid": "SCR"
},
"name": "SciCrunch Registry",
"pattern": "^\\d+$",
@@ -49522,6 +52186,9 @@
"pubmed": "26599696",
"title": "The Resource Identification Initiative: A Cultural Shift in Publishing",
"year": 2016
+ },
+ {
+ "pubmed": "22434839"
}
],
"synonyms": [
@@ -49579,6 +52246,7 @@
"homepage": "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi",
"mappings": {
"biocontext": "SDBS",
+ "integbio": "nbdc01520",
"miriam": "sdbs",
"n2t": "sdbs"
},
@@ -49590,7 +52258,6 @@
"sdgio": {
"contact": {
"email": "pier.buttigieg@awi.de",
- "github": null,
"name": "Pier Luigi Buttigieg",
"orcid": "0000-0002-4366-3088"
},
@@ -49600,7 +52267,8 @@
"homepage": "https://github.com/SDG-InterfaceOntology/sdgio",
"keywords": [
"environmental science",
- "ontology"
+ "ontology",
+ "sustainability"
],
"mappings": {
"agroportal": "SDGIO",
@@ -49641,6 +52309,7 @@
"diseases",
"selventa"
],
+ "license": "Apache-2.0",
"name": "Selventa Diseases",
"pattern": "^D\\d{4}$",
"preferred_prefix": "sdis",
@@ -49736,7 +52405,6 @@
"pattern": "^\\d+$",
"preferred_prefix": "seinet",
"reviewer": {
- "email": null,
"github": "callahantiff",
"name": "Tiffany J. Callahan",
"orcid": "0000-0002-8169-9049"
@@ -49772,7 +52440,6 @@
{
"name": "Semanticly",
"partnered": true,
- "ror": null,
"wikidata": "Q115518213"
}
],
@@ -49782,6 +52449,18 @@
],
"uri_format": "https://w3id.org/semapv/vocab/$1"
},
+ "semion": {
+ "description": "identifier of an author or reviewer, in Semion",
+ "example": "22132778",
+ "homepage": "https://www.semion.io",
+ "mappings": {
+ "wikidata": "P7671"
+ },
+ "name": "Semion author ID",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "semion",
+ "uri_format": "https://www.semion.io/Author/$1"
+ },
"senso": {
"contact": {
"email": "brycemecum@gmail.com",
@@ -49817,6 +52496,13 @@
"download_rdf": "https://raw.githubusercontent.com/saidfathalla/SEOontology/master/SEO.ttl",
"example": "Symposium",
"homepage": "https://w3id.org/seo",
+ "keywords": [
+ "academy",
+ "events"
+ ],
+ "mappings": {
+ "lov": "seo"
+ },
"name": "Scientific Event Ontology",
"preferred_prefix": "seo",
"uri_format": "https://w3id.org/seo#$1"
@@ -49824,9 +52510,7 @@
"sep": {
"contact": {
"email": "psidev-gps-dev@lists.sourceforge.net",
- "github": null,
- "name": "SEP developers via the PSI and MSI mailing lists",
- "orcid": null
+ "name": "SEP developers via the PSI and MSI mailing lists"
},
"deprecated": true,
"description": "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments.",
@@ -49893,7 +52577,7 @@
"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_$1",
- "version": "2023-02-21"
+ "version": "2023-06-13"
},
"sfam": {
"contributor": {
@@ -49910,6 +52594,7 @@
"protein families",
"selventa"
],
+ "license": "Apache-2.0",
"name": "Selventa Families",
"pattern": "^F\\d{4}$",
"preferred_prefix": "sfam",
@@ -49928,16 +52613,19 @@
"proteomics",
"transcriptomics"
],
+ "license": "CC-BY-4.0",
"mappings": {
"biocontext": "SGD",
"edam": "2632",
"fairsharing": "FAIRsharing.pzvw40",
"go": "SGD",
+ "integbio": "nbdc00202",
"miriam": "sgd",
"n2t": "sgd",
"ncbi": "SGD",
"prefixcommons": "sgd",
"re3data": "r3d100010419",
+ "togoid": "Sgd",
"uniprot": "DB-0095",
"wikidata": "P3406"
},
@@ -50004,7 +52692,6 @@
"year": 1997
},
{
- "doi": null,
"pmc": "PMC3057085",
"pubmed": "9169866",
"title": "Genetic and physical maps of Saccharomyces cerevisiae",
@@ -50018,8 +52705,6 @@
"year": 1997
},
{
- "doi": null,
- "pmc": null,
"pubmed": "7660459",
"title": "Genetic nomenclature guide. Saccharomyces cerevisiae",
"year": 1995
@@ -50250,7 +52935,6 @@
},
{
"doi": "10.1016/s0076-6879(02)50972-1",
- "pmc": null,
"pubmed": "12073322",
"title": "Saccharomyces Genome Database",
"year": 2002
@@ -50278,17 +52962,12 @@
},
{
"doi": "10.1002/9780470089941.et1104s01",
- "pmc": null,
- "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
+ "title": "Expanding yeast knowledge online."
}
],
"twitter": "yeastgenome",
@@ -50350,9 +53029,11 @@
"biocontext": "SGN",
"fairsharing": "FAIRsharing.3zqvaf",
"go": "SGN",
+ "integbio": "nbdc02414",
"miriam": "sgn",
"n2t": "sgn",
"ncbi": "SGN",
+ "pathguide": "433",
"prefixcommons": "sgn",
"re3data": "r3d100012078"
},
@@ -50408,10 +53089,14 @@
"informatics",
"knowledge and information systems",
"ontology",
- "ontology and terminology"
+ "ontology and terminology",
+ "quality",
+ "w3c rec"
],
"mappings": {
- "fairsharing": "FAIRsharing.f1449d"
+ "fairsharing": "FAIRsharing.f1449d",
+ "lov": "sh",
+ "zazuko": "sh"
},
"name": "Shapes Constraint Language",
"preferred_prefix": "sh",
@@ -50584,6 +53269,11 @@
"uri_format": "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"
},
"shex": {
+ "contact": {
+ "email": "gregg@greggkellogg.net",
+ "github": "gkellogg",
+ "name": "Gregg Kellogg"
+ },
"contributor": {
"email": "cthoyt@gmail.com",
"github": "cthoyt",
@@ -50591,6 +53281,7 @@
"orcid": "0000-0003-4423-4370"
},
"description": "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces.",
+ "download_rdf": "https://www.w3.org/ns/shex.ttl",
"example": "TripleExpression",
"homepage": "http://www.w3.org/ns/shex#",
"keywords": [
@@ -50598,8 +53289,13 @@
"rdf",
"semantic web"
],
+ "mappings": {
+ "zazuko": "shex"
+ },
"name": "Shape Expression Vocabulary",
+ "pattern": "^\\w+$",
"preferred_prefix": "shex",
+ "repository": "https://github.com/shexspec/shexspec.github.io",
"uri_format": "http://www.w3.org/ns/shex#$1"
},
"shibase": {
@@ -50636,7 +53332,6 @@
"sibo": {
"contact": {
"email": "cjmungall@lbl.gov",
- "github": null,
"name": "Chris Mungall",
"orcid": "0000-0002-6601-2165"
},
@@ -50715,6 +53410,9 @@
"life sciences",
"vendor"
],
+ "mappings": {
+ "pathguide": "236"
+ },
"name": "Sigma Aldrich",
"preferred_prefix": "sigmaaldrich",
"uri_format": "https://www.sigmaaldrich.com/US/en/product/sigma/$1"
@@ -50732,6 +53430,7 @@
"biocontext": "SIGNALING-GATEWAY",
"miriam": "signaling-gateway",
"n2t": "signaling-gateway",
+ "pathguide": "87",
"prefixcommons": "signaling-gateway"
},
"name": "Signaling Gateway",
@@ -50763,7 +53462,6 @@
},
{
"doi": "10.1038/nature01307",
- "pmc": null,
"pubmed": "12478304",
"title": "The Molecule Pages database",
"year": 2002
@@ -50774,7 +53472,6 @@
"signor": {
"contact": {
"email": "gianni.cesareni@torvergata.it",
- "github": null,
"name": "Gianni Cesareni",
"orcid": "0000-0002-9528-6018"
},
@@ -50784,15 +53481,24 @@
"keywords": [
"biology"
],
+ "license": "CC-BY-NC-4.0",
"mappings": {
"fairsharing": "FAIRsharing.ss78t4",
"miriam": "signor",
+ "pathguide": "599",
"uniprot": "DB-0206"
},
"name": "Signaling Network Open Resource",
"pattern": "^SIGNOR\\-[A-Z]+\\d+$",
"preferred_prefix": "signor",
"publications": [
+ {
+ "doi": "10.1093/nar/gkac883",
+ "pmc": "PMC9825604",
+ "pubmed": "36243968",
+ "title": "SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update",
+ "year": 2022
+ },
{
"doi": "10.1093/nar/gkv1048",
"pmc": "PMC4702784",
@@ -50845,6 +53551,8 @@
"example": "000912",
"homepage": "https://github.com/micheldumontier/semanticscience",
"keywords": [
+ "biology",
+ "knowledge representation",
"natural science",
"ontology",
"subject agnostic"
@@ -50856,6 +53564,7 @@
"biolink": "SIO",
"bioportal": "SIO",
"fairsharing": "FAIRsharing.dpkb5f",
+ "lov": "sio",
"miriam": "sio",
"ols": "sio",
"ontobee": "SIO"
@@ -50880,7 +53589,6 @@
"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"
},
@@ -50902,8 +53610,6 @@
"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
}
@@ -50919,7 +53625,6 @@
"sisu": {
"contact": {
"email": "hannele.laivuori@helsinki.fi",
- "github": null,
"name": "Hannele Laivuori",
"orcid": "0000-0003-3212-7826"
},
@@ -51045,18 +53750,22 @@
"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://www.w3.org/TR/skos-reference/skos.rdf",
+ "download_owl": "http://aber-owl.net/media/ontologies/skos/1/skos.owl",
+ "download_rdf": "http://www.w3.org/TR/skos-reference/skos.rdf",
"example": "prefLabel",
"homepage": "https://www.w3.org/2004/02/skos/",
"keywords": [
"ontology",
- "subject agnostic"
+ "subject agnostic",
+ "w3c rec"
],
"mappings": {
"aberowl": "skos",
"biocontext": "skos",
"fairsharing": "FAIRsharing.48e326",
- "ols": "skos"
+ "lov": "skos",
+ "ols": "skos",
+ "zazuko": "skos"
},
"name": "Simple Knowledge Organization System",
"preferred_prefix": "skos",
@@ -51076,8 +53785,13 @@
"data model",
"metadata",
"semantic web",
- "skos"
+ "skos",
+ "w3c rec"
],
+ "mappings": {
+ "lov": "skosxl",
+ "zazuko": "skosxl"
+ },
"name": "Simple Knowledge Organization System eXtension for Labels",
"preferred_prefix": "skosxl",
"uri_format": "http://www.w3.org/2008/05/skos-xl#$1"
@@ -51116,26 +53830,27 @@
"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",
+ "download_rdf": "file:///nfs/production/parkinso/spot/ols4/prod/local_ontologies/swisslipids.ttl",
"example": "000000341",
"homepage": "http://www.swisslipids.org/#/",
"keywords": [
"life science",
- "metabolomics",
- "ontology"
+ "metabolomics"
],
"mappings": {
"biocontext": "SWISSLIPID",
"fairsharing": "FAIRsharing.pxr7x2",
+ "integbio": "nbdc02026",
"miriam": "slm",
"n2t": "swisslipid",
"ols": "slm",
+ "pathguide": "687",
"re3data": "r3d100012603",
+ "togoid": "Swisslipids",
"uniprot": "DB-0197",
"wikidata": "P8691"
},
@@ -51158,6 +53873,36 @@
],
"uri_format": "https://www.swisslipids.org/#/entity/SLM:$1"
},
+ "slso": {
+ "contact": {
+ "email": "daniel.c.berrios@nasa.gov",
+ "github": "DanBerrios",
+ "name": "Dan Berrios",
+ "orcid": "0000-0003-4312-9552"
+ },
+ "description": "The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.",
+ "download_json": "http://purl.obolibrary.org/obo/slso.json",
+ "download_obo": "http://purl.obolibrary.org/obo/slso.obo",
+ "download_owl": "http://purl.obolibrary.org/obo/slso.owl",
+ "example": "0000000",
+ "homepage": "https://github.com/nasa/LSDAO",
+ "keywords": [
+ "obo",
+ "ontology"
+ ],
+ "license": "CC-BY-3.0",
+ "mappings": {
+ "aberowl": "SLSO",
+ "bioportal": "SLSO",
+ "obofoundry": "slso",
+ "ontobee": "SLSO"
+ },
+ "name": "Space Life Sciences Ontology",
+ "preferred_prefix": "SLSO",
+ "rdf_uri_format": "http://purl.obolibrary.org/obo/SLSO_$1",
+ "repository": "https://github.com/nasa/LSDAO",
+ "uri_format": "http://purl.obolibrary.org/obo/SLSO_$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",
@@ -51172,9 +53917,11 @@
"biocontext": "SMART",
"fairsharing": "FAIRsharing.hsbpq3",
"go": "SMART",
+ "integbio": "nbdc00682",
"miriam": "smart",
"n2t": "smart",
"prefixcommons": "smart",
+ "togoid": "Smart",
"uniprot": "DB-0097"
},
"name": "Simple Modular Architecture Research Tool",
@@ -51255,17 +54002,13 @@
},
{
"doi": "10.1016/s0959-440x(99)80055-4",
- "pmc": null,
"pubmed": "10361098",
"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
+ "title": "Protein families in multicellular organisms."
}
],
"uri_format": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"
@@ -51292,8 +54035,7 @@
"contact": {
"email": "tim.vandermeersch@gmail.com",
"github": "timvdm",
- "name": "Tim Vandermeersch",
- "orcid": null
+ "name": "Tim Vandermeersch"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -51301,6 +54043,13 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
+ "contributor_extras": [
+ {
+ "github": "NishaSharma14",
+ "name": "Nisha Sharma",
+ "orcid": "0009-0006-4755-1039"
+ }
+ ],
"description": "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.",
"example": "CC2(C)C\\1CCC(C)/C=C/12",
"homepage": "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html",
@@ -51315,6 +54064,92 @@
"name": "Simplified molecular-input line-entry system",
"pattern": "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$",
"preferred_prefix": "smiles",
+ "providers": [
+ {
+ "code": "cms.canonicalize",
+ "description": "Canonicalizes a given SMILES string according to the allowed toolkits.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_Canonicalise_convert_canonicalsmiles_get",
+ "name": "Canonicalizes a SMILES via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/canonicalsmiles?smiles=$1"
+ },
+ {
+ "code": "cms.convert",
+ "description": "Convert SMILES to various molecular formats using different toolkits.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_convert_to_Formats_convert_formats_get",
+ "name": "Convert SMILES to various molecular formats via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/formats?smiles=$1"
+ },
+ {
+ "code": "cms.coordinates2d",
+ "description": "Generates 2D Coordinates using the CDK Structure diagram generator/RDKit/Open Babel and returns the mol block.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/Create2D_Coordinates_convert_mol2D_get",
+ "name": "Generate 2D coordinates via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/mol2D?smiles=$1"
+ },
+ {
+ "code": "cms.coordinates3d",
+ "description": "Generates a random 3D conformer from SMILES using the specified molecule toolkit.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/Create3D_Coordinates_convert_mol3D_get",
+ "name": "Generate 3D conformer via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/mol3D?smiles=$1"
+ },
+ {
+ "code": "cms.cxsmiles",
+ "description": "Convert SMILES to CXSMILES. For more informations.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_CXSMILES_convert_cxsmiles_get",
+ "name": "Convert SMILES to CXSMILES via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/cxsmiles?smiles=$1"
+ },
+ {
+ "code": "cms.depict2d",
+ "description": "Generates a 2D depiction of a molecule using CDK or RDKit with the given parameters.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/depict/Depict2D_molecule_depict_2D_get",
+ "name": "Depict 2D via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/depict/2D?smiles=$1"
+ },
+ {
+ "code": "cms.depict3d",
+ "description": "Generate 3D depictions of molecules using OpenBabel or RDKit.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/depict/Depict3D_Molecule_depict_3D_get",
+ "name": "Depict 3D via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/depict/3D?smiles=$1"
+ },
+ {
+ "code": "cms.descriptor",
+ "description": "Returns descriptors calculated from the molecule with RDKit",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/chem/get_descriptors_chem_descriptors_get",
+ "name": "RDKit Descriptor via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/chem/descriptors?smiles=$1"
+ },
+ {
+ "code": "cms.inchi",
+ "description": "Convert SMILES to InChI.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChI_convert_inchi_get",
+ "name": "Convert SMILES to InChI via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/inchi?smiles=$1"
+ },
+ {
+ "code": "cms.inchikey",
+ "description": "Convert SMILES to InChIKey.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_InChIKey_convert_inchikey_get",
+ "name": "Convert SMILES to InChIKey via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/inchikey?smiles=$1"
+ },
+ {
+ "code": "cms.iupac",
+ "description": "Generates IUPAC name for given SMILES using [STOUT](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00512-4) package.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/SMILES_to_IUPACname_convert_iupac_get",
+ "name": "Generate IUPAC name from SMILES via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/iupac?smiles=$1"
+ },
+ {
+ "code": "cms.selfies",
+ "description": "Generates SELFIES string for a given SMILES string.",
+ "homepage": "https://api.naturalproducts.net/latest/docs#/convert/encode_SELFIES_convert_selfies_get",
+ "name": "Generates SELFIES for a SMILES via the Cheminformatics Microservice",
+ "uri_format": "https://api.naturalproducts.net/latest/convert/selfies?smiles=$1"
+ }
+ ],
"publications": [
{
"doi": "10.1186/1758-2946-4-24",
@@ -51325,28 +54160,25 @@
},
{
"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
}
],
+ "references": [
+ "https://github.com/biopragmatics/bioregistry/issues/931"
+ ],
"repository": "https://github.com/timvdm/OpenSMILES/blob/master/discussion_summary.txt",
- "uri_format": "https://chemapps.stolaf.edu/jmol/jmol.php?model=$1"
+ "uri_format": "https://www.simolecule.com/cdkdepict/depict/bow/svg?smi=$1&zoom=2.0&annotate=cip"
},
"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.",
@@ -51364,8 +54196,10 @@
"biolink": "PathWhiz",
"edam": "2659",
"fairsharing": "FAIRsharing.y1zyaq",
+ "integbio": "nbdc00908",
"miriam": "smpdb",
"n2t": "smpdb",
+ "pathguide": "311",
"prefixcommons": "smpdb"
},
"name": "Small Molecule Pathway Database",
@@ -51397,10 +54231,7 @@
},
{
"doi": "doi:10.1093/nar/gkp1002",
- "pmc": null,
- "pubmed": null,
- "title": "SMPDB: The Small Molecule Pathway Database.",
- "year": null
+ "title": "SMPDB: The Small Molecule Pathway Database."
}
],
"synonyms": [
@@ -51426,6 +54257,7 @@
"protein"
],
"mappings": {
+ "pathguide": "494",
"prefixcommons": "snap"
},
"name": "Snapshot",
@@ -51441,12 +54273,24 @@
],
"uri_format": "http://www.ifomis.org/bfo/1.1/snap#$1"
},
+ "snctp": {
+ "comment": "it appears they cede information into WHO",
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]",
+ "example": "SNCTP000005580",
+ "homepage": "https://kofam.ch/en/snctp-portal",
+ "name": "Swiss National Clinical Trials Portal",
+ "preferred_prefix": "snctp"
+ },
"snomedct": {
"contact": {
- "email": "custserv@nlm.nih.gov",
- "github": null,
- "name": "NLM Customer Service",
- "orcid": null
+ "email": "willisj@mail.nlm.nih.gov",
+ "name": "Jan Willis, NLM"
},
"contributor_extras": [
{
@@ -51467,6 +54311,7 @@
"ontology",
"preclinical studies"
],
+ "license": "https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf",
"mappings": {
"aberowl": "SNOMEDCT",
"biocontext": "SNOMEDCT",
@@ -51495,7 +54340,6 @@
"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
@@ -51530,6 +54374,10 @@
"SNOMEDCT_US_2022_09_01",
"SNOMEDCT_US_2022_12_31",
"SNOMEDCT_US_2023_02_28",
+ "SNOMEDCT_US_2023_03_01",
+ "SNOMEDCT_US_2023_09_01",
+ "SNOMEDCT_US_2023_10_01",
+ "SNOMEDCT_US_2023_11_01",
"SNOMED_CT",
"SNOMED_CT_US_2018_03_01",
"SNOWMEDCT",
@@ -51553,6 +54401,7 @@
"rna"
],
"mappings": {
+ "integbio": "nbdc00323",
"prefixcommons": "snornalbmedb"
},
"name": "snoRNABase",
@@ -51631,11 +54480,18 @@
"keywords": [
"bioinformatics",
"biology",
+ "deoxyribonucleic acid",
"dna",
+ "gene",
+ "genome",
"life science",
"obo",
"ontology",
+ "ribonucleic acid",
"rna",
+ "sequence",
+ "sequence annotation",
+ "sequence feature",
"structure"
],
"license": "CC-BY-4.0",
@@ -51692,13 +54548,12 @@
],
"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"
+ "uri_format": "http://purl.obolibrary.org/obo/SO_$1",
+ "version": "2024-04-10"
},
"sopharm": {
"contact": {
"email": "adrien.coulet@loria.fr",
- "github": null,
"name": "Adrien Coulet",
"orcid": "0000-0002-1466-062X"
},
@@ -51724,7 +54579,6 @@
"soybase": {
"contact": {
"email": "Jacqueline.Campbell@usda.gov",
- "github": null,
"name": "Jacqueline Campbell",
"orcid": "0000-0003-2787-3955"
},
@@ -51744,9 +54598,11 @@
"mappings": {
"biocontext": "SOYBASE",
"fairsharing": "FAIRsharing.z4agsr",
+ "integbio": "nbdc01817",
"miriam": "soybase",
"n2t": "soybase",
"ncbi": "SoyBase",
+ "pathguide": "44",
"prefixcommons": "soy",
"re3data": "r3d100010846"
},
@@ -51803,6 +54659,7 @@
"rna"
],
"mappings": {
+ "integbio": "nbdc00686",
"prefixcommons": "spbase"
},
"name": "SpBase",
@@ -51838,6 +54695,7 @@
"homepage": "http://research.amnh.org/atol/files/",
"keywords": [
"anatomy",
+ "behavior",
"life science",
"obo",
"ontology",
@@ -51870,16 +54728,13 @@
"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
}
],
"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": "1.0"
+ "uri_format": "http://purl.obolibrary.org/obo/SPD_$1"
},
"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.",
@@ -51897,7 +54752,6 @@
"sphn": {
"contact": {
"email": "Sabine.Oesterle@sib.swiss",
- "github": null,
"name": "Sabine Oesterle",
"orcid": "0000-0003-3248-7899"
},
@@ -52024,7 +54878,6 @@
"spp": {
"contact": {
"email": "nmckenna@bcm.edu",
- "github": null,
"name": "Neil McKenna",
"orcid": "0000-0001-6689-0104"
},
@@ -52069,14 +54922,18 @@
"keywords": [
"agriculture",
"biomedical science",
+ "classification",
"computer science",
"earth science",
"environmental science",
+ "fair",
"humanities",
"life science",
+ "metadata standardization",
"metascience",
"natural science",
"ontology",
+ "resource metadata",
"topics"
],
"mappings": {
@@ -52090,7 +54947,7 @@
"repository": "https://github.com/FAIRsharing/subject-ontology",
"twitter": "FAIRsharing_org",
"uri_format": "http://www.fairsharing.org/ontology/subject/SRAO_$1",
- "version": "0.3.0"
+ "version": "2023-10-10"
},
"ssbd.dataset": {
"contributor": {
@@ -52154,11 +55011,14 @@
},
"description": "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace.",
"example": "mapping_justification",
+ "example_extras": [
+ "superClassOf"
+ ],
"github_request_issue": 759,
"homepage": "https://w3id.org/sssom",
"license": "BSD-3-Clause",
"name": "Simple Standard for Sharing Ontological Mappings",
- "pattern": "^[a-z_]+$",
+ "pattern": "^[A-Za-z_]+$",
"preferred_prefix": "sssom",
"repository": "https://github.com/mapping-commons/sssom",
"reviewer": {
@@ -52221,7 +55081,6 @@
"publications": [
{
"doi": "10.1093/bioinformatics/btv595",
- "pmc": null,
"pubmed": "26504145",
"title": "NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores",
"year": 2015
@@ -52235,7 +55094,6 @@
},
{
"doi": "10.1002/prot.24265",
- "pmc": null,
"pubmed": "23408564",
"title": "Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach",
"year": 2013
@@ -52256,6 +55114,7 @@
"psdo",
"scdo"
],
+ "banana": "STATO",
"contact": {
"email": "alejandra.gonzalez.beltran@gmail.com",
"github": "agbeltran",
@@ -52268,9 +55127,13 @@
"homepage": "http://stato-ontology.org/",
"keywords": [
"data visualization",
+ "experimental measurement",
+ "graph",
"obo",
"ontology",
- "statistics"
+ "protocol",
+ "statistics",
+ "study design"
],
"license": "CC-BY-3.0",
"logo": "https://raw.githubusercontent.com/ISA-tools/stato/dev/images/stato-logo-3.png",
@@ -52279,11 +55142,13 @@
"biocontext": "STATO",
"bioportal": "STATO",
"fairsharing": "FAIRsharing.na5xp",
+ "miriam": "stato",
"obofoundry": "stato",
"ols": "stato",
"ontobee": "STATO"
},
"name": "The Statistical Methods Ontology",
+ "namespace_in_lui": true,
"pattern": "^\\d{7}$",
"preferred_prefix": "STATO",
"rdf_uri_format": "http://purl.obolibrary.org/obo/STATO_$1",
@@ -52306,7 +55171,9 @@
"fairsharing": "FAIRsharing.zhwa8x",
"miriam": "stitch",
"n2t": "stitch",
- "prefixcommons": "stitch"
+ "pathguide": "313",
+ "prefixcommons": "stitch",
+ "re3data": "r3d100012165"
},
"name": "Search Tool for Interactions of Chemicals",
"pattern": "^\\w{14}$",
@@ -52352,11 +55219,23 @@
],
"uri_format": "http://stitch.embl.de/interactions/$1"
},
+ "stn": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "The pre-IND tracking number for submissions to the FDA",
+ "example": "125768",
+ "homepage": "https://www.fda.gov/media/128698/download",
+ "name": "FDA Submission Tracking Number",
+ "preferred_prefix": "stn"
+ },
"storedb": {
"banana": "STOREDB",
"contact": {
"email": "PNS12@cam.ac.uk",
- "github": null,
"name": "Dr Paul Schofield",
"orcid": "0000-0002-5111-7263"
},
@@ -52373,6 +55252,7 @@
"mappings": {
"biocontext": "STOREDB",
"fairsharing": "FAIRsharing.6h8d2r",
+ "integbio": "nbdc02191",
"miriam": "storedb",
"n2t": "storedb",
"re3data": "r3d100011049"
@@ -52445,7 +55325,6 @@
"string": {
"contact": {
"email": "bork@embl.de",
- "github": null,
"name": "Peer Bork",
"orcid": "0000-0002-2627-833X"
},
@@ -52462,8 +55341,10 @@
"biocontext": "STRING",
"edam": "2302",
"fairsharing": "FAIRsharing.9b7wvk",
+ "integbio": "nbdc00690",
"miriam": "string",
"n2t": "string",
+ "pathguide": "93",
"prefixcommons": "string",
"re3data": "r3d100010604",
"uniprot": "DB-0141"
@@ -52537,9 +55418,7 @@
"sty": {
"contact": {
"email": "support@bioontology.org",
- "github": null,
- "name": "bioportal",
- "orcid": null
+ "name": "bioportal"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -52642,6 +55521,7 @@
"mappings": {
"biocontext": "SUBTIWIKI",
"fairsharing": "FAIRsharing.2ck3st",
+ "integbio": "nbdc00693",
"miriam": "subtiwiki",
"n2t": "subtiwiki",
"prefixcommons": "subtiwiki"
@@ -52675,7 +55555,6 @@
},
{
"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
@@ -52686,11 +55565,11 @@
"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.",
+ "download_owl": "http://aber-owl.net/media/ontologies/SUGARBIND/1/sugarbind.owl",
"example": "lectins/172",
"homepage": "http://sugarbind.expasy.org/",
"keywords": [
@@ -52699,9 +55578,11 @@
"ontology"
],
"mappings": {
+ "aberowl": "SUGARBIND",
"biocontext": "SUGARBIND",
"bioportal": "SUGARBIND",
"fairsharing": "FAIRsharing.d064y6",
+ "integbio": "nbdc02224",
"miriam": "sugarbind",
"n2t": "sugarbind"
},
@@ -52718,8 +55599,6 @@
},
{
"doi": "10.1007/978-4-431-56454-6_13",
- "pmc": null,
- "pubmed": null,
"title": "SugarBindDB",
"year": 2016
}
@@ -52757,9 +55636,12 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gky1130",
+ "pubmed": "30445555"
+ },
{
"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
@@ -52807,7 +55689,6 @@
"swiss-model": {
"contact": {
"email": "help-swissmodel@unibas.ch",
- "github": null,
"name": "Torsten Schwede",
"orcid": "0000-0003-2715-335X"
},
@@ -52870,7 +55751,6 @@
"swissregulon": {
"contact": {
"email": "erik.vannimwegen@unibas.ch",
- "github": null,
"name": "Erik van Nimwegen",
"orcid": "0000-0001-6338-1312"
},
@@ -52883,6 +55763,7 @@
"mappings": {
"biocontext": "SWISSREGULON",
"fairsharing": "FAIRsharing.7fnx38",
+ "integbio": "nbdc02225",
"miriam": "swissregulon",
"n2t": "swissregulon"
},
@@ -52908,6 +55789,9 @@
"uri_format": "http://swissregulon.unibas.ch/query/$1"
},
"swo": {
+ "appears_in": [
+ "mcro"
+ ],
"contact": {
"email": "allyson.lister@oerc.ox.ac.uk",
"github": "allysonlister",
@@ -52921,10 +55805,13 @@
"example": "0000144",
"homepage": "https://github.com/allysonlister/swo",
"keywords": [
+ "algorithm",
"bioinformatics",
"computer science",
"obo",
- "ontology"
+ "ontology",
+ "software",
+ "workflow"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -53008,6 +55895,12 @@
"description": "SWRL enables Horn-like rules to be combined with an OWL knowledge base.",
"example": "Variable",
"homepage": "https://www.w3.org/2003/11/swrl#",
+ "keywords": [
+ "vocabularies"
+ ],
+ "mappings": {
+ "lov": "swrl"
+ },
"name": "A Semantic Web Rule Language Combining OWL and RuleML",
"preferred_prefix": "swrl",
"uri_format": "http://www.w3.org/2003/11/swrl#$1"
@@ -53030,10 +55923,13 @@
"homepage": "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page",
"keywords": [
"biomedical science",
+ "diagnosis",
+ "disease",
"life science",
"obo",
"ontology",
- "pain medicine"
+ "pain medicine",
+ "patient care"
],
"license": "CC0-1.0",
"mappings": {
@@ -53080,8 +55976,22 @@
"synonyms": [
"SYMP"
],
- "uri_format": "https://www.ebi.ac.uk/ols/ontologies/symp/terms?iri=http://purl.obolibrary.org/obo/SYMP_$1",
- "version": "2022-11-30"
+ "uri_format": "http://purl.obolibrary.org/obo/SYMP_$1",
+ "version": "2024-02-09"
+ },
+ "synapse": {
+ "description": "Synapse is a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate.",
+ "example": "41455251.1",
+ "homepage": "https://sagebionetworks.org",
+ "mappings": {
+ "integbio": "nbdc02162",
+ "miriam": "synapse",
+ "re3data": "r3d100011894"
+ },
+ "name": "Synapse Data Repository",
+ "pattern": "^[0-9]*\\.*[0-9]*$",
+ "preferred_prefix": "synapse",
+ "uri_format": "https://repo-prod.prod.sagebase.org/ga4gh/drs/v1/objects/syn$1"
},
"syoid": {
"contributor": {
@@ -53100,7 +56010,6 @@
"t3db": {
"contact": {
"email": "david.wishart@ualberta.ca",
- "github": null,
"name": "David Wishart",
"orcid": "0000-0002-3207-2434"
},
@@ -53119,6 +56028,7 @@
"fairsharing": "FAIRsharing.psn0h2",
"miriam": "t3db",
"n2t": "t3db",
+ "pathguide": "326",
"prefixcommons": "t3db",
"re3data": "r3d100012189"
},
@@ -53172,11 +56082,15 @@
"example": "0000127",
"homepage": "https://github.com/terms4fairskills/FAIRterminology",
"keywords": [
+ "curated information",
+ "digital curation",
+ "fair",
"obo",
"ontology",
"subject agnostic"
],
"license": "CC-BY-4.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBZ1VDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--692c3b4cc5ea2f7aa8cc80267dad833f16dcccbb/terms4FAIRskills.png?disposition=inline",
"mappings": {
"aberowl": "T4FS",
"fairsharing": "FAIRsharing.fb99fa",
@@ -53190,15 +56104,11 @@
"publications": [
{
"doi": "10.5281/zenodo.4772741",
- "pmc": null,
- "pubmed": null,
"title": "EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report",
"year": 2021
},
{
"doi": "10.5281/zenodo.4705219",
- "pmc": null,
- "pubmed": null,
"title": "EOSC Co-creation funded project 074: Delivery of a proof of concept for terms4FAIRskills: Technical report",
"year": 2021
}
@@ -53211,7 +56121,6 @@
"tads": {
"contact": {
"email": "dsonensh@odu.edu",
- "github": null,
"name": "Daniel Sonenshine",
"orcid": "0000-0001-9370-918X"
},
@@ -53243,7 +56152,6 @@
"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
@@ -53257,9 +56165,7 @@
"tahe": {
"contact": {
"email": "pierre.sprumont@unifr.ch",
- "github": null,
- "name": "Pierre Sprumont",
- "orcid": null
+ "name": "Pierre Sprumont"
},
"deprecated": true,
"keywords": [
@@ -53278,9 +56184,7 @@
"tahh": {
"contact": {
"email": "pierre.sprumont@unifr.ch",
- "github": null,
- "name": "Pierre Sprumont",
- "orcid": null
+ "name": "Pierre Sprumont"
},
"deprecated": true,
"keywords": [
@@ -53327,7 +56231,6 @@
"publications": [
{
"doi": "10.1007/s10142-002-0077-z",
- "pmc": null,
"pubmed": "12444417",
"title": "TAIR: a resource for integrated Arabidopsis data",
"year": 2002
@@ -53380,7 +56283,6 @@
"publications": [
{
"doi": "10.1007/s10142-002-0077-z",
- "pmc": null,
"pubmed": "12444417",
"title": "TAIR: a resource for integrated Arabidopsis data",
"year": 2002
@@ -53418,7 +56320,6 @@
"publications": [
{
"doi": "10.1007/s10142-002-0077-z",
- "pmc": null,
"pubmed": "12444417",
"title": "TAIR: a resource for integrated Arabidopsis data",
"year": 2002
@@ -53429,7 +56330,6 @@
"tao": {
"contact": {
"email": "wasila.dahdul@usd.edu",
- "github": null,
"name": "Wasila Dahdul",
"orcid": "0000-0003-3162-7490"
},
@@ -53493,8 +56393,10 @@
"mappings": {
"biocontext": "TARBASE",
"fairsharing": "FAIRsharing.a0k4cd",
+ "integbio": "nbdc02102",
"miriam": "tarbase",
- "n2t": "tarbase"
+ "n2t": "tarbase",
+ "pathguide": "283"
},
"name": "TarBase",
"pattern": "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$",
@@ -53547,11 +56449,13 @@
"life science",
"obo",
"ontology",
+ "taxonomic classification",
"taxonomy"
],
"license": "CC0-1.0",
"mappings": {
"aberowl": "TAXRANK",
+ "agroportal": "TAXRANK",
"biocontext": "TAXRANK",
"bioportal": "TAXRANK",
"fairsharing": "FAIRsharing.p1sejz",
@@ -53634,7 +56538,6 @@
"tcdb": {
"contact": {
"email": "msaier@ucsd.edu",
- "github": null,
"name": "Milton H. Saier, Jr.",
"orcid": "0000-0001-5530-0017"
},
@@ -53657,6 +56560,7 @@
"go": "TC",
"miriam": "tcdb",
"n2t": "tcdb",
+ "pathguide": "104",
"prefixcommons": "tcdb",
"uniprot": "DB-0135",
"wikidata": "P7260"
@@ -53695,20 +56599,6 @@
"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",
- "pubmed": "19022853",
- "title": null,
- "year": null
- },
{
"doi": "10.1093/nar/gkn862",
"pmc": "PMC2686586",
@@ -53774,13 +56664,19 @@
"example": "2.1.1",
"homepage": "http://tfclass.bioinf.med.uni-goettingen.de",
"keywords": [
+ "binding",
+ "binding site",
"bioinformatics",
+ "expression data",
"phylogenetics",
+ "transcription factor",
+ "transcription factor binding site prediction",
"transcriptomics"
],
"mappings": {
"fairsharing": "FAIRsharing.XykycZ",
- "go": "TFClass"
+ "go": "TFClass",
+ "pathguide": "666"
},
"name": "Classification of Transcription Factors in Mammalia",
"preferred_prefix": "tfclass",
@@ -53826,7 +56722,6 @@
"tgma": {
"contact": {
"email": "topalis@imbb.forth.gr",
- "github": null,
"name": "Pantelis Topalis",
"orcid": "0000-0002-1635-4810"
},
@@ -53869,7 +56764,6 @@
"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
@@ -53888,6 +56782,7 @@
"orcid": "0000-0003-4423-4370"
},
"deprecated": true,
+ "description": "TGN is a structured vocabulary currently containing around 1,106,000 names and other information about places. Names for a place may include names in the vernacular language, English, other languages, historical names, names and in natural order and inverted order. Among these names, one is flagged as the preferred name. TGN is a thesaurus, compliant with ISO and NISO standards for thesaurus construction; it contains hierarchical, equivalence, and associative relationships. Note that TGN is not a GIS (Geographic Information System). While many records in TGN include coordinates, these coordinates are approximate and are intended for reference only. The focus of each TGN record is a place. There are around 912,000 places in the TGN. In the database, each place record (also called a subject) is identified by a unique numeric ID. Linked to the record for the place are names, the place's parent or position in the hierarchy, other relationships, geographic coordinates, notes, sources for the data, and place types, which are terms describing the role of the place (e.g., inhabited place and state capital). The temporal coverage of the TGN ranges from prehistory to the present and the scope is global. The TGN is a hierarchical database; its trees branch from a root called Top of the TGN hierarchies (Subject_ID: 1000000). Currently there are two TGN facets, World and Extraterrestrial Places. Under the facet World, places are arranged in hierarchies generally representing the current political and physical world, although some historical nations and empires are also included. There may be multiple broader contexts, making the TGN polyhierarchical. The primary users of the Getty vocabularies include museums, art libraries, archives, visual resource collection catalogers, bibliographic projects concerned with art, researchers in art and art history, and the information specialists who are dealing with the needs of these users. In addition, a significant number of users of the Getty vocabularies are students or members of the general public.",
"example": "1023371",
"homepage": "https://www.getty.edu/research/tools/vocabularies/tgn/",
"mappings": {
@@ -54004,13 +56899,20 @@
"github_request_issue": 505,
"homepage": "https://www.w3.org/TR/owl-time/",
"keywords": [
+ "data coordination",
+ "data model",
+ "metadata standardization",
"ontology",
- "subject agnostic"
+ "resource metadata",
+ "subject agnostic",
+ "time"
],
"mappings": {
"aberowl": "TIME",
"bioportal": "TIME",
- "fairsharing": "FAIRsharing.hw3bh2"
+ "fairsharing": "FAIRsharing.hw3bh2",
+ "lov": "time",
+ "zazuko": "time"
},
"name": "Time Ontology in OWL",
"preferred_prefix": "time",
@@ -54036,7 +56938,7 @@
"uri_format": "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"
},
"tngb": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "67035",
"homepage": "http://biobanknetwork.telethon.it/",
"mappings": {
@@ -54064,9 +56966,12 @@
"homepage": "http://browser.planteome.org/amigo",
"keywords": [
"botany",
+ "life cycle",
"obo",
"ontology",
+ "phenotype",
"plant",
+ "structure",
"trait"
],
"license": "CC-BY-4.0",
@@ -54106,14 +57011,48 @@
"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"
+ "version": "2023-07-17"
+ },
+ "togoid": {
+ "contact": {
+ "email": "ktym@dbcls.jp",
+ "github": "ktym",
+ "name": "Toshiaki Katayama",
+ "orcid": "0000-0003-2391-0384"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "TogoID is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. (from https://togoid.dbcls.jp/)",
+ "download_rdf": "https://raw.githubusercontent.com/togoid/togoid-config/main/ontology/togoid-ontology.ttl",
+ "example": "AffyProbeset",
+ "homepage": "https://togoid.dbcls.jp/ontology",
+ "name": "TogoID Ontology",
+ "preferred_prefix": "togoid",
+ "publications": [
+ {
+ "doi": "10.1093/bioinformatics/btac491",
+ "pmc": "PMC9438948",
+ "pubmed": "35801937",
+ "title": "TogoID: an exploratory ID converter to bridge biological datasets",
+ "year": 2022
+ }
+ ],
+ "rdf_uri_format": "https://togoid.dbcls.jp/ontology#$1",
+ "repository": "https://github.com/dbcls/togoid/togoid-config",
+ "uri_format": "https://togoid.dbcls.jp/#$1"
},
"togovar": {
"description": "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.",
"example": "tgv139393198",
"homepage": "https://grch38.togovar.org/",
"mappings": {
- "miriam": "togovar"
+ "integbio": "nbdc02359",
+ "miriam": "togovar",
+ "togoid": "Togovar"
},
"name": "TogoVar",
"pattern": "^tgv[0-9]+$",
@@ -54221,7 +57160,6 @@
},
{
"doi": "10.1038/nmeth.1669",
- "pmc": null,
"pubmed": "21822272",
"title": "TopFIND, a knowledgebase linking protein termini with function",
"year": 2011
@@ -54313,6 +57251,7 @@
"protein"
],
"mappings": {
+ "pathguide": "105",
"prefixcommons": "transportdb"
},
"name": "TransportDB",
@@ -54357,6 +57296,7 @@
"regulation"
],
"mappings": {
+ "pathguide": "167",
"prefixcommons": "tred"
},
"name": "Transcriptional Regulatory Element Database",
@@ -54396,6 +57336,7 @@
"mappings": {
"biocontext": "TREEBASE",
"fairsharing": "FAIRsharing.zcn4w4",
+ "integbio": "nbdc01882",
"miriam": "treebase",
"n2t": "treebase",
"prefixcommons": "treebase",
@@ -54436,6 +57377,7 @@
],
"mappings": {
"biocontext": "TREEFAM",
+ "integbio": "nbdc01596",
"miriam": "treefam",
"n2t": "treefam",
"prefixcommons": "treefam",
@@ -54464,10 +57406,21 @@
],
"uri_format": "http://www.treefam.org/family/$1"
},
+ "tricdb": {
+ "description": "Tri©DB is a newly developed integrated platform functioning as a knowledge base and reporting system for cancer precision medicine. This platform harmonizes and mines cancer-related data from various aspects, presenting them on a centralized platform with enhanced accessibility, rich annotations, and robust analysis capabilities. The development of Tri©DB is aimed at meeting the needs of a broad range of researchers, thereby propelling both foundational and translational research in cancer precision medicine.",
+ "example": "1eec8393-e598-41ed-9d8b-6d5b0db94470",
+ "homepage": "http://www.biomeddb.org/",
+ "mappings": {
+ "miriam": "tricdb"
+ },
+ "name": "tricdb",
+ "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$",
+ "preferred_prefix": "tricdb",
+ "uri_format": "http://biomeddb.org/Disease/Details?DISEASEID=$1"
+ },
"trichdb": {
"contact": {
"email": "oharb@pcbi.upenn.edu",
- "github": null,
"name": "Omar Harb",
"orcid": "0000-0003-4446-6200"
},
@@ -54480,6 +57433,7 @@
"mappings": {
"biocontext": "TRICHDB",
"fairsharing": "FAIRsharing.pv0ezt",
+ "integbio": "nbdc01785",
"miriam": "trichdb",
"n2t": "trichdb",
"re3data": "r3d100012461"
@@ -54502,7 +57456,6 @@
"tritrypdb": {
"contact": {
"email": "oharb@pcbi.upenn.edu",
- "github": null,
"name": "Omar Harb",
"orcid": "0000-0003-4446-6200"
},
@@ -54518,6 +57471,7 @@
"biocontext": "TRITRYPDB",
"fairsharing": "FAIRsharing.fs1z27",
"go": "TriTrypDB",
+ "integbio": "nbdc01786",
"miriam": "tritrypdb",
"n2t": "tritrypdb",
"re3data": "r3d100011479"
@@ -54549,6 +57503,7 @@
"rna"
],
"mappings": {
+ "integbio": "nbdc00720",
"prefixcommons": "trnadbce"
},
"name": "tRNA Gene Database",
@@ -54571,6 +57526,32 @@
},
"uri_format": "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"
},
+ "tsc": {
+ "description": "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]",
+ "example": "SD00043",
+ "homepage": "https://tetrahymena.vet.cornell.edu/",
+ "keywords": [
+ "biology",
+ "cell",
+ "cellular",
+ "culture",
+ "eukaryota",
+ "genetics",
+ "model",
+ "molecular",
+ "protozoan",
+ "repository",
+ "research",
+ "tetrahymena thermophila"
+ ],
+ "mappings": {
+ "rrid": "TSC"
+ },
+ "name": "Tetrahymena Stock Center",
+ "pattern": "^SD\\d+$",
+ "preferred_prefix": "tsc",
+ "uri_format": "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1"
+ },
"ttd.drug": {
"description": "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target.",
"example": "DAP000773",
@@ -54618,7 +57599,8 @@
"life science",
"obo",
"ontology",
- "phenotype"
+ "phenotype",
+ "taxonomic classification"
],
"license": "CC0-1.0",
"mappings": {
@@ -54646,8 +57628,6 @@
"publications": [
{
"doi": "10.1038/npre.2010.4629.1",
- "pmc": null,
- "pubmed": null,
"title": "The Teleost Taxonomy Ontology",
"year": 2010
}
@@ -54733,10 +57713,18 @@
"orcid": "0000-0002-6601-2165"
},
"depends_on": [
+ "bfo",
+ "bspo",
"chebi",
"cl",
+ "envo",
"go",
- "pr"
+ "nbo",
+ "ncbitaxon",
+ "omo",
+ "pato",
+ "pr",
+ "ro"
],
"description": "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.",
"download_json": "http://purl.obolibrary.org/obo/uberon.json",
@@ -54766,6 +57754,7 @@
"obofoundry": "uberon",
"ols": "uberon",
"ontobee": "UBERON",
+ "togoid": "Uberon",
"wikidata": "P1554"
},
"name": "Uber Anatomy Ontology",
@@ -54773,6 +57762,13 @@
"pattern": "^\\d+$",
"preferred_prefix": "UBERON",
"providers": [
+ {
+ "code": "cellguide",
+ "description": "CellGuide is a comprehensive resource for knowledge about cell types.",
+ "homepage": "https://cellxgene.cziscience.com/cellguide",
+ "name": "Cell Guide",
+ "uri_format": "https://cellxgene.cziscience.com/cellguide/tissues/UBERON_$1"
+ },
{
"code": "cellxgene",
"description": "Explore single cell data through the CZ CELLxGENE portal",
@@ -54805,8 +57801,8 @@
"Uberon"
],
"twitter": "uberanat",
- "uri_format": "https://www.ebi.ac.uk/ols4/ontologies/uberon/terms?obo_id=UBERON:$1",
- "version": "2023-05-23"
+ "uri_format": "http://purl.obolibrary.org/obo/UBERON_$1",
+ "version": "2024-03-22"
},
"ubio.namebank": {
"description": "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context.",
@@ -54927,12 +57923,17 @@
],
"homepage": "https://ucum.org",
"keywords": [
- "subject agnostic"
+ "data identity and mapping",
+ "general & upper",
+ "measurement",
+ "subject agnostic",
+ "unit"
],
"mappings": {
"bartoc": "1895",
"fairsharing": "FAIRsharing.27w8k0",
- "hl7": "2.16.840.1.113883.6.8"
+ "hl7": "2.16.840.1.113883.6.8",
+ "lov": "ucum"
},
"name": "Unified Code for Units of Measure",
"preferred_prefix": "ucum",
@@ -55087,6 +58088,9 @@
"description": "An additional Japanese clinical trial registry",
"example": "UMIN000049383",
"homepage": "https://www.umin.ac.jp/ctr/index.htm",
+ "mappings": {
+ "integbio": "nbdc01470"
+ },
"name": "University hospital Medical Information Network Clinical Trial Registry",
"pattern": "^UMIN\\d+$",
"preferred_prefix": "uminctr",
@@ -55098,6 +58102,8 @@
"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",
+ "license": "https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html",
+ "logo": "https://uts.nlm.nih.gov/uts/assets/images/umls_tree_sm.jpg",
"mappings": {
"bartoc": "20052",
"biocontext": "UMLS",
@@ -55116,7 +58122,7 @@
"UMLS_CUI",
"umls.cui"
],
- "uri_format": "http://linkedlifedata.com/resource/umls/id/$1"
+ "uri_format": "https://uts.nlm.nih.gov/uts/umls/concept/$1"
},
"umls.aui": {
"contributor": {
@@ -55162,6 +58168,7 @@
"mappings": {
"biocontext": "UNIGENE",
"fairsharing": "FAIRsharing.ge1c3p",
+ "integbio": "nbdc00220",
"miriam": "unigene",
"n2t": "unigene",
"prefixcommons": "unigene",
@@ -55217,7 +58224,7 @@
},
"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",
+ "download_owl": "https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/unimod.owl",
"example": "1200",
"homepage": "http://www.unimod.org/",
"keywords": [
@@ -55238,7 +58245,6 @@
"publications": [
{
"doi": "10.1002/pmic.200300744",
- "pmc": null,
"pubmed": "15174123",
"title": "Unimod: Protein modifications for mass spectrometry",
"year": 2004
@@ -55327,7 +58333,8 @@
"homepage": "http://www.uniprot.org",
"keywords": [
"biology",
- "protein"
+ "protein",
+ "taxonomic classification"
],
"mappings": {
"aberowl": "UP",
@@ -55337,11 +58344,13 @@
"edam": "3021",
"fairsharing": "FAIRsharing.wf28wm",
"go": "UniProtKB",
+ "integbio": "nbdc00221",
"miriam": "uniprot",
"n2t": "uniprot",
"ncbi": "UniProt",
"prefixcommons": "uniprot",
"re3data": "r3d100011521",
+ "togoid": "Uniprot",
"wikidata": "P352"
},
"name": "UniProt Protein",
@@ -55355,6 +58364,13 @@
"name": "Bio2RDF",
"uri_format": "http://bio2rdf.org/uniprot:$1"
},
+ {
+ "code": "drugbank",
+ "description": "DrugBank PolyPeptide.",
+ "homepage": "https://go.drugbank.com",
+ "name": "DrugBank Polypeptide",
+ "uri_format": "https://go.drugbank.com/polypeptides/$1"
+ },
{
"code": "indra",
"description": "A large scale database of biomedical statements.",
@@ -55429,6 +58445,9 @@
"example": "ARBA00000001",
"github_request_issue": 620,
"homepage": "https://www.uniprot.org/arba",
+ "mappings": {
+ "go": "ARBA"
+ },
"name": "Association-Rule-Based Annotator",
"pattern": "^ARBA\\d+$",
"preferred_prefix": "uniprot.arba",
@@ -55459,6 +58478,25 @@
],
"uri_format": "http://purl.uniprot.org/annotation/$1"
},
+ "uniprot.core": {
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "Properties and classes used for protein annotation",
+ "example": "certain",
+ "homepage": "http://purl.uniprot.org/core/",
+ "keywords": [
+ "biology"
+ ],
+ "mappings": {
+ "lov": "uniprot"
+ },
+ "name": "Uniprot Core Ontology",
+ "preferred_prefix": "uniprot.core"
+ },
"uniprot.disease": {
"contributor": {
"email": "cthoyt@gmail.com",
@@ -55800,7 +58838,6 @@
"unite": {
"contact": {
"email": "urmas.koljalg@ut.ee",
- "github": null,
"name": "Urmas Kõljalg",
"orcid": "0000-0002-5171-1668"
},
@@ -55841,7 +58878,6 @@
"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
@@ -55864,7 +58900,6 @@
"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
@@ -55905,12 +58940,15 @@
"keywords": [
"life science",
"mathematics",
+ "measurement",
"obo",
- "ontology"
+ "ontology",
+ "unit"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "UO",
+ "agroportal": "UO",
"biocontext": "UO",
"bioportal": "UO",
"fairsharing": "FAIRsharing.mjnypw",
@@ -55979,6 +59017,7 @@
"obofoundry": "upa",
"ols": "upa",
"ontobee": "UPA",
+ "pathguide": "414",
"prefixcommons": "unipathway"
},
"name": "Unipathway",
@@ -56010,7 +59049,7 @@
"unipathway.pathway"
],
"uri_format": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1",
- "version": "2018-12-12"
+ "version": "2024-03-06"
},
"upheno": {
"contact": {
@@ -56026,9 +59065,11 @@
"evolutionary biology",
"obo",
"ontology",
- "phenomics"
+ "phenomics",
+ "phenotype"
],
"license": "CC0-1.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBa01CIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--3f5258d2bcf30a7e127b5a9fe209b27e25e88883/up.png?disposition=inline",
"mappings": {
"aberowl": "UPHENO",
"biocontext": "UPHENO",
@@ -56050,7 +59091,6 @@
"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"
@@ -56090,6 +59130,7 @@
"example": "5UTR_107_ENST00000517291.2",
"homepage": "https://utrdb.cloud.ba.infn.it/utrdb/index_107.html",
"mappings": {
+ "integbio": "nbdc00730",
"miriam": "utrdb"
},
"name": "UTRdb",
@@ -56120,7 +59161,6 @@
"validatordb": {
"contact": {
"email": "david.sehnal@gmail.com",
- "github": null,
"name": "David Sehnal",
"orcid": "0000-0002-0682-3089"
},
@@ -56133,6 +59173,7 @@
"mappings": {
"biocontext": "VALIDATORDB",
"fairsharing": "FAIRsharing.c9psgb",
+ "integbio": "nbdc02174",
"miriam": "validatordb",
"n2t": "validatordb"
},
@@ -56154,9 +59195,7 @@
"vandf": {
"contact": {
"email": "michael.lincoln@med.va.gov",
- "github": null,
- "name": "Michael Lincoln",
- "orcid": null
+ "name": "Michael Lincoln"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -56169,6 +59208,8 @@
"homepage": "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF",
"keywords": [
"biomedical science",
+ "drug",
+ "drug interaction",
"ontology",
"pharmacology"
],
@@ -56184,7 +59225,6 @@
"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",
@@ -56197,8 +59237,7 @@
"contact": {
"email": "nospam@iandavis.com",
"github": "iand",
- "name": "Ian Davis",
- "orcid": null
+ "name": "Ian Davis"
},
"contributor": {
"email": "cthoyt@gmail.com",
@@ -56209,6 +59248,13 @@
"description": "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes.",
"example": "usageNote",
"homepage": "https://vocab.org/vann/",
+ "keywords": [
+ "metadata"
+ ],
+ "mappings": {
+ "lov": "vann",
+ "zazuko": "vann"
+ },
"name": "A vocabulary for annotating vocabulary descriptions",
"preferred_prefix": "vann",
"uri_format": "https://vocab.org/vann/$1"
@@ -56228,9 +59274,14 @@
"example": "0376",
"homepage": "http://variationontology.org",
"keywords": [
+ "deoxyribonucleic acid",
+ "dna structural variation",
"genetics",
"obo",
- "ontology"
+ "ontology",
+ "protein",
+ "ribonucleic acid",
+ "sequence variant"
],
"license": "CC-BY-4.0",
"mappings": {
@@ -56268,14 +59319,12 @@
},
{
"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
@@ -56302,7 +59351,6 @@
"vbase2": {
"contact": {
"email": "wmueller@gbf.de",
- "github": null,
"name": "Werner Müller",
"orcid": "0000-0002-1297-9725"
},
@@ -56316,6 +59364,7 @@
"mappings": {
"biocontext": "VBASE2",
"fairsharing": "FAIRsharing.qvxhb1",
+ "integbio": "nbdc01897",
"miriam": "vbase2",
"n2t": "vbase2",
"ncbi": "VBASE2",
@@ -56367,6 +59416,7 @@
"license": "CC-BY-4.0",
"mappings": {
"aberowl": "VBO",
+ "bioportal": "VBO",
"obofoundry": "vbo",
"ols": "vbo",
"ontobee": "VBO"
@@ -56377,7 +59427,7 @@
"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": "2023-06-02"
+ "version": "2024-04-18"
},
"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.",
@@ -56415,8 +59465,31 @@
"preferred_prefix": "vcell",
"uri_format": "https://vcell.org/biomodel-$1"
},
+ "vdrc": {
+ "description": "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]",
+ "example": "100291",
+ "homepage": "http://stockcenter.vdrc.at/control/main",
+ "keywords": [
+ "biomaterial supply resource",
+ "drosophila",
+ "fly lines"
+ ],
+ "mappings": {
+ "rrid": "VDRC"
+ },
+ "name": "Vienna Drosophila Resource Center",
+ "pattern": "^\\d+$",
+ "preferred_prefix": "vdrc",
+ "uri_format": "https://shop.vbc.ac.at/vdrc_store/$1.html"
+ },
"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.",
+ "contact": {
+ "email": "d.e.starns@liv.ac.uk",
+ "github": "obsidian83",
+ "name": "David Starns",
+ "orcid": "0000-0001-6583-9067"
+ },
+ "description": "VectorBase is part of the VEuPathDB, a NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens and related species of interest. Currently, VectorBase contains genome information for approximately 80 organisms: mosquitoes, bed bugs, biting midges, ticks, tsetse flies, mites, sand flies, house flies, body lice, stable flies, kissing bugs, and a snail which is an intermediate host.",
"example": "ISCW007415",
"homepage": "https://www.vectorbase.org/",
"keywords": [
@@ -56432,6 +59505,7 @@
"mappings": {
"biocontext": "VECTORBASE",
"fairsharing": "FAIRsharing.3etvdn",
+ "integbio": "nbdc01909",
"miriam": "vectorbase",
"n2t": "vectorbase",
"ncbi": "VectorBase",
@@ -56486,7 +59560,6 @@
"vega": {
"contact": {
"email": "jla1@sanger.ac.uk",
- "github": null,
"name": "Jennifer L Harrow",
"orcid": "0000-0003-0338-3070"
},
@@ -56559,7 +59632,6 @@
],
"contact": {
"email": "DBrodbelt@RVC.AC.UK",
- "github": null,
"name": "David Brodbelt",
"orcid": "0000-0001-5628-4194"
},
@@ -56583,7 +59655,6 @@
"vfb": {
"contact": {
"email": "r.court@ed.ac.uk",
- "github": null,
"name": "Robert Court",
"orcid": "0000-0002-0173-9080"
},
@@ -56613,24 +59684,19 @@
},
{
"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
},
{
"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
+ "title": "Web tools for large-scale 3D biological images and atlases"
}
],
"uri_format": "http://virtualflybrain.org/reports/$1"
@@ -56675,6 +59741,7 @@
"fairsharing": "FAIRsharing.5NhJFK",
"miriam": "vgnc",
"ncbi": "VGNC",
+ "togoid": "Vgnc",
"uniprot": "DB-0226"
},
"name": "Vertebrate Gene Nomenclature Committee",
@@ -56694,9 +59761,7 @@
"vhog": {
"contact": {
"email": "bgee@isb-sib.ch",
- "github": null,
- "name": "Bgee team",
- "orcid": null
+ "name": "Bgee team"
},
"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.",
@@ -56740,8 +59805,13 @@
"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",
+ "keywords": [
+ "centrally registered identifier",
+ "knowledge and information systems"
+ ],
"mappings": {
"bartoc": "2053",
+ "fairsharing": "FAIRsharing.a15ac6",
"miriam": "viaf",
"n2t": "viaf"
},
@@ -56759,6 +59829,7 @@
{
"code": "viaf.https",
"description": "A duplicate endpoint over HTTPS",
+ "first_party": true,
"homepage": "http://viaf.org",
"name": "VIAF (https)",
"uri_format": "https://viaf.org/$1"
@@ -56836,6 +59907,7 @@
"structure"
],
"mappings": {
+ "integbio": "nbdc00835",
"prefixcommons": "viperdb",
"re3data": "r3d100012362"
},
@@ -56856,7 +59928,6 @@
"vipr": {
"contact": {
"email": "rscheuermann@jcvi.org",
- "github": null,
"name": "Richard Scheuermann",
"orcid": "0000-0003-1355-892X"
},
@@ -56901,14 +59972,12 @@
{
"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
}
@@ -56919,7 +59988,6 @@
"viralzone": {
"contact": {
"email": "Philippe.Lemercier@sib.swiss",
- "github": null,
"name": "Philippe Le Mercier",
"orcid": "0000-0001-8528-090X"
},
@@ -56937,6 +60005,7 @@
"biocontext": "VIRALZONE",
"fairsharing": "FAIRsharing.tppk10",
"go": "VZ",
+ "integbio": "nbdc02226",
"miriam": "viralzone",
"n2t": "viralzone",
"prefixcommons": "vz",
@@ -57080,6 +60149,7 @@
"virus"
],
"mappings": {
+ "integbio": "nbdc02395",
"prefixcommons": "virushostdb"
},
"name": "Virus-HostDB",
@@ -57201,17 +60271,21 @@
"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",
+ "homepage": "https://violinet.org/vaccineontology",
"keywords": [
+ "biological process",
"biomedical science",
"immunology",
"obo",
"ontology",
"pathobiochemistry",
+ "pathogen",
"small molecule",
+ "vaccination",
"vaccine"
],
- "license": "CC-BY-3.0",
+ "license": "CC-BY-4.0",
+ "logo": "https://api.fairsharing.org/rails/active_storage/blobs/redirect/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBaUFDIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--0d3898a5618b34c0bc948bb0d101e906f212f05f/vo_banner.png?disposition=inline",
"mappings": {
"aberowl": "VO",
"biocontext": "VO",
@@ -57238,7 +60312,6 @@
"publications": [
{
"doi": "10.2174/1381612826666201125112131",
- "pmc": null,
"pubmed": "33238868",
"title": "Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development",
"year": 2021
@@ -57263,19 +60336,43 @@
"pubmed": "20875156",
"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_$1",
- "version": "1.1.218"
+ "version": "2024-04-09"
+ },
+ "voc4cat": {
+ "comment": "The most current version of a concept can be accessed so * https://w3id.org/nfdi4cat/voc4cat_0000123 other/older versions from releases like so * https://w3id.org/nfdi4cat/voc4cat/v2023-08-17/voc4cat_0000123. This is pretty unique and isn't tracked by the Bioregistry currently.",
+ "contact": {
+ "email": "nikolaos.moustakas@catalysis.de",
+ "github": "nmoust",
+ "name": "Nikolaos Moustakas",
+ "orcid": "0000-0002-6242-2167"
+ },
+ "contributor": {
+ "email": "David.Linke@catalysis.de",
+ "github": "dalito",
+ "name": "David Linke",
+ "orcid": "0000-0002-5898-1820"
+ },
+ "description": "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.",
+ "example": "0000123",
+ "github_request_issue": 957,
+ "homepage": "https://nfdi4cat.github.io/voc4cat/",
+ "license": "CC0-1.0",
+ "name": "A vocabulary for the catalysis disciplines",
+ "pattern": "^\\d{7,}$",
+ "preferred_prefix": "voc4cat",
+ "repository": "https://github.com/nfdi4cat/voc4cat",
+ "reviewer": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "uri_format": "https://w3id.org/nfdi4cat/voc4cat_$1"
},
"void": {
"contributor": {
@@ -57287,8 +60384,13 @@
"description": "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary.",
"example": "feature",
"homepage": "http://vocab.deri.ie/void",
+ "keywords": [
+ "metadata"
+ ],
"mappings": {
- "biocontext": "void"
+ "biocontext": "void",
+ "lov": "void",
+ "zazuko": "void"
},
"name": "Vocabulary of Interlinked Datasets",
"preferred_prefix": "void",
@@ -57297,7 +60399,6 @@
"vsao": {
"contact": {
"email": "wasila.dahdul@usd.edu",
- "github": null,
"name": "Wasila Dahdul",
"orcid": "0000-0003-3162-7490"
},
@@ -57305,7 +60406,7 @@
"description": "Vertebrate skeletal anatomy ontology.",
"download_obo": "http://aber-owl.net/media/ontologies/VSAO/20/vsao.obo",
"download_owl": "http://purl.obolibrary.org/obo/vsao.owl",
- "example": "VSAO_0000183",
+ "example": "0000183",
"homepage": "https://www.nescent.org/phenoscape/Main_Page",
"keywords": [
"anatomy",
@@ -57322,6 +60423,7 @@
"prefixcommons": "vao"
},
"name": "Vertebrate Skeletal Anatomy Ontology",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "VSAO",
"providers": [
{
@@ -57387,9 +60489,7 @@
"vso": {
"contact": {
"email": "albertgoldfain@gmail.com",
- "github": null,
- "name": "Albert Goldfain",
- "orcid": null
+ "name": "Albert Goldfain"
},
"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",
@@ -57397,6 +60497,8 @@
"homepage": "https://bioportal.bioontology.org/ontologies/VSO",
"keywords": [
"biomedical science",
+ "blood",
+ "experimental measurement",
"health",
"health science",
"ontology",
@@ -57406,7 +60508,8 @@
"aberowl": "VSO",
"bioportal": "VSO",
"fairsharing": "FAIRsharing.jjb2p2",
- "prefixcommons": "vso"
+ "prefixcommons": "vso",
+ "zazuko": "vso"
},
"name": "Vital Sign Ontology",
"pattern": "^\\d{7}$",
@@ -57432,7 +60535,7 @@
"name": "Carissa Park",
"orcid": "0000-0002-2346-5201"
},
- "description": "An ontology of traits covering vertebrates",
+ "description": "The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.",
"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",
@@ -57441,8 +60544,10 @@
"animal physiology",
"biology",
"developmental biology",
+ "morphology",
"obo",
"ontology",
+ "phenotype",
"physiology",
"trait",
"vertebrate"
@@ -57482,7 +60587,8 @@
],
"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"
+ "uri_format": "http://purl.obolibrary.org/obo/VT_$1",
+ "version": "2024-04-23"
},
"vto": {
"contact": {
@@ -57497,6 +60603,7 @@
"example": "9008500",
"homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology",
"keywords": [
+ "bone",
"obo",
"ontology",
"taxonomy"
@@ -57574,6 +60681,7 @@
"homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology",
"keywords": [
"anatomy",
+ "cell",
"life science",
"obo",
"ontology",
@@ -57618,8 +60726,8 @@
"synonyms": [
"WBbt"
],
- "uri_format": "http://wormbase.org/db/ontology/anatomy?name=$1",
- "version": "2023-04-07"
+ "uri_format": "http://purl.obolibrary.org/obo/WBbt_$1",
+ "version": "2024-04-01"
},
"wbls": {
"contact": {
@@ -57636,6 +60744,8 @@
"keywords": [
"development",
"developmental biology",
+ "life cycle",
+ "life cycle stage",
"life science",
"obo",
"ontology",
@@ -57680,8 +60790,8 @@
"synonyms": [
"WBls"
],
- "uri_format": "http://www.wormbase.org/get?name=$1",
- "version": "2023-05-17"
+ "uri_format": "http://purl.obolibrary.org/obo/WBls_$1",
+ "version": "2024-04-09"
},
"wbphenotype": {
"contact": {
@@ -57742,7 +60852,7 @@
"WBPhenotype"
],
"uri_format": "http://purl.obolibrary.org/obo/WBPhenotype_$1",
- "version": "2023-05-18"
+ "version": "2024-04-09"
},
"webelements": {
"contributor": {
@@ -57772,15 +60882,19 @@
"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",
+ "keywords": [
+ "geography"
+ ],
"mappings": {
- "biolink": "wgs"
+ "biolink": "wgs",
+ "lov": "geo"
},
"name": "WGS84 Geo Positioning",
"preferred_prefix": "wgs84",
"uri_format": "http://www.w3.org/2003/01/geo/wgs84_pos#$1"
},
"wicell": {
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "ai10e-kctd13b",
"homepage": "https://www.wicell.org",
"mappings": {
@@ -57792,7 +60906,7 @@
},
"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",
+ "example": "Q47475003",
"homepage": "https://www.wikidata.org/",
"keywords": [
"chemistry",
@@ -57801,6 +60915,7 @@
"proteomics",
"subject agnostic"
],
+ "license": "CC0-1.0",
"mappings": {
"bartoc": "1940",
"biocontext": "WIKIDATA",
@@ -57826,8 +60941,6 @@
"publications": [
{
"doi": "10.1145/2187980.2188242",
- "pmc": null,
- "pubmed": null,
"title": "Wikidata",
"year": 2012
}
@@ -57849,6 +60962,7 @@
"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",
+ "license": "CC0-1.0",
"mappings": {
"biocontext": "WD_Prop",
"biolink": "WIKIDATA_PROPERTY"
@@ -57902,8 +61016,16 @@
"example": "WP732",
"homepage": "http://www.wikipathways.org/",
"keywords": [
+ "biological regulation",
+ "drug interaction",
"epidemiology",
+ "genetic interaction",
+ "molecular interaction",
"pathway",
+ "pathway model",
+ "protein interaction",
+ "reaction data",
+ "signaling",
"virology"
],
"license": "CC0-1.0",
@@ -57912,10 +61034,13 @@
"biocontext": "WIKIPATHWAYS",
"edam": "3952",
"fairsharing": "FAIRsharing.g7b4rj",
+ "integbio": "nbdc02116",
"miriam": "wikipathways",
"n2t": "wikipathways",
+ "pathguide": "237",
"prefixcommons": "wikipathways",
"re3data": "r3d100013316",
+ "togoid": "Wikipathways",
"wikidata": "P2410"
},
"mastodon": "wikipathways@fosstodon.org",
@@ -57939,6 +61064,13 @@
}
],
"publications": [
+ {
+ "doi": "10.1093/nar/gkad960",
+ "pmc": "PMC10767877",
+ "pubmed": "37941138",
+ "title": "WikiPathways 2024: next generation pathway database",
+ "year": 2024
+ },
{
"doi": "10.1093/nar/gkaa1024",
"pmc": "PMC7779061",
@@ -58076,6 +61208,7 @@
],
"mappings": {
"biocontext": "WORFDB",
+ "integbio": "nbdc00738",
"miriam": "worfdb",
"n2t": "worfdb",
"ncbi": "WorfDB",
@@ -58124,7 +61257,6 @@
"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
@@ -58179,21 +61311,43 @@
"homepage": "https://www.wormbase.org/",
"keywords": [
"anatomy",
+ "blast",
+ "c elegans",
+ "catalog",
+ "database",
+ "faseb list",
"gene",
+ "gene expression",
+ "gene function",
+ "gene mapping",
+ "gene prediction",
+ "geneotype",
"genome",
- "life science"
+ "genomic sequence",
+ "genomics",
+ "life science",
+ "ortholog",
+ "orthology assignment",
+ "phenotype",
+ "roundworm",
+ "transposon family",
+ "wormmart"
],
+ "license": "CC0-1.0",
"mappings": {
"biocontext": "WormBase",
"biolink": "WBVocab",
"edam": "1805",
"fairsharing": "FAIRsharing.zx1td8",
"go": "WB_REF",
+ "integbio": "nbdc00740",
"miriam": "wb",
"n2t": "wb",
"ncbi": "WormBase",
+ "pathguide": "426",
"prefixcommons": "wormbase",
"re3data": "r3d100010424",
+ "rrid": "WB-STRAIN:WBStrain",
"uniprot": "DB-0110",
"wikidata": "P3860"
},
@@ -58238,6 +61392,9 @@
"title": "WormBase 2017: molting into a new stage",
"year": 2018
},
+ {
+ "pubmed": "24194605"
+ },
{
"doi": "10.1186/1471-2105-12-175",
"pmc": "PMC3213741",
@@ -58301,6 +61458,12 @@
"title": "nGASP--the nematode genome annotation assessment project",
"year": 2008
},
+ {
+ "pubmed": "17991679"
+ },
+ {
+ "pubmed": "15608221"
+ },
{
"doi": "10.1093/nar/29.1.82",
"pmc": "PMC29781",
@@ -58310,6 +61473,7 @@
}
],
"synonyms": [
+ "WB",
"WB_REF",
"wb",
"wormbase"
@@ -58348,7 +61512,6 @@
"worms": {
"contact": {
"email": "leen.vandepitte@vliz.be",
- "github": null,
"name": "Leen Vandepitte",
"orcid": "0000-0002-8160-7941"
},
@@ -58407,7 +61570,19 @@
"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"
+ "uri_format": "https://www.webofscience.com/wos/woscc/full-record/WOS:$1"
+ },
+ "wos.researcher": {
+ "description": "identifier for a researcher in a system for scientific authors, redirects to a Web of Science ID, along with P3829",
+ "example": "B-5720-2018",
+ "homepage": "https://access.clarivate.com/login?app=wos",
+ "mappings": {
+ "wikidata": "P1053"
+ },
+ "name": "ResearcherID",
+ "pattern": "^[A-Z]{1,3}-\\d{4}-(19|20)\\d\\d$",
+ "preferred_prefix": "wos.researcher",
+ "uri_format": "https://www.webofscience.com/wos/author/record/$1"
},
"wwf.ecoregion": {
"comment": "ENVO includes xrefs to this resource. See EnvironmentOntology/envo#658",
@@ -58456,9 +61631,13 @@
"keywords": [
"anatomy",
"developmental biology",
+ "life cycle",
+ "life cycle stage",
"life science",
+ "morphology",
"obo",
- "ontology"
+ "ontology",
+ "structure"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -58489,13 +61668,6 @@
"pubmed": "18817563",
"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",
@@ -58520,11 +61692,17 @@
"example": "0000780",
"homepage": "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000",
"keywords": [
+ "assay",
"biomedical science",
+ "experimental condition",
+ "experimental measurement",
+ "experimentally determined",
"life science",
"measurement",
"obo",
- "ontology"
+ "ontology",
+ "protocol",
+ "study design"
],
"license": "CC0-1.0",
"logo": "http://rgd.mcw.edu/common/images/rgd_LOGO_blue_rgd.gif",
@@ -58569,8 +61747,8 @@
"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": "4.46"
+ "uri_format": "http://purl.obolibrary.org/obo/XCO_$1",
+ "version": "4.165"
},
"xenbase": {
"contact": {
@@ -58691,17 +61869,11 @@
},
{
"doi": "doi:10.3389/fphys.2019.00154",
- "pmc": null,
- "pubmed": null,
- "title": "Xenbase: Facilitating the Use of Xenopus to Model Human Disease.",
- "year": null
+ "title": "Xenbase: Facilitating the Use of Xenopus to Model Human Disease."
},
{
"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
+ "title": "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database."
}
],
"synonyms": [
@@ -58717,7 +61889,7 @@
"name": "Charles Tapley Hoyt",
"orcid": "0000-0003-4423-4370"
},
- "description": "Cell line collections",
+ "description": "Cell line collections (Providers)",
"example": "151022",
"homepage": "https://ximbio.com",
"mappings": {
@@ -58731,11 +61903,7 @@
"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",
@@ -58747,10 +61915,10 @@
},
"xlmod": {
"contact": {
- "email": "lutz.fischer@tu-berlin.de",
- "github": "lutzfischer",
- "name": "Lutz Fischer",
- "orcid": "0000-0003-4978-0864"
+ "email": "gerhard.mayer@rub.de",
+ "github": "germa",
+ "name": "Gerhard Mayer",
+ "orcid": "0000-0002-1767-2343"
},
"description": "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.",
"download_obo": "http://purl.obolibrary.org/obo/xlmod.obo",
@@ -58758,13 +61926,20 @@
"example": "00050",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"keywords": [
+ "chemical biology",
+ "experimental measurement",
+ "mass spectrometry assay",
+ "mass spectrum",
+ "metabolomics",
"obo",
+ "omics",
"ontology"
],
"license": "CC-BY-3.0",
"mappings": {
"aberowl": "XLMOD",
"bioportal": "XLMOD",
+ "fairsharing": "FAIRsharing.6ccbe6",
"obofoundry": "xlmod",
"ols": "xlmod",
"ontobee": "XLMOD"
@@ -58865,7 +62040,7 @@
"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": "2022-09-15"
+ "version": "2024-04-18"
},
"xsd": {
"contributor": {
@@ -58877,8 +62052,13 @@
"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",
+ "keywords": [
+ "w3c rec"
+ ],
"mappings": {
- "biocontext": "xsd"
+ "biocontext": "xsd",
+ "lov": "xsd",
+ "zazuko": "xsd"
},
"name": "XML Schema Definition",
"preferred_prefix": "xsd",
@@ -58952,6 +62132,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.mphj4z",
+ "pathguide": "205",
"prefixcommons": "yeastract"
},
"name": "Yeast Searching for Transcriptional Regulators and Consensus Tracking",
@@ -59080,6 +62261,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.tawpg2",
+ "pathguide": "388",
"re3data": "r3d100012733"
},
"name": "Yeast Metabolome Database",
@@ -59100,7 +62282,6 @@
"ypo": {
"contact": {
"email": "cherry@genome.stanford.edu",
- "github": null,
"name": "Mike Cherry",
"orcid": "0000-0001-9163-5180"
},
@@ -59122,7 +62303,6 @@
"yrcpdr": {
"contact": {
"email": "mriffle@u.washington.edu",
- "github": null,
"name": "Michael Riffle",
"orcid": "0000-0003-1633-8607"
},
@@ -59156,17 +62336,37 @@
],
"uri_format": "http://yeastrc.org/pdr/viewProtein.do?id=$1"
},
+ "zazuko": {
+ "contact": {
+ "email": "ktk@netlabs.org",
+ "github": "ktk",
+ "name": "Adrian Gschwend",
+ "orcid": "0000-0002-2079-9636"
+ },
+ "contributor": {
+ "email": "cthoyt@gmail.com",
+ "github": "cthoyt",
+ "name": "Charles Tapley Hoyt",
+ "orcid": "0000-0003-4423-4370"
+ },
+ "description": "This service fills a gap between services like prefix.cc and LOV or looking up the original vocabulary specification. Not all vocabularies (or schema or ontology, whatever you want to call them) provide an HTML view. If you resolve some of the common prefixes all you get back is some RDF serialization which is not ideal. (from )",
+ "example": "frbr",
+ "homepage": "https://prefix.zazuko.com/",
+ "license": "MIT",
+ "name": "Zazuko Prefix Server",
+ "preferred_prefix": "zazuko",
+ "uri_format": "https://prefix.zazuko.com/prefix/$1:"
+ },
"zea": {
"contact": {
"email": "Leszek@missouri.edu",
- "github": null,
"name": "Leszek Vincent",
"orcid": "0000-0002-9316-2919"
},
"deprecated": true,
"description": "Maize gross anatomy",
"download_obo": "http://aber-owl.net/media/ontologies/ZEA/2/zea.obo",
- "example": "ZEA_0015177",
+ "example": "0015177",
"homepage": "http://www.maizemap.org/",
"keywords": [
"anatomy",
@@ -59182,6 +62382,7 @@
"prefixcommons": "zea"
},
"name": "Maize gross anatomy",
+ "pattern": "^\\d{7}$",
"preferred_prefix": "ZEA",
"providers": [
{
@@ -59212,12 +62413,21 @@
"example": "0000171",
"homepage": "https://github.com/ybradford/zebrafish-experimental-conditions-ontology",
"keywords": [
+ "allele",
"animal physiology",
+ "bibliography",
"developmental biology",
+ "disease process modeling",
+ "expression data",
+ "gene",
"genetics",
+ "genome",
"genomics",
+ "model organism",
+ "mutation",
"obo",
- "ontology"
+ "ontology",
+ "phenotype"
],
"license": "CC-BY-3.0",
"mappings": {
@@ -59240,7 +62450,6 @@
"zenodo.record": {
"contact": {
"email": "lars.holm.nielsen@cern.ch",
- "github": null,
"name": "Lars Holm Nielsen",
"orcid": "0000-0001-8135-3489"
},
@@ -59260,6 +62469,7 @@
],
"mappings": {
"fairsharing": "FAIRsharing.wy4egf",
+ "integbio": "nbdc02187",
"re3data": "r3d100010468",
"wikidata": "P4901"
},
@@ -59297,9 +62507,13 @@
"keywords": [
"anatomy",
"developmental biology",
+ "life cycle",
+ "life cycle stage",
"life science",
+ "morphology",
"obo",
"ontology",
+ "structure",
"zebrafish"
],
"license": "CC-BY-3.0",
@@ -59345,7 +62559,6 @@
"zfin": {
"contact": {
"email": "dhowe@zfin.org",
- "github": null,
"name": "Doug Howe",
"orcid": "0000-0001-5831-7439"
},
@@ -59353,23 +62566,34 @@
"example": "ZDB-GENE-041118-11",
"homepage": "http://zfin.org",
"keywords": [
+ "adult",
"animal physiology",
+ "antibody",
+ "cdna",
"developmental biology",
+ "embryo",
+ "expressed sequence tag",
+ "fish",
"gene",
"genetics",
"genome",
"genomics",
- "zebrafish"
+ "pathology",
+ "research",
+ "zebrafish",
+ "zebrafish line"
],
"mappings": {
"biocontext": "ZFIN",
"fairsharing": "FAIRsharing.ybxnhg",
"go": "ZFIN",
+ "integbio": "nbdc00746",
"miriam": "zfin",
"n2t": "zfin",
"ncbi": "ZFIN",
"prefixcommons": "zfin",
"re3data": "r3d100010421",
+ "rrid": "ZIRC",
"uniprot": "DB-0113",
"wikidata": "P3870"
},
@@ -59402,31 +62626,23 @@
},
{
"doi": "10.1093/nar/gks938",
- "pmc": null,
"pubmed": "23074187",
- "title": "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics",
- "year": null
+ "title": "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics"
},
{
"doi": "10.1016/b978-0-12-374814-0.00017-3",
- "pmc": null,
"pubmed": "21924170",
- "title": "Data extraction, transformation, and dissemination through ZFIN",
- "year": null
+ "title": "Data extraction, transformation, and dissemination through ZFIN"
},
{
"doi": "10.1093/nar/gkq1077",
- "pmc": null,
"pubmed": "21036866",
- "title": "ZFIN: enhancements and updates to the Zebrafish Model Organism Database",
- "year": null
+ "title": "ZFIN: enhancements and updates to the Zebrafish Model Organism Database"
},
{
"doi": "10.1002/0471250953.bi0118s31.",
- "pmc": null,
"pubmed": "20836073",
- "title": "Exploring zebrafish genomic, functional and phenotypic data using ZFIN",
- "year": null
+ "title": "Exploring zebrafish genomic, functional and phenotypic data using ZFIN"
},
{
"doi": "10.1093/nar/gkm956",
@@ -59437,31 +62653,22 @@
},
{
"doi": "10.1093/nar/gkj086",
- "pmc": null,
"pubmed": "16381936",
- "title": "The Zebrafish Information Network: the zebrafish model organism database",
- "year": null
+ "title": "The Zebrafish Information Network: the zebrafish model organism database"
},
{
"doi": "10.1093/nar/gkg027",
- "pmc": null,
"pubmed": "12519991",
- "title": "The Zebrafish Information Network (ZFIN): the zebrafish model organism database",
- "year": null
+ "title": "The Zebrafish Information Network (ZFIN): the zebrafish model organism database"
},
{
"doi": "10.1016/s0168-9525(99)01741-2",
- "pmc": null,
"pubmed": "10354586",
- "title": "Zebrafish in the Net",
- "year": null
+ "title": "Zebrafish in the Net"
},
{
"doi": "10.1016/B978-0-12-374814-0.00017-3",
- "pmc": null,
- "pubmed": null,
- "title": "Data extraction, transformation, and dissemination through ZFIN.",
- "year": null
+ "title": "Data extraction, transformation, and dissemination through ZFIN."
}
],
"synonyms": [
@@ -59483,8 +62690,10 @@
"example": "0000050",
"homepage": "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources",
"keywords": [
+ "aging",
"anatomy",
"developmental biology",
+ "life cycle",
"marine biology",
"obo",
"ontology",
@@ -59564,6 +62773,6 @@
"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": "2022-12-17"
+ "version": "2024-04-18"
}
}
\ 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 978547aa..0b164564 100644
--- a/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java
+++ b/paxtools-console/src/main/java/org/biopax/paxtools/Commands.java
@@ -527,8 +527,6 @@ static Set identifiers(final PhysicalEntity entity, final String xrefdb,
Set children = fetcher.fetch(entity, XReferrable.class);
children.add(entity); //include itself
-
-
for(XReferrable child : children) {//ignore some classes, such as controlled vocabularies, interactions, etc.
if (child instanceof PhysicalEntity || child instanceof EntityReference || child instanceof Gene)
for (Xref x : child.getXref()) {